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Integrate method for the OPLS OBC parameters #78
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SupportA new branch called |
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_molecule = molecule.rdkit_molecule
atom_degrees = list()
for atom in rdkit_molecule.GetAtoms():
atom_degrees.append(atom.GetDegree()) |
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 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 |
ImplementationThe method _add_GBSA_solvent_parameters() has been filled with the parameterization pipeline from the Different features from the
TestsThe function |
Description
PELE
has a script to obtain the OBC parameters given a small molecule. This script is quite old though and presents many compatibility problems. Maybe we can incorporate this script into theoffpele
package to automatize the parameterization workflow. We could also look at its compatibility issues to try to improve it.Solution
This would be a new
Solvent
class, that given aMolecule
representation, parameterized withOPLS2005
would use atom types to assign the OBC parameters. Then, it should write the template file in the corresponding format file expected by PELE.The text was updated successfully, but these errors were encountered: