From d64f9a78ac909306b8746272bad59f2229a6d240 Mon Sep 17 00:00:00 2001
From: PauAndrio <andriopau@gmail.com>
Date: Mon, 4 Nov 2024 11:55:51 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bioexcel?=
 =?UTF-8?q?/biobb=5Fcmip@7c184dc55e33e39d6bab41e88b53f7b2455c5682=20?=
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MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 coverage/class_index.html                     | 12 ++--
 coverage/coverage.xml                         |  7 +-
 coverage/coveragebadge.svg                    |  2 +-
 coverage/function_index.html                  | 12 ++--
 coverage/index.html                           | 12 ++--
 coverage/status.json                          |  2 +-
 ...e0a65b75_test_cmip_ignore_residues_py.html |  4 +-
 ...9514e0a65b75_test_cmip_prepare_pdb_py.html |  4 +-
 ...a65b75_test_cmip_prepare_structure_py.html |  4 +-
 .../z_60079514e0a65b75_test_cmip_run_py.html  |  4 +-
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 .../z_8c1d59f76554b5b6_cmip_titration_py.html | 18 ++---
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 coverage/z_edf6e6b2d5ce0b2c___init___py.html  |  4 +-
 flake8/index.html                             |  2 +-
 junit/junit.xml                               |  2 +-
 junit/report.html                             |  6 +-
 24 files changed, 112 insertions(+), 111 deletions(-)

diff --git a/coverage/class_index.html b/coverage/class_index.html
index e15d767..de9b0eb 100644
--- a/coverage/class_index.html
+++ b/coverage/class_index.html
@@ -55,7 +55,7 @@ <h2>
         </h2>
         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
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@@ -285,10 +285,10 @@ <h2>
             <tr class="total">
                 <td class="name left">Total</td>
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+                <td>898</td>
                 <td>460</td>
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-                <td class="right" data-ratio="437 897">49%</td>
+                <td class="right" data-ratio="438 898">49%</td>
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@@ -300,7 +300,7 @@ <h2>
     <div class="content">
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+            created at 2024-11-04 11:55 +0000
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diff --git a/coverage/coverage.xml b/coverage/coverage.xml
index 2dcabd3..fe4f49d 100644
--- a/coverage/coverage.xml
+++ b/coverage/coverage.xml
@@ -1,5 +1,5 @@
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@@ -19,7 +19,7 @@
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-		<package name="biobb_cmip.cmip" line-rate="0.4956" branch-rate="0" complexity="0">
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 				<class name="__init__.py" filename="biobb_cmip/cmip/__init__.py" complexity="0" line-rate="1" branch-rate="0">
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-				<class name="common.py" filename="biobb_cmip/cmip/common.py" complexity="0" line-rate="0.4435" branch-rate="0">
+				<class name="common.py" filename="biobb_cmip/cmip/common.py" complexity="0" line-rate="0.445" branch-rate="0">
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index 00d8199..d72ebba 100644
--- a/coverage/coveragebadge.svg
+++ b/coverage/coveragebadge.svg
@@ -1 +1 @@
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\ No newline at end of file
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index fe3f1de..7637e80 100644
--- a/coverage/function_index.html
+++ b/coverage/function_index.html
@@ -55,7 +55,7 @@ <h2>
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         <p class="text">
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-            created at 2024-11-04 11:52 +0000
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-                <td class="right" data-ratio="6 8">75%</td>
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diff --git a/coverage/index.html b/coverage/index.html
index 1792155..3a9bc4b 100644
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@@ -54,7 +54,7 @@ <h2>
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+            created at 2024-11-04 11:55 +0000
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index b6abb2c..f8be19f 100644
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-            created at 2024-11-04 11:52 +0000
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     <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">                <span class="nam">warnings</span><span class="op">.</span><span class="nam">filterwarnings</span><span class="op">(</span><span class="str">"ignore"</span><span class="op">,</span> <span class="nam">category</span><span class="op">=</span><span class="nam">UserWarning</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'Reading: {top_file} to extract charges'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="fst">Reading: </span><span class="op">{</span><span class="nam">top_file</span><span class="op">}</span><span class="fst"> to extract charges</span><span class="fst">'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">                <span class="nam">charges_list</span> <span class="op">=</span> <span class="nam">get_topology_charges</span><span class="op">(</span><span class="nam">top_file</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'Reading: {top_file} to extract elements'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="fst">Reading: </span><span class="op">{</span><span class="nam">top_file</span><span class="op">}</span><span class="fst"> to extract elements</span><span class="fst">'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">                <span class="nam">elements_list</span> <span class="op">=</span> <span class="nam">get_topology_cmip_elements_canonical</span><span class="op">(</span><span class="nam">top_file</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">                <span class="nam">two_letter_elements</span> <span class="op">=</span> <span class="op">{</span><span class="str">"CL"</span><span class="op">:</span> <span class="str">"Cl"</span><span class="op">,</span> <span class="str">"NA"</span><span class="op">:</span> <span class="str">"Na"</span><span class="op">,</span> <span class="str">"ZN"</span><span class="op">:</span> <span class="str">"Zn"</span><span class="op">,</span> <span class="str">"MG"</span><span class="op">:</span> <span class="str">"Mg"</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">                <span class="nam">elements_list</span> <span class="op">=</span> <span class="op">[</span><span class="nam">two_letter_elements</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="nam">element</span><span class="op">,</span> <span class="nam">element</span><span class="op">)</span> <span class="key">for</span> <span class="nam">element</span> <span class="key">in</span> <span class="nam">elements_list</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -248,7 +248,7 @@ <h2>
             <a class="nav" href="z_8c1d59f76554b5b6_cmip_run_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8c1d59f76554b5b6_cmip_run_py.html b/coverage/z_8c1d59f76554b5b6_cmip_run_py.html
index a8ae6f7..e42e1c2 100644
--- a/coverage/z_8c1d59f76554b5b6_cmip_run_py.html
+++ b/coverage/z_8c1d59f76554b5b6_cmip_run_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8c1d59f76554b5b6_cmip_titration_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -189,7 +189,7 @@ <h2>
     <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">params</span> <span class="op">=</span> <span class="op">{</span><span class="nam">k</span><span class="op">:</span> <span class="nam">str</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span> <span class="key">for</span> <span class="nam">k</span><span class="op">,</span> <span class="nam">v</span> <span class="key">in</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'params'</span><span class="op">,</span> <span class="nam">dict</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">.</span><span class="nam">items</span><span class="op">(</span><span class="op">)</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'input_vdw_params_path'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_vdw_params_path'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{os.environ.get('CONDA_PREFIX')}/share/cmip/dat/vdwprm"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_vdw_params_path'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">os</span><span class="op">.</span><span class="nam">environ</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'CONDA_PREFIX'</span><span class="op">)</span><span class="op">}</span><span class="fst">/share/cmip/dat/vdwprm</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'combined_params_path'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'combined_params_path'</span><span class="op">,</span> <span class="str">'params'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
@@ -208,31 +208,31 @@ <h2>
     <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_pdb_path'</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_pdb_path'</span><span class="op">]</span><span class="op">.</span><span class="nam">endswith</span><span class="op">(</span><span class="str">'.pdb'</span><span class="op">)</span><span class="op">)</span> <span class="key">or</span> <span class="xx">\</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">               <span class="op">(</span><span class="str">"_"</span> <span class="key">in</span> <span class="nam">str</span><span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_pdb_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"ERROR: output_pdb_path ({self.io_dict['out']['output_pdb_path']}) "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                       <span class="str">f"name must end in .pdb and not contain underscores"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">f"ERROR: output_pdb_path ({self.io_dict['out']['output_pdb_path']})"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">                                 <span class="str">f"name must end in .pdb and not contain underscores"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">ERROR: output_pdb_path (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_pdb_path'</span><span class="op">]</span><span class="op">}</span><span class="fst">) </span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                       <span class="fst">f"</span><span class="fst">name must end in .pdb and not contain underscores</span><span class="fst">"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="fst">f"</span><span class="fst">ERROR: output_pdb_path (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_pdb_path'</span><span class="op">]</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">                                 <span class="fst">f"</span><span class="fst">name must end in .pdb and not contain underscores</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">params_preset_dict</span><span class="op">:</span> <span class="nam">dict</span><span class="op">[</span><span class="nam">str</span><span class="op">,</span> <span class="nam">Any</span><span class="op">]</span> <span class="op">=</span> <span class="nam">params_preset</span><span class="op">(</span><span class="nam">execution_type</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">execution_type</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">"input_json_external_box_path"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">params_preset_dict</span><span class="op">[</span><span class="str">"readgrid0"</span><span class="op">]</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">origin</span><span class="op">,</span> <span class="nam">size</span><span class="op">,</span> <span class="nam">grid_params</span> <span class="op">=</span> <span class="nam">get_grid</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">"input_json_external_box_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">params_preset_dict</span><span class="op">[</span><span class="str">'grid_int0'</span><span class="op">]</span> <span class="op">=</span> <span class="xx">\</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">                <span class="str">f"INTX0={grid_params['INT'][0]},INTY0={grid_params['INT'][1]},INTZ0={grid_params['INT'][2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">                <span class="fst">f"</span><span class="fst">INTX0=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'INT'</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTY0=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'INT'</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTZ0=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'INT'</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">params_preset_dict</span><span class="op">[</span><span class="str">'grid_cen0'</span><span class="op">]</span> <span class="op">=</span> <span class="xx">\</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">                <span class="str">f"CENX0={grid_params['CEN'][0]},CENY0={grid_params['CEN'][1]},CENZ0={grid_params['CEN'][2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">                <span class="fst">f"</span><span class="fst">CENX0=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'CEN'</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,CENY0=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'CEN'</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,CENZ0=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'CEN'</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="nam">params_preset_dict</span><span class="op">[</span><span class="str">'grid_dim0'</span><span class="op">]</span> <span class="op">=</span> <span class="xx">\</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">                <span class="str">f"DIMX0={grid_params['DIM'][0]},DIMY0={grid_params['DIM'][1]},DIMZ0={grid_params['DIM'][2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">                <span class="fst">f"</span><span class="fst">DIMX0=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'DIM'</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,DIMY0=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'DIM'</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,DIMZ0=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'DIM'</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">"input_json_box_path"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">params_preset_dict</span><span class="op">[</span><span class="str">"readgrid"</span><span class="op">]</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">origin</span><span class="op">,</span> <span class="nam">size</span><span class="op">,</span> <span class="nam">grid_params</span> <span class="op">=</span> <span class="nam">get_grid</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">"input_json_box_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">params_preset_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">=</span> <span class="xx">\</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="str">f"INTX={grid_params['INT'][0]},INTY={grid_params['INT'][1]},INTZ={grid_params['INT'][2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="fst">f"</span><span class="fst">INTX=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'INT'</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTY=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'INT'</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTZ=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'INT'</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">params_preset_dict</span><span class="op">[</span><span class="str">'grid_cen'</span><span class="op">]</span> <span class="op">=</span> <span class="xx">\</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">                <span class="str">f"CENX={grid_params['CEN'][0]},CENY={grid_params['CEN'][1]},CENZ={grid_params['CEN'][2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">                <span class="fst">f"</span><span class="fst">CENX=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'CEN'</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,CENY=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'CEN'</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,CENZ=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'CEN'</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">params_preset_dict</span><span class="op">[</span><span class="str">'grid_dim'</span><span class="op">]</span> <span class="op">=</span> <span class="xx">\</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="str">f"DIMX={grid_params['DIM'][0]},DIMY={grid_params['DIM'][1]},DIMZ={grid_params['DIM'][2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="fst">f"</span><span class="fst">DIMX=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'DIM'</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,DIMY=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'DIM'</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,DIMZ=</span><span class="op">{</span><span class="nam">grid_params</span><span class="op">[</span><span class="str">'DIM'</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_json_box_path'</span><span class="op">]</span> <span class="key">or</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_json_external_box_path'</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">params_preset_dict</span><span class="op">[</span><span class="str">'WRITELOG'</span><span class="op">]</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
@@ -314,7 +314,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="key">elif</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">output_pdb_path</span> <span class="op">+</span> <span class="str">".pdb"</span><span class="op">)</span><span class="op">.</span><span class="nam">exists</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">                <span class="nam">shutil</span><span class="op">.</span><span class="nam">move</span><span class="op">(</span><span class="nam">output_pdb_path</span> <span class="op">+</span> <span class="str">".pdb"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'output_pdb_path'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">            <span class="key">elif</span> <span class="key">not</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">output_pdb_path</span><span class="op">)</span><span class="op">.</span><span class="nam">exists</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"WARNING: File not found output_pdb_path: {output_pdb_path}"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">WARNING: File not found output_pdb_path: </span><span class="op">{</span><span class="nam">output_pdb_path</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="com"># Replace "ATOMTM" tag for "ATOM  "</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -327,7 +327,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">                    <span class="key">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">list_pdb_lines</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">                        <span class="nam">pdb_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">line</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">'ATOMTM'</span><span class="op">,</span> <span class="str">'ATOM  '</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"WARNING: File not found output_pdb_path: {output_pdb_path} Abs Path: {Path(output_pdb_path).resolve()}"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">WARNING: File not found output_pdb_path: </span><span class="op">{</span><span class="nam">output_pdb_path</span><span class="op">}</span><span class="fst"> Abs Path: </span><span class="op">{</span><span class="nam">Path</span><span class="op">(</span><span class="nam">output_pdb_path</span><span class="op">)</span><span class="op">.</span><span class="nam">resolve</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="com"># Create json_box_path file from CMIP log file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'output_json_box_path'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -443,7 +443,7 @@ <h2>
             <a class="nav" href="z_8c1d59f76554b5b6_cmip_titration_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8c1d59f76554b5b6_cmip_titration_py.html b/coverage/z_8c1d59f76554b5b6_cmip_titration_py.html
index 60ea637..9b7b787 100644
--- a/coverage/z_8c1d59f76554b5b6_cmip_titration_py.html
+++ b/coverage/z_8c1d59f76554b5b6_cmip_titration_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8c1d59f76554b5b6_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -170,7 +170,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'titration'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">output_params_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'output_params_path'</span><span class="op">,</span> <span class="str">'params'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'input_vdw_params_path'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_vdw_params_path'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{os.environ.get('CONDA_PREFIX')}/share/cmip/dat/vdwprm"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_vdw_params_path'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">os</span><span class="op">.</span><span class="nam">environ</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'CONDA_PREFIX'</span><span class="op">)</span><span class="op">}</span><span class="fst">/share/cmip/dat/vdwprm</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">params</span><span class="op">:</span> <span class="nam">dict</span><span class="op">[</span><span class="nam">str</span><span class="op">,</span> <span class="nam">Any</span><span class="op">]</span> <span class="op">=</span> <span class="op">{</span><span class="nam">k</span><span class="op">:</span> <span class="nam">str</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span> <span class="key">for</span> <span class="nam">k</span><span class="op">,</span> <span class="nam">v</span> <span class="key">in</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'params'</span><span class="op">,</span> <span class="nam">dict</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">.</span><span class="nam">items</span><span class="op">(</span><span class="op">)</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">energy_cutoff</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'energy_cutoff'</span><span class="op">,</span> <span class="num">9999.9</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -206,12 +206,12 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="key">elif</span> <span class="nam">int</span><span class="op">(</span><span class="nam">round</span><span class="op">(</span><span class="nam">charge</span><span class="op">)</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">params</span><span class="op">[</span><span class="str">'titip'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">abs</span><span class="op">(</span><span class="nam">int</span><span class="op">(</span><span class="nam">round</span><span class="op">(</span><span class="nam">charge</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'Neutral flag activated however no positive or negative ions will be added because the system '</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                       <span class="str">f'is already neutralized. System charge: {round(charge, 3)}'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'Neutral flag activated. Current system charge: {round(charge, 3)}, '</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                   <span class="str">f'positive ions to be added: {self.params["titip"]}, '</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                   <span class="str">f'negative ions to be added: {self.params["titim"]}, '</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">                   <span class="str">f'final residual charge: {round(charge + int(self.params["titip"]) - int(self.params["titim"]), 3)}'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="fst">Neutral flag activated however no positive or negative ions will be added because the system </span><span class="fst">'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                       <span class="fst">f'</span><span class="fst">is already neutralized. System charge: </span><span class="op">{</span><span class="nam">round</span><span class="op">(</span><span class="nam">charge</span><span class="op">,</span> <span class="num">3</span><span class="op">)</span><span class="op">}</span><span class="fst">'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="fst">Neutral flag activated. Current system charge: </span><span class="op">{</span><span class="nam">round</span><span class="op">(</span><span class="nam">charge</span><span class="op">,</span> <span class="num">3</span><span class="op">)</span><span class="op">}</span><span class="fst">, </span><span class="fst">'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                   <span class="fst">f'</span><span class="fst">positive ions to be added: </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">params</span><span class="op">[</span><span class="str">"titip"</span><span class="op">]</span><span class="op">}</span><span class="fst">, </span><span class="fst">'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                   <span class="fst">f'</span><span class="fst">negative ions to be added: </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">params</span><span class="op">[</span><span class="str">"titim"</span><span class="op">]</span><span class="op">}</span><span class="fst">, </span><span class="fst">'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">                   <span class="fst">f'</span><span class="fst">final residual charge: </span><span class="op">{</span><span class="nam">round</span><span class="op">(</span><span class="nam">charge</span> <span class="op">+</span> <span class="nam">int</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">params</span><span class="op">[</span><span class="str">"titip"</span><span class="op">]</span><span class="op">)</span> <span class="op">-</span> <span class="nam">int</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">params</span><span class="op">[</span><span class="str">"titim"</span><span class="op">]</span><span class="op">)</span><span class="op">,</span> <span class="num">3</span><span class="op">)</span><span class="op">}</span><span class="fst">'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">energy_cutoff</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">params</span><span class="op">[</span><span class="str">'titcut'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">energy_cutoff</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -289,7 +289,7 @@ <h2>
             <a class="nav" href="z_8c1d59f76554b5b6_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8c1d59f76554b5b6_common_py.html b/coverage/z_8c1d59f76554b5b6_common_py.html
index 1033075..8f7fb85 100644
--- a/coverage/z_8c1d59f76554b5b6_common_py.html
+++ b/coverage/z_8c1d59f76554b5b6_common_py.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-    <title>Coverage for biobb_cmip/cmip/common.py: 44%</title>
+    <title>Coverage for biobb_cmip/cmip/common.py: 45%</title>
     <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
     <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
     <script src="coverage_html_cb_6fb7b396.js" defer></script>
@@ -12,7 +12,7 @@
     <div class="content">
         <h1>
             <span class="text">Coverage for </span><b>biobb_cmip/cmip/common.py</b>:
-            <span class="pc_cov">44%</span>
+            <span class="pc_cov">45%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">372 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">165<span class="text"> run</span></button>
+            <span class="text">373 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">166<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">207<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_edf6e6b2d5ce0b2c___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -184,7 +184,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">parent_dir</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">.</span><span class="nam">cwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">    <span class="key">if</span> <span class="key">not</span> <span class="nam">extension</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="nam">extension</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">    <span class="key">while</span> <span class="key">True</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">    <span class="key">while</span> <span class="key">True</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">name</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">uuid</span><span class="op">.</span><span class="nam">uuid4</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">+</span><span class="nam">extension</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">file_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">parent_dir</span><span class="op">)</span><span class="op">.</span><span class="nam">resolve</span><span class="op">(</span><span class="op">)</span><span class="op">,</span> <span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">file_path</span><span class="op">.</span><span class="nam">exists</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -314,13 +314,13 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="key">if</span> <span class="nam">nomr</span> <span class="op">==</span> <span class="str">"HIS"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">                <span class="nam">nomr</span> <span class="op">=</span> <span class="str">"HID"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">                <span class="key">if</span> <span class="nam">residue_num</span> <span class="op">!=</span> <span class="nam">line</span><span class="op">[</span><span class="num">23</span><span class="op">:</span><span class="num">27</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                    <span class="nam">print</span><span class="op">(</span><span class="str">f"WARNING replacing HIS:{line[23:27]} by HID"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                    <span class="nam">print</span><span class="op">(</span><span class="fst">f"</span><span class="fst">WARNING replacing HIS:</span><span class="op">{</span><span class="nam">line</span><span class="op">[</span><span class="num">23</span><span class="op">:</span><span class="num">27</span><span class="op">]</span><span class="op">}</span><span class="fst"> by HID</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">                    <span class="nam">residue_num</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">23</span><span class="op">:</span><span class="num">27</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">            <span class="com"># Thats not correct REVIEW this should be done for all the atoms in the residue</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">            <span class="com"># not just the oxigen</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">            <span class="key">if</span> <span class="nam">nomat</span> <span class="op">==</span> <span class="str">"OXT"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">                <span class="nam">nomr</span> <span class="op">=</span> <span class="nam">nomr</span> <span class="op">+</span> <span class="str">"C"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">                <span class="nam">print</span><span class="op">(</span><span class="str">f"WARNING replacing {nomr[:-1]}:{line[23:27]} by {nomr}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">                <span class="nam">print</span><span class="op">(</span><span class="fst">f"</span><span class="fst">WARNING replacing </span><span class="op">{</span><span class="nam">nomr</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">:</span><span class="op">{</span><span class="nam">line</span><span class="op">[</span><span class="num">23</span><span class="op">:</span><span class="num">27</span><span class="op">]</span><span class="op">}</span><span class="fst"> by </span><span class="op">{</span><span class="nam">nomr</span><span class="op">}</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">            <span class="com">######################################################</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">            <span class="nam">parms</span> <span class="op">=</span> <span class="nam">aaLib</span><span class="op">.</span><span class="nam">getParams</span><span class="op">(</span><span class="nam">nomr</span><span class="op">,</span> <span class="nam">nomat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">            <span class="nam">charges_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">parms</span><span class="op">.</span><span class="nam">charg</span><span class="op">)</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
