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Soft core force field includes torsions with wildcards #308

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Oct 3, 2024
Merged

Soft core force field includes torsions with wildcards #308

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889d566
Soft core force field includes torsions with wildcards
peastman Sep 30, 2024
32ebcd7
Bug fixes
peastman Oct 3, 2024
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52 changes: 23 additions & 29 deletions devtools/createSoftForcefield.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,18 +51,21 @@
omitTypes = set()
omitClasses = set()
for atomType in forcefield._atomTypes:
(atomClass, mass, element) = forcefield._atomTypes[atomType]
if element is None or element == elem.hydrogen:
data = forcefield._atomTypes[atomType]
if data.element is None or data.element == elem.hydrogen:
omitTypes.add(atomType)
omitClasses.add(atomClass)
omitClasses.add(data.atomClass)
else:
print(' <Type name="%s" class="%s" element="%s" mass="%g"/>' % (atomType, atomClass, element.symbol, mass))
print(' <Type name="%s" class="%s" element="%s" mass="%g"/>' % (atomType, data.atomClass, data.element.symbol, data.mass))
print(' </AtomTypes>')

# Print the residue templates.

print(' <Residues>')
skipTemplates = ('ASH', 'CYM', 'GLH', 'HID', 'HIE', 'LYN')
for template in forcefield._templates.values():
if template.name in skipTemplates or template.name[1:] in skipTemplates:
continue
print(' <Residue name="%s">' % template.name)
atomIndex = {}
for i, atom in enumerate(template.atoms):
Expand All @@ -86,8 +89,8 @@
type1 = next(iter(bonds.types1[i]))
type2 = next(iter(bonds.types2[i]))
if type1 not in omitTypes and type2 not in omitTypes:
class1 = forcefield._atomTypes[type1][0]
class2 = forcefield._atomTypes[type2][0]
class1 = forcefield._atomTypes[type1].atomClass
class2 = forcefield._atomTypes[type2].atomClass
print(' <Bond class1="%s" class2="%s" length="%g" k="%g"/>' % (class1, class2, bonds.length[i], bondK))
print(' </HarmonicBondForce>')

Expand All @@ -100,41 +103,32 @@
type2 = next(iter(angles.types2[i]))
type3 = next(iter(angles.types3[i]))
if type1 not in omitTypes and type2 not in omitTypes and type3 not in omitTypes:
class1 = forcefield._atomTypes[type1][0]
class2 = forcefield._atomTypes[type2][0]
class3 = forcefield._atomTypes[type3][0]
class1 = forcefield._atomTypes[type1].atomClass
class2 = forcefield._atomTypes[type2].atomClass
class3 = forcefield._atomTypes[type3].atomClass
print(' <Angle class1="%s" class2="%s" class3="%s" angle="%g" k="%g"/>' % (class1, class2, class3, angles.angle[i], angleK))
print(' </HarmonicAngleForce>')

# Print the periodic torsions.

print(' <PeriodicTorsionForce>')
torsions = [f for f in forcefield._forces if isinstance(f, ff.PeriodicTorsionGenerator)][0]
wildcardType = forcefield._atomClasses['']
for torsion in torsions.proper:
type1 = next(iter(torsion.types1))
type2 = next(iter(torsion.types2))
type3 = next(iter(torsion.types3))
type4= next(iter(torsion.types4))
if type1 not in omitTypes and type2 not in omitTypes and type3 not in omitTypes and type4 not in omitTypes:
class1 = forcefield._atomTypes[type1][0]
class2 = forcefield._atomTypes[type2][0]
class3 = forcefield._atomTypes[type3][0]
class4 = forcefield._atomTypes[type4][0]
print(' <Proper class1="%s" class2="%s" class3="%s" class4="%s"' % (class1, class2, class3, class4), end=' ')
type = [next(iter(torsion.types1)), next(iter(torsion.types2)), next(iter(torsion.types3)), next(iter(torsion.types4))]
wildcard = [torsion.types1 == wildcardType, torsion.types2 == wildcardType, torsion.types3 == wildcardType, torsion.types4 == wildcardType]
if all(type[i] not in omitTypes or wildcard[i] for i in range(4)):
classes = tuple('' if wildcard[i] else forcefield._atomTypes[type[i]].atomClass for i in range(4))
print(' <Proper class1="%s" class2="%s" class3="%s" class4="%s"' % classes, end=' ')
for i in range(len(torsion.k)):
print(' periodicity%d="%d" phase%d="%g" k%d="%g"' % (i+1, torsion.periodicity[i], i+1, torsion.phase[i], i+1, torsion.k[i]), end=' ')
print('/>')
for torsion in torsions.improper:
type1 = next(iter(torsion.types1))
type2 = next(iter(torsion.types2))
type3 = next(iter(torsion.types3))
type4= next(iter(torsion.types4))
if type1 not in omitTypes and type2 not in omitTypes and type3 not in omitTypes and type4 not in omitTypes:
class1 = forcefield._atomTypes[type1][0]
class2 = forcefield._atomTypes[type2][0]
class3 = forcefield._atomTypes[type3][0]
class4 = forcefield._atomTypes[type4][0]
print(' <Improper class1="%s" class2="%s" class3="%s" class4="%s"' % (class1, class2, class3, class4), end=' ')
type = [next(iter(torsion.types1)), next(iter(torsion.types2)), next(iter(torsion.types3)), next(iter(torsion.types4))]
wildcard = [torsion.types1 == wildcardType, torsion.types2 == wildcardType, torsion.types3 == wildcardType, torsion.types4 == wildcardType]
if all(type[i] not in omitTypes or wildcard[i] for i in range(4)):
classes = tuple('' if wildcard[i] else forcefield._atomTypes[type[i]].atomClass for i in range(4))
print(' <Improper class1="%s" class2="%s" class3="%s" class4="%s"' % classes, end=' ')
for i in range(len(torsion.k)):
print(' periodicity%d="%d" phase%d="%g" k%d="%g"' % (i+1, torsion.periodicity[i], i+1, torsion.phase[i], i+1, torsion.k[i]), end=' ')
print('/>')
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