RustOpenMM/openmm
1
0
Fork 0
mirror of https://github.com/openmm/openmm synced 2026-06-03 06:39:48 +09:00
Code Issues Packages Projects Releases Wiki Activity
Files
master
openmm/wrappers/python/tests/TestPatches.py
Peter Eastman e53bdc5eab Top level Python module is now "openmm" (#3000) 
* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning
2021-02-01 09:40:37 -08:00

326 lines
13 KiB
Python
Raw Permalink Blame History

import unittest
from openmm.app import *
from openmm import *
from openmm.unit import *
import openmm.app.forcefield as forcefield
import math
try:
from cStringIO import StringIO
except ImportError:
from io import StringIO
import os
class TestPatches(unittest.TestCase):
"""Test ForceFields that use patches."""
def testParsePatch(self):
"""Test parsing a <Patch> tag."""
xml = """
<ForceField>
<AtomTypes>
<Type name="A type" class="A class" element="O" mass="15.99943"/>
<Type name="B type" class="B class" element="H" mass="1.007947"/>
</AtomTypes>
<Patches>
<Patch name="Test">
<AddAtom name="A" type="A type"/>
<ChangeAtom name="B" type="B type"/>
<RemoveAtom name="C"/>
<AddBond atomName1="A" atomName2="B"/>
<RemoveBond atomName1="B" atomName2="C"/>
<AddExternalBond atomName="A"/>
<RemoveExternalBond atomName="C"/>
<ApplyToResidue name="RES"/>
<VirtualSite type="average2" siteName="A" atomName1="B" atomName2="B" weight1="0.8" weight2="0.2"/>
</Patch>
</Patches>
</ForceField>"""
ff = ForceField(StringIO(xml))
self.assertEqual(1, len(ff._patches))
patch = ff._patches['Test']
self.assertEqual(1, len(patch.addedAtoms))
self.assertEqual(1, len(patch.addedAtoms[0]))
self.assertEqual(1, len(patch.changedAtoms))
self.assertEqual(1, len(patch.changedAtoms[0]))
self.assertEqual(1, len(patch.deletedAtoms))
self.assertEqual(1, len(patch.addedBonds))
self.assertEqual(1, len(patch.deletedBonds))
self.assertEqual(1, len(patch.addedExternalBonds))
self.assertEqual(1, len(patch.deletedExternalBonds))
self.assertEqual(1, len(patch.virtualSites))
self.assertEqual(1, len(ff._templatePatches))
self.assertEqual(1, len(ff._templatePatches['RES']))
self.assertEqual('A', patch.addedAtoms[0][0].name)
self.assertEqual('A type', patch.addedAtoms[0][0].type)
self.assertEqual('B', patch.changedAtoms[0][0].name)
self.assertEqual('B type', patch.changedAtoms[0][0].type)
self.assertEqual('C', patch.deletedAtoms[0].name)
self.assertEqual(0, patch.deletedAtoms[0].residue)
self.assertEqual('A', patch.addedBonds[0][0].name)
self.assertEqual(0, patch.addedBonds[0][0].residue)
self.assertEqual('B', patch.addedBonds[0][1].name)
self.assertEqual(0, patch.addedBonds[0][1].residue)
self.assertEqual('B', patch.deletedBonds[0][0].name)
self.assertEqual(0, patch.deletedBonds[0][0].residue)
self.assertEqual('C', patch.deletedBonds[0][1].name)
self.assertEqual(0, patch.deletedBonds[0][1].residue)
self.assertEqual('A', patch.addedExternalBonds[0].name)
self.assertEqual(0, patch.addedExternalBonds[0].residue)
self.assertEqual('C', patch.deletedExternalBonds[0].name)
self.assertEqual(0, patch.deletedExternalBonds[0].residue)
self.assertEqual(0, patch.virtualSites[0][0].index)
self.assertEqual([1, 1], patch.virtualSites[0][0].atoms)
self.assertEqual([0.8, 0.2], patch.virtualSites[0][0].weights)
patch = list(ff._templatePatches['RES'])[0]
self.assertEqual('Test', patch[0])
self.assertEqual(0, patch[1])
def testParseMultiresiduePatch(self):
"""Test parsing a <Patch> tag that affects two residues."""
