def resume(filename, _self=cmd):
'''
DESCRIPTION
"resume" executes a log file and opens it for recording of
additional commands.
USAGE
resume filename
SEE ALSO
log, log_close
'''
pymol = _self._pymol
r = DEFAULT_ERROR
if os.path.exists(filename):
if (re.search(r"\.py$|\.PY$|\.pym$|.PYM$", filename)):
r = _self.do("run %s" % filename)
else:
r = _self.do("@%s" % filename)
if is_ok(r):
r = _self.do("log_open %s,a" % filename)
if _self._raising(r, _self): raise pymol.CmdException
return r
def count_states(selection="(all)", quiet=1, _self=cmd):
'''
DESCRIPTION
"count_states" returns the number of states in the selection.
USAGE
count_states
PYMOL API
cmd.count_states(string selection)
SEE ALSO
frame
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.count_states(_self._COb,selection)
finally:
_self.unlock(r,_self)
if is_ok(r):
if not quiet:
print " cmd.count_states: %d states."%r
if _raising(r,_self): raise pymol.CmdException
return r
def count_states(selection="(all)", quiet=1, _self=cmd):
'''
DESCRIPTION
"count_states" returns the number of states in the selection.
USAGE
count_states
PYMOL API
cmd.count_states(string selection)
SEE ALSO
frame
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.count_states(_self._COb, selection)
finally:
_self.unlock(r, _self)
if is_ok(r):
if not quiet:
print " cmd.count_states: %d states." % r
if _raising(r, _self): raise pymol.CmdException
return r
def resume(filename, _self=cmd):
'''
DESCRIPTION
"resume" executes a log file and opens it for recording of
additional commands.
USAGE
resume filename
SEE ALSO
log, log_close
'''
pymol=_self._pymol
r = DEFAULT_ERROR
if os.path.exists(filename):
if(re.search(r"\.py$|\.PY$|\.pym$|.PYM$",filename)):
r = _self.do("run %s"%filename)
else:
r = _self.do("@%s"%filename)
if is_ok(r):
r = _self.do("log_open %s,a"%filename)
if _self._raising(r,_self): raise pymol.CmdException
return r
def get_session(names='',
partial=0,
quiet=1,
compress=-1,
cache=-1,
_self=cmd):
session = {}
r = DEFAULT_SUCCESS
cache = int(cache)
compress = int(compress)
if cache:
cache_opt = int(_self.get('session_cache_optimize'))
if cache != 0:
cache_mode = int(_self.get('cache_mode'))
if ((cache_mode > 0) and (cache_opt != 0)) or (cache_opt == 1):
_self.cache('optimize')
for a in _self._pymol._session_save_tasks:
if a == None:
try:
_self.lock(_self)
r = _cmd.get_session(_self._COb, session, str(names),
int(partial), int(quiet))
finally:
_self.unlock(r, _self)
try:
session['session'] = copy.deepcopy(_self._pymol.session)
if cache and hasattr(_self._pymol, '_cache'):
session['cache'] = _self._pymol._cache
except:
traceback.print_exc()
else:
try:
if is_error(apply(a, (session, ), {'_self': _self})):
r = DEFAULT_ERROR
except:
traceback.print_exc()
print "Error: An error occurred when trying to generate session."
print "Error: The resulting session file may be incomplete."
if is_ok(r):
if (compress < 0):
compress = _self.get_setting_boolean('session_compression')
if (compress):
import zlib
session = zlib.compress(io.pkl.toString(session))
return session
elif _self._raising(r, _self):
raise QuietException
return r
def get_session(names='', partial=0, quiet=1, compress=-1, cache=-1, _self=cmd):
session = {}
r = DEFAULT_SUCCESS
cache = int(cache)
compress = int(compress)
if cache:
cache_opt = int(_self.get('session_cache_optimize'))
if cache != 0:
cache_mode = int(_self.get('cache_mode'))
if ((cache_mode > 0) and (cache_opt != 0)) or (cache_opt==1):
_self.cache('optimize')
for a in _self._pymol._session_save_tasks:
if a==None:
try:
_self.lock(_self)
r = _cmd.get_session(_self._COb,session,str(names),
int(partial),int(quiet))
finally:
_self.unlock(r,_self)
try:
session['session'] = copy.deepcopy(_self._pymol.session)
if cache and hasattr(_self._pymol,'_cache'):
session['cache'] = _self._pymol._cache
except:
traceback.print_exc()
else:
try:
if is_error(apply(a,(session,),{'_self':_self})):
r = DEFAULT_ERROR
except:
traceback.print_exc()
print "Error: An error occurred when trying to generate session."
print "Error: The resulting session file may be incomplete."
if is_ok(r):
if(compress<0):
compress = _self.get_setting_boolean('session_compression')
if(compress):
import zlib
session = zlib.compress(io.pkl.toString(session))
return session
elif _self._raising(r,_self):
raise QuietException
return r
def pop(name, source, enable=-1, quiet=1, _self=cmd):
'''
DESCRIPTION
"pop" provides a mechanism of iterating through an atom selection
atom by atom, where each atom is sequentially assigned to the
named selection.
USAGE
pop name, source
EXAMPLE
select src, name ca
python
while cmd.pop("tmp","src"):
cmd.zoom("tmp",2, animate=1)
for a in range(30):
cmd.refresh()
time.sleep(0.05)
python end
PYMOL API
cmd.deselect()
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.pop(_self._COb,str(name),str(source),int(quiet))
if is_ok(r):
enable = int(enable)
if enable>0:
r = _cmd.onoff(_self._COb,str(name),1,0);
elif enable == 0:
r = _cmd.onoff(_self._COb,str(name),0,0)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def distance(name=None, selection1="(pk1)", selection2="(pk2)",
cutoff=None, mode=None, zoom=0, width=None, length=None,
gap=None, label=1, quiet=1, reset=0, state=0, _self=cmd):
'''
DESCRIPTION
"distance" creates a new distance object between two selections.
USAGE
distance [name [, selection1 [, selection2 [, cutoff [, mode ]]]]]
ARGUMENTS
name = string: name of the distance object to create
selection1 = string: first atom selection
selection2 = string: second atom selection
cutoff = float: longest distance to show
mode = 0: all interatomic distances
mode = 1: only bond distances
mode = 2: only show polar contact distances
EXAMPLES
distance mydist, 14/CA, 29/CA
distance hbonds, all, all, 3.2, mode=2
NOTES
The distance wizard makes measuring distances easier than using
the "dist" command for real-time operations.
"dist" alone will show distances between selections (pk1) and (pk1),
which can be set using the PkAt mouse action (usually CTRL-middle-click).
PYMOL API
cmd.distance(string name, string selection1, string selection2,
string cutoff, string mode )
'''
# handle unnamed distance
r = DEFAULT_SUCCESS
if name!=None:
if len(name):
if name[0]=='(' or ' ' in name or '/' in name: # we're one argument off...
if cutoff!=None:
mode = cutoff
if selection2!="(pk2)":
cutoff = selection2
if selection1!="(pk1)":
selection2 = selection1
selection1=name
name = None
if selection1=="(pk1)":
if "pk1" not in _self.get_names('selections'):
if _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: The 'pk1' selection is undefined."
r = DEFAULT_ERROR
if selection2=="(pk2)":
if "pk2" not in _self.get_names('selections'):
if _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: The 'pk2' selection is undefined."
r = DEFAULT_ERROR
if is_ok(r):
r = DEFAULT_ERROR
# if unlabeled, then get next name in series
if name!=None:
nam=name
else:
try:
_self.lock(_self)
cnt = _cmd.get(_self._COb,"dist_counter") + 1.0
r = _cmd.legacy_set(_self._COb,"dist_counter","%1.0f" % cnt)
nam = "dist%02.0f" % cnt
finally:
_self.unlock(r,_self)
# defaults
if mode == None:
mode = 0
if cutoff == None:
cutoff = -1.0
# preprocess selections
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
# now do the deed
try:
_self.lock(_self)
if selection2!="same":
selection2 = "("+selection2+")"
r = _cmd.dist(_self._COb,str(nam),"("+str(selection1)+")",
str(selection2),int(mode),float(cutoff),
int(label),int(quiet),int(reset),
int(state)-1,int(zoom))
if width!=None:
_self.set("dash_width",width,nam)
if length!=None:
_self.set("dash_length",length,nam)
if gap!=None:
_self.set("dash_gap",gap,nam)
finally:
_self.unlock(r,_self)
if (r<0.0) and (not quiet):
# a negative value is an warning signal from PyMOL...
r = DEFAULT_ERROR
if _raising(r,_self): raise pymol.CmdException
return r
def dihedral(name=None, selection1="(pk1)", selection2="(pk2)",
selection3="(pk3)", selection4="(pk4)", mode=None,
label=1, reset=0, zoom=0, state=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"dihedral" shows dihedral angles formed between any four atoms.
USAGE
dihedral [ name [, selection1 [, selection2 [, selection3 [, selection4 ]]]]]
NOTES
"dihedral" alone will show the dihedral angle formed by selections
(pk1), (pk2), (pk3), and (pk4), which can be set using the "PkAt"
mouse action (typically, Ctrl-middle-click)
PYMOL API
cmd.dihedral(string name, string selection1, string selection2,
string selection3, string selection4)
SEE ALSO
distance, angle
'''
r = DEFAULT_SUCCESS
if selection1=="(pk1)":
if "pk1" not in _self.get_names('selections'):
if _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: The 'pk1' selection is undefined."
r = DEFAULT_ERROR
if selection2=="(pk2)":
if "pk2" not in _self.get_names('selections'):
if _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: The 'pk2' selection is undefined."
r = DEFAULT_ERROR
if selection3=="(pk3)":
if "pk3" not in _self.get_names('selections'):
if _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: The 'pk3' selection is undefined."
r = DEFAULT_ERROR
if selection3=="(pk4)":
if "pk4" not in _self.get_names('selections'):
if _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: The 'pk4' selection is undefined."
r = DEFAULT_ERROR
if is_ok(r):
r = DEFAULT_ERROR
# if unlabeled, then get next name in series
if name!=None:
nam=name
else:
try:
_self.lock(_self)
cnt = _cmd.get(_self._COb,"dist_counter") + 1.0
r = _cmd.legacy_set(_self._COb,"dist_counter","%1.0f" % cnt)
nam = "dihedral%02.0f" % cnt
finally:
_self.unlock(r,_self)
# defaults
if mode == None:
mode = 0
# preprocess selections
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
selection3 = selector.process(selection3)
selection4 = selector.process(selection4)
# now do the deed
try:
_self.lock(_self)
if selection2!="same":
selection2 = "("+selection2+")"
if selection3!="same":
selection3 = "("+selection3+")"
if selection4!="same":
selection4 = "("+selection4+")"
r = _cmd.dihedral(_self._COb,str(nam),"("+str(selection1)+")",
str(selection2),
str(selection3),
str(selection4),
int(mode),int(label),
int(reset),int(zoom),
int(quiet),int(state)-1)
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def _load(oname,
finfo,
state,
ftype,
finish,
discrete,
quiet=1,
multiplex=0,
zoom=-1,
mimic=1,
_self=cmd):
# WARNING: internal routine, subject to change
# caller must already hold API lock
# NOTE: state index assumes 1-based state
r = DEFAULT_ERROR
size = 0
if ftype not in (loadable.model, loadable.brick):
if ftype == loadable.r3d:
import cgo
obj = cgo.from_r3d(finfo)
if is_ok(obj):
r = _cmd.load_object(_self._COb, str(oname), obj,
int(state) - 1, loadable.cgo, int(finish),
int(discrete), int(quiet), int(zoom))
else:
print "Load-Error: Unable to open file '%s'." % finfo
elif ftype == loadable.cc1: # ChemDraw 3D
obj = io.cc1.fromFile(finfo)
if obj:
r = _cmd.load_object(_self._COb, str(oname), obj,
int(state) - 1, loadable.model,
int(finish), int(discrete), int(quiet),
int(zoom))
elif ftype == loadable.moe:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import moe
moe_str = file_read(finfo)
r = moe.read_moestr(moe_str,
str(oname),
int(state),
int(finish),
int(discrete),
int(quiet),
int(zoom),
_self=_self)
# END PROPRIETARY CODE SEGMENT
except ImportError:
print "Error: .MOE format not supported by this PyMOL build."
