Merge pull request #20 from martimunicoy/devel

Minor release 0.2.1

docs/charge.rst

@@ -0,0 +1,20 @@
+.. _charge ::
+
+Charge methods
+==============
+
+This module provides different methods to calculate partial charges
+for PELE.
+
+.. currentmodule:: offpele.charge
+
+Primary objects
+---------------
+
+.. autosummary::
+    :nosignatures:
+    :toctree: api/autogenerated
+    :template: class.rst
+
+    Am1bccCalculator
+    GasteigerCalculator

docs/index.rst

@@ -13,6 +13,7 @@ User guide
   :maxdepth: 1
 
   installation
+  releasehistory
 
 
 API documentation
@@ -24,3 +25,4 @@ API documentation
   topology
   template
   solvent
+  charge

docs/installation.rst

@@ -3,11 +3,81 @@
 Installation
 ************
 
-Installing via PyPI
-===================
+Installing via `conda`
+======================
+The more straightforward way to install `offpele` along with the required
+dependencies is through the `conda <http://www.continuum.io/blog/conda>`_
+package manager.
 
-It can be easily install through PyPI with the following command:
+First, you need to install the
+`miniconda <http://conda.pydata.org/miniconda.html>`_ distribution, which is
+the minimal installation of the Anaconda Python package.
+
+To install the Python 3 version on ``linux`` (on ``bash`` systems):
+
+.. code-block:: bash
+
+   $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+   $ bash ./Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3
+
+It can also be installed on ``osx`` with:
+
+.. code-block:: bash
+
+   $ curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O
+   $ bash ./Miniconda3-latest-MacOSX-x86_64.sh -b -p $HOME/miniconda3
+
+Once installed, the bases environment of `conda` can be loaded with
+the following commands:
+
+.. code-block:: bash
+
+   $ source ~/miniconda3/etc/profile.d/conda.sh
+   $ conda activate base
+
+You can also create a custom conda environment to handle offpele:
+
+.. code-block:: bash
+
+   $ conda create --name offpele_env
+
+which can be activated and deactivated with the two commands from below:
+
+.. code-block:: bash
+
+   $ conda activate offpele_env
+   $ conda deactivate
+
+To install de dependencies of offpele, the following `conda` channels need
+to be added and updated:
+
+.. code-block:: bash
+
+   $ conda config --add channels omnia --add channels conda-forge --add channels martimunicoy
+   $ conda update --all
+
+Finally, you can install the latest stable build of `offpele`
+
+.. code-block:: bash
+
+   $ conda install offpele
+
+
+Installing via `PyPI`
+=====================
+
+`offpele` can also be installed through `PyPI <https://pypi.org>`_
+with the following command:
 
 .. code-block:: bash
 
    $ pip install offpele
+
+However, with `PyPI` some of the required dependencies of `offpele` are not
+installed and have to be installed manually such as:
+
+- Open Force Field Toolkit
+- RDKit
+- AmberTools
+
+For this reason, the installation through `conda` is recommended.

docs/releasehistory.rst

@@ -1,4 +1,51 @@
-Release history
-###############
+Release History
+===============
 
-To do
+Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https://www.python.org/dev/peps/pep-0440/#final-releases>`_, where
+
+* ``major`` increments denote a change that may break API compatibility with previous ``major`` releases
+* ``minor`` increments add features but do not break API compatibility
+* ``micro`` increments represent bugfix releases or improvements in documentation
+
+0.3.0 - Current development
+-------------------------
+
+This is still a preliminary version of the Open Force Field to PELE package.
+
+
+0.2.1
+-----
+
+This is a micro release that includes new features and parameters to configurate the behaviour of the program.
+It is designed to be employed to run the first benchmarks of the implementation in PELE. 
+It also includes many stability improvements and an extended test coverage.
+
+New features
+""""""""""""
+- `PR #15 <https://github.com/martimunicoy/offpele/pull/15>`_: Adds a new method (Antechamber's gasteiger) to calculate partial charges.
+- `PR #19 <https://github.com/martimunicoy/offpele/pull/19>`_: Adds a new option to ignore terminal rotatable bonds of each rotamer's branch.
+- `PR #17 <https://github.com/martimunicoy/offpele/pull/17>`_: Adds and updates the documentation. However, it is still not completed.
+
+Bugfixes
+""""""""
+- `PR #18 <https://github.com/martimunicoy/offpele/pull/18>`_: Fixes some problems with proper and improper constructors.
+
+Tests added
+"""""""""""
+- `PR #15 <https://github.com/martimunicoy/offpele/pull/15>`_: Adds tests ensuring that the run_offpele call from main and the partial charge calculators work as expected.
+- `PR #19 <https://github.com/martimunicoy/offpele/pull/19>`_: Adds tests to validate the construction of the `RotamerLibrary` class and the filtering of terminal rotatable bonds.
+
+
+0.2.0
+-----
+
+This is a preliminary version of the Open Force Field to PELE package.
+
+New features
+""""""""""""
+
+A first implementation of the package that allows to:
+
+- Build a rotamer library for a small molecule using RDKit's API
+- Build a template with the Molecular Mechanics' parameters for a small molecule using the Open Force Field Toolkit
+- Assign the OBC implicit solvent parameters to a small molecule using the Open Force Field Toolkit