@@ -351,13 +351,13 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">            <span class="key">if</span> <span class="nam">nomr</span> <span class="op">==</span> <span class="str">"HIS"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">                <span class="nam">nomr</span> <span class="op">=</span> <span class="str">"HID"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">                <span class="key">if</span> <span class="nam">residue_num</span> <span class="op">!=</span> <span class="nam">line</span><span class="op">[</span><span class="num">23</span><span class="op">:</span><span class="num">27</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">                    <span class="nam">print</span><span class="op">(</span><span class="str">f"WARNING replacing HIS:{line[23:27]} by HID"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">                    <span class="nam">print</span><span class="op">(</span><span class="fst">f"</span><span class="fst">WARNING replacing HIS:</span><span class="op">{</span><span class="nam">line</span><span class="op">[</span><span class="num">23</span><span class="op">:</span><span class="num">27</span><span class="op">]</span><span class="op">}</span><span class="fst"> by HID</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">                    <span class="nam">residue_num</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">23</span><span class="op">:</span><span class="num">27</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">            <span class="com"># Thats not correct REVIEW this should be done for all the atoms in the residue</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">            <span class="com"># not just the oxigen</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">            <span class="key">if</span> <span class="nam">nomat</span> <span class="op">==</span> <span class="str">"OXT"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">                <span class="nam">nomr</span> <span class="op">=</span> <span class="nam">nomr</span> <span class="op">+</span> <span class="str">"C"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">                <span class="nam">print</span><span class="op">(</span><span class="str">f"WARNING replacing {nomr[:-1]}:{line[23:27]} by {nomr}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">                <span class="nam">print</span><span class="op">(</span><span class="fst">f"</span><span class="fst">WARNING replacing </span><span class="op">{</span><span class="nam">nomr</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">:</span><span class="op">{</span><span class="nam">line</span><span class="op">[</span><span class="num">23</span><span class="op">:</span><span class="num">27</span><span class="op">]</span><span class="op">}</span><span class="fst"> by </span><span class="op">{</span><span class="nam">nomr</span><span class="op">}</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">            <span class="com">######################################################</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">            <span class="nam">parms</span> <span class="op">=</span> <span class="nam">aaLib</span><span class="op">.</span><span class="nam">getParams</span><span class="op">(</span><span class="nam">nomr</span><span class="op">,</span> <span class="nam">nomat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">            <span class="nam">elements_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">parms</span><span class="op">.</span><span class="nam">atType</span><span class="op">)</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
@@ -378,10 +378,10 @@ <h2>
     <p class="run"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t"><span class="key">def</span> <span class="nam">probe_params_grid</span><span class="op">(</span><span class="nam">probe_id</span><span class="op">:</span> <span class="nam">int</span> <span class="op">=</span> <span class="num">0</span><span class="op">,</span> <span class="nam">readgrid</span><span class="op">:</span> <span class="nam">int</span> <span class="op">=</span> <span class="num">2</span><span class="op">,</span> <span class="nam">pbfocus</span><span class="op">:</span> <span class="nam">int</span> <span class="op">=</span> <span class="num">1</span><span class="op">,</span> <span class="nam">perfill</span><span class="op">:</span> <span class="nam">float</span> <span class="op">=</span> <span class="num">0.6</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">                      <span class="nam">grid_int</span><span class="op">:</span> <span class="nam">tuple</span><span class="op">[</span><span class="nam">float</span><span class="op">,</span> <span class="nam">float</span><span class="op">,</span> <span class="nam">float</span><span class="op">]</span> <span class="op">=</span> <span class="op">(</span><span class="num">0.5</span><span class="op">,</span> <span class="num">0.5</span><span class="op">,</span> <span class="num">0.5</span><span class="op">)</span><span class="op">)</span> <span class="op">-></span> <span class="nam">dict</span><span class="op">[</span><span class="nam">str</span><span class="op">,</span> <span class="nam">str</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">    <span class="nam">grid_dict</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="str">f"readgrid{probe_id}"</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{readgrid}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="str">f"perfill{probe_id}"</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{perfill}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'pbfocus'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{pbfocus}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"INTX{probe_id}={grid_int[0]},INTY{probe_id}={grid_int[1]},INTZ{probe_id}={grid_int[2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="fst">f"</span><span class="fst">readgrid</span><span class="op">{</span><span class="nam">probe_id</span><span class="op">}</span><span class="fst">"</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">readgrid</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="fst">f"</span><span class="fst">perfill</span><span class="op">{</span><span class="nam">probe_id</span><span class="op">}</span><span class="fst">"</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">perfill</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'pbfocus'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">pbfocus</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">INTX</span><span class="op">{</span><span class="nam">probe_id</span><span class="op">}</span><span class="fst">=</span><span class="op">{</span><span class="nam">grid_int</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTY</span><span class="op">{</span><span class="nam">probe_id</span><span class="op">}</span><span class="fst">=</span><span class="op">{</span><span class="nam">grid_int</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTZ</span><span class="op">{</span><span class="nam">probe_id</span><span class="op">}</span><span class="fst">=</span><span class="op">{</span><span class="nam">grid_int</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">    <span class="key">return</span> <span class="nam">grid_dict</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -397,15 +397,15 @@ <h2>
     <p class="pln"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">    <span class="com">#     cmip, titration, pbsolvation = 2, >3</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">    <span class="nam">grid_dict</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="str">"readgrid"</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{readgrid}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">    <span class="nam">grid_dict</span><span class="op">[</span><span class="str">"readgrid"</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">readgrid</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">    <span class="key">if</span> <span class="nam">grid_type</span> <span class="key">in</span> <span class="op">[</span><span class="str">'pb_interaction_energy'</span><span class="op">,</span> <span class="str">'mip_pos'</span><span class="op">,</span> <span class="str">'mip_neu'</span><span class="op">,</span> <span class="str">'mip_neg'</span><span class="op">,</span> <span class="str">'docking'</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_cen'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"CENX={grid_cen[0]},CENY={grid_cen[1]},CENZ={grid_cen[2]}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_dim'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"DIMX={grid_dim[0]},DIMY={grid_dim[1]},DIMZ={grid_dim[2]}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"INTX={grid_int[0]},INTY={grid_int[1]},INTZ={grid_int[2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_cen'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">CENX=</span><span class="op">{</span><span class="nam">grid_cen</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,CENY=</span><span class="op">{</span><span class="nam">grid_cen</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,CENZ=</span><span class="op">{</span><span class="nam">grid_cen</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_dim'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">DIMX=</span><span class="op">{</span><span class="nam">grid_dim</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,DIMY=</span><span class="op">{</span><span class="nam">grid_dim</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,DIMZ=</span><span class="op">{</span><span class="nam">grid_dim</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">INTX=</span><span class="op">{</span><span class="nam">grid_int</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTY=</span><span class="op">{</span><span class="nam">grid_int</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTZ=</span><span class="op">{</span><span class="nam">grid_int</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">    <span class="key">elif</span> <span class="nam">grid_type</span> <span class="key">in</span> <span class="op">[</span><span class="str">'solvation'</span><span class="op">,</span> <span class="str">'titration'</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'perfill'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{perfill}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"INTX={grid_int[0]},INTY={grid_int[1]},INTZ={grid_int[2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'perfill'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">perfill</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">        <span class="nam">grid_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">INTX=</span><span class="op">{</span><span class="nam">grid_int</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTY=</span><span class="op">{</span><span class="nam">grid_int</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">,INTZ=</span><span class="op">{</span><span class="nam">grid_int</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t">    <span class="key">return</span> <span class="nam">grid_dict</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t329" href="#t329">329</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -564,19 +564,19 @@ <h2>
     <p class="pln"><span class="n"><a id="t482" href="#t482">482</a></span><span class="t">                <span class="com"># Grid Values</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t483" href="#t483">483</a></span><span class="t">                <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">param_key</span><span class="op">)</span> <span class="op">></span> <span class="num">3</span> <span class="key">and</span> <span class="nam">param_key</span><span class="op">[</span><span class="op">:</span><span class="num">3</span><span class="op">]</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">'INT'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t484" href="#t484">484</a></span><span class="t">                    <span class="key">if</span> <span class="nam">params_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'grid_int'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t485" href="#t485">485</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">+=</span> <span class="str">f",{param_key}={param_value}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t485" href="#t485">485</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">+=</span> <span class="fst">f"</span><span class="fst">,</span><span class="op">{</span><span class="nam">param_key</span><span class="op">}</span><span class="fst">=</span><span class="op">{</span><span class="nam">param_value</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t486" href="#t486">486</a></span><span class="t">                    <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t487" href="#t487">487</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{param_key}={param_value}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t487" href="#t487">487</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_int'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">param_key</span><span class="op">}</span><span class="fst">=</span><span class="op">{</span><span class="nam">param_value</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t488" href="#t488">488</a></span><span class="t">                <span class="key">elif</span> <span class="nam">len</span><span class="op">(</span><span class="nam">param_key</span><span class="op">)</span> <span class="op">></span> <span class="num">3</span> <span class="key">and</span> <span class="nam">param_key</span><span class="op">[</span><span class="op">:</span><span class="num">3</span><span class="op">]</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">'CEN'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t489" href="#t489">489</a></span><span class="t">                    <span class="key">if</span> <span class="nam">params_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'grid_cen'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t490" href="#t490">490</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_cen'</span><span