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tsoc
openmm
Commits
e79f1488
Commit
e79f1488
authored
Dec 30, 2015
by
Jason Swails
Browse files
Remove unnecessary trailing ;
parent
fd74112b
Changes
1
Show whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
26 additions
and
26 deletions
+26
-26
wrappers/python/simtk/openmm/app/gromacstopfile.py
wrappers/python/simtk/openmm/app/gromacstopfile.py
+26
-26
No files found.
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @
e79f1488
...
@@ -259,7 +259,7 @@ class GromacsTopFile(object):
...
@@ -259,7 +259,7 @@ class GromacsTopFile(object):
"""Process the [ defaults ] line."""
"""Process the [ defaults ] line."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
4
:
if
len
(
fields
)
<
4
:
raise
ValueError
(
'Too few fields in [ defaults ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ defaults ] line: '
+
line
)
if
fields
[
0
]
!=
'1'
:
if
fields
[
0
]
!=
'1'
:
raise
ValueError
(
'Unsupported nonbonded type: '
+
fields
[
0
])
raise
ValueError
(
'Unsupported nonbonded type: '
+
fields
[
0
])
if
fields
[
1
]
!=
'2'
:
if
fields
[
1
]
!=
'2'
:
...
@@ -272,7 +272,7 @@ class GromacsTopFile(object):
...
@@ -272,7 +272,7 @@ class GromacsTopFile(object):
"""Process a line in the [ moleculetypes ] category."""
"""Process a line in the [ moleculetypes ] category."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
1
:
if
len
(
fields
)
<
1
:
raise
ValueError
(
'Too few fields in [ moleculetypes ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ moleculetypes ] line: '
+
line
)
type
=
GromacsTopFile
.
_MoleculeType
()
type
=
GromacsTopFile
.
_MoleculeType
()
self
.
_moleculeTypes
[
fields
[
0
]]
=
type
self
.
_moleculeTypes
[
fields
[
0
]]
=
type
self
.
_currentMoleculeType
=
type
self
.
_currentMoleculeType
=
type
...
@@ -281,7 +281,7 @@ class GromacsTopFile(object):
...
@@ -281,7 +281,7 @@ class GromacsTopFile(object):
"""Process a line in the [ molecules ] category."""
"""Process a line in the [ molecules ] category."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
2
:
if
len
(
fields
)
<
2
:
raise
ValueError
(
'Too few fields in [ molecules ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ molecules ] line: '
+
line
)
self
.
_molecules
.
append
((
fields
[
0
],
int
(
fields
[
1
])))
self
.
_molecules
.
append
((
fields
[
0
],
int
(
fields
[
1
])))
def
_processAtom
(
self
,
line
):
def
_processAtom
(
self
,
line
):
...
@@ -290,7 +290,7 @@ class GromacsTopFile(object):
...
@@ -290,7 +290,7 @@ class GromacsTopFile(object):
raise
ValueError
(
'Found [ atoms ] section before [ moleculetype ]'
)
raise
ValueError
(
'Found [ atoms ] section before [ moleculetype ]'
)
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
5
:
if
len
(
fields
)
<
5
:
raise
ValueError
(
'Too few fields in [ atoms ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ atoms ] line: '
+
line
)
self
.
_currentMoleculeType
.
atoms
.
append
(
fields
)
self
.
_currentMoleculeType
.
atoms
.
append
(
fields
)
def
_processBond
(
self
,
line
):
def
_processBond
(
self
,
line
):
...
@@ -299,9 +299,9 @@ class GromacsTopFile(object):
...
@@ -299,9 +299,9 @@ class GromacsTopFile(object):
raise
ValueError
(
'Found [ bonds ] section before [ moleculetype ]'
)
raise
ValueError
(
'Found [ bonds ] section before [ moleculetype ]'
)
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
3
:
if
len
(
fields
)
<
3
:
raise
ValueError
(
'Too few fields in [ bonds ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ bonds ] line: '
+
line
)
if
fields
[
2
]
!=
'1'
:
if
fields
[
2
]
!=
'1'
:
raise
ValueError
(
'Unsupported function type in [ bonds ] line: '
+
line
)
;
raise
ValueError
(
'Unsupported function type in [ bonds ] line: '
+
line
)
self
.
_currentMoleculeType
.
bonds
.
append
(
fields
)
self
.
_currentMoleculeType
.
bonds
.
append
(
fields
)
def
_processAngle
(
self
,
line
):
def
_processAngle
(
self
,
line
):
...
@@ -310,9 +310,9 @@ class GromacsTopFile(object):
...
@@ -310,9 +310,9 @@ class GromacsTopFile(object):
raise
ValueError
(
'Found [ angles ] section before [ moleculetype ]'
)
raise
ValueError
(
'Found [ angles ] section before [ moleculetype ]'
)
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
4
:
if
len
(
fields
)
<
4
:
raise
ValueError
(
'Too few fields in [ angles ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ angles ] line: '
+
line
)
if
fields
[
3
]
not
in
(
'1'
,
'5'
):
if
fields
[
3
]
not
in
(
'1'
,
'5'
):
raise
ValueError
(
'Unsupported function type in [ angles ] line: '
+
line
)
;
raise
ValueError
(
'Unsupported function type in [ angles ] line: '
+
line
)
self
.
_currentMoleculeType
.
angles
.
append
(
fields
)
self
.
_currentMoleculeType
.
angles
.
append
(
fields
)
def
_processDihedral
(
self
,
line
):
def
_processDihedral
(
self
,
line
):
...
@@ -321,9 +321,9 @@ class GromacsTopFile(object):
...
@@ -321,9 +321,9 @@ class GromacsTopFile(object):
raise
ValueError
(
'Found [ dihedrals ] section before [ moleculetype ]'
)
raise
ValueError
(
'Found [ dihedrals ] section before [ moleculetype ]'
)
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
5
:
if
len
(
fields
)
<
5
:
raise
ValueError
(
'Too few fields in [ dihedrals ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ dihedrals ] line: '
+
line
)
if
fields
[
4
]
not
in
(
'1'
,
'2'
,
'3'
,
'4'
,
'9'
):
if
fields
[
4
]
not
in
(
'1'
,
'2'
,
'3'
,
'4'
,
'9'
):
raise
ValueError
(
'Unsupported function type in [ dihedrals ] line: '
+
line
)
;
raise
ValueError
(
'Unsupported function type in [ dihedrals ] line: '
+
line
)
self
.
_currentMoleculeType
.
dihedrals
.
append
(
fields
)
self
.
_currentMoleculeType
.
dihedrals
.
append
(
fields
)
def
_processExclusion
(
self
,
line
):
def
_processExclusion
(
self
,
line
):
...
@@ -332,7 +332,7 @@ class GromacsTopFile(object):
...
@@ -332,7 +332,7 @@ class GromacsTopFile(object):
raise
ValueError
(
'Found [ exclusions ] section before [ moleculetype ]'
)
raise
ValueError
(
'Found [ exclusions ] section before [ moleculetype ]'
)
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
2
:
if
len
(
fields
)
<
2
:
raise
ValueError
(
'Too few fields in [ exclusions ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ exclusions ] line: '
+
line
)
self
.
_currentMoleculeType
.
exclusions
.
append
(
fields
)
self
.
_currentMoleculeType
.
exclusions
.
append
(
fields
)
def
_processPair
(
self
,
line
):
def
_processPair
(
self
,
line
):
...
@@ -341,9 +341,9 @@ class GromacsTopFile(object):
...