xml = """
<ForceField>
<AtomTypes>
<Type name="A type" class="A class" element="O" mass="15.99943"/>
<Type name="B type" class="B class" element="H" mass="1.007947"/>
</AtomTypes>
<Patches>
<Patch name="Test" residues="2">
<AddAtom name="1:A" type="A type"/>
<ChangeAtom name="2:B" type="B type"/>
<AddBond atomName1="1:A" atomName2="2:B"/>
<ApplyToResidue name="1:RESA"/>
<ApplyToResidue name="2:RESB"/>
</Patch>
</Patches>
</ForceField>"""
ff = ForceField(StringIO(xml))
self.assertEqual(1, len(ff._patches))
patch = ff._patches['Test']
self.assertEqual(2, len(patch.addedAtoms))
self.assertEqual(1, len(patch.addedAtoms[0]))
self.assertEqual(0, len(patch.addedAtoms[1]))
self.assertEqual(2, len(patch.changedAtoms))
self.assertEqual(0, len(patch.changedAtoms[0]))
self.assertEqual(1, len(patch.changedAtoms[1]))
self.assertEqual(1, len(patch.addedBonds))
self.assertEqual(2, len(ff._templatePatches))
self.assertEqual(1, len(ff._templatePatches['RESA']))
self.assertEqual(1, len(ff._templatePatches['RESB']))
self.assertEqual('A', patch.addedAtoms[0][0].name)
self.assertEqual('A type', patch.addedAtoms[0][0].type)
self.assertEqual('B', patch.changedAtoms[1][0].name)
self.assertEqual('B type', patch.changedAtoms[1][0].type)
self.assertEqual('A', patch.addedBonds[0][0].name)
self.assertEqual(0, patch.addedBonds[0][0].residue)
self.assertEqual('B', patch.addedBonds[0][1].name)
self.assertEqual(1, patch.addedBonds[0][1].residue)
patchA = list(ff._templatePatches['RESA'])[0]
self.assertEqual('Test', patchA[0])
self.assertEqual(0, patchA[1])
patchB = list(ff._templatePatches['RESB'])[0]
self.assertEqual('Test', patchB[0])
self.assertEqual(1, patchB[1])
def testApplyPatch(self):
"""Test applying a patch to a template."""
xml = """
<ForceField>
<AtomTypes>
<Type name="A type" class="A class" element="O" mass="15.99943"/>
<Type name="B type" class="B class" element="H" mass="1.007947"/>
<Type name="C type" class="C class" element="H" mass="1.007947"/>
<Type name="D type" class="D class" element="C" mass="12.010000"/>
</AtomTypes>
<Residues>
<Residue name="RES">
<Atom name="A" type="A type"/>
<Atom name="B" type="B type"/>
<Atom name="C" type="C type"/>
<Bond atomName1="A" atomName2="B"/>
<Bond atomName1="B" atomName2="C"/>
<ExternalBond atomName="C"/>
<VirtualSite type="average2" siteName="C" atomName1="B" atomName2="C" weight1="0.6" weight2="0.4"/>
</Residue>
</Residues>
<Patches>
<Patch name="Test">
<AddAtom name="D" type="D type"/>
<ChangeAtom name="B" type="A type"/>
<RemoveAtom name="A"/>
<AddBond atomName1="B" atomName2="D"/>
<RemoveBond atomName1="A" atomName2="B"/>
<AddExternalBond atomName="D"/>
<RemoveExternalBond atomName="C"/>
<ApplyToResidue name="RES"/>
</Patch>
</Patches>
</ForceField>"""
ff = ForceField(StringIO(xml))
self.assertEqual(1, len(ff._patches))
patch = ff._patches['Test']