class="op">]</span> <span class="op">+=</span> <span class="str">f",{param_key}={param_value}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t490" href="#t490">490</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_cen'</span><span class="op">]</span> <span class="op">+=</span> <span class="fst">f"</span><span class="fst">,</span><span class="op">{</span><span class="nam">param_key</span><span class="op">}</span><span class="fst">=</span><span class="op">{</span><span class="nam">param_value</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t491" href="#t491">491</a></span><span class="t">                    <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t492" href="#t492">492</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_cen'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{param_key}={param_value}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t492" href="#t492">492</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_cen'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">param_key</span><span class="op">}</span><span class="fst">=</span><span class="op">{</span><span class="nam">param_value</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t493" href="#t493">493</a></span><span class="t">                <span class="key">elif</span> <span class="nam">len</span><span class="op">(</span><span class="nam">param_key</span><span class="op">)</span> <span class="op">></span> <span class="num">3</span> <span class="key">and</span> <span class="nam">param_key</span><span class="op">[</span><span class="op">:</span><span class="num">3</span><span class="op">]</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">'DIM'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t494" href="#t494">494</a></span><span class="t">                    <span class="key">if</span> <span class="nam">params_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'grid_dim'</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t495" href="#t495">495</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_dim'</span><span class="op">]</span> <span class="op">+=</span> <span class="str">f",{param_key}={param_value}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t495" href="#t495">495</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_dim'</span><span class="op">]</span> <span class="op">+=</span> <span class="fst">f"</span><span class="fst">,</span><span class="op">{</span><span class="nam">param_key</span><span class="op">}</span><span class="fst">=</span><span class="op">{</span><span class="nam">param_value</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t496" href="#t496">496</a></span><span class="t">                    <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t497" href="#t497">497</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_dim'</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{param_key}={param_value}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t497" href="#t497">497</a></span><span class="t">                        <span class="nam">params_dict</span><span class="op">[</span><span class="str">'grid_dim'</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">param_key</span><span class="op">}</span><span class="fst">=</span><span class="op">{</span><span class="nam">param_value</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t498" href="#t498">498</a></span><span class="t">                <span class="com"># Rest of parameters</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t499" href="#t499">499</a></span><span class="t">                <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t500" href="#t500">500</a></span><span class="t">                    <span class="nam">params_dict</span><span class="op">[</span><span class="nam">param_key</span><span class="op">]</span> <span class="op">=</span> <span class="nam">param_value</span>&nbsp;</span><span class="r"></span></p>
@@ -585,13 +585,13 @@ <h2>
     <p class="pln"><span class="n"><a id="t503" href="#t503">503</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t504" href="#t504">504</a></span><span class="t"><span class="key">def</span> <span class="nam">write_params_file</span><span class="op">(</span><span class="nam">output_params_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">params_dict</span><span class="op">:</span> <span class="nam">dict</span><span class="op">[</span><span class="nam">str</span><span class="op">,</span> <span class="nam">str</span><span class="op">]</span><span class="op">)</span> <span class="op">-></span> <span class="nam">str</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t505" href="#t505">505</a></span><span class="t">    <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">output_params_path</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">output_params_file</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t506" href="#t506">506</a></span><span class="t">        <span class="nam">output_params_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">f"{params_dict.pop('title', 'Untitled')}\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t506" href="#t506">506</a></span><span class="t">        <span class="nam">output_params_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">params_dict</span><span class="op">.</span><span class="nam">pop</span><span class="op">(</span><span class="str">'title'</span><span class="op">,</span> <span class="str">'Untitled'</span><span class="op">)</span><span class="op">}</span><span class="fst">\n</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t507" href="#t507">507</a></span><span class="t">        <span class="nam">output_params_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"&amp;cntrl\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t508" href="#t508">508</a></span><span class="t">        <span class="key">for</span> <span class="nam">params_key</span><span class="op">,</span> <span class="nam">params_value</span> <span class="key">in</span> <span class="nam">params_dict</span><span class="op">.</span><span class="nam">items</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t509" href="#t509">509</a></span><span class="t">            <span class="key">if</span> <span class="nam">params_key</span> <span class="key">in</span> <span class="op">[</span><span class="str">'grid_int'</span><span class="op">,</span> <span class="str">'grid_cen'</span><span class="op">,</span> <span class="str">'grid_dim'</span><span class="op">,</span> <span class="str">'grid_int0'</span><span class="op">,</span> <span class="str">'grid_cen0'</span><span class="op">,</span> <span class="str">'grid_dim0'</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t510" href="#t510">510</a></span><span class="t">                <span class="nam">output_params_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">f" {params_value}\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t510" href="#t510">510</a></span><span class="t">                <span class="nam">output_params_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="fst">f"</span><span class="fst"> </span><span class="op">{</span><span class="nam">params_value</span><span class="op">}</span><span class="fst">\n</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t511" href="#t511">511</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t512" href="#t512">512</a></span><span class="t">                <span class="nam">output_params_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">f" {params_key} = {params_value}\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t512" href="#t512">512</a></span><span class="t">                <span class="nam">output_params_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="fst">f"</span><span class="fst"> </span><span class="op">{</span><span class="nam">params_key</span><span class="op">}</span><span class="fst"> = </span><span class="op">{</span><span class="nam">params_value</span><span class="op">}</span><span class="fst">\n</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t513" href="#t513">513</a></span><span class="t">        <span class="nam">output_params_file</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"&amp;end\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t514" href="#t514">514</a></span><span class="t">    <span class="key">return</span> <span class="nam">output_params_path</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t515" href="#t515">515</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -633,7 +633,7 @@ <h2>
     <p class="run"><span class="n"><a id="t551" href="#t551">551</a></span><span class="t">    <span class="key">if</span> <span class="key">not</span> <span class="nam">residue_list</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t552" href="#t552">552</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">"Empty residue_list all residues will be marked"</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t553" href="#t553">553</a></span><span class="t">    <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t554" href="#t554">554</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Residue list: {residue_list}"</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t554" href="#t554">554</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Residue list: </span><span class="op">{</span><span class="nam">residue_list</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t555" href="#t555">555</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t556" href="#t556">556</a></span><span class="t">    <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">input_cmip_pdb_path</span><span class="op">)</span> <span class="key">as</span> <span class="nam">pdb_file_in</span><span class="op">,</span> <span class="nam">open</span><span class="op">(</span><span class="nam">output_cmip_pdb_path</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">pdb_file_out</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t557" href="#t557">557</a></span><span class="t">        <span class="nam">residue_set_used</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -648,12 +648,12 @@ <h2>
     <p class="run"><span class="n"><a id="t566" href="#t566">566</a></span><span class="t">                    <span class="nam">residue_set_used</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">used_residue</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t567" href="#t567">567</a></span><span class="t">                    <span class="nam">line</span> <span class="op">=</span> <span class="nam">_mark_pdb_atom</span><span class="op">(</span><span class="nam">line</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t568" href="#t568">568</a></span><span class="t">            <span class="nam">pdb_file_out</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">line</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t569" href="#t569">569</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"{res_counter} residues have been marked"</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t569" href="#t569">569</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">res_counter</span><span class="op">}</span><span class="fst"> residues have been marked</span><span class="fst">"</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t570" href="#t570">570</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t571" href="#t571">571</a></span><span class="t">        <span class="key">if</span> <span class="nam">residue_list</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t572" href="#t572">572</a></span><span class="t">            <span class="nam">unused_residues</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">residue_list</span><span class="op">)</span> <span class="op">-</span> <span class="nam">residue_set_used</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t573" href="#t573">573</a></span><span class="t">            <span class="key">if</span> <span class="nam">unused_residues</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t574" href="#t574">574</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"The following residues where present in the residue_list and have not been marked: {unused_residues}"</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t574" href="#t574">574</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">The following residues where present in the residue_list and have not been marked: </span><span class="op">{</span><span class="nam">unused_residues</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t575" href="#t575">575</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t576" href="#t576">576</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t577" href="#t577">577</a></span><span class="t"><span class="key">def</span> <span class="nam">_mark_pdb_atom</span><span class="op">(</span><span class="nam">line</span><span class="op">:</span> <span class="nam">str</span><span class="op">)</span> <span class="op">-></span> <span class="nam">str</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -702,7 +702,7 @@ <h2>
             <a class="nav" href="z_edf6e6b2d5ce0b2c___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_edf6e6b2d5ce0b2c___init___py.html b/coverage/z_edf6e6b2d5ce0b2c___init___py.html
index c4b465e..1bbcaab 100644
--- a/coverage/z_edf6e6b2d5ce0b2c___init___py.html
+++ b/coverage/z_edf6e6b2d5ce0b2c___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_60079514e0a65b75_test_cmip_ignore_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -89,7 +89,7 @@ <h2>
             <a class="nav" href="z_60079514e0a65b75_test_cmip_ignore_residues_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:52 +0000
+            created at 2024-11-04 11:55 +0000
         </p>
     </div>
 </footer>
diff --git a/flake8/index.html b/flake8/index.html
index ba2a257..16c567b 100644
--- a/flake8/index.html
+++ b/flake8/index.html
@@ -9,7 +9,7 @@
       <div id="masthead" class="sev-4"></div>
       <div id="page">
           <h1>flake8 violations</h1>
-         <p id="versions">Generated on 2024-11-04 11:51
+         <p id="versions">Generated on 2024-11-04 11:53
             with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.12.1, pyflakes: 3.2.0
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diff --git a/junit/junit.xml b/junit/junit.xml
index f9b4366..3cb410e 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="4" time="27.685" timestamp="2024-11-04T11:51:43.390347+00:00" hostname="biobb-runners"><testcase classname="biobb_cmip.test.unitests.test_cmip.test_cmip_ignore_residues.TestCmipIgnoreResidues" name="test_cmip_ignore_residues" time="0.371" /><testcase classname="biobb_cmip.test.unitests.test_cmip.test_cmip_prepare_pdb.TestCmipPreparePDB" name="test_cmip_prepare_pdb" time="1.340" /><testcase classname="biobb_cmip.test.unitests.test_cmip.test_cmip_prepare_structure.TestCmipPrepareStructureTopology" name="test_cmip_prepare_structure_Topology" time="7.403" /><testcase classname="biobb_cmip.test.unitests.test_cmip.test_cmip_run.TestCmipRunEnergy" name="test_cmip_run_energy" time="17.683" /></testsuite></testsuites>
\ No newline at end of file
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="4" time="112.060" timestamp="2024-11-04T11:53:47.459145+00:00" hostname="biobb-runners"><testcase classname="biobb_cmip.test.unitests.test_cmip.test_cmip_ignore_residues.TestCmipIgnoreResidues" name="test_cmip_ignore_residues" time="0.640" /><testcase classname="biobb_cmip.test.unitests.test_cmip.test_cmip_prepare_pdb.TestCmipPreparePDB" name="test_cmip_prepare_pdb" time="1.039" /><testcase classname="biobb_cmip.test.unitests.test_cmip.test_cmip_prepare_structure.TestCmipPrepareStructureTopology" name="test_cmip_prepare_structure_Topology" time="6.727" /><testcase classname="biobb_cmip.test.unitests.test_cmip.test_cmip_run.TestCmipRunEnergy" name="test_cmip_run_energy" time="102.222" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index 44f82f5..9b47822 100644
