Read the Docs fixes

biobb_cmip/cmip/__init__.py

@@ -1,2 +1,2 @@
 name = "cmip"
-__all__ = ["cmip_titration", "cmip_run", "cmip_prepare_structure", "cmip_prepare_pdb", "cmip_ignore_residues"]
+__all__ = ["cmip_titration", "cmip_run", "cmip_prepare_structure", "cmip_prepare_pdb", "cmip_ignore_residues"]

biobb_cmip/cmip/cmip_ignore_residues.py

@@ -75,7 +75,7 @@ def launch(self) -> int:
             return 0
 
         if not self.ignore_all and not self.residue_list:
-            fu.log(f"Residue_list is empty and ignore_all is false nothing will be done.", self.out_log, self.global_log)
+            fu.log("Residue_list is empty and ignore_all is false nothing will be done.", self.out_log, self.global_log)
             shutil.copyfile(self.io_dict["in"]["input_cmip_pdb_path"], self.io_dict["out"]["output_cmip_pdb_path"])
             return self.return_code
 

biobb_cmip/cmip/cmip_run.py

@@ -114,7 +114,6 @@ def __init__(self, input_pdb_path: str, input_probe_pdb_path: str = None, output
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`Cmip <cmip.cmip.Cmip>` object."""
-        tmp_files = []
 
         # Setup Biobb
         if self.check_restart():

biobb_cmip/cmip/cmip_titration.py

@@ -3,13 +3,11 @@
 """Module containing the Titration class and the command line interface."""
 import os
 import argparse
-import shutil
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
-from biobb_common.command_wrapper import cmd_wrapper
 from biobb_cmip.cmip.common import create_params_file
 from biobb_cmip.cmip.common import params_preset
 from biobb_cmip.cmip.common import get_pdb_total_charge

biobb_cmip/cmip/common.py

@@ -52,7 +52,7 @@ def _get_grid_from_text(cmip_log_path: Union[str, Path], external: bool = False)
                 int_match = re.match(r"Grid units:\s+([-+]?(?:\d*\.\d+|\d+))\s+([-+]?(?:\d*\.\d+|\d+))\s+([-+]?(?:\d*\.\d+|\d+))", line.strip())
                 if int_match:
                     grid_params['INT'] = float(int_match.group(1)), float(int_match.group(2)), float(int_match.group(3))
-                cen_match = re.match(r"Grid center:\s+([-+]?(?:\d*\.\d+|\d+))\s+([-+]?(?:\d*\.\d+|\d+))\s+([-+]?(?:\d*\.\d+|\d+))",line.strip())
+                cen_match = re.match(r"Grid center:\s+([-+]?(?:\d*\.\d+|\d+))\s+([-+]?(?:\d*\.\d+|\d+))\s+([-+]?(?:\d*\.\d+|\d+))", line.strip())
                 if cen_match:
                     grid_params['CEN'] = float(cen_match.group(1)), float(cen_match.group(2)), float(cen_match.group(3))
                 dim_match = re.match(r"Grid density:\s+([-+]?(?:\d*\.\d+|\d+))\s+([-+]?(?:\d*\.\d+|\d+))\s+([-+]?(?:\d*\.\d+|\d+))", line.strip())
@@ -86,7 +86,7 @@ def _get_grid_from_key_value(cmip_log_path: Union[str, Path], external: bool = F
                 int_match = re.match(r"spacing=\s+([-+]?(?:\d*\.\d+|\d+))\s*,\s*([-+]?(?:\d*\.\d+|\d+))\s*,\s*([-+]?(?:\d*\.\d+|\d+))", line.strip())
                 if int_match:
                     grid_params['INT'] = float(int_match.group(1)), float(int_match.group(2)), float(int_match.group(3))
-                cen_match = re.match(r"center=\s+([-+]?(?:\d*\.\d+|\d+))\s*,\s*([-+]?(?:\d*\.\d+|\d+))\s*,\s*([-+]?(?:\d*\.\d+|\d+))",line.strip())
+                cen_match = re.match(r"center=\s+([-+]?(?:\d*\.\d+|\d+))\s*,\s*([-+]?(?:\d*\.\d+|\d+))\s*,\s*([-+]?(?:\d*\.\d+|\d+))", line.strip())
                 if cen_match:
                     grid_params['CEN'] = float(cen_match.group(1)), float(cen_match.group(2)), float(cen_match.group(3))
                 dim_match = re.match(r"dim=\s+([-+]?(?:\d*\.\d+|\d+))\s*,\s*([-+]?(?:\d*\.\d+|\d+))\s*,\s*([-+]?(?:\d*\.\d+|\d+))", line.strip())
@@ -97,7 +97,6 @@ def _get_grid_from_key_value(cmip_log_path: Union[str, Path], external: bool = F
     return origin, size, grid_params
 
