Merge branch 'pdb_class' of https://github.com/martimunicoy/peleffy i…

…nto pdb_class

docs/releasehistory.rst

@@ -7,6 +7,17 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``minor`` increments add features but do not break API compatibility
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
+1.3.0 - Current development
+---------------------------
+
+New features
+""""""""""""
+- `PR #137 <https://github.com/martimunicoy/peleffy/pull/137>`_: New PDB class that allows to handle an input PDB file with multiple molecules. 
+
+Tests added
+"""""""""""
+- `PR #137 <https://github.com/martimunicoy/peleffy/pull/137>`_: Adds tests to validate the new PDB class that allows to handle an input PDB file with multiple molecules.
+
 
 1.2.1 - API Documentation and improvements
 ------------------------------------------

docs/usage.rst

@@ -104,6 +104,7 @@ arguments. To obtain the full list of flags you can type:
                              The name of the method to use to compute charges
        --charges_from_file PATH
                              The path to the file with charges
+       --chain CHAIN         Chain of the molecule to parameterize
        --include_terminal_rotamers
                              Not exclude terminal rotamers when building the
                              rotamer library
@@ -221,6 +222,18 @@ It sets the method to load external partial charges.
 
         $ python -m peleffy.main path/to/my_ligand.pdb --charges_from_file path/to/my_ligand.mae
 
+Chain
+-----
+It defines the chain of the molecule to parameterize from the input PDB file.
+
+- Flag: ``--chain``
+- Default: ``None``
+- Example: the code below will parameterize the hetero molecule in the chain L of the input file
+
+  .. code-block:: bash
+
+        $ python -m peleffy.main path/to/my_system.pdb --chain L
+        
 Include terminal rotamers
 -------------------------
 It always includes terminal rotamers, even if they belong to a terminal methyl group whose rotation is trivial in PELE.