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Support for neutral point mutation #98

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Support for neutral point mutation #98

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3a27d07
improving parametr handling
JohannesKarwou Nov 15, 2022
2ec0e83
Fix code style issues with Black
lint-action Nov 15, 2022
ea374e9
supporting a first point mutation
JohannesKarwou Nov 15, 2022
ca092bb
Fix code style issues with Black
lint-action Nov 15, 2022
dc19d70
setting NGRP section to zero
JohannesKarwou Nov 15, 2022
f647c16
Merge branch 'support_point_mutation' of github.com:wiederm/transform…
JohannesKarwou Nov 15, 2022
4763c89
Fix code style issues with Black
lint-action Nov 15, 2022
8d9c0ca
minor comments
JohannesKarwou Nov 15, 2022
5745122
Merge branch 'support_point_mutation' of github.com:wiederm/transform…
JohannesKarwou Nov 15, 2022
d1d06e8
paramters which are used by tf are now written out to toppar.st
JohannesKarwou Nov 16, 2022
d0b390e
Merge branch 'parameter_handling' of github.com:wiederm/transformato …
JohannesKarwou Nov 16, 2022
99fe889
Fix code style issues with Black
lint-action Nov 16, 2022
bc0908f
removing ligand1 and ligand2 from parameterset
JohannesKarwou Nov 16, 2022
bcbafc3
Fix code style issues with Black
lint-action Nov 16, 2022
19a022c
extending function to work with asfe
JohannesKarwou Nov 17, 2022
c657551
strange merge conflict
JohannesKarwou Nov 17, 2022
04a2beb
assure that only chain A is mutated
JohannesKarwou Nov 25, 2022
87c5850
Fix code style issues with Black
lint-action Nov 25, 2022
89ae17f
Merge branch 'support_point_mutation' into parameter_handling
JohannesKarwou Nov 27, 2022
33e4d6a
Fix code style issues with Black
lint-action Nov 27, 2022
96b5ab9
Merge pull request #100 from wiederm/parameter_handling
JohannesKarwou Nov 27, 2022
d0123f0
consider empty tlc for s2
JohannesKarwou Nov 27, 2022
d3c724b
Fix code style issues with Black
lint-action Nov 27, 2022
559f0c9
remove unnecessary print statements
JohannesKarwou Nov 28, 2022
a19eda0
comments + way of copying ligand specific files if necessary
JohannesKarwou Nov 28, 2022
aa1f3a0
Fix code style issues with Black
lint-action Nov 28, 2022
575ed84
automatic common core transformation
JohannesKarwou Nov 29, 2022
d821c88
Fix code style issues with Black
lint-action Nov 29, 2022
0380568
create again corrected psf for the tests
JohannesKarwou Nov 29, 2022
4d94b82
Merge branch 'support_point_mutation' of github.com:wiederm/transform…
JohannesKarwou Nov 29, 2022
a536d96
Update mutate.py
JohannesKarwou Jan 13, 2023
92168a6
Update system.py
JohannesKarwou Jan 13, 2023
2915b8c
Fix code style issues with Black
lint-action Jan 13, 2023
5fb7353
Update mutate.py
JohannesKarwou Jan 16, 2023
65bcaba
Fix code style issues with Black
lint-action Jan 16, 2023
bd3a580
handling of different residue names
JohannesKarwou Jan 16, 2023
bdc06b5
Fix code style issues with Black
lint-action Jan 16, 2023
aced89e
avoid parameter changes for dummy atoms in last step
JohannesKarwou Jan 27, 2023
8040e2b
Fix code style issues with Black
lint-action Jan 27, 2023
bd2abe9
remove redundant and statement
JohannesKarwou Jan 30, 2023
f7cc923
Merge branch 'support_point_mutation' of github.com:wiederm/transform…
JohannesKarwou Jan 30, 2023
10793e7
remove unnecessary and statement
JohannesKarwou Jan 30, 2023
e7587ec
compare only within tlc of mutation
JohannesKarwou May 17, 2023
3acaaff
adding addtional toppar file for modified nucleobases
JohannesKarwou May 25, 2023
58191de
Merge branch 'master' into support_point_mutation
JohannesKarwou May 25, 2023
5221929
Fix code style issues with Black
lint-action May 25, 2023
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93 changes: 47 additions & 46 deletions transformato/mutate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1221,8 +1221,8 @@ def _transform_common_core(self) -> list:
logger.warning(f"Charge parameters mutation: {charge_mutation}.")