--- a/junit/report.html
+++ b/junit/report.html
@@ -7,7 +7,7 @@
   </head>
   <body>
     <h1 id="title">report.html</h1>
-    <p>Report generated on 04-Nov-2024 at 11:52:11 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 04-Nov-2024 at 11:55:39 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
         v4.1.1</p>
     <div id="environment-header">
       <h2>Environment</h2>
@@ -61,7 +61,7 @@ <h2>Environment</h2>
         <h2>Summary</h2>
         <div class="additional-summary prefix">
         </div>
-        <p class="run-count">4 tests took 00:00:27.</p>
+        <p class="run-count">4 tests took 00:01:51.</p>
         <p class="filter">(Un)check the boxes to filter the results.</p>
         <div class="summary__reload">
           <div class="summary__reload__button hidden" onclick="location.reload()">
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.9.20&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-200-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.3&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py::TestCmipIgnoreResidues::test_cmip_ignore_residues&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py::TestCmipIgnoreResidues::test_cmip_ignore_residues&#34;, &#34;duration&#34;: &#34;371 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py::TestCmipIgnoreResidues::test_cmip_ignore_residues&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;371 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 11:51:44,108 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_ignore_residues Version: 5.0.0\n2024-11-04 11:51:44,109 [MainThread  ] [INFO ]  Residue list: [&amp;#x27;:3&amp;#x27;]\n2024-11-04 11:51:44,136 [MainThread  ] [INFO ]  17 residues have been marked\n2024-11-04 11:51:44,137 [MainThread  ] [INFO ]  Removed: []\n2024-11-04 11:51:44,137 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/cmip_ignore_residues/ignore_residues_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_8/cmip_ignore_residues/ignore_residues_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/ignore_res_gln3.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3173\n     Atoms ALIGNED in PDB_B: 3173\n     RMS: 1.0024822746830985e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_ignore_residues Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 Residue list: [&amp;#x27;:3&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 17 residues have been marked\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 Removed: []\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py::TestCmipPreparePDB::test_cmip_prepare_pdb&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py::TestCmipPreparePDB::test_cmip_prepare_pdb&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py::TestCmipPreparePDB::test_cmip_prepare_pdb&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 11:51:44,501 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_prepare_pdb Version: 5.0.0\n2024-11-04 11:51:44,501 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961 directory successfully created\n2024-11-04 11:51:44,501 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/1aki.pdb to /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961\n2024-11-04 11:51:44,502 [MainThread  ] [INFO ]  check_structure -v -i /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961/1aki.pdb -o /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961/1aki_cmip.pdb --output_format cmip --non_interactive command_list --list &amp;#x27;water --remove yes; backbone --add_caps none; fixside --fix All; add_hydrogen --add_mode auto --add_charges CMIP&amp;#x27;\n\n2024-11-04 11:51:45,631 [MainThread  ] [INFO ]  Executing: check_structure -v -i /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75...\n2024-11-04 11:51:45,632 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 11:51:45,632 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\n\nStep 1: water --remove yes\nRunning water. Options: --remove yes\nDetected 78 Water molecules\nRemoved 78 Water molecules\n\nStep 2:  backbone --add_caps none\nRunning backbone. Options: --add_caps none\nFound No residues with missing backbone atoms\nNo backbone breaks\nNo unexpected backbone links\nCapping terminal ends\nTrue terminal residues: A1,A129\nNothing to do\nNo caps added\n\nStep 3:  fixside --fix All\nRunning fixside. Options: --fix All\nFound no residues with missing or unknown side chain atoms\n\nStep 4:  add_hydrogen --add_mode auto --add_charges CMIP\nRunning add_hydrogen. Options: --add_mode auto --add_charges CMIP\nFound 38 Residues requiring selection on adding H atoms\n CYS A6,A30,A64,A76,A80,A94,A115,A127\n ASP A18,A48,A52,A66,A87,A101,A119\n GLU A7,A35\n HIS A15\n LYS A1,A13,A33,A96,A97,A116\n ARG A5,A14,A21,A45,A61,A68,A73,A112,A114,A125,A128\n TYR A20,A23,A53\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A15 by HIE\nUpdating partial charges and atom types\nTotal assigned charge:       8.00\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  129\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 129 (total 967 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1968\nStructure saved on /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961/1aki_cmip.pdb\n\n2024-11-04 11:51:45,633 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961&amp;#x27;]\n2024-11-04 11:51:45,633 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/cmip_prepare_pdb/1aki_cmip.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_8/cmip_prepare_pdb/1aki_cmip.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/1aki_cmip.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 1001\n     Atoms ALIGNED in PDB_B: 1001\n     RMS: 1.4828848083881487e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_prepare_pdb Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:82 /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961 directory successfully created\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/1aki.pdb to /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:63 check_structure -v -i /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961/1aki.pdb -o /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961/1aki_cmip.pdb --output_format cmip --non_interactive command_list --list &amp;#x27;water --remove yes; backbone --add_caps none; fixside --fix All; add_hydrogen --add_mode auto --add_charges CMIP&amp;#x27;\n\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:36 Executing: check_structure -v -i /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75...\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\n\nStep 1: water --remove yes\nRunning water. Options: --remove yes\nDetected 78 Water molecules\nRemoved 78 Water molecules\n\nStep 2:  backbone --add_caps none\nRunning backbone. Options: --add_caps none\nFound No residues with missing backbone atoms\nNo backbone breaks\nNo unexpected backbone links\nCapping terminal ends\nTrue terminal residues: A1,A129\nNothing to do\nNo caps added\n\nStep 3:  fixside --fix All\nRunning fixside. Options: --fix All\nFound no residues with missing or unknown side chain atoms\n\nStep 4:  add_hydrogen --add_mode auto --add_charges CMIP\nRunning add_hydrogen. Options: --add_mode auto --add_charges CMIP\nFound 38 Residues requiring selection on adding H atoms\n CYS A6,A30,A64,A76,A80,A94,A115,A127\n ASP A18,A48,A52,A66,A87,A101,A119\n GLU A7,A35\n HIS A15\n LYS A1,A13,A33,A96,A97,A116\n ARG A5,A14,A21,A45,A61,A68,A73,A112,A114,A125,A128\n TYR A20,A23,A53\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A15 by HIE\nUpdating partial charges and atom types\nTotal assigned charge:       8.00\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  129\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 129 (total 967 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1968\nStructure saved on /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961/1aki_cmip.pdb\n\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_5a4cc2fd-75a2-4856-b793-867f84a52961&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 11:51:45,845 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_prepare_structure Version: 5.0.0\n2024-11-04 11:51:45,849 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\n2024-11-04 11:51:45,849 [MainThread  ] [INFO ]  to:\n2024-11-04 11:51:45,849 [MainThread  ] [INFO ]  [&amp;#x27;ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_posre.itp&amp;#x27;]\n2024-11-04 11:51:45,849 [MainThread  ] [INFO ]  Unzipping: \n2024-11-04 11:51:45,849 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\n2024-11-04 11:51:45,849 [MainThread  ] [INFO ]  To: \n2024-11-04 11:51:45,849 [MainThread  ] [INFO ]  ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_p2g.top\n2024-11-04 11:51:45,849 [MainThread  ] [INFO ]  ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_posre.itp\n2024-11-04 11:51:45,849 [MainThread  ] [INFO ]  Reading: ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_p2g.top to extract charges\n2024-11-04 11:51:49,151 [MainThread  ] [INFO ]  Reading: ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_p2g.top to extract elements\n2024-11-04 11:51:52,939 [MainThread  ] [INFO ]  Removed: [&amp;#x27;ecd926bc-0087-4f5b-91d5-474b454c82ea&amp;#x27;]\n2024-11-04 11:51:52,939 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/cmip_prepare_structure_topology/prepare_structure_topology_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_8/cmip_prepare_structure_topology/prepare_structure_topology_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/egfr_cmip.pdb\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2872\n     Atoms ALIGNED in PDB_B: 2872\n     RMS: 1.1126217417895259e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_prepare_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:174 [&amp;#x27;ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_posre.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:256 ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_p2g.top\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:256 ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_posre.itp\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Reading: ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_p2g.top to extract charges\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Reading: ecd926bc-0087-4f5b-91d5-474b454c82ea/pdb2gmx_p2g.top to extract elements\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Removed: [&amp;#x27;ecd926bc-0087-4f5b-91d5-474b454c82ea&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&#34;, &#34;duration&#34;: &#34;00:00:18&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:18&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 11:51:53,252 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_run Version: 5.0.0\n2024-11-04 11:51:53,253 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d directory successfully created\n2024-11-04 11:51:53,253 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.hACE2.cmip.pdb to /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d\n2024-11-04 11:51:53,254 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.RBD.cmip.pdb to /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d\n2024-11-04 11:51:53,254 [MainThread  ] [INFO ]  Copy: /home/user/micromamba/envs/test_environment/share/cmip/dat/vdwprm to /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d\n2024-11-04 11:51:53,254 [MainThread  ] [INFO ]  Copy: 14c9501f-af0e-4317-9a1d-50d437725fca/params to /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d\n2024-11-04 11:51:53,255 [MainThread  ] [INFO ]  cmip -i /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/params -vdw /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/vdwprm -hs /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/RBD-hACE2.hACE2.cmip.pdb -pr /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/RBD-hACE2.RBD.cmip.pdb -byat /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/output_byat.out\n\n2024-11-04 11:52:10,888 [MainThread  ] [INFO ]  Executing: cmip -i /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404...\n2024-11-04 11:52:10,889 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 11:52:10,889 [MainThread  ] [INFO ]   =================================================\n =                                               =\n =                C M I P  (2.7.0)               =\n =          J. Ll. Gelpi, A. Morreale,           =\n =            F. J. Luque, M.Orozco              =\n =      Dept. Biochemistry. Univ. Barcelona      =\n =                  1999-2021                    =\n =================================================\n\n  Code for ASA calculation by Juan F. Recio       \n\n#T Run started at   11:51:53 h on  4-11-2024\n SIZES\n -----\n MAXTIP:           100\n MAXATH:            80000\n MAXATP x MAXCONF: 100000\n\n INPUT FILES\n -----------\n    Calc. settings: /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/params                                                                    \n VdW Parameters:      /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/vdwprm                                                                    \n PDB Host:            /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/RBD-hACE2.hACE2.cmip.pdb                                                  \n PDB Guest:           /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/RBD-hACE2.RBD.cmip.pdb                                                    \n Conf. energies:      energies                                                                                                                                              \n\n OUTPUT FILES\n ------------\n LOG file:            output                                                                                                                                                \n Grid Out:            gridout                                                                                                                                               \n Output PDB coords:          outpdb                                                                                                                                                \n\n Parameters\n ----------\nDocking Interaction energy calculation. PB electrostatics                       \n&amp;amp;cntrl                                                                          \n tipcalc = 3                                                                    \n calcgrid = 1                                                                   \n irest = 0                                                                      \n orest = 0                                                                      \n coorfmt = 2                                                                    \n fvdw = 0.8                                                                     \n pbelec = 1                                                                     \n pbinic = 2                                                                     \n wgp = 0                                                                        \n ebyatom = 1                                                                    \n readgrid = 2                                                                   \n CENX=0.0,CENY=0.0,CENZ=0.0                                                     \n DIMX=64,DIMY=64,DIMZ=64                                                        \n INTX0=1.5,INTY0=1.5,INTZ0=1.5                                                  \n readgrid0 = 2                                                                  \n perfill0 = 0.6                                                                 \n pbfocus = 1                                                                    \n IREST = 0                                                                      \n&amp;amp;end                                                                            \n\n 18 VdW parameters loaded successfully\n\n Host:      9519 atoms loaded, charge   -27.000\n\n TYPE OF CALCULATION: DOCKING\n Single point\n\n Guest: 3000 atom(s), charge -11.145,    1 conformation(s) loaded\n\n PB Focussing requested\n AUTOMATIC OUTER GRID\n --------------------\n Fill:    0.600\nAutomatic Outer Grid                                                                                                                \n Grid Size:      96.000 138.000 108.000  90.000  90.000  90.000\n Grid density:    64   92   72\n Grid units:      1.500   1.500   1.500\n Grid origin:    23.610  -1.245   2.315\n Grid center:    71.610  67.755  56.315\n     441285 Grid points\n\n AUTOMATIC GRID\n --------------\n Fill:    0.800\nAutomatic Grid                                                                                                                      \n Grid Size:      72.000 103.000  81.500  90.000  90.000  90.000\n Grid density:   144  206  163\n Grid units:      0.500   0.500   0.500\n Grid origin:    35.610  16.255  15.565\n Grid center:    71.610  67.755  56.315\n    4922460 Grid points\n\n All input data read succesfully\n\n Warning: Dielectric grid computed at double density\n Mapping host molecule to outer grid\n   Total charge            :   -27.0000248    \n   Low diel. grid points   :                230941 (   97428.2344     A3)\n   High diel. grid points  :               3229484\n   I Str=0 grid points     :                441285\n   Boundary grid points    :                 57064\n Mapping host molecule to grid\n   Total charge            :   -27.0000019    \n   Low diel. grid points   :               5855067 (   91485.4219      A3)\n   High diel. grid points  :              33174672\n   I Str=0 grid points     :               4922460\n   Boundary grid points    :                550671\n\n CLHOST=           0\n EXTERNAL CUTOFF=   999999.000    \n Checking potentials to calculate...