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Bug fixes
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@peastman
peastman committed Oct 3, 2024
1 parent 889d566 commit 32ebcd7
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Showing 2 changed files with 13 additions and 113 deletions.
18 changes: 7 additions & 11 deletions devtools/createSoftForcefield.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -62,8 +62,9 @@
# Print the residue templates.

print(' <Residues>')
skipTemplates = ('ASH', 'CYM', 'GLH', 'HID', 'HIE', 'LYN')
for template in forcefield._templates.values():
if template.name in ('ASH', 'CYM', 'GLH', 'HID', 'HIE', 'LYN'):
if template.name in skipTemplates or template.name[1:] in skipTemplates:
continue
print(' <Residue name="%s">' % template.name)
atomIndex = {}
Expand Down Expand Up @@ -123,16 +124,11 @@
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].atomClass
class2 = forcefield._atomTypes[type2].atomClass
class3 = forcefield._atomTypes[type3].atomClass
class4 = forcefield._atomTypes[type4].atomClass
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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108 changes: 6 additions & 102 deletions pdbfixer/soft.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1523,56 +1523,6 @@
<Bond from="2" to="4"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="CHID">
<Atom name="N" type="477"/>
<Atom name="CA" type="479"/>
<Atom name="CB" type="481"/>
<Atom name="CG" type="483"/>
<Atom name="ND1" type="484"/>
<Atom name="CE1" type="486"/>
<Atom name="NE2" type="488"/>
<Atom name="CD2" type="489"/>
<Atom name="C" type="491"/>
<Atom name="O" type="492"/>
<Atom name="OXT" type="493"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<Bond from="8" to="10"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="CHIE">
<Atom name="N" type="494"/>
<Atom name="CA" type="496"/>
<Atom name="CB" type="498"/>
<Atom name="CG" type="500"/>
<Atom name="ND1" type="501"/>
<Atom name="CE1" type="502"/>
<Atom name="NE2" type="504"/>
<Atom name="CD2" type="506"/>
<Atom name="C" type="508"/>
<Atom name="O" type="509"/>
<Atom name="OXT" type="510"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<Bond from="8" to="10"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="CHIP">
<Atom name="N" type="511"/>
<Atom name="CA" type="513"/>
Expand Down Expand Up @@ -2877,52 +2827,6 @@
<Atom name="N" type="704"/>
<ExternalBond from="0"/>
</Residue>
<Residue name="NHID">
<Atom name="N" type="816"/>
<Atom name="CA" type="818"/>
<Atom name="CB" type="820"/>
<Atom name="CG" type="822"/>
<Atom name="ND1" type="823"/>
<Atom name="CE1" type="825"/>
<Atom name="NE2" type="827"/>
<Atom name="CD2" type="828"/>
<Atom name="C" type="830"/>
<Atom name="O" type="831"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<ExternalBond from="8"/>
</Residue>
<Residue name="NHIE">
<Atom name="N" type="832"/>
<Atom name="CA" type="834"/>
<Atom name="CB" type="836"/>
<Atom name="CG" type="838"/>
<Atom name="ND1" type="839"/>
<Atom name="CE1" type="840"/>
<Atom name="NE2" type="842"/>
<Atom name="CD2" type="844"/>
<Atom name="C" type="846"/>
<Atom name="O" type="847"/>
<Bond from="0" to="1"/>
<Bond from="1" to="2"/>
<Bond from="1" to="8"/>
<Bond from="2" to="3"/>
<Bond from="3" to="4"/>
<Bond from="3" to="7"/>
<Bond from="4" to="5"/>
<Bond from="5" to="6"/>
<Bond from="6" to="7"/>
<Bond from="8" to="9"/>
<ExternalBond from="8"/>
</Residue>
<Residue name="NHIP">
<Atom name="N" type="848"/>
<Atom name="CA" type="850"/>
Expand Down Expand Up @@ -4343,8 +4247,8 @@
<Proper class1="" class2="C" class3="CB" class4="" periodicity1="2" phase1="3.14159" k1="12.552" />
<Proper class1="" class2="C" class3="CA" class4="" periodicity1="2" phase1="3.14159" k1="15.167" />
<Proper class1="" class2="C" class3="C" class4="" periodicity1="2" phase1="3.14159" k1="15.167" />
<Improper class1="C5" class2="CA" class3="CA" class4="O" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C6" class2="CA" class3="O2" class4="O2" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C5" class2="" class3="" class4="O" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C6" class2="" class3="O2" class4="O2" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="N" class2="C5" class3="CT" class4="O" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="N" class2="C" class3="CT" class4="O" periodicity1="2" phase1="3.14159" k1="4.6024" />
<Improper class1="CA" class2="CA" class3="CA" class4="OH" periodicity1="2" phase1="3.14159" k1="4.6024" />
Expand All @@ -4361,10 +4265,10 @@
<Improper class1="C" class2="CT" class3="O" class4="OH" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="N*" class2="C" class3="CM" class4="CT" periodicity1="2" phase1="3.14159" k1="4.184" />
<Improper class1="N*" class2="CB" class3="CK" class4="CT" periodicity1="2" phase1="3.14159" k1="4.184" />
<Improper class1="N" class2="CA" class3="CT" class4="CT" periodicity1="2" phase1="3.14159" k1="4.184" />
<Improper class1="CA" class2="CA" class3="N2" class4="N2" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C" class2="CA" class3="O2" class4="O2" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C" class2="CA" class3="CA" class4="O" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="N" class2="" class3="CT" class4="CT" periodicity1="2" phase1="3.14159" k1="4.184" />
<Improper class1="CA" class2="" class3="N2" class4="N2" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C" class2="" class3="O2" class4="O2" periodicity1="2" phase1="3.14159" k1="43.932" />
<Improper class1="C" class2="" class3="" class4="O" periodicity1="2" phase1="3.14159" k1="43.932" />
</PeriodicTorsionForce>
<Script>
import openmm as mm
Expand Down

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