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A summary of the question or discussion topic.
I've realized over the last couple weeks working with @Argon1999 to improve our OPLS coverage that the instructions for doing so aren't immediately clear nor well-documented. As we continue to improve our OPLS.xml I wanted to make sure the steps for doing so are clearly outlined:
Define SMARTS strings and description for each type. Add bond, angle, dihedral definitions for the atom type if not already done so.
Generate and add GROMACS gro and top files into a directory that corresponds to a molecule in opls_validation (Make sure these structure files are for a single molecule) These files will be used to test that the molecule can be correctly atom-typed.
in foyer/tests run python test_opls.py. This will run the find_correctly_implemented function that will attempt to atom-type the molecules contained within opls_validation. If the new molecules are correctly atom-typed by the new SMARTS definitions, then the molecule names will be appended to implemented_opls.txt.
Run pytest test_opls.py. If all tests pass, then the SMARTS definitions have been correctly implemented.
The text was updated successfully, but these errors were encountered:
A summary of the question or discussion topic.
I've realized over the last couple weeks working with @Argon1999 to improve our OPLS coverage that the instructions for doing so aren't immediately clear nor well-documented. As we continue to improve our OPLS.xml I wanted to make sure the steps for doing so are clearly outlined:
gro
andtop
files into a directory that corresponds to a molecule inopls_validation
(Make sure these structure files are for a single molecule) These files will be used to test that the molecule can be correctly atom-typed.foyer/tests
runpython test_opls.py
. This will run thefind_correctly_implemented
function that will attempt to atom-type the molecules contained withinopls_validation
. If the new molecules are correctly atom-typed by the new SMARTS definitions, then the molecule names will be appended toimplemented_opls.txt
.pytest test_opls.py
. If all tests pass, then the SMARTS definitions have been correctly implemented.The text was updated successfully, but these errors were encountered: