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 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 create(name, selection, source_state=0,
target_state=0, discrete=0, zoom=-1, quiet=1,
singletons=0, extract=None, _self=cmd):
'''
DESCRIPTION
"create" creates a new molecule object from a selection. It can
also be used to create states in an existing object.
USAGE
create name, selection [,source_state [,target_state ] ]
ARGUMENTS
name = string: name of object to create or modify
selection = string: atoms to include in the new object
source_state = integer: {default: 0 -- copy all states}
target_state = integer: {default: 0}
PYMOL API
cmd.create(string name, string selection, int state,
int target_state, int discrete)
NOTES
If the source and target states are zero (default), then all
states will be copied. Otherwise, only the indicated states will
be copied.
SEE ALSO
load, copy, extract
'''
r = DEFAULT_ERROR
# preprocess selection
selection = selector.process(selection)
#
try:
_self.lock(_self)
if name==None:
avoid = {}
for obj in cmd.get_names("all"):
avoid[obj] = 1
sel_cnt = _cmd.get(_self._COb,"sel_counter")
while 1:
sel_cnt = sel_cnt + 1.0
name = "obj%02.0f" % sel_cnt
if not avoid.has_key(name):
_cmd.legacy_set(_self._COb,"sel_counter","%1.0f" % sel_cnt)
break
r = _cmd.create(_self._COb,str(name),"("+str(selection)+")",
int(source_state)-1,int(target_state)-1,
int(discrete),int(zoom),int(quiet),int(singletons))
finally:
_self.unlock(r,_self)
if not is_error(r): # temporary inefficient implementation
if extract not in (None, 0, '0'):
if extract not in (1, '1'):
extract = selector.process(extract)
else:
extract = selection
_self.remove("(("+extract+") in (%s)) and not (%s)"%(name,name))
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
