Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
tsoc
openmm
Commits
80528f3b
Commit
80528f3b
authored
Jan 18, 2018
by
Alan Grossfield
Browse files
removed default call to condense altogether
parent
75b8c17c
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
1 addition
and
15 deletions
+1
-15
wrappers/python/simtk/openmm/app/charmmparameterset.py
wrappers/python/simtk/openmm/app/charmmparameterset.py
+0
-14
wrappers/python/simtk/openmm/app/charmmpsffile.py
wrappers/python/simtk/openmm/app/charmmpsffile.py
+1
-1
No files found.
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @
80528f3b
...
@@ -116,9 +116,6 @@ class CharmmParameterSet(object):
...
@@ -116,9 +116,6 @@ class CharmmParameterSet(object):
self
.
nbfix_types
=
dict
()
self
.
nbfix_types
=
dict
()
self
.
parametersets
=
[]
self
.
parametersets
=
[]
# Allow the user to skip parameter condensing
self
.
_noCondense
=
False
# Load all of the files
# Load all of the files
tops
,
pars
,
strs
=
[],
[],
[]
tops
,
pars
,
strs
=
[],
[],
[]
for
arg
in
args
:
for
arg
in
args
:
...
@@ -606,14 +603,6 @@ class CharmmParameterSet(object):
...
@@ -606,14 +603,6 @@ class CharmmParameterSet(object):
self
.
readParameterFile
(
section
)
self
.
readParameterFile
(
section
)
title
,
section
=
f
.
next_section
()
title
,
section
=
f
.
next_section
()
def
noCondense
(
self
):
"""
If you have a very large number of interaction types, condensing
can be a slow operation. Allow the user to specify that it
should be skipped.
"""
self
.
_noCondense
=
True
def
condense
(
self
):
def
condense
(
self
):
"""
"""
This function goes through each of the parameter type dicts and
This function goes through each of the parameter type dicts and
...
@@ -625,9 +614,6 @@ class CharmmParameterSet(object):
...
@@ -625,9 +614,6 @@ class CharmmParameterSet(object):
-------
-------
>>> params = CharmmParameterSet('charmm.prm').condense()
>>> params = CharmmParameterSet('charmm.prm').condense()
"""
"""
if
self
.
_noCondense
:
return
self
# First scan through all of the bond types
# First scan through all of the bond types
self
.
_condense_types
(
self
.
bond_types
)
self
.
_condense_types
(
self
.
bond_types
)
self
.
_condense_types
(
self
.
angle_types
)
self
.
_condense_types
(
self
.
angle_types
)
...
...
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @
80528f3b
...
@@ -740,7 +740,7 @@ class CharmmPsfFile(object):
...
@@ -740,7 +740,7 @@ class CharmmPsfFile(object):
raise a ValueError
raise a ValueError
"""
"""
# Load the parameter set
# Load the parameter set
self
.
loadParameters
(
params
.
condense
()
)
self
.
loadParameters
(
params
)
hasbox
=
self
.
topology
.
getUnitCellDimensions
()
is
not
None
hasbox
=
self
.
topology
.
getUnitCellDimensions
()
is
not
None
# Check GB input parameters
# Check GB input parameters
if
implicitSolvent
is
not
None
and
gbsaModel
not
in
(
'ACE'
,
None
):
if
implicitSolvent
is
not
None
and
gbsaModel
not
in
(
'ACE'
,
None
):
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment