Merge pull request #136 from martimunicoy/devel

1.2.1 Release
martimunicoy · Apr 7, 2021 · 31a1487 · 31a1487
2 parents a81633a + de108f4
commit 31a1487
Show file tree

Hide file tree

Showing 10 changed files with 278 additions and 31 deletions.
diff --git a/docs/forcefield.rst b/docs/forcefield.rst
@@ -1,7 +1,7 @@
-.. _forcefield ::
+.. _forcefield :
 
 Forcefield methods
-==============
+==================
 
 This module defines the different force fields that are available
 in `peleffy` to parameterize molecules for PELE.
@@ -13,8 +13,8 @@ Primary objects
 
 .. autosummary::
     :nosignatures:
-    :toctree: api/autogenerated
     :template: class.rst
+    :toctree: api/autogenerated
 
     OpenForceField
     OPLS2005ForceField
@@ -26,8 +26,8 @@ Secondary objects
 
 .. autosummary::
     :nosignatures:
-    :toctree: api/autogenerated
     :template: class.rst
+    :toctree: api/autogenerated
 
     calculators.Am1bccCalculator
     calculators.GasteigerCalculator

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -6,7 +6,7 @@ Installation
 Installing via `conda`
 ======================
 The more straightforward way to install `peleffy` along with the required
-dependencies is through the `conda <http://www.continuum.io/blog/conda>`_
+dependencies is through the `conda <https://docs.conda.io/en/latest/>`_
 package manager.
 
 First, you need to install the

diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -7,6 +7,26 @@ 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
 
+
+1.2.1 - API Documentation and improvements
+------------------------------------------
+
+This is a micro release of peleffy that includes and new method to load parameters from a JSON file and solves different bugs in the documentation and the OPLS parametrization. 
+
+New features
+""""""""""""
+- `PR #131 <https://github.com/martimunicoy/peleffy/pull/131>`_: New method to load parameters from a JSON file.
+
+Tests added
+"""""""""""
+- `PR #131 <https://github.com/martimunicoy/peleffy/pull/131>`_: Adds tests to validate the new method to load parameters from a JSON file.
+
+Bugfixes
+""""""""
+- `PR #129 <https://github.com/martimunicoy/peleffy/pull/129>`_: Some format errors in the API documentation are fixed. Links to the PELE documentation are updated.
+- `PR #134 <https://github.com/martimunicoy/peleffy/pull/134>`_: Fixes bug when parsing the parameters of the ligand when OPLS is used to parameterize. 
+
+
 1.2.0 - New tools for parameters and templates
 ----------------------------------------------
 

diff --git a/docs/solvent.rst b/docs/solvent.rst
@@ -1,4 +1,4 @@
-.. _solvent ::
+.. _solvent :
 
 Solvent models
 ==============
@@ -13,8 +13,8 @@ Primary objects
 
 .. autosummary::
     :nosignatures:
-    :toctree: api/autogenerated
     :template: class.rst
+    :toctree: api/autogenerated
 
     OBC2
     OPLSOBC
@@ -25,7 +25,7 @@ Secondary objects
 
 .. autosummary::
     :nosignatures:
-    :toctree: api/autogenerated
     :template: class.rst
+    :toctree: api/autogenerated
 
     OBC1
diff --git a/docs/template.rst b/docs/template.rst
@@ -1,4 +1,4 @@
-.. _template ::
+.. _template :
 
 Template handlers
 =================
@@ -12,8 +12,8 @@ Primary objects
 
 .. autosummary::
     :nosignatures:
-    :toctree: api/autogenerated
     :template: class.rst
+    :toctree: api/autogenerated
 
     Impact
 
@@ -23,8 +23,8 @@ Secondary objects
 
 .. autosummary::
     :nosignatures:
-    :toctree: api/autogenerated
     :template: class.rst
+    :toctree: api/autogenerated
 
     impact.WritableWrapper
     impact.WritableAtom

diff --git a/docs/topology.rst b/docs/topology.rst
@@ -1,4 +1,4 @@
-.. _topology ::
+.. _topology :
 
 Topology representations
 ========================
@@ -14,8 +14,8 @@ Primary objects
 
 .. autosummary::
     :nosignatures:
-    :toctree: api/autogenerated
     :template: class.rst
+    :toctree: api/autogenerated
 
     Molecule
     Topology
@@ -26,8 +26,8 @@ Secondary objects
 
 .. autosummary::
     :nosignatures:
-    :toctree: api/autogenerated
     :template: class.rst
+    :toctree: api/autogenerated
 