if _self._raising(-1, _self): raise pymol.CmdException
elif ftype == loadable.mae:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import mae
mae_str = file_read(finfo)
r = mae.read_maestr(mae_str,
str(oname),
int(state),
int(finish),
int(discrete),
int(quiet),
int(zoom),
int(multiplex),
int(mimic),
_self=_self)
# END PROPRIETARY CODE SEGMENT
except ValueError:
print "Error: .MAE format not supported by this PyMOL build."
if _self._raising(-1, _self): raise pymol.CmdException
else:
if ftype in _load2str and ('://' in finfo
or cmd.gz_ext_re.search(finfo)):
# NOTE: we could safely always do this, not only for URLs and
# compressed files. But I don't want to change the old behavior
# that regular files are read from the C function.
finfo = file_read(finfo)
ftype = _load2str[ftype]
r = _cmd.load(_self._COb, str(oname), finfo,
int(state) - 1, int(ftype), int(finish),
int(discrete), int(quiet), int(multiplex), int(zoom))
else:
try:
x = io.pkl.fromFile(finfo)
if isinstance(x, types.ListType) or isinstance(x, types.TupleType):
for a in x:
r = _cmd.load_object(_self._COb, str(oname), a,
int(state) - 1, int(ftype), 0,
int(discrete), int(quiet), int(zoom))
if (state > 0):
state = state + 1
_cmd.finish_object(_self._COb, str(oname))
else:
r = _cmd.load_object(_self._COb, str(oname), x,
int(state) - 1, int(ftype), int(finish),
int(discrete), int(quiet), int(zoom))
except:
# traceback.print_exc()
print "Load-Error: Unable to load file '%s'." % finfo
return r
def select(name, selection="", enable=-1, quiet=1, merge=0, state=0, domain='',_self=cmd):
'''
DESCRIPTION
"select" creates a named atom selection from a
selection-expression.
USAGE
select name, selection [, enable [, quiet [, merge [, state [, domain ]]]]]
ARGUMENTS
name = a unique name for the selection
selection = a selection-expression
NOTES
If a selection-expression with explicit surrounding parethenses is
provided as the first argument, then the default selection name
is used as the name argument.
EXAMPLES
select chA, chain A
select ( resn his )
select near142, resi 142 around 5
PYMOL API
cmd.select(string name, string selection)
SEE ALSO
delete
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
if selection=="":
selection = name
if _cmd.get(_self._COb,"auto_number_selections")!=0.0:
sel_cnt = _cmd.get(_self._COb,"sel_counter") + 1.0
_cmd.legacy_set(_self._COb,"sel_counter","%1.0f" % sel_cnt)
name = "sel%02.0f" % sel_cnt
else:
name = "sele"
if name == None:
sel_cnt = _cmd.get(_self._COb,"sel_counter") + 1.0
_cmd.legacy_set(_self._COb,"sel_counter","%1.0f" % sel_cnt)
name = "sel%02.0f" % sel_cnt
# preprocess selection (note: inside TRY)
selection = selector.process(selection)
merge = int(merge)
if merge==1:
selection = "("+selection+") or ?"+name # merge if exists
elif merge==2:
selection = "("+selection+") or ??"+name # merge if exists and active
#
r = _cmd.select(_self._COb,str(name),str(selection),int(quiet),int(state)-1,str(domain))
enable = int(enable)
if is_ok(r) and enable>0:
_cmd.onoff(_self._COb,str(name),1,0);
elif enable == 0:
_cmd.onoff(_self._COb,str(name),0,0)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def _load(oname,finfo,state,ftype,finish,discrete,
quiet=1,multiplex=0,zoom=-1,mimic=1,
_self=cmd):
# WARNING: internal routine, subject to change
# caller must already hold API lock
# NOTE: state index assumes 1-based state
r = DEFAULT_ERROR
size = 0
if ftype not in (loadable.model,loadable.brick):
if ftype == loadable.r3d:
import cgo
obj = cgo.from_r3d(finfo)
if is_ok(obj):
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.cgo,
int(finish),int(discrete),int(quiet),
int(zoom))
else:
print "Load-Error: Unable to open file '%s'."%finfo
elif ftype == loadable.cc1: # ChemDraw 3D
obj = io.cc1.fromFile(finfo)
if obj:
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.model,
int(finish),int(discrete),
int(quiet),int(zoom))
elif ftype == loadable.moe:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import moe
if (string.find(finfo,":")>1):
import urllib
moe_file = urllib.urlopen(finfo)
else:
moe_file = open(finfo)
moe_str = moe_file.read()
moe_file.close()
r = moe.read_moestr(moe_str,str(oname),int(state),
int(finish),int(discrete),int(quiet),int(zoom),_self=_self)
# END PROPRIETARY CODE SEGMENT
except ImportError:
print "Error: .MOE format not supported by this PyMOL build."