 
-
 def create_unique_file_path(parent_dir: Union[str, Path] = None, extension: str = None) -> str:
     if not parent_dir:
         parent_dir = Path.cwd
@@ -198,14 +197,14 @@ def __init__(self, fname):
                     continue
                 data = line.split()
                 r = Residue(data)
-                self.RData[r.id]=r
+                self.RData[r.id] = r
             self.nres = len(self.RData)
 
     def getParams(self, resid, atid):
         if resid+':'+atid in self.RData:
             return self.RData[resid+':'+atid]
         else:
-            print("WARNING: atom not found in library (",resid+':'+atid,')')
+            print("WARNING: atom not found in library (", resid+':'+atid, ')')
             return {}
 
 
@@ -248,7 +247,7 @@ def get_pdb_charges(input_pdb_filename: str, residue_library_path: str = None) -
 
 def get_pdb_cmip_elements_canonical(input_pdb_filename: str, residue_library_path: str = None) -> List:
     if not residue_library_path:
-        residue_library_path = str(Path(__file__).parent.joinpath("dat","aa.lib").resolve())
+        residue_library_path = str(Path(__file__).parent.joinpath("dat", "aa.lib").resolve())
 
     aaLib = ResiduesDataLib(residue_library_path)
     print("{} residue/atom pairs loaded from {}".format(aaLib.nres, residue_library_path))
@@ -316,7 +315,7 @@ def params_grid(grid_type: str, readgrid: int = 0, perfill: float = 0.8,
     #     cmip, titration, pbsolvation = 2, >3
 
     grid_dict = {}
-    grid_dict[f"readgrid"] = f"{readgrid}"
+    grid_dict["readgrid"] = f"{readgrid}"
 
     if grid_type in ['pb_interaction_energy', 'mip_pos', 'mip_neu', 'mip_neg', 'docking']:
         grid_dict['grid_cen'] = f"CENX={grid_cen[0]},CENY={grid_cen[1]},CENZ={grid_cen[2]}"
@@ -335,7 +334,7 @@ def params_preset(execution_type: str) -> Dict[str, str]:
     probe_grid_dict = {}
     execution_type = execution_type.strip()
     if execution_type == 'titration':
-        grid_dict = params_grid(grid_type=execution_type, readgrid=2, perfill=0.8, grid_int=(0.5, 0.5, 0.5) )
+        grid_dict = params_grid(grid_type=execution_type, readgrid=2, perfill=0.8, grid_int=(0.5, 0.5, 0.5))
         params_dict = {
             'title': 'Titration',
             'tipcalc': 1,
@@ -356,11 +355,11 @@ def params_preset(execution_type: str) -> Dict[str, str]:
             'irest': 0,
             'orest': 0,
             'coorfmt': 2,
-            'dields':  2,
+            'dields': 2,
             'cubeoutput': 1,
             'fvdw': 0.8,
             'carmip': 1,
-            'tipatmip' : "'OW'"
+            'tipatmip': "'OW'"
         }
     elif execution_type == 'mip_neu':
         grid_dict = params_grid(grid_type=execution_type, readgrid=2)
@@ -371,11 +370,11 @@ def params_preset(execution_type: str) -> Dict[str, str]:
             'irest': 0,
             'orest': 0,
             'coorfmt': 2,
-            'dields':  2,
+            'dields': 2,
             'cubeoutput': 1,
             'fvdw': 0.8,
             'carmip': 0,
-            'tipatmip' : "'OW'"
+            'tipatmip': "'OW'"
         }
     elif execution_type == 'mip_neg':
         grid_dict = params_grid(grid_type=execution_type, readgrid=2)
@@ -386,13 +385,13 @@ def params_preset(execution_type: str) -> Dict[str, str]:
             'irest': 0,
             'orest': 0,
             'coorfmt': 2,
-            'dields':  2,
+            'dields': 2,
             'cubeoutput': 1,
             'fvdw': 0.8,
             'carmip': -1,
-            'tipatmip' : "'OW'"
+            'tipatmip': "'OW'"
         }
-#TODO 'carmip': 1,
+    # TODO 'carmip': 1,
     # wat: tipcalc: 1 + titration: 'inifoc': 2, 'cutfoc': -0.5, 'focus': 1, 'ninter': 10,
     elif execution_type == 'solvation':
         grid_dict = params_grid(grid_type=execution_type, readgrid=2, perfill=0.2,
@@ -404,13 +403,13 @@ def params_preset(execution_type: str) -> Dict[str, str]:
             'irest': 0,
             'orest': 0,
             'coorfmt': 2,
-            'cubeoutput': 1, 'vdw': 0,  'pbelec': 1,
+            'cubeoutput': 1, 'vdw': 0, 'pbelec': 1,
             'novdwgrid': 1, 'solvenergy': 1, 'dielc': 1, 'dielsol': 80
         }
 