@@ -341,9 +341,9 @@ class GromacsTopFile(object):
raise
ValueError
(
'Found [ pairs ] section before [ moleculetype ]'
)
raise
ValueError
(
'Found [ pairs ] section before [ moleculetype ]'
)
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
3
:
if
len
(
fields
)
<
3
:
raise
ValueError
(
'Too few fields in [ pairs ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ pairs ] line: '
+
line
)
if
fields
[
2
]
!=
'1'
:
if
fields
[
2
]
!=
'1'
:
raise
ValueError
(
'Unsupported function type in [ pairs ] line: '
+
line
)
;
raise
ValueError
(
'Unsupported function type in [ pairs ] line: '
+
line
)
self
.
_currentMoleculeType
.
pairs
.
append
(
fields
)
self
.
_currentMoleculeType
.
pairs
.
append
(
fields
)
def
_processCmap
(
self
,
line
):
def
_processCmap
(
self
,
line
):
...
@@ -352,14 +352,14 @@ class GromacsTopFile(object):
...
@@ -352,14 +352,14 @@ class GromacsTopFile(object):
raise
ValueError
(
'Found [ cmap ] section before [ moleculetype ]'
)
raise
ValueError
(
'Found [ cmap ] section before [ moleculetype ]'
)
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
6
:
if
len
(
fields
)
<
6
:
raise
ValueError
(
'Too few fields in [ cmap ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ cmap ] line: '
+
line
)
self
.
_currentMoleculeType
.
cmaps
.
append
(
fields
)
self
.
_currentMoleculeType
.
cmaps
.
append
(
fields
)
def
_processAtomType
(
self
,
line
):
def
_processAtomType
(
self
,
line
):
"""Process a line in the [ atomtypes ] category."""
"""Process a line in the [ atomtypes ] category."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
6
:
if
len
(
fields
)
<
6
:
raise
ValueError
(
'Too few fields in [ atomtypes ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ atomtypes ] line: '
+
line
)
if
len
(
fields
[
3
])
==
1
:
if
len
(
fields
[
3
])
==
1
:
# Bonded type and atomic number are both missing.
# Bonded type and atomic number are both missing.
fields
.
insert
(
1
,
None
)
fields
.
insert
(
1
,
None
)
...
@@ -377,27 +377,27 @@ class GromacsTopFile(object):
...
@@ -377,27 +377,27 @@ class GromacsTopFile(object):
"""Process a line in the [ bondtypes ] category."""
"""Process a line in the [ bondtypes ] category."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
5
:
if
len
(
fields
)
<
5
:
raise
ValueError
(
'Too few fields in [ bondtypes ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ bondtypes ] line: '
+
line
)
if
fields
[
2
]
!=
'1'
:
if
fields
[
2
]
!=
'1'
:
raise
ValueError
(
'Unsupported function type in [ bondtypes ] line: '
+
line
)
;
raise
ValueError
(
'Unsupported function type in [ bondtypes ] line: '
+
line
)
self
.
_bondTypes
[
tuple
(
fields
[:
2
])]
=
fields
self
.
_bondTypes
[
tuple
(
fields
[:
2
])]
=
fields
def
_processAngleType
(
self
,
line
):
def
_processAngleType
(
self
,
line
):
"""Process a line in the [ angletypes ] category."""
"""Process a line in the [ angletypes ] category."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
6
:
if
len
(
fields
)
<
6
:
raise
ValueError
(
'Too few fields in [ angletypes ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ angletypes ] line: '
+
line
)
if
fields
[
3
]
not
in
(
'1'
,
'5'
):
if
fields
[
3
]
not
in
(
'1'
,
'5'
):
raise
ValueError
(
'Unsupported function type in [ angletypes ] line: '
+
line
)
;
raise
ValueError
(
'Unsupported function type in [ angletypes ] line: '
+
line
)
self
.
_angleTypes
[
tuple
(
fields
[:
3
])]
=
fields
self
.
_angleTypes
[
tuple
(
fields
[:
3
])]
=
fields
def
_processDihedralType
(
self
,
line
):
def
_processDihedralType
(
self
,
line
):
"""Process a line in the [ dihedraltypes ] category."""
"""Process a line in the [ dihedraltypes ] category."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
7
:
if
len
(
fields
)
<
7
:
raise
ValueError
(
'Too few fields in [ dihedraltypes ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ dihedraltypes ] line: '
+
line
)
if
fields
[
4
]
not
in
(
'1'
,
'2'
,
'3'
,
'4'
,
'9'
):
if
fields
[
4
]
not
in
(
'1'
,
'2'
,
'3'
,
'4'
,
'9'
):
raise
ValueError
(
'Unsupported function type in [ dihedraltypes ] line: '
+
line
)
;
raise
ValueError
(
'Unsupported function type in [ dihedraltypes ] line: '
+
line
)
key
=
tuple
(
fields
[:
5
])
key
=
tuple
(
fields
[:
5
])
if
fields
[
4
]
==
'9'
and
key
in
self
.
_dihedralTypes
:
if
fields
[
4
]
==
'9'
and
key
in
self
.
_dihedralTypes
:
# There are multiple dihedrals defined for these atom types.
# There are multiple dihedrals defined for these atom types.
...
@@ -409,25 +409,25 @@ class GromacsTopFile(object):
...
@@ -409,25 +409,25 @@ class GromacsTopFile(object):
"""Process a line in the [ implicit_genborn_params ] category."""
"""Process a line in the [ implicit_genborn_params ] category."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
6
:
if
len
(
fields
)
<
6
:
raise
ValueError
(
'Too few fields in [ implicit_genborn_params ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ implicit_genborn_params ] line: '
+
line
)
self
.
_implicitTypes
[
fields
[
0
]]
=
fields
self
.
_implicitTypes
[
fields
[
0
]]
=
fields
def
_processPairType
(
self
,
line
):
def
_processPairType
(
self
,
line
):
"""Process a line in the [ pairtypes ] category."""
"""Process a line in the [ pairtypes ] category."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
5
:
if
len
(
fields
)
<
5
:
raise
ValueError
(
'Too few fields in [ pairtypes] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ pairtypes] line: '
+
line
)
if
fields
[
2
]
!=
'1'
:
if
fields
[
2
]
!=
'1'
:
raise
ValueError
(
'Unsupported function type in [ pairtypes ] line: '
+
line
)
;
raise
ValueError
(
'Unsupported function type in [ pairtypes ] line: '
+
line
)
self
.
_pairTypes
[
tuple
(
fields
[:
2
])]
=
fields
self
.
_pairTypes
[
tuple
(
fields
[:
2
])]
=
fields
def
_processCmapType
(
self
,
line
):
def
_processCmapType
(
self
,
line
):
"""Process a line in the [ cmaptypes ] category."""
"""Process a line in the [ cmaptypes ] category."""
fields
=
line
.
split
()
fields
=
line
.
split
()
if
len
(
fields
)
<
8
or
len
(
fields
)
<
8
+
int
(
fields
[
6
])
*
int
(
fields
[
7
]):
if
len
(
fields
)
<
8
or
len
(
fields
)
<
8
+
int
(
fields
[
6
])
*
int
(
fields
[
7
]):
raise
ValueError
(
'Too few fields in [ cmaptypes ] line: '
+
line
)
;
raise
ValueError
(
'Too few fields in [ cmaptypes ] line: '
+
line
)
if
fields
[
5
]
!=
'1'
:
if
fields
[
5
]
!=
'1'
:
raise
ValueError
(
'Unsupported function type in [ cmaptypes ] line: '
+
line
)
;
raise
ValueError
(
'Unsupported function type in [ cmaptypes ] line: '
+
line
)
self
.
_cmapTypes
[
tuple
(
fields
[:
5
])]
=
fields
self
.
_cmapTypes
[
tuple
(
fields
[:
5
])]
=
fields
def
__init__
(
self
,
file
,
periodicBoxVectors
=
None
,
unitCellDimensions
=
None
,
includeDir
=
None
,
defines
=
None
):
def
__init__
(
self
,
file
,
periodicBoxVectors
=
None
,
unitCellDimensions
=
None
,
includeDir
=
None
,
defines
=
None
):
...
...
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