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Commit 1cf42774 authored by Evan Pretti's avatar Evan Pretti
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Additional explanation messages for special cases and tests

parent 71208da2
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Showing with 171 additions and 57 deletions
wrappers/python/openmm/app/forcefield.py
View file @ 1cf42774
...@@ -41,6 +41,7 @@ import warnings ...@@ -41,6 +41,7 @@ import warnings
from math import sqrt, cos from math import sqrt, cos
from copy import deepcopy from copy import deepcopy
from collections import Counter, defaultdict from collections import Counter, defaultdict
from difflib import SequenceMatcher
import openmm as mm import openmm as mm
import openmm.unit as unit import openmm.unit as unit
from . import element as elem from . import element as elem
...@@ -1878,23 +1879,49 @@ def _findMatchErrors(forcefield, res): ...@@ -1878,23 +1879,49 @@ def _findMatchErrors(forcefield, res):
messages.append(f'is missing {message}') messages.append(f'is missing {message}')
if extra: if extra:
message = joinMessages(f'{diff} {formatter(key, diff)}' for key, diff in sorted(extra)) message = joinMessages(f'{diff} {formatter(key, diff)}' for key, diff in sorted(extra))
messages.append(f'has {message} extra') messages.append(f'has {message} too many')
return joinMessages(messages) return joinMessages(messages)
def formatAtomDiff(key, diff): def formatAtomDiff(key, diff):
"""Formats a string describing an element associated with a different number of atoms.""" """Formats a string describing an element associated with a different number of atoms."""
return (f'{elem.Element.getByAtomicNumber(key).symbol} atom' if key else 'site') + ('' if diff == 1 else 's') return (f'{elem.Element.getByAtomicNumber(key).symbol} atom' if key else 'extra site') + ('' if diff == 1 else 's')
def formatBondDiff(key, diff): def formatBondDiff(key, diff):
"""Formats a string describing elements associated with a different number of bonds.""" """Formats a string describing elements associated with a different number of bonds."""
name1 = elem.Element.getByAtomicNumber(key[0]).symbol if key else 'site' name1 = elem.Element.getByAtomicNumber(key[0]).symbol if key else 'extra site'
name2 = elem.Element.getByAtomicNumber(key[1]).symbol if key else 'site' name2 = elem.Element.getByAtomicNumber(key[1]).symbol if key else 'extra site'
return f'{name1}-{name2} bond' + ('' if diff == 1 else 's') return f'{name1}-{name2} bond' + ('' if diff == 1 else 's')
# Prepare fingerprints of the residue and templates based on counts of the def pickBestMatch(bestMatches):
# elements of their atoms. """If there are multiple best-scoring matches, pick one with the closest name to the residue. Call only with a non-empty list."""
if not res.name:
return bestMatches[0]
return max(bestMatches, key=lambda match: SequenceMatcher(a=res.name.strip(), b=match.strip(), autojunk=False).ratio())
# First check to see if there are no templates in the force field.
if not forcefield._templates:
return f'The force field contains no residue templates.'
# Get all elements in all templates in the force field and see if this
# residue uses an element not supported. Otherwise, prepare fingerprints of
# the residue and templates based on counts of the elements of their atoms.
supportedElements = set(elemToNum(atom.element) for template in forcefield._templates.values() for atom in template.atoms)
residueAtomCounts = Counter(elemToNum(atom.element) for atom in res.atoms()) residueAtomCounts = Counter(elemToNum(atom.element) for atom in res.atoms())
unsupportedElements = set(residueAtomCounts.keys()) - supportedElements
if unsupportedElements:
unsupportedMessage = joinMessages(formatAtomDiff(elemNum, 0) for elemNum in sorted(unsupportedElements))
return f'The residue contains {unsupportedMessage}, which are not supported by any template in the force field.'
# It will be useful to provide a special message if this is a terminal
# residue of the chain, since this is a common cause of topology problems.
chainResidues = list(res.chain.residues())
if len(chainResidues) > 1 and (res == chainResidues[0] or res == chainResidues[-1]):
terminalMessage = ' Is the chain terminated in a way that is unsupported by the force field?'
else:
terminalMessage = ''
def makeTemplateAtomDiff(templateName): def makeTemplateAtomDiff(templateName):
"""Prepares a Counter describing the difference between a residue's and a template's atoms.""" """Prepares a Counter describing the difference between a residue's and a template's atoms."""
...@@ -1913,10 +1940,23 @@ def _findMatchErrors(forcefield, res): ...@@ -1913,10 +1940,23 @@ def _findMatchErrors(forcefield, res):
# If there are matches found and the best score's sum is non-zero # If there are matches found and the best score's sum is non-zero
# (an imperfect match), return. Otherwise, if the best matches are # (an imperfect match), return. Otherwise, if the best matches are
# perfect, keep filtering with additional criteria. # perfect, keep filtering with additional criteria.
return f'The set of atoms is similar to {bestMatches[0]}, but {formatDiffMessage(templatesAtomDiffs[bestMatches[0]], formatAtomDiff)}.' bestMatch = pickBestMatch(bestMatches)
return f'The set of atoms is similar to {bestMatch}, but {formatDiffMessage(templatesAtomDiffs[bestMatch], formatAtomDiff)}.{terminalMessage}'
bestMatches, bestScore = bestMatchAtom(templatesAtomDiffs, bestMatches, False) bestMatches, bestScore = bestMatchAtom(templatesAtomDiffs, bestMatches, False)
if bestMatches and bestScore[1]: if bestMatches and bestScore[1]:
return f'The set of heavy atoms matches {bestMatches[0]}, but the residue {formatDiffMessage(templatesAtomDiffs[bestMatches[0]], formatAtomDiff)}.' bestMatch = pickBestMatch(bestMatches)
bestMatchDiffs = templatesAtomDiffs[bestMatch]
# Give additional help in the special cases where the residue is missing
# sites or hydrogen atoms and nothing else.
if bestMatchDiffs[0] < 0 and all(diff == 0 for key, diff in bestMatchDiffs.items() if key != 0):
specialLabel = 'it' if bestMatchDiffs[0] == -1 else 'them'
specialMessage = f' You may be able to add {specialLabel} with Modeller.addExtraParticles().'
elif bestMatchDiffs[1] < 0 and all(diff == 0 for key, diff in bestMatchDiffs.items() if key != 1):
specialLabel = 'it' if bestMatchDiffs[1] == -1 else 'them'
specialMessage = f' You may be able to add {specialLabel} with Modeller.addHydrogens().'
else:
specialMessage = terminalMessage
return f'The set of heavy atoms matches {bestMatch}, but the residue {formatDiffMessage(bestMatchDiffs, formatAtomDiff)}.{specialMessage}'
# We found templates that are atom-for-atom matches to the residue, so now # We found templates that are atom-for-atom matches to the residue, so now
# prepare fingerprints of the residue and templates based on their bonds. # prepare fingerprints of the residue and templates based on their bonds.
...@@ -1930,11 +1970,17 @@ def _findMatchErrors(forcefield, res): ...@@ -1930,11 +1970,17 @@ def _findMatchErrors(forcefield, res):
return counterSubtract(residueIntBondCounts, Counter(makeIntBondSpec((template.atoms[atom1], template.atoms[atom2])) for atom1, atom2 in template.bonds)) return counterSubtract(residueIntBondCounts, Counter(makeIntBondSpec((template.atoms[atom1], template.atoms[atom2])) for atom1, atom2 in template.bonds))
# We only need to prepare data for the templates remaining in bestMatches. # We only need to prepare data for the templates remaining in bestMatches.
templatesIntBondDiffs = {templateName: makeTemplateIntBondDiff(templateName) for templateName in bestMatches} templatesIntBondDiffs = {templateName: makeTemplateIntBondDiff(templateName) for templateName in bestMatches}
bestMatches, bestScore = bestMatchBond(templatesIntBondDiffs, bestMatches) bestMatches, bestScore = bestMatchBond(templatesIntBondDiffs, bestMatches)
if bestMatches and bestScore[1]: if bestMatches and bestScore[1]:
return f'The set of atoms matches {bestMatches[0]}, but the residue {formatDiffMessage(templatesIntBondDiffs[bestMatches[0]], formatBondDiff)}.' bestMatch = pickBestMatch(bestMatches)
if not tuple(res.internal_bonds()):
# Special message when the residue is missing all internal bonds.
return (f'The set of atoms matches {bestMatch}, but the residue has no bonds between its atoms. '
'If the topology was read from a PDB, it may contain non-standard residues/names and/or be missing CONECT records.')
return f'The set of atoms matches {bestMatch}, but the residue {formatDiffMessage(templatesIntBondDiffs[bestMatch], formatBondDiff)}.'
# Finally, check external bonds. Normally these should always be from heavy # Finally, check external bonds. Normally these should always be from heavy
# atoms, so don't do separate checks excluding vs. including non-heavy atoms # atoms, so don't do separate checks excluding vs. including non-heavy atoms
...@@ -1951,14 +1997,24 @@ def _findMatchErrors(forcefield, res): ...@@ -1951,14 +1997,24 @@ def _findMatchErrors(forcefield, res):
bestMatches, bestScore = bestMatchAtom(templatesExtBondDiffs, bestMatches, False) bestMatches, bestScore = bestMatchAtom(templatesExtBondDiffs, bestMatches, False)
if bestMatches and bestScore[1]: if bestMatches and bestScore[1]:
return f'The residue matches {bestMatches[0]}, but the set of externally bonded atoms {formatDiffMessage(templatesExtBondDiffs[bestMatches[0]], formatAtomDiff)}.' bestMatch = pickBestMatch(bestMatches)
bestMatchDiffs = templatesExtBondDiffs[bestMatch]
if all(value <= 0 for value in bestMatchDiffs.values()):
# Special message if external bonds are missing only, not different.
specialMessage = ' Is the chain missing a terminal capping group?'
else:
specialMessage = terminalMessage
return f'The atoms and bonds in the residue match {bestMatch}, but the set of externally bonded atoms {formatDiffMessage(bestMatchDiffs, formatAtomDiff)}.{specialMessage}'
# If we have matches at this point, atoms and bonds match perfectly, so the # If we have matches at this point, atoms and bonds match perfectly, so the
# connectivity must be different. If bestMatches is empty, something else # connectivity must be different. If bestMatches is empty, something else
# went wrong, so return a generic error message. # went wrong, so return a generic error message.
if bestMatches: if bestMatches:
return f'The atoms and bonds in the residue match {bestMatches[0]}, but the connectivity is different.' # Display all possible matching templates at this point to try to help,
# since we can't give any more detailed information.
return f'The atoms and bonds in the residue match {joinMessages(bestMatches)}, but the connectivity is different.'
return 'This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field.' return 'This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field.'
def _createResidueTemplate(residue): def _createResidueTemplate(residue):
......
wrappers/python/tests/TestForceField.py
View file @ 1cf42774
...@@ -835,27 +835,27 @@ class TestForceField(unittest.TestCase): ...@@ -835,27 +835,27 @@ class TestForceField(unittest.TestCase):
"""Test match error detection and diagnostics""" """Test match error detection and diagnostics"""
# Load a force field to test with and prepare some lines with which to build topologies from PDB files. # Load a force field to test with and prepare some lines with which to build topologies from PDB files.