     elif execution_type == 'pb_interaction_energy':
-        grid_dict = params_grid(grid_type=execution_type, readgrid= 2)
-        probe_grid_dict = probe_params_grid(probe_id= 0, readgrid= 2, pbfocus= 1, perfill= 0.6,
+        grid_dict = params_grid(grid_type=execution_type, readgrid=2)
+        probe_grid_dict = probe_params_grid(probe_id=0, readgrid=2, pbfocus=1, perfill=0.6,
                                             grid_int=(1.5, 1.5, 1.5))
 
         # TODO Check for external box file or parameters
@@ -425,7 +424,7 @@ def params_preset(execution_type: str) -> Dict[str, str]:
         }
 
     elif execution_type == 'docking':
-        grid_dict = params_grid(grid_type=execution_type, readgrid= 2)
+        grid_dict = params_grid(grid_type=execution_type, readgrid=2)
 
         params_dict = {
             'title': 'Docking Mehler Solmajer dielectric',
@@ -474,7 +473,8 @@ def read_params_file(input_params_path: str) -> Dict[str, str]:
         params_dict['title']: input_params_file.readline()
         for line in input_params_file:
             line = line.replace(' ', '')
-            if line.startswith('&'): continue
+            if line.startswith('&'):
+                continue
             param_list = line.split(',')
             for param in param_list:
                 param_key, param_value = param.split("=")
@@ -504,13 +504,13 @@ def read_params_file(input_params_path: str) -> Dict[str, str]:
 def write_params_file(output_params_path: str, params_dict: Mapping[str, str]) -> str:
     with open(output_params_path, 'w') as output_params_file:
         output_params_file.write(f"{params_dict.pop('title', 'Untitled')}\n")
-        output_params_file.write(f"&cntrl\n")
+        output_params_file.write("&cntrl\n")
         for params_key, params_value in params_dict.items():
             if params_key in ['grid_int', 'grid_cen', 'grid_dim', 'grid_int0', 'grid_cen0', 'grid_dim0']:
                 output_params_file.write(f" {params_value}\n")
             else:
                 output_params_file.write(f" {params_key} = {params_value}\n")
-        output_params_file.write(f"&end\n")
+        output_params_file.write("&end\n")
     return output_params_path
 
 
@@ -539,6 +539,7 @@ def create_params_file(output_params_path: str, input_params_path: str = None,
 
     return write_params_file(output_params_path, params_dict)
 
+
 def mark_residues(residue_list: Sequence[str], input_cmip_pdb_path: str, output_cmip_pdb_path: str, out_log: logging.Logger = None, global_log: logging.Logger = None) -> None:
     """Marks using an "X" before the atom type all the residues in *residue_list* and writes the result in *output_cmip_pdb_path*.
 
