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added option for skipping dihedrals which end only in hydrogens
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@stefdoerr
stefdoerr committed Oct 10, 2023
1 parent 32e43c6 commit 9289b1e
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86 changes: 86 additions & 0 deletions moleculekit/test-data/test-detect/m19.cif
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Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
data_MOL
#
#
_chem_comp.id MOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_formal_charge -2
##
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
MOL N . N 0 0.0 39.214 9.077 15.861 39.214 9.077 15.861
MOL C . C 0 0.0 40.483 9.570 16.159 40.483 9.570 16.159
MOL C1 . C 0 0.0 41.481 8.732 16.673 41.481 8.732 16.673
MOL C2 . C 0 0.0 42.751 9.242 16.942 42.751 9.242 16.942
MOL C3 . C 0 0.0 43.042 10.580 16.671 43.042 10.580 16.671
MOL C4 . C 0 0.0 42.058 11.435 16.160 42.058 11.435 16.160
MOL C5 . C 0 0.0 42.347 12.825 15.829 42.347 12.825 15.829
MOL S . S 0 0.0 43.437 13.782 16.801 43.437 13.782 16.801
MOL C6 . C 0 0.0 43.208 15.199 15.794 43.208 15.199 15.794
MOL C7 . C 0 0.0 43.954 16.419 16.179 43.954 16.419 16.179
MOL O . O 0 0.0 43.812 17.451 15.487 43.812 17.451 15.487
MOL O1 . O -1 0.0 44.704 16.389 17.181 44.704 16.389 17.181
MOL C8 . C 0 0.0 42.325 14.933 14.753 42.325 14.933 14.753
MOL O2 . O 0 0.0 41.965 15.835 13.815 41.965 15.835 13.815
MOL C9 . C 0 0.0 40.772 16.545 14.120 40.772 16.545 14.120
MOL C10 . C 0 0.0 40.416 17.529 13.003 40.416 17.529 13.003
MOL O3 . O 0 0.0 39.425 18.276 13.167 39.425 18.276 13.167
MOL O4 . O -1 0.0 41.162 17.531 11.999 41.162 17.531 11.999
MOL C11 . C 0 0.0 41.877 13.615 14.780 41.877 13.615 14.780
MOL Br . Br 0 0.0 40.711 12.963 13.419 40.711 12.963 13.419
MOL C12 . C 0 0.0 40.776 10.916 15.950 40.776 10.916 15.950
MOL H . H 0 0.0 38.988 8.099 15.971 38.988 8.099 15.971
MOL H1 . H 0 0.0 38.500 9.668 15.457 38.500 9.668 15.457
MOL H2 . H 0 0.0 41.276 7.688 16.862 41.276 7.688 16.862
MOL H3 . H 0 0.0 43.512 8.600 17.361 43.512 8.600 17.361
MOL H4 . H 0 0.0 44.040 10.950 16.855 44.040 10.950 16.855
MOL H5 . H 0 0.0 39.933 15.861 14.253 39.933 15.861 14.253
MOL H6 . H 0 0.0 40.903 17.091 15.055 40.903 17.091 15.055
MOL H7 . H 0 0.0 39.996 11.586 15.620 39.996 11.586 15.620
##
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
MOL N C SING
MOL N H SING
MOL N H1 SING
MOL C C12 SING
MOL C C1 DOUB
MOL C1 C2 SING
MOL C1 H2 SING
MOL C2 C3 DOUB
MOL C2 H3 SING
MOL C3 C4 SING
MOL C3 H4 SING
MOL C4 C5 SING
MOL C4 C12 DOUB
MOL C5 C11 DOUB
MOL C5 S SING
MOL S C6 SING
MOL C6 C7 SING
MOL C6 C8 DOUB
MOL C7 O DOUB
MOL C7 O1 SING
MOL C8 O2 SING
MOL C8 C11 SING
MOL O2 C9 SING
MOL C9 C10 SING
MOL C9 H5 SING
MOL C9 H6 SING
MOL C10 O3 DOUB
MOL C10 O4 SING
MOL C11 Br SING
MOL C12 H7 SING
##
49 changes: 47 additions & 2 deletions moleculekit/tools/detect.py
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Original file line number Diff line number Diff line change
Expand Up @@ -325,7 +325,9 @@ def connected_component_subgraphs(graph):
)


def detectParameterizableCores(graph, skip_methyl=True, skip_hydroxyl=False):
def detectParameterizableCores(
graph, skip_methyl=True, skip_hydroxyl=False, skip_terminal_hs=False
):
"""
Detect parametrizable dihedral angle cores (central atom pairs)
Expand Down Expand Up @@ -371,6 +373,15 @@ def detectParameterizableCores(graph, skip_methyl=True, skip_hydroxyl=False):
if graph.nodes[core[1]]["element"] == "C" and graph.degree(core[1]) == 2:
continue

# Skip if side contains only Hs
if skip_terminal_hs:
keys_0 = [x for x in sideGraphs[0].nodes if x != core[0]]
keys_1 = [x for x in sideGraphs[1].nodes if x != core[1]]
if all([graph.nodes[i]["element"] == "H" for i in keys_0]):
continue
if all([graph.nodes[i]["element"] == "H" for i in keys_1]):
continue

all_core_sides.append((core, sideGraphs))

return all_core_sides
Expand Down Expand Up @@ -457,6 +468,7 @@ def detectParameterizableDihedrals(
return_all_dihedrals=False,
skip_methyl=True,
skip_hydroxyl=False,
skip_terminal_hs=False,
):
"""
Detect parameterizable dihedral angles
Expand All @@ -474,6 +486,8 @@ def detectParameterizableDihedrals(
Setting to True will skip dihedrals whose terminal is a methyl group
skip_hydroxyl : bool
Setting to True will skip dihedrals whose terminal is a hydroxyl group
skip_terminal_hs : bool
Setting to True will skip dihedrals ending in hydrogens
Return
------
Expand Down Expand Up @@ -555,7 +569,10 @@ def detectParameterizableDihedrals(
# Get parameterizable dihedral angles
dihedrals = []
for core, sides in detectParameterizableCores(
graph, skip_methyl=skip_methyl, skip_hydroxyl=skip_hydroxyl
graph,
skip_methyl=skip_methyl,
skip_hydroxyl=skip_hydroxyl,
skip_terminal_hs=skip_terminal_hs,
):
if return_all_dihedrals:
all_terminals = [
Expand Down Expand Up @@ -670,6 +687,34 @@ def test_charged_detection(self):
self._compare(eqatoms, eqatoms_ref)
self._compare(eqgroupbyatom, eqgroupbyatom_ref)

def test_detect_dihedrals(self):
import os
from moleculekit.home import home
from moleculekit.molecule import Molecule
import numpy as np

mol = Molecule(os.path.join(home(dataDir="test-detect"), "m19.cif"))
res1 = detectParameterizableDihedrals(mol, skip_terminal_hs=False)
ref1 = [
[(10, 9, 8, 12)],
[(12, 13, 14, 15)],
[(13, 14, 15, 16)],
[(14, 13, 12, 18)],
[(18, 6, 5, 20)],
[(20, 1, 0, 21), (20, 1, 0, 22)],
]
assert res1 == ref1

res2 = detectParameterizableDihedrals(mol, skip_terminal_hs=True)
ref2 = [
[(10, 9, 8, 12)],
[(12, 13, 14, 15)],
[(13, 14, 15, 16)],
[(14, 13, 12, 18)],
[(18, 6, 5, 20)],
]
assert res2 == ref2


if __name__ == "__main__":
import sys
Expand Down

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