template = ff._templates['RES']
newTemplates = patch.createPatchedTemplates([template])
self.assertEqual(1, len(newTemplates))
t = newTemplates[0]
self.assertEqual(3, len(t.atoms))
self.assertTrue(any(a.name == 'B' and a.type == 'A type' for a in t.atoms))
self.assertTrue(any(a.name == 'C' and a.type == 'C type' for a in t.atoms))
self.assertTrue(any(a.name == 'D' and a.type == 'D type' for a in t.atoms))
indexMap = dict([(a.name, i) for i, a in enumerate(t.atoms)])
self.assertEqual(2, len(t.bonds))
self.assertTrue((indexMap['B'], indexMap['C']) in t.bonds)
self.assertTrue((indexMap['B'], indexMap['D']) in t.bonds)
self.assertEqual(1, len(t.externalBonds))
self.assertTrue(indexMap['D'] in t.externalBonds)
self.assertEqual(1, len(t.virtualSites))
v = t.virtualSites[0]
self.assertEqual('average2', v.type)
self.assertEqual(0.6, v.weights[0])
self.assertEqual(0.4, v.weights[1])
self.assertEqual(indexMap['C'], v.index)
self.assertEqual(indexMap['B'], v.atoms[0])
self.assertEqual(indexMap['C'], v.atoms[1])
def testAlaAlaAla(self):
"""Test constructing a System that involves two patches."""
xml = """
<ForceField>
<AtomTypes>
<Type name="N" class="N" element="N" mass="14.00672"/>
<Type name="H" class="H" element="H" mass="1.007947"/>
<Type name="CT" class="CT" element="C" mass="12.01078"/>
<Type name="H1" class="H1" element="H" mass="1.007947"/>
<Type name="HC" class="HC" element="H" mass="1.007947"/>
<Type name="C" class="C" element="C" mass="12.01078"/>
<Type name="O" class="O" element="O" mass="15.99943"/>
<Type name="O2" class="O2" element="O" mass="15.99943"/>
<Type name="N3" class="N3" element="N" mass="14.00672"/>
</AtomTypes>
<Residues>
<Residue name="ALA">
<Atom name="N" type="N"/>
<Atom name="H" type="H"/>
<Atom name="CA" type="CT"/>
<Atom name="HA" type="H1"/>
<Atom name="CB" type="CT"/>
<Atom name="HB1" type="HC"/>
<Atom name="HB2" type="HC"/>
<Atom name="HB3" type="HC"/>
<Atom name="C" type="C"/>
<Atom name="O" type="O"/>
<Bond from="0" to="1"/>
<Bond from="0" to="2"/>
<Bond from="2" to="3"/>
<Bond from="2" to="4"/>
<Bond from="2" to="8"/>
<Bond from="4" to="5"/>
<Bond from="4" to="6"/>
<Bond from="4" to="7"/>
<Bond from="8" to="9"/>
<ExternalBond from="0"/>
<ExternalBond from="8"/>
<AllowPatch name="CTER"/>
<AllowPatch name="NTER"/>
</Residue>
</Residues>
<Patches>
<Patch name="CTER">
<AddAtom name="OXT" type="O2"/>
<ChangeAtom name="O" type="O2"/>
<AddBond atomName1="C" atomName2="OXT"/>
<RemoveExternalBond atomName="C"/>
</Patch>
<Patch name="NTER">
<RemoveAtom name="H"/>
<AddAtom name="H1" type="H"/>
<AddAtom name="H2" type="H"/>
<AddAtom name="H3" type="H"/>
<ChangeAtom name="N" type="N3"/>
<RemoveBond atomName1="N" atomName2="H"/>
<AddBond atomName1="N" atomName2="H1"/>
<AddBond atomName1="N" atomName2="H2"/>
<AddBond atomName1="N" atomName2="H3"/>