@@ -548,7 +549,7 @@ def mark_residues(residue_list: Sequence[str], input_cmip_pdb_path: str, output_
             global_log (:obj:`logging.Logger`): global log object.
         """
     if not residue_list:
-        fu.log(f"Empty residue_list all residues will be marked", out_log, global_log)
+        fu.log("Empty residue_list all residues will be marked", out_log, global_log)
     else:
         fu.log(f"Residue list: {residue_list}", out_log, global_log)
 
@@ -572,11 +573,13 @@ def mark_residues(residue_list: Sequence[str], input_cmip_pdb_path: str, output_
             if unused_residues:
                 fu.log(f"The following residues where present in the residue_list and have not been marked: {unused_residues}", out_log, global_log)
 
+
 def _mark_pdb_atom(line: str) -> str:
     line = list(line)
     line.insert(64, 'X')
     return ''.join(line)
 
+
 def _get_residue_code_in_list(input_residue, residue_list):
     if not residue_list:
         return None
@@ -597,11 +600,14 @@ def _get_residue_code_in_list(input_residue, residue_list):
 def _get_residue_code(line: str) -> str:
     return _get_chain(line)+":"+_get_resnum(line)
 
+
 def _get_chain(line: str) -> str:
     return line[21].upper()
 
+
 def _get_resnum(line: str) -> str:
     return line[22:27].strip()
 
+
 def _is_atom(line: str) -> str:
     return line[0:6].strip().upper() in ["ATOM", "HETATM"]

biobb_cmip/docs/source/command_line.md

@@ -13,7 +13,20 @@ Command:
 ```python
 cmip_prepare_pdb -h
 ```
-    /bin/sh: cmip_prepare_pdb: command not found
+    usage: cmip_prepare_pdb [-h] [-c CONFIG] -i INPUT_PDB_PATH -o OUTPUT_CMIP_PDB_PATH
+
+    Model the missing atoms in the backbone of a PDB structure.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -c CONFIG, --config CONFIG
+                            This file can be a YAML file, JSON file or JSON string
+
+    required arguments:
+      -i INPUT_PDB_PATH, --input_pdb_path INPUT_PDB_PATH
+                            Input PDB file name
+      -o OUTPUT_CMIP_PDB_PATH, --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH
+                            Output PDB file name
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
@@ -63,7 +76,20 @@ Command:
 ```python
 cmip_ignore_residues -h
 ```
-    /bin/sh: cmip_ignore_residues: command not found
+    usage: cmip_ignore_residues [-h] [-c CONFIG] -i INPUT_CMIP_PDB_PATH -o OUTPUT_CMIP_PDB_PATH
+
+    Mark residues which charges will be ignored in the CMIP potential calculations.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -c CONFIG, --config CONFIG
+                            This file can be a YAML file, JSON file or JSON string
+
+    required arguments:
+      -i INPUT_CMIP_PDB_PATH, --input_cmip_pdb_path INPUT_CMIP_PDB_PATH
+                            Input PDB file name
+      -o OUTPUT_CMIP_PDB_PATH, --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH
+                            Output PDB file name
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
@@ -112,7 +138,20 @@ Command:
 ```python
 cmip_titration -h
 ```
-    /bin/sh: cmip_titration: command not found
+    usage: cmip_titration [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH --output_pdb_path OUTPUT_PDB_PATH [--input_vdw_params_path INPUT_VDW_PARAMS_PATH] [--input_params_path INPUT_PARAMS_PATH]
+
+    Wrapper of the CMIP Titration module.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -c CONFIG, --config CONFIG
+                            This file can be a YAML file, JSON file or JSON string
+      --input_vdw_params_path INPUT_VDW_PARAMS_PATH
+      --input_params_path INPUT_PARAMS_PATH
+
+    required arguments:
+      --input_pdb_path INPUT_PDB_PATH
+      --output_pdb_path OUTPUT_PDB_PATH
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
@@ -214,7 +253,30 @@ Command:
 ```python
 cmip_run -h
 ```
-    /bin/sh: cmip_run: command not found
+    usage: cmip_run [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH [--input_probe_pdb_path INPUT_PROBE_PDB_PATH] [--output_pdb_path OUTPUT_PDB_PATH] [--output_grd_path OUTPUT_GRD_PATH] [--output_cube_path OUTPUT_CUBE_PATH] [--output_rst_path OUTPUT_RST_PATH] [--output_byat_path OUTPUT_BYAT_PATH] [--output_log_path OUTPUT_LOG_PATH] [--input_vdw_params_path INPUT_VDW_PARAMS_PATH] [--input_params_path INPUT_PARAMS_PATH] [--output_json_box_path OUTPUT_JSON_BOX_PATH] [--output_json_external_box_path OUTPUT_JSON_EXTERNAL_BOX_PATH] [--input_json_box_path INPUT_JSON_BOX_PATH] [--input_json_external_box_path INPUT_JSON_EXTERNAL_BOX_PATH]
+
+    Wrapper of the CMIP cmip module.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -c CONFIG, --config CONFIG
+                            This file can be a YAML file, JSON file or JSON string
+      --input_probe_pdb_path INPUT_PROBE_PDB_PATH
+      --output_pdb_path OUTPUT_PDB_PATH
+      --output_grd_path OUTPUT_GRD_PATH
+      --output_cube_path OUTPUT_CUBE_PATH
+      --output_rst_path OUTPUT_RST_PATH
+      --output_byat_path OUTPUT_BYAT_PATH
+      --output_log_path OUTPUT_LOG_PATH
+      --input_vdw_params_path INPUT_VDW_PARAMS_PATH
+      --input_params_path INPUT_PARAMS_PATH
+      --output_json_box_path OUTPUT_JSON_BOX_PATH
+      --output_json_external_box_path OUTPUT_JSON_EXTERNAL_BOX_PATH
+      --input_json_box_path INPUT_JSON_BOX_PATH
+      --input_json_external_box_path INPUT_JSON_EXTERNAL_BOX_PATH
+
+    required arguments:
+      --input_pdb_path INPUT_PDB_PATH
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
@@ -325,7 +387,19 @@ Command:
 ```python
 cmip_prepare_structure -h
 ```
-    /bin/sh: cmip_prepare_structure: command not found
+    usage: cmip_prepare_structure [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH [--input_topology_path INPUT_TOPOLOGY_PATH]
+
+    Wrapper of the cmip prepare_structure module.
+
+    optional arguments:
+      -h, --help            show this help message and exit
+      -c CONFIG, --config CONFIG
+                            This file can be a YAML file, JSON file or JSON string
+      --input_topology_path INPUT_TOPOLOGY_PATH
+
+    required arguments:
+      --input_pdb_path INPUT_PDB_PATH
+      --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 