\n - Vdw: C   \n - Vdw: N   \n - Vdw: S   \n - Vdw: HO  \n - Vdw: HN  \n - Vdw: H   \n - Vdw: O   \n - Electrostatic \n     Dielectric type    :            0\n     Dielectric constant:    2.00000000    \n Vdw energies:\n  -C    -2.15     0.254E+21\n  -N    -2.73     0.266E+21\n  -S    -3.82     0.557E+21\n  -HO    0.00      0.00    \n  -HN  -0.344     0.116E+18\n  -H   -0.860     0.268E+20\n  -O    -2.87     0.169E+21\n     Poisson-Boltzmann calculation requested\n     Focussing          :            1\n     Initial potentials :            2\n     Solute  Dielectric :    2.00000000    \n     Solvent Dielectric :    79.8000031    \n     Solvent radius     :    1.39999998    \n     Convergence crit.  :    9.99999975E-05\n     Ionic strength     :    0.00000000    \n Outer grid\n          20  0.147574857       14.6699677    \n          40   2.98345201E-02   3.29004049    \n          60   6.40256703E-03  0.731274426    \n          80   1.45485543E-03  0.142998144    \n         100   3.46234767E-04   1.59425586E-02\n         120   8.31682264E-05   2.48038885E-03\n         140   1.97630197E-05   8.35724466E-04\n Converged at   157 iterations (Mean:       0.543E-05, Max:      0.988E-04)\n Potentials:   -145.994   169.029\n Inner Grid limits\n Potentials:   -128.467   156.689\n          20  0.879424989       44.1415787    \n          40  0.403403550       18.3190784    \n          60  0.196925744       11.3940735    \n          80   9.77351442E-02   6.85034180    \n         100   4.82290089E-02   3.02071834    \n         120   2.38220431E-02   1.71308899    \n         140   1.16539244E-02  0.880086958    \n         160   5.68585796E-03  0.497510821    \n         180   2.73818872E-03  0.352287740    \n         200   1.29141530E-03  0.225940496    \n         220   5.93792938E-04  0.122722477    \n         240   2.68824253E-04   4.83854339E-02\n         260   1.19691191E-04   1.86853185E-02\n         280   5.35512190E-05   5.89078385E-03\n         300   2.40280260E-05   2.55507161E-03\n         320   1.08220156E-05   1.01418095E-03\n         340   4.89427066E-06   3.80280049E-04\n         360   2.25906979E-06   1.78266186E-04\n Converged at   376 iterations (Mean:       0.125E-05, Max:      0.966E-04)\n Potentials:   -739.519  1051.831\n Internal:        4.20389539E-42  kcal/mol\n Van der Waals:         Infinity  kcal/mol\n Electrostatic:   90.0757980     kcal/mol\n Total Energy :         Infinity kcal/mol\n\n#T Run finished at  11:52:10 h on  4-11-2024\n\n#T       T I M I N G S \n#T       ---------------\n#T         Input:     0.180 s,   1.02%\n#T         Setup:     2.318 s,  13.18%\n#T         Grids:    15.086 s,  85.76%\n#T        Energy:     0.008 s,   0.04%\n#T        Output:     0.000 s,   0.00%\n ----------------------------------\n#T         TOTAL:    17.592 s ( 0.00 h)\n\n2024-11-04 11:52:10,890 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d&amp;#x27;, &amp;#x27;14c9501f-af0e-4317-9a1d-50d437725fca&amp;#x27;]\n2024-11-04 11:52:10,891 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/cmip_run/output_byat.out\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_run Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:82 /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d directory successfully created\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.hACE2.cmip.pdb to /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.RBD.cmip.pdb to /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/micromamba/envs/test_environment/share/cmip/dat/vdwprm to /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: 14c9501f-af0e-4317-9a1d-50d437725fca/params to /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:cmd_wrapper.py:63 cmip -i /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/params -vdw /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/vdwprm -hs /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/RBD-hACE2.hACE2.cmip.pdb -pr /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/RBD-hACE2.RBD.cmip.pdb -byat /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/output_byat.out\n\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:cmd_wrapper.py:36 Executing: cmip -i /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404...\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:cmd_wrapper.py:41  =================================================\n =                                               =\n =                C M I P  (2.7.0)               =\n =          J. Ll. Gelpi, A. Morreale,           =\n =            F. J. Luque, M.Orozco              =\n =      Dept. Biochemistry. Univ. Barcelona      =\n =                  1999-2021                    =\n =================================================\n\n  Code for ASA calculation by Juan F. Recio       \n\n#T Run started at   11:51:53 h on  4-11-2024\n SIZES\n -----\n MAXTIP:           100\n MAXATH:            80000\n MAXATP x MAXCONF: 100000\n\n INPUT FILES\n -----------\n    Calc. settings: /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/params                                                                    \n VdW Parameters:      /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/vdwprm                                                                    \n PDB Host:            /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/RBD-hACE2.hACE2.cmip.pdb                                                  \n PDB Guest:           /tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d/RBD-hACE2.RBD.cmip.pdb                                                    \n Conf. energies:      energies                                                                                                                                              \n\n OUTPUT FILES\n ------------\n LOG file:            output                                                                                                                                                \n Grid Out:            gridout                                                                                                                                               \n Output PDB coords:          outpdb                                                                                                                                                \n\n Parameters\n ----------\nDocking Interaction energy calculation. PB electrostatics                       \n&amp;amp;cntrl                                                                          \n tipcalc = 3                                                                    \n calcgrid = 1                                                                   \n irest = 0                                                                      \n orest = 0                                                                      \n coorfmt = 2                                                                    \n fvdw = 0.8                                                                     \n pbelec = 1                                                                     \n pbinic = 2                                                                     \n wgp = 0                                                                        \n ebyatom = 1                                                                    \n readgrid = 2                                                                   \n CENX=0.0,CENY=0.0,CENZ=0.0                                                     \n DIMX=64,DIMY=64,DIMZ=64                                                        \n INTX0=1.5,INTY0=1.5,INTZ0=1.5                                                  \n readgrid0 = 2                                                                  \n perfill0 = 0.6                                                                 \n pbfocus = 1                                                                    \n IREST = 0                                                                      \n&amp;amp;end                                                                            \n\n 18 VdW parameters loaded successfully\n\n Host:      9519 atoms loaded, charge   -27.000\n\n TYPE OF CALCULATION: DOCKING\n Single point\n\n Guest: 3000 atom(s), charge -11.145,    1 conformation(s) loaded\n\n PB Focussing requested\n AUTOMATIC OUTER GRID\n --------------------\n Fill:    0.600\nAutomatic Outer Grid                                                                                                                \n Grid Size:      96.000 138.000 108.000  90.000  90.000  90.000\n Grid density:    64   92   72\n Grid units:      1.500   1.500   1.500\n Grid origin:    23.610  -1.245   2.315\n Grid center:    71.610  67.755  56.315\n     441285 Grid points\n\n AUTOMATIC GRID\n --------------\n Fill:    0.800\nAutomatic Grid                                                                                                                      \n Grid Size:      72.000 103.000  81.500  90.000  90.000  90.000\n Grid density:   144  206  163\n Grid units:      0.500   0.500   0.500\n Grid origin:    35.610  16.255  15.565\n Grid center:    71.610  67.755  56.315\n    4922460 Grid points\n\n All input data read succesfully\n\n Warning: Dielectric grid computed at double density\n Mapping host molecule to outer grid\n   Total charge            :   -27.0000248    \n   Low diel. grid points   :                230941 (   97428.2344     A3)\n   High diel. grid points  :               3229484\n   I Str=0 grid points     :                441285\n   Boundary grid points    :                 57064\n Mapping host molecule to grid\n   Total charge            :   -27.0000019    \n   Low diel. grid points   :               5855067 (   91485.4219      A3)\n   High diel. grid points  :              33174672\n   I Str=0 grid points     :               4922460\n   Boundary grid points    :                550671\n\n CLHOST=           0\n EXTERNAL CUTOFF=   999999.000    \n Checking potentials to calculate...\n - Vdw: C   \n - Vdw: N   \n - Vdw: S   \n - Vdw: HO  \n - Vdw: HN  \n - Vdw: H   \n - Vdw: O   \n - Electrostatic \n     Dielectric type    :            0\n     Dielectric constant:    2.00000000    \n Vdw energies:\n  -C    -2.15     0.254E+21\n  -N    -2.73     0.266E+21\n  -S    -3.82     0.557E+21\n  -HO    0.00      0.00    \n  -HN  -0.344     0.116E+18\n  -H   -0.860     0.268E+20\n  -O    -2.87     0.169E+21\n     Poisson-Boltzmann calculation requested\n     Focussing          :            1\n     Initial potentials :            2\n     Solute  Dielectric :    2.00000000    \n     Solvent Dielectric :    79.8000031    \n     Solvent radius     :    1.39999998    \n     Convergence crit.  :    9.99999975E-05\n     Ionic strength     :    0.00000000    \n Outer grid\n          20  0.147574857       14.6699677    \n          40   2.98345201E-02   3.29004049    \n          60   6.40256703E-03  0.731274426    \n          80   1.45485543E-03  0.142998144    \n         100   3.46234767E-04   1.59425586E-02\n         120   8.31682264E-05   2.48038885E-03\n         140   1.97630197E-05   8.35724466E-04\n Converged at   157 iterations (Mean:       0.543E-05, Max:      0.988E-04)\n Potentials:   -145.994   169.029\n Inner Grid limits\n Potentials:   -128.467   156.689\n          20  0.879424989       44.1415787    \n          40  0.403403550       18.3190784    \n          60  0.196925744       11.3940735    \n          80   9.77351442E-02   6.85034180    \n         100   4.82290089E-02   3.02071834    \n         120   2.38220431E-02   1.71308899    \n         140   1.16539244E-02  0.880086958    \n         160   5.68585796E-03  0.497510821    \n         180   2.73818872E-03  0.352287740    \n         200   1.29141530E-03  0.225940496    \n         220   5.93792938E-04  0.122722477    \n         240   2.68824253E-04   4.83854339E-02\n         260   1.19691191E-04   1.86853185E-02\n         280   5.35512190E-05   5.89078385E-03\n         300   2.40280260E-05   2.55507161E-03\n         320   1.08220156E-05   1.01418095E-03\n         340   4.89427066E-06   3.80280049E-04\n         360   2.25906979E-06   1.78266186E-04\n Converged at   376 iterations (Mean:       0.125E-05, Max:      0.966E-04)\n Potentials:   -739.519  1051.831\n Internal:        4.20389539E-42  kcal/mol\n Van der Waals:         Infinity  kcal/mol\n Electrostatic:   90.0757980     kcal/mol\n Total Energy :         Infinity kcal/mol\n\n#T Run finished at  11:52:10 h on  4-11-2024\n\n#T       T I M I N G S \n#T       ---------------\n#T         Input:     0.180 s,   1.02%\n#T         Setup:     2.318 s,  13.18%\n#T         Grids:    15.086 s,  85.76%\n#T        Energy:     0.008 s,   0.04%\n#T        Output:     0.000 s,   0.00%\n ----------------------------------\n#T         TOTAL:    17.592 s ( 0.00 h)\n\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/cmip_run/sandbox_4b1b3cb8-7086-43e0-85c6-076710404f5d&amp;#x27;, &amp;#x27;14c9501f-af0e-4317-9a1d-50d437725fca&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.12.7&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-200-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.3&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py::TestCmipIgnoreResidues::test_cmip_ignore_residues&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py::TestCmipIgnoreResidues::test_cmip_ignore_residues&#34;, &#34;duration&#34;: &#34;640 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py::TestCmipIgnoreResidues::test_cmip_ignore_residues&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;640 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 11:53:48,837 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_ignore_residues Version: 5.0.0\n2024-11-04 11:53:48,837 [MainThread  ] [INFO ]  Residue list: [&amp;#x27;:3&amp;#x27;]\n2024-11-04 11:53:48,865 [MainThread  ] [INFO ]  17 residues have been marked\n2024-11-04 11:53:48,865 [MainThread  ] [INFO ]  Removed: []\n2024-11-04 11:53:48,865 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/cmip_ignore_residues/ignore_residues_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_8/cmip_ignore_residues/ignore_residues_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/ignore_res_gln3.