     Atom
     Bond

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -5,9 +5,9 @@ Generate PELE parameter files
 
 The main purpose of `peleffy` is to build the parameter files for PELE. Basically, PELE requires two files for each non-standard residue found in the system:
 
-- `IMPACT template <https://eapm-bsc.github.io/PELE-repo/fileFormats.html#impact-template-file-format>`_: a file containing the atom types and parameters of the ligand. Its job is to link each atom with the corresponding parameters using PDB atom names. Thus, PDB atom names in the input PDB file must match with the expected PDB atom names in the Impact file. This file intrinsically contains the information about the topology and connectivity of each residue.
+- `IMPACT template <https://nostrumbiodiscovery.github.io/pele_docs/fileFormats.html#sec-fileformats-impact>`_: a file containing the atom types and parameters of the ligand. Its job is to link each atom with the corresponding parameters using PDB atom names. Thus, PDB atom names in the input PDB file must match with the expected PDB atom names in the Impact file. This file intrinsically contains the information about the topology and connectivity of each residue.
 
-- `Rotamer library <https://eapm-bsc.github.io/PELE-repo/fileFormats.html#ligand-rotamer-library-file>`_: a file containing the branches that can rotate with respect to a central atomic core. Each branch consists in a set of consecutive rotatable bonds.
+- `Rotamer library <https://nostrumbiodiscovery.github.io/pele_docs/fileFormats.html#sec-fileformats-ligandrotamers>`_: a file containing the branches that can rotate with respect to a central atomic core. Each branch consists in a set of consecutive rotatable bonds.
 
 Besides, a third file with the `Solvent parameters` might be required when employing the OBC implicit solvent.
 
@@ -102,6 +102,8 @@ arguments. To obtain the full list of flags you can type:
                              hierarchy
        -c NAME, --charge_method NAME
                              The name of the method to use to compute charges
+       --charges_from_file PATH
+                             The path to the file with charges
        --include_terminal_rotamers
                              Not exclude terminal rotamers when building the
                              rotamer library

diff --git a/peleffy/forcefield/parameters.py b/peleffy/forcefield/parameters.py
@@ -215,6 +215,107 @@ def to_json(self, output_path):
             json.dump(convert_all_quantities_to_string(self), f,
                       indent=4, sort_keys=True)
 
+    def from_json(self, input_path):
+        """
+        It loads a json file containing the parameters into the parameter
+        wrapper.
+
+        Parameters
+        ----------
+        input_path : str
+            The path to the json file to load the parameters from
+
+        Returns
+        -------
+        self : a BaseParameterWrapper object
+            The resulting parameters wrapper
+        """
+        import json
+        def correct_type(label, value):
+            """
+            It converts the parameters loaded from the JSON file into the
+            expected data type in the parameter wrapper.
+
+            Parameters
+            ----------
+            label : str
+                Label for the parameters
+            value : list
+                Set of parameters
+
+            Returns
+            -------
+            correct_value : list
+                Set of paramaeters with the expected data type
+            """
+            import simtk.unit
+            from peleffy.utils import string_to_quantity
+
+            # Dictionary relating parameters key with the expected data type
+            dict_units = {
+                'alphas': float, 'gammas': float,
+                'charges':  simtk.unit.quantity.Quantity,
+                'sigmas' : 'list_Quantity', 'epsilons' : 'list_Quantity',
+                'SGB_radii' : 'list_Quantity','vdW_radii' : 'list_Quantity',
+                'angles': dict, 'bonds': dict, 'impropers': dict,
+                'propers': dict, 'GBSA_radii': 'list_Quantity',
+                'GBSA_scales': 'list_Quantity',
+                'atom_names': str, 'atom_types' : str
+                }
+
+            # Skip data type transformation if the list is empty or None values
+            if value == [None,] * len(value):
+                return value
+            if value == []:
+                return None
+
+            # Perform data type transformation, if needed
+            else:
+                if dict_units[label] is str:
+                    correct_value = value
+
+                if dict_units[label] is float:
+                    correct_value  = [float(v) if not v is None else v
+                    for v in value]
+
+                if dict_units[label] is simtk.unit.quantity.Quantity:
+                    correct_value = string_to_quantity(value)
+                    return correct_value
+
+                if dict_units[label] == 'list_Quantity':
+                    correct_value = \
+                            [unit.Quantity(value=string_to_quantity(v)._value,
+                                           unit=string_to_quantity(v).unit)
+                            for v in value]
+
+                if dict_units[label] is dict:
+                    correct_value = []
+                    for element in value:
+                        correct_dict = dict()
+                        for k,v in element.items():
+                            if 'idx' in k:
+                                correct_dict[k] = int(v)
+                            else:
+                                try:
+                                    correct_dict[k] = unit.Quantity(
+                                            value=string_to_quantity(v)._value,
+                                            unit=string_to_quantity(v).unit)
+                                except:
+                                    correct_dict[k] = v
+                        correct_value.append(correct_dict)
+                return correct_value
+
+        # Load the dict from the JSON file
+        with open(input_path) as f:
+            data = json.load(f)
+
+        # Correct the data type format and fetch the BaseParameterWrapper
+        for key, value in data.items():
+            value_correct = correct_type(key, value)
+            if not value_correct is None:
+                self.add_parameters(key, value_correct)
+        return self
+
     @property
     def atom_iterator(self):
         """
@@ -299,7 +400,7 @@ def from_impact_template(molecule, impact_template_path):
         >>> from peleffy.forcefield.parameters import \
                 OpenForceFieldParametersWrapper
 