offpele/charge/__init__.py

@@ -0,0 +1 @@
+from .charges import Am1bccCalculator, GasteigerCalculator

offpele/charge/charges.py

@@ -0,0 +1,74 @@
+"""
+This module handles all classes and functions related with partial charge
+calculators.
+"""
+
+
+from offpele.utils.toolkits import AmberToolkitWrapper
+
+
+class _PartialChargesCalculator(object):
+    """
+    Base class for partial charges calculators.
+    """
+
+    _name = None
+    _amber_toolkit = AmberToolkitWrapper()
+
+    def __init__(self, molecule):
+        """
+        It initiates a PartialChargesCalculator object.
+
+        Parameters
+        ----------
+        molecule : An offpele.topology.Molecule
+            The partial charges of this Molecule object will be calculated
+        """
+        self._molecule = molecule
+
+    @property
+    def molecule(self):
+        """
+        The offpele's Molecule.
+
+        Returns
+        -------
+        molecule : an offpele.topology.Molecule
+            The offpele's Molecule object
+        """
+        return self._molecule
+
+    @property
+    def name(self):
+        return self._name
+
+    def get_partial_charges(self):
+        """
+        It returns the partial charges that correspond to the molecule's
+        atoms.
+
+        Returns
+        -------
+        charges : simtk.unit.Quantity
+            The array of partial charges
+        """
+
+        return self._amber_toolkit.compute_partial_charges(self.molecule,
+                                                           method=self.name)
+
+
+class Am1bccCalculator(_PartialChargesCalculator):
+    """
+    Implementation of the AM1-BCC partial charges calculator (using RDKit).
+    """
+
+    _name = 'am1bcc'
+
+
+class GasteigerCalculator(_PartialChargesCalculator):
+    """
+    Implementation of the gasteiger partial charges calculator (using
+    RDKit).
+    """
+
+    _name = 'gasteiger'

offpele/main.py

@@ -18,9 +18,11 @@
 
 DEFAULT_OFF_FORCEFIELD = 'openff_unconstrained-1.2.0.offxml'
 DEFAULT_RESOLUTION = int(30)
+DEFAULT_CHARGES_METHOD = 'am1bcc'
 IMPACT_TEMPLATE_PATH = 'DataLocal/Templates/OFF/Parsley/HeteroAtoms/'
 ROTAMER_LIBRARY_PATH = 'DataLocal/LigandRotamerLibs/'
 SOLVENT_TEMPLATE_PATH = 'DataLocal/OBC/'
+DEFAULT_TERMINAL_ROT_TO_IGNORE = 1
 
 
 def parse_args():
@@ -52,6 +54,13 @@ def parse_args():
     parser.add_argument('--as_DataLocal', dest='as_datalocal',
                         help="Output will be saved following PELE's DataLocal "
                         + "hierarchy", action='store_true')
+    parser.add_argument('-c', '--charges_method', metavar="NAME",
+                        type=str, help="The name of the method to use to "
+                        + "compute charges", default=DEFAULT_CHARGES_METHOD)
+    parser.add_argument('-t', '--terminal_rotamers_to_ignore', metavar="INT",
+                        type=str, help="The number of terminal rotamers " +
+                        " to ignore when building the rotamer library",
+                        default=DEFAULT_TERMINAL_ROT_TO_IGNORE)
 
     parser.set_defaults(as_datalocal=False)
     parser.set_defaults(with_solvent=False)
@@ -112,8 +121,10 @@ def handle_output_paths(molecule, output, as_datalocal):
 
 
 def run_offpele(pdb_file, forcefield=DEFAULT_OFF_FORCEFIELD,
-                  resolution=DEFAULT_RESOLUTION, output=None,
-                  with_solvent=False, as_datalocal=False,):
+                resolution=DEFAULT_RESOLUTION,
+                charges_method=DEFAULT_CHARGES_METHOD,
+                terminal_rotamers_to_ignore=DEFAULT_TERMINAL_ROT_TO_IGNORE,
+                output=None, with_solvent=False, as_datalocal=False):
     """
     It runs offpele.
 