t = CommonCoreTransformation(
self.get_common_core_idx_mol1() + self.dummy_region_cc1.lj_default,
self.get_common_core_idx_mol2() + self.dummy_region_cc2.lj_default,
self.get_common_core_idx_mol1(),
self.get_common_core_idx_mol2(),
self.psfs["m1"],
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I don't know if we can remove the self.dummy_region_cc1.lj_default variable, but in my opinion I think it's not necessary since this atom (the lj default atom) is not part of the common core anymore and thus can vary between different ligands

self.psfs["m2"],
self.s1_tlc,
Expand Down Expand Up @@ -1461,50 +1461,51 @@ def _get_atom_mapping(self) -> dict:
logger.info(f"CC Struc2: {cc_names_struc2}")

### DANGER ONLY FOR ONE MUTATION NEEEDS TO BE FIXED #####
match_atom_names_cc1_to_cc2 = {
"O5'": "O5'",
"H5T": "H5T",
"C5'": "C5'",
"H5''": "H5''",
"H5'": "H5'",
"C4'": "C4'",
"H4'": "H4'",
"O4'": "O4'",
"C1'": "C1'",
"C2'": "C2'",
"C3'": "C3'",
"H3'": "H3'",
"O3'": "O3'",
"P": "P",
"O2P": "O2P",
"O1P": "O1P",
"H1'": "H1'",
"H2''": "H2''",
"O2'": "O2'",
"H2'": "H2'",
"N1": "N1",
"C6": "C6",
"H6": "H6",
"C5": "C5",
"H5": "H5",
"C4": "C4",
"N3": "N3",
"C2": "C2",
"O2": "O2",
"N4": "N4",
"H42": "H42",
"H41": "H41",
"N9": "N9",
"N7": "N7",
"C8": "C8",
"H8": "H8",
"N2": "N2",
"H21": "H21",
"H22": "H22",
"H1": "H1",
"O6": "O6",
"H3T": "H3T",
}
# match_atom_names_cc1_to_cc2 = {
# "O5'": "O5'",
# "H5T": "H5T",
# "C5'": "C5'",
# "H5''": "H5''",
# "H5'": "H5'",
# "C4'": "C4'",
# "H4'": "H4'",
# "O4'": "O4'",
# "C1'": "C1'",
# "C2'": "C2'",
# "C3'": "C3'",
# "H3'": "H3'",
# "O3'": "O3'",
# "P": "P",
# "O2P": "O2P",
# "O1P": "O1P",
# "H1'": "H1'",
# "H2''": "H2''",
# "O2'": "O2'",
# "H2'": "H2'",
# "N1": "N1",
# "C6": "C6",
# "H6": "H6",
# "C5": "C5",
# "H5": "H5",
# "C4": "C4",
# "N3": "N3",
# "C2": "C2",
# "O2": "O2",
# "N4": "N4",
# "H42": "H42",
# "H41": "H41",
# "N9": "N9",
# "N7": "N7",
# "C8": "C8",
# "H8": "H8",
# "N2": "N2",
# "H21": "H21",
# "H22": "H22",
# "H1": "H1",
# "O6": "O6",
# "H3T": "H3T",
# }

return match_atom_names_cc1_to_cc2

def _mutate_charges(self, psf: pm.charmm.CharmmPsfFile, scale: float):
Expand Down
11 changes: 5 additions & 6 deletions transformato/tests/test_point_mutation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,12 +23,11 @@
warnings.filterwarnings("ignore", module="parmed")


# @pytest.mark.rbfe
# @pytest.mark.requires_parmed_supporting_lp
# @pytest.mark.skipif(
# os.getenv("CI") == "true",
# reason="Skipping tests that cannot pass in github actions",
# )
@pytest.mark.point_mutation
@pytest.mark.skipif(
os.getenv("CI") == "true",
reason="Skipping tests that cannot pass in github actions",
)
def test_setting_up_point_mutation():

configuration = load_config_yaml(
Expand Down