-        >>> wrapper_off = OpenForceFieldParameterWrapper()
+        >>> wrapper_off = OpenForceFieldParametersWrapper()
         >>> parameters = wrapper_off.from_impact_template(
                 molecule, impact_template_path)
 
@@ -952,7 +1053,7 @@ def from_ffld_output(molecule, ffld_output):
                 assert len(fields) > 7, 'Unexpected number of fields ' \
                     + 'found at line {}'.format(line)
 
-                name_to_index[line[0:4]] = len(name_to_index)
+                name_to_index[line[0:8]] = len(name_to_index)
 
                 params['atom_types'].append(fields[3])
                 params['charges'].append(
@@ -971,8 +1072,8 @@ def from_ffld_output(molecule, ffld_output):
                     + 'found at line {}'.format(line)
 
                 params['bonds'].append(
-                    {'atom1_idx': name_to_index[line[0:4]],
-                     'atom2_idx': name_to_index[line[8:12]],
+                    {'atom1_idx': name_to_index[line[0:8]],
+                     'atom2_idx': name_to_index[line[8:16]],
                      'spring_constant': unit.Quantity(
                         float(fields[2]), unit.kilocalorie
                         / (unit.angstrom ** 2 * unit.mole)),
@@ -986,9 +1087,9 @@ def from_ffld_output(molecule, ffld_output):
                     + 'found at line {}'.format(line)
 
                 params['angles'].append(
-                    {'atom1_idx': name_to_index[line[0:4]],
-                     'atom2_idx': name_to_index[line[8:12]],
-                     'atom3_idx': name_to_index[line[16:20]],
+                    {'atom1_idx': name_to_index[line[0:8]],
+                     'atom2_idx': name_to_index[line[8:16]],
+                     'atom3_idx': name_to_index[line[16:24]],
                      'spring_constant': unit.Quantity(
                         float(fields[3]), unit.kilocalorie
                         / (unit.radian ** 2 * unit.mole)),
@@ -1001,10 +1102,10 @@ def from_ffld_output(molecule, ffld_output):
                 assert len(fields) > 9, 'Unexpected number of fields ' \
                     + 'found at line {}'.format(line)
 
-                atom1_idx = name_to_index[line[0:4]]
-                atom2_idx = name_to_index[line[8:12]]
-                atom3_idx = name_to_index[line[16:20]]
-                atom4_idx = name_to_index[line[24:28]]
+                atom1_idx = name_to_index[line[0:8]]
+                atom2_idx = name_to_index[line[8:16]]
+                atom3_idx = name_to_index[line[16:24]]
+                atom4_idx = name_to_index[line[24:32]]
 
                 for k, periodicity, phase in zip(
                         fields[4:8], [1, 2, 3, 4],
@@ -1051,10 +1152,10 @@ def from_ffld_output(molecule, ffld_output):
                                   unit.kilocalorie / unit.mole)
 
                 params['impropers'].append(
-                    {'atom1_idx': name_to_index[line[0:4]],
-                     'atom2_idx': name_to_index[line[8:12]],
-                     'atom3_idx': name_to_index[line[16:20]],
-                     'atom4_idx': name_to_index[line[24:28]],
+                    {'atom1_idx': name_to_index[line[0:8]],
+                     'atom2_idx': name_to_index[line[8:16]],
+                     'atom3_idx': name_to_index[line[16:24]],
+                     'atom4_idx': name_to_index[line[24:32]],
                      'periodicity': 2,
                      'phase': unit.Quantity(180.0, unit.degree),
                      'k': k / 2.0,  # PELE works with half of Schrodinger's force constant