@@ -124,7 +135,13 @@ def run_offpele(pdb_file, forcefield=DEFAULT_OFF_FORCEFIELD,
     forcefield : str
         The name of an OpenForceField's forcefield
     resolution : float
-        The resolution in degrees for the rotamer library
+        The resolution in degrees for the rotamer library. Default is 30
+    charges_method : str
+        The name of the method to use to compute partial charges. Default
+        is 'am1bcc'
+    terminal_rotamers_to_ignore : int
+        The number of terminal rotamers to ignore when building the
+        rotamer library. Default is 1
     output : str
         Path where output files will be saved
     with_solvent : bool
@@ -135,12 +152,15 @@ def run_offpele(pdb_file, forcefield=DEFAULT_OFF_FORCEFIELD,
         not
     """
     print('-' * 60)
-    print('Open Force Field parameterizer for PELE v'
+    print('Open Force Field parameterizer for PELE '
           '{}'.format(offpele.__version__))
     print('-' * 60)
     print(' - PDB to parameterize: {}'.format(pdb_file))
     print(' - Force field: {}'.format(forcefield))
     print(' - Rotamer library resolution: {}'.format(resolution))
+    print(' - Charges method: {}'.format(charges_method))
+    print(' - Terminal rotamers to ignore: {}'.format(
+        terminal_rotamers_to_ignore))
     print(' - Output path: {}'.format(output))
     print(' - Write solvent parameters: {}'.format(with_solvent))
     print(' - DataLocal-like output: {}'.format(as_datalocal))
@@ -158,11 +178,13 @@ def run_offpele(pdb_file, forcefield=DEFAULT_OFF_FORCEFIELD,
         output = os.getcwd()
 
     molecule = Molecule(pdb_file)
-    molecule.parameterize(forcefield)
+    molecule.parameterize(forcefield, charges_method=charges_method)
 
     rotlib_out, impact_out, solvent_out = handle_output_paths(molecule, output, as_datalocal)
 
-    molecule.build_rotamer_library(resolution=resolution)
+    molecule.build_rotamer_library(
+        resolution=resolution,
+        n_rot_bonds_to_ignore=terminal_rotamers_to_ignore)
     molecule.rotamer_library.to_file(rotlib_out)
     impact = Impact(molecule)
     impact.write(impact_out)
@@ -177,20 +199,22 @@ def run_offpele(pdb_file, forcefield=DEFAULT_OFF_FORCEFIELD,
 
 def main():
     """
-    It reads the command-line arguments and calls offpele.
+    It reads the command-line arguments and runs offpele.
 
     Examples
     --------
 
     From the command-line:
 
     >>> python main.py molecule.pdb -f openff_unconstrained-1.1.1.offxml -r 30
-        -o output_path/ --with_solvent --as_DataLocal
+        -o output_path/ --with_solvent --as_DataLocal -c gasteiger
 
     """
     args = parse_args()
-    run_offpele(args.pdb_file, args.forcefield, args.resolution, args.output,
-                  args.with_solvent, args.as_datalocal)
+    run_offpele(args.pdb_file, args.forcefield, args.resolution,
+                args.charges_method, args.terminal_rotamers_to_ignore,
+                args.output, args.with_solvent,
+                args.as_datalocal)
 
 
 if __name__ == '__main__':

offpele/solvent/solvent.py

@@ -240,7 +240,7 @@ class OBC2(_SolventWrapper):
     Implementation of the OBC2 solvent.
     """
 
-    _ff_file = get_data_file_path('forcefields/GBSA_OBC1-1.0.offxml')
+    _ff_file = get_data_file_path('forcefields/GBSA_OBC2-1.0.offxml')
     _name = 'OBC2'
 
     def __init__(self, molecule):