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tsoc
openmm
Commits
7aacdeb1
"docs/OpenMMUsersGuide.doc" did not exist on "9eb00769b406be53c7c68719b377acaef6e12b48"
Commit
7aacdeb1
authored
Jan 20, 2016
by
John Chodera (MSKCC)
Browse files
Fix test
parent
06b61c6e
Changes
2
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2 changed files
with
4 additions
and
4 deletions
+4
-4
wrappers/python/simtk/openmm/app/forcefield.py
wrappers/python/simtk/openmm/app/forcefield.py
+1
-1
wrappers/python/tests/TestForceField.py
wrappers/python/tests/TestForceField.py
+3
-3
No files found.
wrappers/python/simtk/openmm/app/forcefield.py
View file @
7aacdeb1
...
@@ -1103,7 +1103,7 @@ def _createResidueTemplate(residue):
...
@@ -1103,7 +1103,7 @@ def _createResidueTemplate(residue):
"""
"""
template
=
ForceField
.
_TemplateData
(
residue
.
name
)
template
=
ForceField
.
_TemplateData
(
residue
.
name
)
for
atom
in
residue
.
atoms
():
for
atom
in
residue
.
atoms
():
template
.
atoms
.
append
(
ForceField
.
_TemplateAtomData
(
atom
.
name
,
'X'
,
atom
.
element
))
template
.
atoms
.
append
(
ForceField
.
_TemplateAtomData
(
atom
.
name
,
None
,
atom
.
element
))
for
(
atom1
,
atom2
)
in
residue
.
internal_bonds
():
for
(
atom1
,
atom2
)
in
residue
.
internal_bonds
():
template
.
addBondByName
(
atom1
.
name
,
atom2
.
name
)
template
.
addBondByName
(
atom1
.
name
,
atom2
.
name
)
residue_atoms
=
[
atom
for
atom
in
residue
.
atoms
()
]
residue_atoms
=
[
atom
for
atom
in
residue
.
atoms
()
]
...
...
wrappers/python/tests/TestForceField.py
View file @
7aacdeb1
...
@@ -419,12 +419,12 @@ class TestForceField(unittest.TestCase):
...
@@ -419,12 +419,12 @@ class TestForceField(unittest.TestCase):
# Create a ForceField object.
# Create a ForceField object.
forcefield
=
ForceField
(
'amber99sb.xml'
,
'tip3p.xml'
,
StringIO
(
simple_ffxml_contents
))
forcefield
=
ForceField
(
'amber99sb.xml'
,
'tip3p.xml'
,
StringIO
(
simple_ffxml_contents
))
# Get list of unique unmatched residues.
# Get list of unique unmatched residues.
[
unique_unmatched_
residues
,
templates
]
=
forcefield
.
getUniqueUnmatchedResidues
(
pdb
.
topology
)
[
residues
,
templates
]
=
forcefield
.
getUniqueUnmatchedResidues
(
pdb
.
topology
)
# Add residue templates to forcefield.
# Add residue templates to forcefield.
for
template
in
templates
:
for
template
in
templates
:
# Replace atom types.
# Replace atom types.
for
(
template_atom
,
residue_atom
)
in
zip
(
template
.
atoms
,
residue
.
atoms
())
:
for
atom
in
template
.
atoms
:
template_
atom
.
type
=
'XXX'
atom
.
type
=
'XXX'
# Register the template.
# Register the template.
forcefield
.
registerResidueTemplate
(
template
)
forcefield
.
registerResidueTemplate
(
template
)
# Parameterize system.
# Parameterize system.
...
...
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