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fix OPLS ligpargen atomtypes
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@fgrunewald
fgrunewald committed Aug 15, 2024
1 parent 98e9f85 commit da3a010
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Showing 3 changed files with 108 additions and 7 deletions.
31 changes: 29 additions & 2 deletions polyply/src/gen_ff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,27 @@
from polyply.src.charges import balance_charges, set_charges
from .load_library import load_ff_library

def is_opls(topology):
atomtypes = list(topology.atom_types.keys())
if "opls" in atomtypes[0]:
return True
return False

def _clean_opls_atomtypes(topology):
old_to_new = {}
unique_atypes = {}

for atype, params in topology.atom_types.items():
nb_vals = (str(params['nb1']), str(params['nb2']))
if nb_vals not in unique_atypes:
unique_atypes[nb_vals] = atype
old_to_new[atype] = unique_atypes[nb_vals]
for mol in topology.molecules:
for node in mol.molecule.nodes:
mol.molecule.nodes[node]["atype"] = old_to_new[mol.molecule.nodes[node]["atype"]]
mol.relabel_and_redo_res_graph(mapping={})
return topology

def _read_itp_file(itppath):
"""
small wrapper for reading itps
Expand All @@ -37,7 +58,7 @@ def _read_itp_file(itppath):

def gen_ff(itppath, smile_str, outpath, inpath=[], res_charges=None):
"""
Main executable for itp to ff tool.
Main executable for gen_ff tool.
"""
# load FF files if given
if inpath:
Expand All @@ -53,7 +74,13 @@ def gen_ff(itppath, smile_str, outpath, inpath=[], res_charges=None):
# read the topology file
if itppath.suffix == ".top":
top = Topology.from_gmx_topfile(itppath, name="test")
target_mol = top.molecules[0].molecule
# opls specific fix
# in LigParGen each atom get's its own atype even though
# they are the same; pretty strange but this confuses
# the terminal modifications module
if top and is_opls(top):
_clean_opls_atomtypes(top)
target_mol = top.molecules[0].molecule
# read itp file
elif itppath.suffix == ".itp":
top = None
Expand Down
74 changes: 74 additions & 0 deletions ...tests/test_data/gen_ff/PEG_PBE/in_itp.itp → ...ply/tests/test_data/gen_ff/PEG_PBE/in.top
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Original file line number Diff line number Diff line change
@@ -1,3 +1,73 @@
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5

[ atomtypes ]
opls_814 C814 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_842 H842 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_862 H862 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_818 C818 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_843 H843 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_807 C807 1 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_836 H836 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_834 H834 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_828 H828 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_806 C806 1 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_860 H860 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_851 H851 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_812 C812 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_819 O819 1 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_815 C815 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_811 C811 1 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_861 H861 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_827 H827 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_801 C801 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_838 H838 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_844 H844 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_857 H857 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_824 C824 1 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_830 H830 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_825 C825 1 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_805 C805 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_848 H848 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_826 H826 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_821 C821 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_837 H837 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_829 H829 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_831 H831 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_832 H832 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_803 C803 1 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_822 O822 1 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_800 C800 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_858 H858 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_846 H846 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_856 H856 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_833 H833 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_810 C810 1 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_813 C813 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_816 O816 1 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_820 C820 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_835 H835 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_841 H841 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_852 H852 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_804 C804 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_855 H855 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_839 H839 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_817 C817 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_809 C809 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_808 C808 1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_850 H850 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_840 H840 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_849 H849 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_823 H823 1 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_847 H847 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_853 H853 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_802 C802 1 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_845 H845 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_854 H854 1 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_859 H859 1 1.0080 0.000 A 2.50000E-01 1.25520E-01



[ moleculetype ]
; Name nrexcl
Expand Down Expand Up @@ -571,3 +641,7 @@ PBE_PEO 3
61 62 1
61 63 1

[system]
test
[molecules]
PBE_PEO 1
10 changes: 5 additions & 5 deletions polyply/tests/test_gen_ff.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,11 +79,11 @@ def itp_equal(ref_mol, new_mol):
[("OHter", 0), ("PEO", 0)],
),
# test case 2 PEO-PBE block cooplymer with two termini
# ("PEG_PBE",
# "in_itp.itp",
# "{[#CH3ter][#PBE]|4[#PEO]|2[#OHter]}.{#PEO=[>]COC[<],#OHter=[<]CO,#CH3ter=[>]C,#PBE=[>]CC[<]C=C}",
# [("CH3ter", 0), ("PBE", 0), ("PEO", 0), ("OHter", 0)],
# ),
("PEG_PBE",
"in.top",
"{[#CH3ter][#PBE]|4[#PEO]|2[#OHter]}.{#PEO=[>]COC[<],#OHter=[<]CO,#CH3ter=[>]C,#PBE=[>]CC[<]C=C}",
[("CH3ter", 0), ("PBE", 0), ("PEO", 0), ("OHter", 0)],
),
# test case 3 complex sequence with charged ion in the center
("ACOL",
"ref.top",
Expand Down

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