Unifying names

.github/workflows/citation.yaml

@@ -14,7 +14,7 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v2
         with:
-          repository: bioexcel/biobb_wf_amber_md_setup
+          repository: bioexcel/biobb_wf_amber
           path: ./
 
       - name: Download file using wget

.gitignore

@@ -38,25 +38,25 @@ mdinfo
 !logo.png
 !requirements.txt
 .ipynb_checkpoints/
-biobb_wf_amber_md_setup/notebooks/*/*/
-biobb_wf_amber_md_setup/notebooks/*/*.web.ipynb
-biobb_wf_amber_md_setup/notebooks/*/*.docs.ipynb
-biobb_wf_amber_md_setup/notebooks/*/*.png
-biobb_wf_amber_md_setup/notebooks/*/*.gif
-biobb_wf_amber_md_setup/notebooks/*/*.rst
-!biobb_wf_amber_md_setup/notebooks/abcsetup/ABCix_config_files/
-!biobb_wf_amber_md_setup/notebooks/abcsetup/ABCix_config_files/*.in
-!biobb_wf_amber_md_setup/notebooks/abcsetup/ABCix_config_files/*.in.ORIG
-!biobb_wf_amber_md_setup/html/abcsetup/sander.md.nc
-!biobb_wf_amber_md_setup/html/abcsetup/structure.ions.parmtop
-!biobb_wf_amber_md_setup/html/abcsetup/structure.leap.4fs.top
-!biobb_wf_amber_md_setup/html/abcsetup/sander.md.ncrst
-!biobb_wf_amber_md_setup/docs/source/_static/abcsetup/sander.md.nc
-!biobb_wf_amber_md_setup/docs/source/_static/abcsetup/structure.ions.parmtop
-!biobb_wf_amber_md_setup/docs/source/_static/abcsetup/structure.leap.4fs.top
-!biobb_wf_amber_md_setup/docs/source/_static/abcsetup/sander.md.ncrst
-biobb_wf_amber_md_setup/docs/notebooks/
-biobb_wf_amber_md_setup/html/abcsetup/biobb_amber_ABC_setup.web.ipynb
-biobb_wf_amber_md_setup/html/mdsetup/biobb_amber_setup_notebook.web.ipynb
-biobb_wf_amber_md_setup/html/mdsetup_lig/biobb_amber_complex_setup_notebook.web.ipynb
-biobb_wf_amber_md_setup/html/mdsetup_ph/biobb_amber_CpHMD_notebook.web.ipynb
+biobb_wf_amber/notebooks/*/*/
+biobb_wf_amber/notebooks/*/*.web.ipynb
+biobb_wf_amber/notebooks/*/*.docs.ipynb
+biobb_wf_amber/notebooks/*/*.png
+biobb_wf_amber/notebooks/*/*.gif
+biobb_wf_amber/notebooks/*/*.rst
+!biobb_wf_amber/notebooks/abc_setup/ABCix_config_files/
+!biobb_wf_amber/notebooks/abc_setup/ABCix_config_files/*.in
+!biobb_wf_amber/notebooks/abc_setup/ABCix_config_files/*.in.ORIG
+!biobb_wf_amber/html/abc_setup/sander.md.nc
+!biobb_wf_amber/html/abc_setup/structure.ions.parmtop
+!biobb_wf_amber/html/abc_setup/structure.leap.4fs.top
+!biobb_wf_amber/html/abc_setup/sander.md.ncrst
+!biobb_wf_amber/docs/source/_static/abc_setup/sander.md.nc
+!biobb_wf_amber/docs/source/_static/abc_setup/structure.ions.parmtop
+!biobb_wf_amber/docs/source/_static/abc_setup/structure.leap.4fs.top
+!biobb_wf_amber/docs/source/_static/abc_setup/sander.md.ncrst
+biobb_wf_amber/docs/notebooks/
+biobb_wf_amber/html/abc_setup/biobb_wf_amber_abc_setup.web.ipynb
+biobb_wf_amber/html/md_setup/biobb_wf_amber_md_setup.web.ipynb
+biobb_wf_amber/html/md_setup_lig/biobb_wf_amber_md_setup_lig.web.ipynb
+biobb_wf_amber/html/md_setup_ph/biobb_wf_amber_md_setup_ph.web.ipynb