if _self._raising(-1,_self): raise pymol.CmdException
elif ftype == loadable.mae:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import mae
if (string.find(finfo,":")>1):
import urllib
mae_file = urllib.urlopen(finfo)
else:
mae_file = open(finfo)
mae_str = mae_file.read()
mae_file.close()
r = mae.read_maestr(mae_str,str(oname),
int(state),
int(finish),int(discrete),
int(quiet),int(zoom),int(multiplex),
int(mimic),
_self=_self)
# END PROPRIETARY CODE SEGMENT
except ValueError:
print "Error: .MAE format not supported by this PyMOL build."
if _self._raising(-1,_self): raise pymol.CmdException
else:
if ftype in _load2str.keys() and (string.find(finfo,":")>1):
gz = re.search("\.gz$",finfo,re.I)
try:
import urllib
tmp_file = urllib.urlopen(finfo)
except:
print "Error: unable to open the URL:\nError: %s"%finfo
# traceback.print_exc()
return 0
finfo = tmp_file.read()
if gz:
import StringIO
fakestream = StringIO.StringIO(finfo)
import gzip
finfo = gzip.GzipFile(fileobj=fakestream).read()
ftype = _load2str[ftype]
tmp_file.close()
elif ftype in _load2str.keys() and re.search("\.gz$",finfo,re.I):
import gzip
finfo = gzip.open(finfo).read()
ftype = _load2str[ftype]
r = _cmd.load(_self._COb,str(oname),finfo,int(state)-1,int(ftype),
int(finish),int(discrete),int(quiet),
int(multiplex),int(zoom))
else:
try:
x = io.pkl.fromFile(finfo)
if isinstance(x,types.ListType) or isinstance(x,types.TupleType):
for a in x:
r = _cmd.load_object(_self._COb,str(oname),a,int(state)-1,
int(ftype),0,int(discrete),int(quiet),
int(zoom))
if(state>0):
state = state + 1
_cmd.finish_object(_self._COb,str(oname))
else:
r = _cmd.load_object(_self._COb,str(oname),x,
int(state)-1,int(ftype),
int(finish),int(discrete),
int(quiet),int(zoom))
except:
# traceback.print_exc()
print "Load-Error: Unable to load file '%s'." % finfo
return r
def _load(oname,finfo,state,ftype,finish,discrete,
quiet=1,multiplex=0,zoom=-1,mimic=1,
_self=cmd):
# WARNING: internal routine, subject to change
# caller must already hold API lock
# NOTE: state index assumes 1-based state
r = DEFAULT_ERROR
size = 0
if ftype not in (loadable.model,loadable.brick):
if ftype == loadable.r3d:
import cgo
obj = cgo.from_r3d(finfo)
if is_ok(obj):
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.cgo,
int(finish),int(discrete),int(quiet),
int(zoom))
else:
print "Load-Error: Unable to open file '%s'."%finfo
elif ftype == loadable.cc1: # ChemDraw 3D
obj = io.cc1.fromFile(finfo)
if obj:
r = _cmd.load_object(_self._COb,str(oname),obj,int(state)-1,loadable.model,
int(finish),int(discrete),
int(quiet),int(zoom))
elif ftype == loadable.moe:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import moe
moe_str = _self.file_read(finfo)
r = moe.read_moestr(moe_str,str(oname),int(state),
int(finish),int(discrete),int(quiet),int(zoom),_self=_self)
# END PROPRIETARY CODE SEGMENT
except ImportError:
print "Error: .MOE format not supported by this PyMOL build."