biobb_cmip/test/unitests/test_cmip/test_cmip_ignore_residues.py

@@ -14,5 +14,3 @@ def test_cmip_ignore_residues(self):
         cmip_ignore_residues(properties=self.properties, **self.paths)
         assert fx.not_empty(self.paths['output_cmip_pdb_path'])
         assert fx.equal(self.paths['output_cmip_pdb_path'], self.paths['ref_output_ignore_residues_pdb_path'])
-
-

biobb_cmip/test/unitests/test_cmip/test_cmip_prepare_pdb.py

@@ -14,5 +14,3 @@ def test_cmip_prepare_pdb(self):
         cmip_prepare_pdb(properties=self.properties, **self.paths)
         assert fx.not_empty(self.paths['output_cmip_pdb_path'])
         assert fx.equal(self.paths['output_cmip_pdb_path'], self.paths['ref_output_prepare_structure_pdb_path'])
-
-

biobb_cmip/test/unitests/test_cmip/test_cmip_run.py

@@ -64,4 +64,4 @@ def test_cmip_run_energy(self):
 #         assert fx.not_empty(self.paths['output_cube_path'])
 #         assert fx.not_empty(self.paths['output_grd_path'])
 #         assert fx.equal(self.paths['output_grd_path'], self.paths['ref_output_cmip_mip_grd_path'])
-#         assert fx.equal(self.paths['output_cube_path'], self.paths['ref_output_cmip_mip_cube_path'])
+#         assert fx.equal(self.paths['output_cube_path'], self.paths['ref_output_cmip_mip_cube_path'])

biobb_cmip/test/unitests/test_cmip/test_cmip_run_docker.py

@@ -66,4 +66,4 @@ def test_cmip_run_energy(self):
 #         assert fx.not_empty(self.paths['output_cube_path'])
 #         assert fx.not_empty(self.paths['output_grd_path'])
 #         assert fx.equal(self.paths['output_grd_path'], self.paths['ref_output_cmip_mip_grd_path'])
-#         assert fx.equal(self.paths['output_cube_path'], self.paths['ref_output_cmip_mip_cube_path'])
+#         assert fx.equal(self.paths['output_cube_path'], self.paths['ref_output_cmip_mip_cube_path'])