Comments (4)
Support
A new branch called OBC_for_OPLS
has been created. It contains a new method called _add_GBSA_solvent_parameters()
to be filled with the parameterization pipeline from the solventOBCParamsGenerator.py script.
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The original script required atom degrees to perform the parameterization. Consequently, we need method to extract atom degrees from our molecule representation. This can be done with RDKit
in a very straightforward way:
rdkit_molecule = molecule.rdkit_molecule
atom_degrees = list()
for atom in rdkit_molecule.GetAtoms():
atom_degrees.append(atom.GetDegree())
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Besides, in case the parent atom of any atom is needed (for instance, thinking on identifying the atom a hydrogen atom is bonded to), the Atom
's attribute parent
stores the reference of the its parent atom. This attribute is set when initializing the Molecule
representation in peleffy
.
Atom
objects are accessible after parameterizing the Molecule
:
molecule = Molecule(smiles='CCC')
molecule.parameterize('openff_unconstrained-1.2.1.offxml')
for atom in molecule.atoms:
if atom.parent is None:
continue
print(atom.parent.index)
Note that there is always an Atom
without a parent Atom
(its parent is set to None). This is the absolute parent atom according to the built molecular graph. However, a terminal atom such as hydrogen should never be the absolute parent atom and, therefore, it will never have a None parent atom.
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Implementation
The method _add_GBSA_solvent_parameters() has been filled with the parameterization pipeline from the solventOBCParamsGenerator.py
script.
Different features from the solventOBCParamsGenerator.py
script have been introduced:
- When only one of the two parameters is found, the default parameters are returned. In the
solventOBCParamsGenerator.py
script, the parameter found was return and the non-found parameter was not defined. - The parameters lists are saved in a JSON file.
Tests
The function test_add_GBSA_solvent_parameters
has been implemented and tests the new method for adding the GBSA solvent parameters for the following ligands: methane.pdb
, melatone.pdb
and ethylene.pdb
.
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Related Issues (20)
- Different names for charge methods in forcefield selector and main for OPLS
- Create new molecule silently HOT 5
- Explanatory error messages when using an invalid Impact template
- Openforcefield-0.8.3 upgrade HOT 1
- Solvent class compatible with multiple topologies HOT 1
- Add CLI option for mae charges HOT 1
- Error in peleffy.topology.molecule.Molecule._pdb_checkup() HOT 2
- Fix documentation API links
- Load parameters from JSON
- Parents order altered
- Peleffy parameters for a macrocycle causes infinte loop in PELE HOT 2
- Support for python 3.8
- Multiple molecules in the input PDB file
- Add examples for peleffy 1.3.0
- Diferent Schrodinger versions causes parsing error in ffld_output
- Extend support to openff 2.0.0 and test it
- Error at generating template files with peleffy HOT 2
- --chain flag error when dealing with pdb containing only the ligand
- Alchemistry docs
- Error when use_peleffy: true in both versions of pele_platform
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