forcefield = ForceField('amber14-all.xml') forcefield = ForceField('amber14-all.xml', 'amber14/opc.xml')
pdbLines = [ pdbLines = [
"ATOM 0 CH3 ACE A 1 0 0 0 C", 'ATOM 0 CH3 ACE A 1 0 0 0 C',
"ATOM 1 HH31 ACE A 1 0 0 0 H", 'ATOM 1 HH31 ACE A 1 0 0 0 H',
"ATOM 2 HH32 ACE A 1 0 0 0 H", 'ATOM 2 HH32 ACE A 1 0 0 0 H',
"ATOM 3 HH33 ACE A 1 0 0 0 H", 'ATOM 3 HH33 ACE A 1 0 0 0 H',
"ATOM 4 C ACE A 1 0 0 0 C", 'ATOM 4 C ACE A 1 0 0 0 C',
"ATOM 5 O ACE A 1 0 0 0 O", 'ATOM 5 O ACE A 1 0 0 0 O',
"ATOM 6 N GLY A 2 0 0 0 N", 'ATOM 6 N GLY A 2 0 0 0 N',
"ATOM 7 H GLY A 2 0 0 0 H", 'ATOM 7 H GLY A 2 0 0 0 H',
"ATOM 8 CA GLY A 2 0 0 0 C", 'ATOM 8 CA GLY A 2 0 0 0 C',
"ATOM 9 HA2 GLY A 2 0 0 0 H", 'ATOM 9 HA2 GLY A 2 0 0 0 H',
"ATOM 10 HA3 GLY A 2 0 0 0 H", 'ATOM 10 HA3 GLY A 2 0 0 0 H',
"ATOM 11 C GLY A 2 0 0 0 C", 'ATOM 11 C GLY A 2 0 0 0 C',
"ATOM 12 O GLY A 2 0 0 0 O", 'ATOM 12 O GLY A 2 0 0 0 O',
"ATOM 13 N NME A 3 0 0 0 N", 'ATOM 13 N NME A 3 0 0 0 N',
"ATOM 14 H NME A 3 0 0 0 H", 'ATOM 14 H NME A 3 0 0 0 H',
"ATOM 15 CH3 NME A 3 0 0 0 C", 'ATOM 15 CH3 NME A 3 0 0 0 C',
"ATOM 16 HH31 NME A 3 0 0 0 H", 'ATOM 16 HH31 NME A 3 0 0 0 H',
"ATOM 17 HH32 NME A 3 0 0 0 H", 'ATOM 17 HH32 NME A 3 0 0 0 H',
"ATOM 18 HH33 NME A 3 0 0 0 H", 'ATOM 18 HH33 NME A 3 0 0 0 H',
] ]
def makeSystem(lines): def makeSystem(lines):
...@@ -864,71 +864,129 @@ class TestForceField(unittest.TestCase): ...@@ -864,71 +864,129 @@ class TestForceField(unittest.TestCase):
# This should succeed and not produce any match errors. # This should succeed and not produce any match errors.
self.assertEqual(makeSystem(pdbLines).getNumParticles(), 19) self.assertEqual(makeSystem(pdbLines).getNumParticles(), 19)
# Add an He atom and B atoms atom to GLY.
with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The residue contains He atoms and B atoms, which are not supported by any template in the force field'):
makeSystem(pdbLines[:9] + [
'ATOM 19 X1 GLY A 2 0 0 0 He',
'ATOM 20 X2 GLY A 2 0 0 0 B',
'ATOM 21 X3 GLY A 2 0 0 0 B',
] + pdbLines[9:])
# Delete CA atom from GLY. # Delete CA atom from GLY.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The set of atoms is similar to GLY, but is missing 1 C atom"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of atoms is similar to GLY, but is missing 1 C atom'):
makeSystem(pdbLines[:8] + pdbLines[9:]) makeSystem(pdbLines[:8] + pdbLines[9:])
# Add an He atom to GLY. # Add an F atom to GLY.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The set of atoms is similar to GLY, but has 1 He atom extra"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of atoms is similar to GLY, but has 1 F atom too many'):
makeSystem(pdbLines[:9] + [ makeSystem(pdbLines[:9] + [
"ATOM 19 X1 GLY A 2 0 0 0 He", 'ATOM 19 X1 GLY A 2 0 0 0 F',
] + pdbLines[9:]) ] + pdbLines[9:])
# Delete CA atom from GLY and add an He atom. # Delete CA atom from GLY and add an F atom.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The set of atoms is similar to GLY, but is missing 1 C atom and has 1 He atom extra"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of atoms is similar to GLY, but is missing 1 C atom and has 1 F atom too many'):
makeSystem(pdbLines[:8] + [ makeSystem(pdbLines[:8] + [
"ATOM 19 X1 GLY A 2 0 0 0 He", 'ATOM 19 X1 GLY A 2 0 0 0 F',
] + pdbLines[9:]) ] + pdbLines[9:])
# Add 1 He atom, 2 Li atoms, and 1 Be atom to GLY. # Add 1 F atom, 2 Cl atoms, and 1 Br atom to GLY.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The set of atoms is similar to GLY, but has 1 He atom, 2 Li atoms, and 1 Be atom extra"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of atoms is similar to GLY, but has 1 F atom, 2 Cl atoms, and 1 Br atom too many'):
makeSystem(pdbLines[:9] + [ makeSystem(pdbLines[:9] + [