if _self._raising(-1,_self): raise pymol.CmdException
elif ftype == loadable.mae:
try:
# BEGIN PROPRIETARY CODE SEGMENT
from epymol import mae
mae_str = _self.file_read(finfo)
r = mae.read_maestr(mae_str,str(oname),
int(state),
int(finish),int(discrete),
int(quiet),int(zoom),int(multiplex),
int(mimic),
_self=_self)
# END PROPRIETARY CODE SEGMENT
except ValueError:
print "Error: .MAE format not supported by this PyMOL build."
if _self._raising(-1,_self): raise pymol.CmdException
else:
if ftype in _load2str and ('://' in finfo or cmd.gz_ext_re.search(finfo)):
# NOTE: we could safely always do this, not only for URLs and
# compressed files. But I don't want to change the old behavior
# that regular files are read from the C function.
finfo = _self.file_read(finfo)
ftype = _load2str[ftype]
r = _cmd.load(_self._COb,str(oname),finfo,int(state)-1,int(ftype),
int(finish),int(discrete),int(quiet),
int(multiplex),int(zoom))
else:
try:
x = io.pkl.fromFile(finfo)
if isinstance(x,types.ListType) or isinstance(x,types.TupleType):
for a in x:
r = _cmd.load_object(_self._COb,str(oname),a,int(state)-1,
int(ftype),0,int(discrete),int(quiet),
int(zoom))
if(state>0):
state = state + 1
_cmd.finish_object(_self._COb,str(oname))
else:
r = _cmd.load_object(_self._COb,str(oname),x,
int(state)-1,int(ftype),
int(finish),int(discrete),
int(quiet),int(zoom))
except:
# traceback.print_exc()
print "Load-Error: Unable to load file '%s'." % finfo
return r
def distance(name=None,
selection1="(pk1)",
selection2="(pk2)",
cutoff=None,
mode=None,
zoom=0,
width=None,
length=None,
gap=None,
label=1,
quiet=1,
reset=0,
state=0,
_self=cmd):
'''
DESCRIPTION
"distance" creates a new distance object between two selections.
USAGE
distance [name [, selection1 [, selection2 [, cutoff [, mode ]]]]]
ARGUMENTS
name = string: name of the distance object to create
selection1 = string: first atom selection
selection2 = string: second atom selection
cutoff = float: longest distance to show
mode = 0: all interatomic distances
mode = 1: only bond distances
mode = 2: only show polar contact distances
EXAMPLES
distance mydist, 14/CA, 29/CA
distance hbonds, all, all, 3.2, mode=2
NOTES
The distance wizard makes measuring distances easier than using
the "dist" command for real-time operations.
"dist" alone will show distances between selections (pk1) and (pk1),
which can be set using the PkAt mouse action (usually CTRL-middle-click).
PYMOL API
cmd.distance(string name, string selection1, string selection2,
string cutoff, string mode )
'''
# handle unnamed distance
r = DEFAULT_SUCCESS
if name != None:
if len(name):
if name[0] == '(' or ' ' in name or '/' in name: # we're one argument off...
if cutoff != None:
mode = cutoff
if selection2 != "(pk2)":
cutoff = selection2
if selection1 != "(pk1)":
selection2 = selection1
selection1 = name
name = None
if selection1 == "(pk1)":
if "pk1" not in _self.get_names('selections'):
if _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: The 'pk1' selection is undefined."