<RemoveExternalBond atomName="N"/>
</Patch>
</Patches>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="N" charge="-0.4157" sigma="0.324999852378" epsilon="0.71128"/>
<Atom type="H" charge="0.2719" sigma="0.106907846177" epsilon="0.0656888"/>
<Atom type="CT" charge="0.0337" sigma="0.339966950842" epsilon="0.4577296"/>
<Atom type="H1" charge="0.0823" sigma="0.247135304412" epsilon="0.0656888"/>
<Atom type="HC" charge="0.0603" sigma="0.264953278775" epsilon="0.0656888"/>
<Atom type="C" charge="0.5973" sigma="0.339966950842" epsilon="0.359824"/>
<Atom type="O" charge="-0.5679" sigma="0.295992190115" epsilon="0.87864"/>
<Atom type="O2" charge="-0.8055" sigma="0.295992190115" epsilon="0.87864"/>
<Atom type="N3" charge="0.1414" sigma="0.324999852378" epsilon="0.71128"/>
</NonbondedForce>
</ForceField>"""
ff = ForceField(StringIO(xml))
pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
system = ff.createSystem(pdb.topology)
nb = system.getForce(0)
expectedCharges = [0.1414, 0.2719, 0.2719, 0.2719, 0.0337, 0.0823, 0.0337, 0.0603, 0.0603, 0.0603, 0.5973, -0.5679,
-0.4157, 0.2719, 0.0337, 0.0823, 0.0337, 0.0603, 0.0603, 0.0603, 0.5973, -0.5679,
0.5973, -0.8055, -0.8055, -0.4157, 0.2719, 0.0337, 0.0823, 0.0337, 0.0603, 0.0603, 0.0603]
for i in range(system.getNumParticles()):
self.assertEqual(expectedCharges[i], nb.getParticleParameters(i)[0].value_in_unit(elementary_charge))
def testDisulfidePatch(self):
pdb = PDBFile(os.path.join('systems', 'bpti.pdb'))
ff = ForceField('amber99sb.xml')
system1 = ff.createSystem(pdb.topology)
# Override the CYX template so it will no longer match.
xml = """
<ForceField>
<Residues>
<Residue name="CYX" override="1">
</Residue>
</Residues>
</ForceField>"""
ff.loadFile(StringIO(xml))
try:
ff.createSystem(pdb.topology)
failed = False
except:
failed = True
self.assertTrue(failed)
# Now add a patch for matching disulfides.
xml = """
<ForceField>
<Patches>
<Patch name="Disulfide" residues="2">
<RemoveAtom name="1:HG"/>
<RemoveAtom name="2:HG"/>
<ChangeAtom name="1:CA" type="83"/>
<ChangeAtom name="2:CA" type="83"/>
<ChangeAtom name="1:HA" type="84"/>
<ChangeAtom name="2:HA" type="84"/>
<ChangeAtom name="1:CB" type="85"/>
<ChangeAtom name="2:CB" type="85"/>
<ChangeAtom name="1:HB2" type="86"/>
<ChangeAtom name="2:HB2" type="86"/>
<ChangeAtom name="1:HB3" type="86"/>
<ChangeAtom name="2:HB3" type="86"/>
<ChangeAtom name="1:SG" type="87"/>
<ChangeAtom name="2:SG" type="87"/>
<AddBond atomName1="1:SG" atomName2="2:SG"/>
<ApplyToResidue name="1:CYS"/>
<ApplyToResidue name="2:CYS"/>
</Patch>
</Patches>
</ForceField>"""
ff.loadFile(StringIO(xml))
system2 = ff.createSystem(pdb.topology)
self.assertEqual(XmlSerializer.serialize(system1), XmlSerializer.serialize(system2))
if __name__ == '__main__':
unittest.main()
Reference in New Issue View Git Blame Copy Permalink