"ATOM 19 X1 GLY A 2 0 0 0 He", 'ATOM 19 X1 GLY A 2 0 0 0 F',
"ATOM 20 X2 GLY A 2 0 0 0 Li", 'ATOM 20 X2 GLY A 2 0 0 0 Cl',
"ATOM 21 X3 GLY A 2 0 0 0 Li", 'ATOM 21 X3 GLY A 2 0 0 0 Cl',
"ATOM 22 X4 GLY A 2 0 0 0 Be", 'ATOM 22 X4 GLY A 2 0 0 0 Br',
] + pdbLines[9:]) ] + pdbLines[9:])
# Add a virtual site to GLY. # Add a virtual site to GLY.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The set of heavy atoms matches GLY, but the residue has 1 site extra"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of heavy atoms matches GLY, but the residue has 1 extra site too many'):
makeSystem(pdbLines[:9] + [ makeSystem(pdbLines[:9] + [
"ATOM 19 X1 GLY A 2 0 0 0 EP", 'ATOM 19 X1 GLY A 2 0 0 0 EP',
] + pdbLines[9:]) ] + pdbLines[9:])
# Delete HA3 atom from GLY. # Delete HA3 atom from GLY.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The set of heavy atoms matches GLY, but the residue is missing 1 H atom"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of heavy atoms matches GLY, but the residue is missing 1 H atom.*You may be able to add it with.*addHydrogens'):
makeSystem(pdbLines[:10] + pdbLines[11:]) makeSystem(pdbLines[:10] + pdbLines[11:])
# Delete HA2 and HA3 atoms from GLY.
with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of heavy atoms matches GLY, but the residue is missing 2 H atoms.*You may be able to add them with.*addHydrogens'):
makeSystem(pdbLines[:9] + pdbLines[11:])
# Delete HA3 atom from GLY and add a virtual site. # Delete HA3 atom from GLY and add a virtual site.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The set of heavy atoms matches GLY, but the residue is missing 1 H atom and has 1 site extra"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of heavy atoms matches GLY, but the residue is missing 1 H atom and has 1 extra site too many'):
makeSystem(pdbLines[:10] + [ makeSystem(pdbLines[:10] + [
"ATOM 19 X1 GLY A 2 0 0 0 EP", 'ATOM 19 X1 GLY A 2 0 0 0 EP',
] + pdbLines[11:]) ] + pdbLines[11:])
# Rename HA3 atom to remove the CA-HA3 bond. # Rename HA3 atom to remove the CA-HA3 bond.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The set of atoms matches GLY, but the residue is missing 1 H-C bond"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of atoms matches GLY, but the residue is missing 1 H-C bond'):
makeSystem(pdbLines[:10] + [ makeSystem(pdbLines[:10] + [
"ATOM 10 X1 GLY A 2 0 0 0 H", 'ATOM 10 X1 GLY A 2 0 0 0 H',
] + pdbLines[11:]) ] + pdbLines[11:])
# Add an extra N-O bond. # Add an extra N-O bond.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The set of atoms matches GLY, but the residue has 1 N-O bond extra"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The set of atoms matches GLY, but the residue has 1 N-O bond too many'):
makeSystem(pdbLines + [ makeSystem(pdbLines + [
"CONECT 6 12" 'CONECT 6 12'
]) ])
# Remove an external bond to NME by renaming its N atom. # Remove an external bond to NME by renaming its N atom.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The residue matches GLY, but the set of externally bonded atoms is missing 1 C atom"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The atoms and bonds in the residue match GLY, but the set of externally bonded atoms is missing 1 C atom'):
makeSystem(pdbLines[:13] + [ makeSystem(pdbLines[:13] + [
"ATOM 13 X1 NME A 3 0 0 0 N", 'ATOM 13 X1 NME A 3 0 0 0 N',
] + pdbLines[14:]) ] + pdbLines[14:])