r = DEFAULT_ERROR
if selection2 == "(pk2)":
if "pk2" not in _self.get_names('selections'):
if _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: The 'pk2' selection is undefined."
r = DEFAULT_ERROR
if is_ok(r):
r = DEFAULT_ERROR
# if unlabeled, then get next name in series
if name != None:
nam = name
else:
try:
_self.lock(_self)
cnt = _cmd.get(_self._COb, "dist_counter") + 1.0
r = _cmd.legacy_set(_self._COb, "dist_counter",
"%1.0f" % cnt)
nam = "dist%02.0f" % cnt
finally:
_self.unlock(r, _self)
# defaults
if mode == None:
mode = 0
if cutoff == None:
cutoff = -1.0
# preprocess selections
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
# now do the deed
try:
_self.lock(_self)
if selection2 != "same":
selection2 = "(" + selection2 + ")"
r = _cmd.dist(_self._COb, str(nam),
"(" + str(selection1) + ")", str(selection2),
int(mode), float(cutoff), int(label), int(quiet),
int(reset),
int(state) - 1, int(zoom))
if width != None:
_self.set("dash_width", width, nam)
if length != None:
_self.set("dash_length", length, nam)
if gap != None:
_self.set("dash_gap", gap, nam)
finally:
_self.unlock(r, _self)
if (r < 0.0) and (not quiet):
# a negative value is an warning signal from PyMOL...
r = DEFAULT_ERROR
if _raising(r, _self): raise pymol.CmdException
return r
def dihedral(name=None,
selection1="(pk1)",
selection2="(pk2)",
selection3="(pk3)",
selection4="(pk4)",
mode=None,
label=1,
reset=0,
zoom=0,
state=0,
quiet=1,
_self=cmd):
'''
DESCRIPTION
"dihedral" shows dihedral angles formed between any four atoms.
USAGE
dihedral [ name [, selection1 [, selection2 [, selection3 [, selection4 ]]]]]
NOTES
"dihedral" alone will show the dihedral angle formed by selections
(pk1), (pk2), (pk3), and (pk4), which can be set using the "PkAt"
mouse action (typically, Ctrl-middle-click)
PYMOL API
cmd.dihedral(string name, string selection1, string selection2,
string selection3, string selection4)
SEE ALSO
distance, angle
'''
r = DEFAULT_SUCCESS
if selection1 == "(pk1)":
if "pk1" not in _self.get_names('selections'):
if _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: The 'pk1' selection is undefined."
r = DEFAULT_ERROR
if selection2 == "(pk2)":
if "pk2" not in _self.get_names('selections'):
if _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: The 'pk2' selection is undefined."
r = DEFAULT_ERROR
if selection3 == "(pk3)":
if "pk3" not in _self.get_names('selections'):
if _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: The 'pk3' selection is undefined."
r = DEFAULT_ERROR
if selection3 == "(pk4)":
if "pk4" not in _self.get_names('selections'):
if _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: The 'pk4' selection is undefined."
r = DEFAULT_ERROR
if is_ok(r):
r = DEFAULT_ERROR
# if unlabeled, then get next name in series
if name != None:
nam = name
else:
try:
_self.lock(_self)
cnt = _cmd.get(_self._COb, "dist_counter") + 1.0
r = _cmd.legacy_set(_self._COb, "dist_counter",
"%1.0f" % cnt)
nam = "dihedral%02.0f" % cnt
finally:
_self.unlock(r, _self)
# defaults
if mode == None:
mode = 0
# preprocess selections
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
selection3 = selector.process(selection3)
selection4 = selector.process(selection4)
# now do the deed
try:
_self.lock(_self)
if selection2 != "same":
selection2 = "(" + selection2 + ")"
if selection3 != "same":
selection3 = "(" + selection3 + ")"
if selection4 != "same":
selection4 = "(" + selection4 + ")"
r = _cmd.dihedral(_self._COb,
str(nam), "(" + str(selection1) + ")",
str(selection2), str(selection3),
str(selection4), int(mode), int(label),
int(reset), int(zoom), int(quiet),
int(state) - 1)
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