.readthedocs.yaml

@@ -12,8 +12,8 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: biobb_wf_amber_md_setup/docs/source/conf.py
+   configuration: biobb_wf_amber/docs/source/conf.py
 
 python:
   install:
-    - requirements: biobb_wf_amber_md_setup/docs/requirements.txt
+    - requirements: biobb_wf_amber/docs/requirements.txt

biobb_wf_amber_md_setup/docs/source/abcsetup_tutorial.md → biobb_wf_amber/docs/source/abc_setup_tutorial.md

@@ -42,7 +42,7 @@ git clone https://github.com/bioexcel/biobb_wf_amber_md_setup.git
 cd biobb_wf_amber_md_setup
 conda env create -f conda_env/environment.yml
 conda activate biobb_wf_amber_md_setup
-jupyter-notebook biobb_wf_amber_md_setup/notebooks/abcsetup/biobb_amber_ABC_setup.ipynb
+jupyter-notebook biobb_wf_amber_md_setup/notebooks/abc_setup/biobb_wf_amber_abc_setup.ipynb
 ```
 
 ***
@@ -107,7 +107,7 @@ if 'google.colab' in sys.modules:
   output.enable_custom_widget_manager()
   # Change working dir
   import os
-  os.chdir("biobb_wf_amber_md_setup/biobb_wf_amber_md_setup/notebooks/abcsetup")
+  os.chdir("biobb_wf_amber_md_setup/biobb_wf_amber_md_setup/notebooks/abc_setup")
   print(f"📂 New working directory: {os.getcwd()}")
 ```
 
@@ -191,7 +191,7 @@ view._remote_call('setSize', target='Widget', args=['','600px'])
 view
 ```
 
-<img src='_static/abcsetup/ngl1.png'></img>
+<img src='_static/abc_setup/ngl1.png'></img>
 
 <a id="top"></a>
 ## Generate Topology
@@ -233,7 +233,7 @@ view._remote_call('setSize', target='Widget', args=['','600px'])
 view
 ```
 
-<img src='_static/abcsetup/ngl2.png'></img>
+<img src='_static/abc_setup/ngl2.png'></img>
 
 <a id="water"></a>
 ## Adding Water Box
@@ -292,7 +292,7 @@ view._remote_call('setSize', target='Widget', args=['','600px'])
 view
 ```
 
-<img src='_static/abcsetup/ngl3.png'></img>
+<img src='_static/abc_setup/ngl3.png'></img>
 
 <a id="ions"></a>
 ## Adding additional ionic concentration
@@ -344,7 +344,7 @@ view._remote_call('setSize', target='Widget', args=['','600px'])
 view
 ```
 
-<img src='_static/abcsetup/ngl4.png'></img>
+<img src='_static/abc_setup/ngl4.png'></img>
 
 <a id="random"></a>
 ## Randomize ions
@@ -390,7 +390,7 @@ view._remote_call('setSize', target='Widget', args=['','600px'])
 view
 ```
 
-<img src='_static/abcsetup/ngl5.png'></img>
+<img src='_static/abc_setup/ngl5.png'></img>
 
 <a id="top4fs"></a>
 ## Generate Topology with Hydrogen Mass Partitioning (4fs)
@@ -547,7 +547,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot01.png'></img>
+<img src='_static/abc_setup/plot01.png'></img>
 
 <a id="eq2"></a>
 ### Equilibration Step 2: NVT equilibration
@@ -667,7 +667,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot02.png'></img>
+<img src='_static/abc_setup/plot02.png'></img>
 
 <a id="eq3"></a>
 ### Equilibration Step 3: System energetic minimization
@@ -778,7 +778,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot03.png'></img>
+<img src='_static/abc_setup/plot03.png'></img>
 
 <a id="eq4"></a>
 ### Equilibration Step 4: System energetic minimization
@@ -889,7 +889,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot04.png'></img>
+<img src='_static/abc_setup/plot04.png'></img>
 
 <a id="eq5"></a>
 ### Equilibration Step 5: System energetic minimization
@@ -997,7 +997,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot05.png'></img>
+<img src='_static/abc_setup/plot05.png'></img>
 
 <a id="eq6"></a>
 ### Equilibration Step 6: NPT equilibration
@@ -1136,7 +1136,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot06.png'></img>
+<img src='_static/abc_setup/plot06.png'></img>
 
 <a id="eq7"></a>
 ### Equilibration Step 7: NPT equilibration
@@ -1276,7 +1276,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot07.png'></img>
+<img src='_static/abc_setup/plot07.png'></img>
 
 <a id="eq8"></a>
 ### Equilibration Step 8: NPT equilibration
@@ -1416,7 +1416,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot08.png'></img>
+<img src='_static/abc_setup/plot08.png'></img>
 
 <a id="eq9"></a>
 ### Equilibration Step 9: NPT equilibration
@@ -1554,7 +1554,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot09.png'></img>
+<img src='_static/abc_setup/plot09.png'></img>
 
 <a id="eq10"></a>
 ### Equilibration Step 10: NPT equilibration
@@ -1693,7 +1693,7 @@ rend = 'colab' if 'google.colab' in sys.modules else ''
 fig.show(renderer=rend)
 ```
 