# Add an extra external bond to NME. # Add an extra external bond to NME.
with self.assertRaisesRegex(ValueError, "No template found for residue.*GLY.*The residue matches GLY, but the set of externally bonded atoms has 1 O atom extra"): with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The atoms and bonds in the residue match GLY, but the set of externally bonded atoms has 1 O atom too many'):
makeSystem(pdbLines + [
'CONECT 12 15'
])
# Delete ACE so that a capping group is missing from GLY.
with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The atoms and bonds in the residue match GLY, but the set of externally bonded atoms is missing 1 N atom.*Is the chain missing a terminal capping group?'):
makeSystem(pdbLines[6:])
# Keep the atom/bond element fingerprint the same but change the connectivity.
with self.assertRaisesRegex(ValueError, 'No template found for residue.*GLY.*The atoms and bonds in the residue match GLY, but the connectivity is different'):
# Rename O to break the C=O bond, but then reattach the O to the CA.
makeSystem(pdbLines[:12] + [
'ATOM 12 X1 GLY A 2 0 0 0 O',
] + pdbLines[13:] + [
'CONECT 8 12'
])
# Make water with incorrect atom names so bonds will be missing.
pdbLines = [
'ATOM 0 X1 HOH A 1 0 0 0 O',
'ATOM 1 X2 HOH A 1 0 0 0 H',
'ATOM 2 X3 HOH A 1 0 0 0 H',
]
# Check for a special message when all bonds are missing.
forcefield = ForceField('opc3.xml')
with self.assertRaisesRegex(ValueError, 'No template found for residue.*HOH.*The set of atoms matches HOH, but the residue has no bonds between its atoms'):
makeSystem(pdbLines)
# Add a site to a residue with a force field that doesn't support sites.
with self.assertRaisesRegex(ValueError, 'No template found for residue.*HOH.*The residue contains extra sites, which are not supported by any template in the force field'):
makeSystem(pdbLines + [ makeSystem(pdbLines + [
"CONECT 12 15" 'ATOM 3 X4 HOH A 1 0 0 0 EP',
]) ])
# Load a force field so that 1 site will be missing.
forcefield = ForceField('opc.xml')
with self.assertRaisesRegex(ValueError, 'No template found for residue.*HOH.*The set of heavy atoms matches HOH, but the residue is missing 1 extra site.*You may be able to add it with.*addExtraParticles'):
makeSystem(pdbLines)
# Load a force field so that 2 sites will be missing.
forcefield = ForceField('tip5p.xml')
with self.assertRaisesRegex(ValueError, 'No template found for residue.*HOH.*The set of heavy atoms matches HOH, but the residue is missing 2 extra sites.*You may be able to add them with.*addExtraParticles'):
makeSystem(pdbLines)
# Use an empty force field so that there are no templates.
forcefield = ForceField()
with self.assertRaisesRegex(ValueError, 'No template found for residue.*HOH.*The force field contains no residue templates'):
makeSystem(pdbLines)
def test_Wildcard(self): def test_Wildcard(self):
"""Test that PeriodicTorsionForces using wildcard ('') for atom types / classes in the ffxml are correctly registered""" """Test that PeriodicTorsionForces using wildcard ('') for atom types / classes in the ffxml are correctly registered"""
......
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