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3173\n     Atoms ALIGNED in PDB_B: 3173\n     RMS: 1.0024822746830985e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_ignore_residues Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 Residue list: [&amp;#x27;:3&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 17 residues have been marked\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409 Removed: []\nINFO     /tmp/biobb/unitests_8/cmip_ignore_residues/cmip_ignore_residues_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py::TestCmipPreparePDB::test_cmip_prepare_pdb&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py::TestCmipPreparePDB::test_cmip_prepare_pdb&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py::TestCmipPreparePDB::test_cmip_prepare_pdb&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 11:53:49,485 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_prepare_pdb Version: 5.0.0\n2024-11-04 11:53:49,485 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf directory successfully created\n2024-11-04 11:53:49,486 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/1aki.pdb to /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf\n2024-11-04 11:53:49,486 [MainThread  ] [INFO ]  check_structure -v -i /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf/1aki.pdb -o /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf/1aki_cmip.pdb --output_format cmip --non_interactive command_list --list &amp;#x27;water --remove yes; backbone --add_caps none; fixside --fix All; add_hydrogen --add_mode auto --add_charges CMIP&amp;#x27;\n\n2024-11-04 11:53:50,373 [MainThread  ] [INFO ]  Executing: check_structure -v -i /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4a...\n2024-11-04 11:53:50,373 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 11:53:50,374 [MainThread  ] [INFO ]  ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\n\nStep 1: water --remove yes\nRunning water. Options: --remove yes\nDetected 78 Water molecules\nRemoved 78 Water molecules\n\nStep 2:  backbone --add_caps none\nRunning backbone. Options: --add_caps none\nFound No residues with missing backbone atoms\nNo backbone breaks\nNo unexpected backbone links\nCapping terminal ends\nTrue terminal residues: A1,A129\nNothing to do\nNo caps added\n\nStep 3:  fixside --fix All\nRunning fixside. Options: --fix All\nFound no residues with missing or unknown side chain atoms\n\nStep 4:  add_hydrogen --add_mode auto --add_charges CMIP\nRunning add_hydrogen. Options: --add_mode auto --add_charges CMIP\nFound 38 Residues requiring selection on adding H atoms\n CYS A6,A30,A64,A76,A80,A94,A115,A127\n ASP A18,A48,A52,A66,A87,A101,A119\n GLU A7,A35\n HIS A15\n LYS A1,A13,A33,A96,A97,A116\n ARG A5,A14,A21,A45,A61,A68,A73,A112,A114,A125,A128\n TYR A20,A23,A53\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A15 by HIE\nUpdating partial charges and atom types\nTotal assigned charge:       8.00\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  129\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 129 (total 967 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1968\nStructure saved on /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf/1aki_cmip.pdb\n\n2024-11-04 11:53:50,374 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf&amp;#x27;]\n2024-11-04 11:53:50,375 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/cmip_prepare_pdb/1aki_cmip.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_8/cmip_prepare_pdb/1aki_cmip.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/1aki_cmip.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 1001\n     Atoms ALIGNED in PDB_B: 1001\n     RMS: 1.4828848083881487e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_prepare_pdb Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:82 /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf directory successfully created\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/1aki.pdb to /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:63 check_structure -v -i /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf/1aki.pdb -o /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf/1aki_cmip.pdb --output_format cmip --non_interactive command_list --list &amp;#x27;water --remove yes; backbone --add_caps none; fixside --fix All; add_hydrogen --add_mode auto --add_charges CMIP&amp;#x27;\n\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:36 Executing: check_structure -v -i /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4a...\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:cmd_wrapper.py:41 ================================================================================\n=                   BioBB structure checking utility v3.13.5                   =\n=            P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23            =\n================================================================================\n\nWarning: sequence features may not be available, use --sequence for  external fasta input\nStructure /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf/1aki.pdb loaded\n PDB id: 1AKI \n Title: the structure of the orthorhombic form of hen egg-white lysozyme at 1.5 angstroms resolution\n Experimental method: x-ray diffraction\n Keywords: hydrolase, glycosidase\n Resolution (A): 1.5\n\n Num. models: 1\n Num. chains: 1 (A: Protein)\n Num. residues:  207\n Num. residues with ins. codes:  0\n Num. residues with H atoms: 0\n Num. HETATM residues:  78\n Num. ligands or modified residues:  0\n Num. water mol.:  78\n Num. atoms:  1079\n\nStep 1: water --remove yes\nRunning water. Options: --remove yes\nDetected 78 Water molecules\nRemoved 78 Water molecules\n\nStep 2:  backbone --add_caps none\nRunning backbone. Options: --add_caps none\nFound No residues with missing backbone atoms\nNo backbone breaks\nNo unexpected backbone links\nCapping terminal ends\nTrue terminal residues: A1,A129\nNothing to do\nNo caps added\n\nStep 3:  fixside --fix All\nRunning fixside. Options: --fix All\nFound no residues with missing or unknown side chain atoms\n\nStep 4:  add_hydrogen --add_mode auto --add_charges CMIP\nRunning add_hydrogen. Options: --add_mode auto --add_charges CMIP\nFound 38 Residues requiring selection on adding H atoms\n CYS A6,A30,A64,A76,A80,A94,A115,A127\n ASP A18,A48,A52,A66,A87,A101,A119\n GLU A7,A35\n HIS A15\n LYS A1,A13,A33,A96,A97,A116\n ARG A5,A14,A21,A45,A61,A68,A73,A112,A114,A125,A128\n TYR A20,A23,A53\nWARNING: fixing side chains, override with --no_fix_side\nRunning fixside. Options: --fix all\nFound no residues with missing or unknown side chain atoms\nSelection: auto\nReplacing HIS A15 by HIE\nUpdating partial charges and atom types\nTotal assigned charge:       8.00\nCommand list completed\nFinal Num. models: 1\nFinal Num. chains: 1 (A: Protein)\nFinal Num. residues:  129\nFinal Num. residues with ins. codes:  0\nFinal Num. residues with H atoms: 129 (total 967 H atoms)\nFinal Num. HETATM residues:  0\nFinal Num. ligands or modified residues:  0\nFinal Num. water mol.:  0\nFinal Num. atoms:  1968\nStructure saved on /tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf/1aki_cmip.pdb\n\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/cmip_prepare_pdb/sandbox_104f5f55-4ae7-4d75-bbcf-4de1f6147bbf&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_prepare_pdb/cmip_prepare_pdb_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_structure.py::TestCmipPrepareStructureTopology::test_cmip_prepare_structure_Topology&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 11:53:50,525 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_prepare_structure Version: 5.0.0\n2024-11-04 11:53:50,533 [MainThread  ] [INFO ]  Extracting: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\n2024-11-04 11:53:50,533 [MainThread  ] [INFO ]  to:\n2024-11-04 11:53:50,533 [MainThread  ] [INFO ]  [&amp;#x27;97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_posre.itp&amp;#x27;]\n2024-11-04 11:53:50,533 [MainThread  ] [INFO ]  Unzipping: \n2024-11-04 11:53:50,534 [MainThread  ] [INFO ]  /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\n2024-11-04 11:53:50,534 [MainThread  ] [INFO ]  To: \n2024-11-04 11:53:50,534 [MainThread  ] [INFO ]  97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_p2g.top\n2024-11-04 11:53:50,534 [MainThread  ] [INFO ]  97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_posre.itp\n2024-11-04 11:53:50,534 [MainThread  ] [INFO ]  Reading: 97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_p2g.top to extract charges\n2024-11-04 11:53:53,522 [MainThread  ] [INFO ]  Reading: 97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_p2g.top to extract elements\n2024-11-04 11:53:56,932 [MainThread  ] [INFO ]  Removed: [&amp;#x27;97f435a0-23db-4730-9b85-f4ba7734a949&amp;#x27;]\n2024-11-04 11:53:56,932 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/cmip_prepare_structure_topology/prepare_structure_topology_output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_8/cmip_prepare_structure_topology/prepare_structure_topology_output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/reference/cmip/egfr_cmip.pdb\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 2872\n     Atoms ALIGNED in PDB_B: 2872\n     RMS: 1.1126217417895259e-14\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_prepare_structure Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:172 Extracting: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:173 to:\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:174 [&amp;#x27;97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_p2g.top&amp;#x27;, &amp;#x27;97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_posre.itp&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:252 Unzipping: \nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:253 /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/egfr_topology.zip\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:254 To: \nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:256 97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_p2g.top\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:256 97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_posre.itp\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Reading: 97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_p2g.top to extract charges\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Reading: 97f435a0-23db-4730-9b85-f4ba7734a949/pdb2gmx_p2g.top to extract elements\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409 Removed: [&amp;#x27;97f435a0-23db-4730-9b85-f4ba7734a949&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_prepare_structure_topology/cmip_prepare_structure_topology_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}], &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&#34;, &#34;duration&#34;: &#34;00:01:42&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_cmip/test/unitests/test_cmip/test_cmip_run.py::TestCmipRunEnergy::test_cmip_run_energy&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:42&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 11:53:57,254 [MainThread  ] [INFO ]  Module: biobb_cmip.cmip.cmip_run Version: 5.0.0\n2024-11-04 11:53:57,255 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26 directory successfully created\n2024-11-04 11:53:57,256 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.hACE2.cmip.pdb to /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26\n2024-11-04 11:53:57,256 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.RBD.cmip.pdb to /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26\n2024-11-04 11:53:57,256 [MainThread  ] [INFO ]  Copy: /home/user/micromamba/envs/test_environment/share/cmip/dat/vdwprm to /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26\n2024-11-04 11:53:57,257 [MainThread  ] [INFO ]  Copy: 2baa347c-4335-4e6e-8eb1-92974d10d1fb/params to /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26\n2024-11-04 11:53:57,257 [MainThread  ] [INFO ]  cmip -i /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/params -vdw /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/vdwprm -hs /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/RBD-hACE2.hACE2.cmip.pdb -pr /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/RBD-hACE2.RBD.cmip.pdb -byat /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/output_byat.out\n\n2024-11-04 11:54:14,674 [MainThread  ] [INFO ]  Executing: cmip -i /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454...\n2024-11-04 11:54:14,674 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 11:54:14,674 [MainThread  ] [INFO ]   =================================================\n =                                               =\n =                C M I P  (2.7.0)               =\n =          J. Ll. Gelpi, A. Morreale,           =\n =            F. J. Luque, M.Orozco              =\n =      Dept. Biochemistry. Univ. Barcelona      =\n =                  1999-2021                    =\n =================================================\n\n  Code for ASA calculation by Juan F. Recio       \n\n#T Run started at   11:53:57 h on  4-11-2024\n SIZES\n -----\n MAXTIP:           100\n MAXATH:            80000\n MAXATP x MAXCONF: 100000\n\n INPUT FILES\n -----------\n    Calc. settings: /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/params                                                                    \n VdW Parameters:      /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/vdwprm                                                                    \n PDB Host:            /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/RBD-hACE2.hACE2.cmip.pdb                                                  \n PDB Guest:           /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/RBD-hACE2.RBD.cmip.pdb                                                    \n Conf. energies:      energies                                                                                                                                              \n\n OUTPUT FILES\n ------------\n LOG file:            output                                                                                                                                                \n Grid Out:            gridout                                                                                                                                               \n Output PDB coords:          outpdb                                                                                                                                                \n\n Parameters\n ----------\nDocking Interaction energy calculation. PB electrostatics                       \n&amp;amp;cntrl                                                                          \n tipcalc = 3                                                                    \n calcgrid = 1                                                                   \n irest = 0                                                                      \n orest = 0                                                                      \n coorfmt = 2                                                                    \n fvdw = 0.8                                                                     \n pbelec = 1                                                                     \n pbinic = 2                                                                     \n wgp = 0                                                                        \n ebyatom = 1                                                                    \n readgrid = 2                                                                   \n CENX=0.0,CENY=0.0,CENZ=0.0                                                     \n DIMX=64,DIMY=64,DIMZ=64                                                        \n INTX0=1.5,INTY0=1.5,INTZ0=1.5                                                  \n readgrid0 = 2                                                                  \n perfill0 = 0.6                                                                 \n pbfocus = 1                                                                    \n IREST = 0                                                                      \n&amp;amp;end                                                                            \n\n 18 VdW parameters loaded successfully\n\n Host:      9519 atoms loaded, charge   -27.000\n\n TYPE OF CALCULATION: DOCKING\n Single point\n\n Guest: 3000 atom(s), charge -11.145,    1 conformation(s) loaded\n\n PB Focussing requested\n AUTOMATIC OUTER GRID\n --------------------\n Fill:    0.600\nAutomatic Outer Grid                                                                                                                \n Grid Size:      96.000 138.000 108.000  90.000  90.000  90.000\n Grid density:    64   92   72\n Grid units:      1.500   1.500   1.500\n Grid origin:    23.610  -1.245   2.315\n Grid center:    71.610  67.755  56.315\n     441285 Grid points\n\n AUTOMATIC GRID\n --------------\n Fill:    0.800\nAutomatic Grid                                                                                                                      \n Grid Size:      72.000 103.000  81.500  90.000  90.000  90.000\n Grid density:   144  206  163\n Grid units:      0.500   0.500   0.500\n Grid origin:    35.610  16.255  15.565\n Grid center:    71.610  67.755  56.315\n    4922460 Grid points\n\n All input data read succesfully\n\n Warning: Dielectric grid computed at double density\n Mapping host molecule to outer grid\n   Total charge            :   -27.0000248    \n   Low diel. grid points   :                230941 (   97428.2344     A3)\n   High diel. grid points  :               3229484\n   I Str=0 grid points     :                441285\n   Boundary grid points    :                 57064\n Mapping host molecule to grid\n   Total charge            :   -27.0000019    \n   Low diel. grid points   :               5855067 (   91485.4219      A3)\n   High diel. grid points  :              33174672\n   I Str=0 grid points     :               4922460\n   Boundary grid points    :                550671\n\n CLHOST=           0\n EXTERNAL CUTOFF=   999999.000    \n Checking potentials to calculate...\n - Vdw: C   \n - Vdw: N   \n - Vdw: S   \n - Vdw: HO  \n - Vdw: HN  \n - Vdw: H   \n - Vdw: O   \n - Electrostatic \n     Dielectric type    :            0\n     Dielectric constant:    2.00000000    \n Vdw energies:\n  -C    -2.15     0.254E+21\n  -N    -2.73     0.266E+21\n  -S    -3.82     0.557E+21\n  -HO    0.00      0.00    \n  -HN  -0.344     0.116E+18\n  -H   -0.860     0.268E+20\n  -O    -2.87     0.169E+21\n     Poisson-Boltzmann calculation requested\n     Focussing          :            1\n     Initial potentials :            2\n     Solute  Dielectric :    2.00000000    \n     Solvent Dielectric :    79.8000031    \n     Solvent radius     :    1.39999998    \n     Convergence crit.  :    9.99999975E-05\n     Ionic strength     :    0.00000000    \n Outer grid\n          20  0.147574857       14.6699677    \n          40   2.98345201E-02   3.29004049    \n          60   6.40256703E-03  0.731274426    \n          80   1.45485543E-03  0.142998144    \n         100   3.42993939E-04   1.78021304E-02\n         120   8.23287264E-05   2.51317094E-03\n         140   1.94953154E-05   8.38404230E-04\n Converged at   158 iterations (Mean:       0.494E-05, Max:      0.923E-04)\n Potentials:   -145.994   169.029\n Inner Grid limits\n Potentials:   -128.467   156.689\n          20  0.878943920       44.1415787    \n          40  0.403151721       18.3211327    \n          60  0.196834385       11.3860836    \n          80   9.76954326E-02   6.86376905    \n         100   4.82133329E-02   3.11586928    \n         120   2.38133743E-02   1.68073165    \n         140   1.16519779E-02  0.922429621    \n         160   5.68284653E-03  0.505116343    \n         180   2.73614028E-03  0.352083772    \n         200   1.29080494E-03  0.225816190    \n         220   5.93372271E-04  0.124706082    \n         240   2.68783973E-04   4.93223928E-02\n         260   1.19772783E-04   1.82762444E-02\n         280   5.36365296E-05   5.83780138E-03\n         300   2.41192101E-05   2.32122769E-03\n         320   1.09052180E-05   9.57663520E-04\n         340   4.97397241E-06   3.95007577E-04\n         360   2.33188575E-06   1.70723855E-04\n Converged at   376 iterations (Mean:       0.132E-05, Max:      0.969E-04)\n Potentials:   -739.519  1051.830\n Internal:        4.20389539E-42  kcal/mol\n Van der Waals:         Infinity  kcal/mol\n Electrostatic:   90.0761948     kcal/mol\n Total Energy :         Infinity kcal/mol\n\n#T Run finished at  11:54:14 h on  4-11-2024\n\n#T       T I M I N G S \n#T       ---------------\n#T         Input:     0.198 s,   1.14%\n#T         Setup:     2.299 s,  13.22%\n#T         Grids:    14.883 s,  85.59%\n#T        Energy:     0.008 s,   0.04%\n#T        Output:     0.000 s,   0.00%\n ----------------------------------\n#T         TOTAL:    17.388 s ( 0.00 h)\n\n2024-11-04 11:55:39,430 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26&amp;#x27;, &amp;#x27;2baa347c-4335-4e6e-8eb1-92974d10d1fb&amp;#x27;]\n2024-11-04 11:55:39,431 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/cmip_run/output_byat.out\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Module: biobb_cmip.cmip.cmip_run Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:82 /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26 directory successfully created\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.hACE2.cmip.pdb to /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_cmip/biobb_cmip/biobb_cmip/test/data/cmip/RBD-hACE2.RBD.cmip.pdb to /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: /home/user/micromamba/envs/test_environment/share/cmip/dat/vdwprm to /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Copy: 2baa347c-4335-4e6e-8eb1-92974d10d1fb/params to /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:cmd_wrapper.py:63 cmip -i /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/params -vdw /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/vdwprm -hs /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/RBD-hACE2.hACE2.cmip.pdb -pr /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/RBD-hACE2.RBD.cmip.pdb -byat /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/output_byat.out\n\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:cmd_wrapper.py:36 Executing: cmip -i /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454...\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:cmd_wrapper.py:41  =================================================\n =                                               =\n =                C M I P  (2.7.0)               =\n =          J. Ll. Gelpi, A. Morreale,           =\n =            F. J. Luque, M.Orozco              =\n =      Dept. Biochemistry. Univ. Barcelona      =\n =                  1999-2021                    =\n =================================================\n\n  Code for ASA calculation by Juan F. Recio       \n\n#T Run started at   11:53:57 h on  4-11-2024\n SIZES\n -----\n MAXTIP:           100\n MAXATH:            80000\n MAXATP x MAXCONF: 100000\n\n INPUT FILES\n -----------\n    Calc. settings: /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/params                                                                    \n VdW Parameters:      /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/vdwprm                                                                    \n PDB Host:            /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/RBD-hACE2.hACE2.cmip.pdb                                                  \n PDB Guest:           /tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26/RBD-hACE2.RBD.cmip.pdb                                                    \n Conf. energies:      energies                                                                                                                                              \n\n OUTPUT FILES\n ------------\n LOG file:            output                                                                                                                                                \n Grid Out:            gridout                                                                                                                                               \n Output PDB coords:          outpdb                                                                                                                                                \n\n Parameters\n ----------\nDocking Interaction energy calculation. PB electrostatics                       \n&amp;amp;cntrl                                                                          \n tipcalc = 3                                                                    \n calcgrid = 1                                                                   \n irest = 0                                                                      \n orest = 0                                                                      \n coorfmt = 2                                                                    \n fvdw = 0.8                                                                     \n pbelec = 1                                                                     \n pbinic = 2                                                                     \n wgp = 0                                                                        \n ebyatom = 1                                                                    \n readgrid = 2                                                                   \n CENX=0.0,CENY=0.0,CENZ=0.0                                                     \n DIMX=64,DIMY=64,DIMZ=64                                                        \n INTX0=1.5,INTY0=1.5,INTZ0=1.5                                                  \n readgrid0 = 2                                                                  \n perfill0 = 0.6                                                                 \n pbfocus = 1                                                                    \n IREST = 0                                                                      \n&amp;amp;end                                                                            \n\n 18 VdW parameters loaded successfully\n\n Host:      9519 atoms loaded, charge   -27.000\n\n TYPE OF CALCULATION: DOCKING\n Single point\n\n Guest: 3000 atom(s), charge -11.145,    1 conformation(s) loaded\n\n PB Focussing requested\n AUTOMATIC OUTER GRID\n --------------------\n Fill:    0.600\nAutomatic Outer Grid                                                                                                                \n Grid Size:      96.000 138.000 108.000  90.000  90.000  90.000\n Grid density:    64   92   72\n Grid units:      1.500   1.500   1.500\n Grid origin:    23.610  -1.245   2.315\n Grid center:    71.610  67.755  56.315\n     441285 Grid points\n\n AUTOMATIC GRID\n --------------\n Fill:    0.800\nAutomatic Grid                                                                                                                      \n Grid Size:      72.000 103.000  81.500  90.000  90.000  90.000\n Grid density:   144  206  163\n Grid units:      0.500   0.500   0.500\n Grid origin:    35.610  16.255  15.565\n Grid center:    71.610  67.755  56.315\n    4922460 Grid points\n\n All input data read succesfully\n\n Warning: Dielectric grid computed at double density\n Mapping host molecule to outer grid\n   Total charge            :   -27.0000248    \n   Low diel. grid points   :                230941 (   97428.2344     A3)\n   High diel. grid points  :               3229484\n   I Str=0 grid points     :                441285\n   Boundary grid points    :                 57064\n Mapping host molecule to grid\n   Total charge            :   -27.0000019    \n   Low diel. grid points   :               5855067 (   91485.4219      A3)\n   High diel. grid points  :              33174672\n   I Str=0 grid points     :               4922460\n   Boundary grid points    :                550671\n\n CLHOST=           0\n EXTERNAL CUTOFF=   999999.000    \n Checking potentials to calculate...\n - Vdw: C   \n - Vdw: N   \n - Vdw: S   \n - Vdw: HO  \n - Vdw: HN  \n - Vdw: H   \n - Vdw: O   \n - Electrostatic \n     Dielectric type    :            0\n     Dielectric constant:    2.00000000    \n Vdw energies:\n  -C    -2.15     0.254E+21\n  -N    -2.73     0.266E+21\n  -S    -3.82     0.557E+21\n  -HO    0.00      0.00    \n  -HN  -0.344     0.116E+18\n  -H   -0.860     0.268E+20\n  -O    -2.87     0.169E+21\n     Poisson-Boltzmann calculation requested\n     Focussing          :            1\n     Initial potentials :            2\n     Solute  Dielectric :    2.00000000    \n     Solvent Dielectric :    79.8000031    \n     Solvent radius     :    1.39999998    \n     Convergence crit.  :    9.99999975E-05\n     Ionic strength     :    0.00000000    \n Outer grid\n          20  0.147574857       14.6699677    \n          40   2.98345201E-02   3.29004049    \n          60   6.40256703E-03  0.731274426    \n          80   1.45485543E-03  0.142998144    \n         100   3.42993939E-04   1.78021304E-02\n         120   8.23287264E-05   2.51317094E-03\n         140   1.94953154E-05   8.38404230E-04\n Converged at   158 iterations (Mean:       0.494E-05, Max:      0.923E-04)\n Potentials:   -145.994   169.029\n Inner Grid limits\n Potentials:   -128.467   156.689\n          20  0.878943920       44.1415787    \n          40  0.403151721       18.3211327    \n          60  0.196834385       11.3860836    \n          80   9.76954326E-02   6.86376905    \n         100   4.82133329E-02   3.11586928    \n         120   2.38133743E-02   1.68073165    \n         140   1.16519779E-02  0.922429621    \n         160   5.68284653E-03  0.505116343    \n         180   2.73614028E-03  0.352083772    \n         200   1.29080494E-03  0.225816190    \n         220   5.93372271E-04  0.124706082    \n         240   2.68783973E-04   4.93223928E-02\n         260   1.19772783E-04   1.82762444E-02\n         280   5.36365296E-05   5.83780138E-03\n         300   2.41192101E-05   2.32122769E-03\n         320   1.09052180E-05   9.57663520E-04\n         340   4.97397241E-06   3.95007577E-04\n         360   2.33188575E-06   1.70723855E-04\n Converged at   376 iterations (Mean:       0.132E-05, Max:      0.969E-04)\n Potentials:   -739.519  1051.830\n Internal:        4.20389539E-42  kcal/mol\n Van der Waals:         Infinity  kcal/mol\n Electrostatic:   90.0761948     kcal/mol\n Total Energy :         Infinity kcal/mol\n\n#T Run finished at  11:54:14 h on  4-11-2024\n\n#T       T I M I N G S \n#T       ---------------\n#T         Input:     0.198 s,   1.14%\n#T         Setup:     2.299 s,  13.22%\n#T         Grids:    14.883 s,  85.59%\n#T        Energy:     0.008 s,   0.04%\n#T        Output:     0.000 s,   0.00%\n ----------------------------------\n#T         TOTAL:    17.388 s ( 0.00 h)\n\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/cmip_run/sandbox_0d54bb7c-c261-4844-93b9-26fbe8454f26&amp;#x27;, &amp;#x27;2baa347c-4335-4e6e-8eb1-92974d10d1fb&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/cmip_run/cmip_run_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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