-<img src='_static/abcsetup/plot10.png'></img>
+<img src='_static/abc_setup/plot10.png'></img>
 
 <a id="free"></a>
 ***
@@ -1787,10 +1787,10 @@ display(FileLink(dna_leap_top_4fs_path))
 display(FileLink(output_md_rst_path))
 ```
 
-<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abcsetup/sander.md.nc' target='_blank'>sander.md.nc</a><br>
-<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abcsetup/structure.ions.parmtop' target='_blank'>structure.ions.parmtop</a><br>
-<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abcsetup/structure.leap.4fs.top' target='_blank'>structure.leap.4fs.top</a><br>
-<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abcsetup/sander.md.ncrst' target='_blank'>sander.md.ncrst</a>
+<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/sander.md.nc' target='_blank'>sander.md.nc</a><br>
+<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/structure.ions.parmtop' target='_blank'>structure.ions.parmtop</a><br>
+<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/structure.leap.4fs.top' target='_blank'>structure.leap.4fs.top</a><br>
+<a href='https://raw.githubusercontent.com/bioexcel/biobb_wf_amber_md_setup/master/biobb_wf_amber_md_setup/html/abc_setup/sander.md.ncrst' target='_blank'>sander.md.ncrst</a>
 
 ***
 <a id="questions"></a>

biobb_wf_amber_md_setup/docs/source/conf.py → biobb_wf_amber/docs/source/conf.py

@@ -66,7 +66,7 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'biobb_wf_amber_md_setup'
+project = u'biobb_wf_amber'
 copyright = u'2021, Bioexcel Project'
 author = u'Bioexcel Project'
 
@@ -224,7 +224,7 @@ def setup(app):
 #html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'biobb_wf_amber_md_setup_doc'
+htmlhelp_basename = 'biobb_wf_amber_doc'
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -246,7 +246,7 @@ def setup(app):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'biobb_wf_amber_md_setup.tex', u'biobb_wf_amber_md_setup Documentation',
+    (master_doc, 'biobb_wf_amber.tex', u'biobb_wf_amber Documentation',
      u'Bioexcel Project', 'manual'),
 ]
 
@@ -276,7 +276,7 @@ def setup(app):
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'biobb_wf_amber_md_setup', u'biobb_wf_amber_md_setup Documentation',
+    (master_doc, 'biobb_wf_amber', u'biobb_wf_amber Documentation',
      [author], 1)
 ]
 
@@ -290,8 +290,8 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'biobb_wf_amber_md_setup', u'biobb_wf_amber_md_setup Documentation',
-     author, 'biobb_wf_amber_md_setup', 'biobb_wf_amber_md_setup molecular dynamics analysis building blocks',
+    (master_doc, 'biobb_wf_amber', u'biobb_wf_amber Documentation',
+     author, 'biobb_wf_amber', 'biobb_wf_amber molecular dynamics analysis building blocks',
      'Miscellaneous'),
 ]
 

biobb_wf_amber_md_setup/docs/source/index.rst → biobb_wf_amber/docs/source/index.rst

@@ -11,12 +11,12 @@ Contents
    :maxdepth: 1
 
    Introduction & installation <readme>
-   MD Setup tutorial <mdsetup_tutorial>
-   Protein-ligand complex MD Setup tutorial <mdsetup_lig_tutorial>
-   Constant pH MD Setup tutorial <mdsetup_ph_tutorial>
-   ABC MD Setup pipeline <abcsetup_tutorial>
+   MD Setup tutorial <md_setup_tutorial>
+   Protein-ligand complex MD Setup tutorial <md_setup_lig_tutorial>
+   Constant pH MD Setup tutorial <md_setup_ph_tutorial>
+   ABC MD Setup pipeline <abc_setup_tutorial>
 
-`Github repository <https://github.com/bioexcel/biobb_wf_amber_md_setup>`_.
+`Github repository <https://github.com/bioexcel/biobb_wf_amber>`_.
 ============================================================================