[DOCS] Adding description to all modules

biobb_pmx/pmxbiobb/pmxanalyse.py

@@ -15,6 +15,7 @@ class Pmxanalyse(BiobbObject):
     """
     | biobb_pmx Pmxanalyse
     | Wrapper class for the `PMX analyse <https://github.com/deGrootLab/pmx>`_ module.
+    | Analyze the work values from the dgdl.xvg files of the A and B states to calculate the free energy difference between two states.
 
     Args:
         input_a_xvg_zip_path (str): Path the zip file containing the dgdl.xvg files of the A state. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/xvg_A.zip>`_. Accepted formats: zip (edam:format_3987).

biobb_pmx/pmxbiobb/pmxatom_mapping.py

@@ -16,6 +16,7 @@ class Pmxatom_mapping(BiobbObject):
     """
     | biobb_pmx Pmxatom_mapping
     | Wrapper class for the `PMX atom_mapping <https://github.com/deGrootLab/pmx>`_ module.
+    | Perform atom mapping between two ligand structures.
 
     Args:
         input_structure1_path (str): Path to the input ligand structure file 1. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.pdb>`_. Accepted formats: pdb (edam:format_1476).

biobb_pmx/pmxbiobb/pmxcreate_top.py

@@ -17,6 +17,7 @@ class Pmxcreate_top(BiobbObject):
     """
     | biobb_pmx Pmxcreate_top
     | Wrapper class for the `PMX create_top <https://github.com/deGrootLab/pmx>`_ module.
+    | Create a complete ligand topology file from two input topology files.
 
     Args:
         input_topology1_path (str): Path to the input topology file 1. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.itp>`_. Accepted formats: itp (edam:format_3883).

biobb_pmx/pmxbiobb/pmxgentop.py

@@ -17,6 +17,7 @@ class Pmxgentop(BiobbObject):
     """
     | biobb_pmx Pmxgentop
     | Wrapper class for the `PMX gentop <https://github.com/deGrootLab/pmx>`_ module.
+    | Generate a topology file for a morphing simulation.
 
     Args:
         input_top_zip_path (str): Path the input GROMACS topology TOP and ITP files in zip format. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/topology.zip>`_. Accepted formats: zip (edam:format_3987).

biobb_pmx/pmxbiobb/pmxligand_hybrid.py

@@ -16,6 +16,7 @@ class Pmxligand_hybrid(BiobbObject):
     """
     | biobb_pmx Pmxligand_hybrid
     | Wrapper class for the `PMX ligand_hybrid <https://github.com/deGrootLab/pmx>`_ module.
+    | Create a hybrid topology and structure based on two ligand structures.
 
     Args:
         input_structure1_path (str): Path to the input ligand structure file 1. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand.pdb>`_. Accepted formats: pdb (edam:format_1476).

biobb_pmx/pmxbiobb/pmxmerge_ff.py

@@ -18,6 +18,7 @@ class Pmxmerge_ff(BiobbObject):
     """
     | biobb_pmx Pmxmerge_ff
     | Wrapper class for the `PMX merge_ff <https://github.com/deGrootLab/pmx>`_ module.
+    | Merge ligand topology files.
 
     Args:
         input_topology_path (str): Path to the input ligand topologies as a zip file containing a list of itp files. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/ligand_itps.zip>`_. Accepted formats: zip (edam:format_3987).

biobb_pmx/pmxbiobb/pmxmutate.py

@@ -18,6 +18,7 @@ class Pmxmutate(BiobbObject):
     """
     | biobb_pmx Pmxmutate
     | Wrapper class for the `PMX mutate <https://github.com/deGrootLab/pmx>`_ module.
+    | Mutate residues in a protein structure.
 
     Args:
         input_structure_path (str): Path to the input structure file. File type: input. `Sample file <https://github.com/bioexcel/biobb_pmx/raw/master/biobb_pmx/test/data/pmx/frame99.pdb>`_. Accepted formats: pdb (edam:format_1476), gro (edam:format_2033).