def id_atom(selection, mode=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"id_atom" returns the original source id of a single atom, or
raises and exception if the atom does not exist or if the selection
corresponds to multiple atoms.
PYMOL API
list = cmd.id_atom(string selection)
'''
r = DEFAULT_ERROR
selection = str(selection)
l = apply(identify, (selection, mode, 1))
ll = len(l)
if not ll:
if _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: atom %s not found by id_atom." % selection
if _self._raising(_self=_self): raise pymol.CmdException
elif ll > 1:
if _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: multiple atoms %s found by id_atom." % selection
if _self._raising(_self=_self): raise pymol.CmdException
else:
r = l[0]
if not quiet:
if mode:
print " cmd.id_atom: (%s and id %d)" % (r[0], r[1])
else:
print " cmd.id_atom: (id %d)" % r
if _raising(r, _self): raise pymol.CmdException
return r
def id_atom(selection,mode=0,quiet=1,_self=cmd):
'''
DESCRIPTION
"id_atom" returns the original source id of a single atom, or
raises and exception if the atom does not exist or if the selection
corresponds to multiple atoms.
PYMOL API
list = cmd.id_atom(string selection)
'''
r = DEFAULT_ERROR
selection = str(selection)
l = apply(identify,(selection,mode,1))
ll = len(l)
if not ll:
if _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: atom %s not found by id_atom." % selection
if _self._raising(_self=_self): raise pymol.CmdException
elif ll>1:
if _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: multiple atoms %s found by id_atom." % selection
if _self._raising(_self=_self): raise pymol.CmdException
else:
r = l[0]
if not quiet:
if mode:
print " cmd.id_atom: (%s and id %d)"%(r[0],r[1])
else:
print " cmd.id_atom: (id %d)"%r
if _raising(r,_self): raise pymol.CmdException
return r
def get_version(quiet=1,_self=cmd):
'''
DESCRIPTION
"get_version" returns a tuple of length three containing text,
floating point, and integer representations of the current PyMOL
version number.
PYMOL API
cmd.get_version(int quiet)
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_version(_self._COb)
finally:
_self.unlock(r,_self)
if _raising(r,_self):
raise pymol.CmdException
else:
if not quiet:
if _feedback(fb_module.cmd,fb_mask.results,_self):
print " version: %s (%8.6f) %d"%r
return r
def phi_psi(selection="(byres pk1)", quiet=1, _self=cmd):
'''
DESCRIPTION
"phi_psi" return the phi and psi angles for a protein atom
selection.
USAGE
'''
r = cmd.get_phipsi(selection)
if r!=None:
kees = r.keys()
kees.sort()
if not quiet:
_self.feedback('push')
_self.feedback('disable','executive','actions')
for a in kees:
_self.iterate("(%s`%d)"%a,"print ' %-9s "+
("( %6.1f, %6.1f )"%r[a])+
"'%(resn+'-'+resi+':')")
_self.feedback('pop')
elif _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: can't compute phi_psi"
if _raising(r,_self): raise pymol.CmdException
return r
def get_version(quiet=1,_self=cmd):
'''
DESCRIPTION
"get_version" returns a tuple of length six containing text,
floating point, and integer representations of the current PyMOL
version number, build date as unix timestamp, GIT SHA and SVN
code revision so far available.
PYMOL API
cmd.get_version(int quiet)
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_version(_self._COb)
finally:
_self.unlock(r,_self)
if _raising(r,_self):
raise pymol.CmdException
else:
quiet = int(quiet)
if quiet < 1 and _feedback(fb_module.cmd, fb_mask.results, _self):
print " version: %s (%2.3f) %d," % r[:3],
print "Incentive Product" if pymol.invocation.options.incentive_product else "Open-Source"
if quiet < 0:
if r[3]:
print ' build date:', time.strftime('%c %Z', time.localtime(r[3]))
if r[4]:
print ' git sha:', r[4]
if r[5]:
print ' svn rev:', r[5]
return r
def get_version(quiet=1, _self=cmd):
'''
DESCRIPTION
"get_version" returns a tuple of length three containing text,
floating point, and integer representations of the current PyMOL
version number.
PYMOL API
cmd.get_version(int quiet)
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_version(_self._COb)
finally:
_self.unlock(r, _self)
if _raising(r, _self):
raise pymol.CmdException
else:
if not quiet:
if _feedback(fb_module.cmd, fb_mask.results, _self):
print " version: %s (%2.3f) %d" % r
return r
def phi_psi(selection="(byres pk1)", quiet=1, _self=cmd):
'''
DESCRIPTION
"phi_psi" return the phi and psi angles for a protein atom
selection.
USAGE
'''
r = cmd.get_phipsi(selection)
if r != None:
kees = r.keys()
kees.sort()
if not quiet:
_self.feedback('push')
_self.feedback('disable', 'executive', 'actions')
for a in kees:
_self.iterate(
"(%s`%d)" % a, "print ' %-9s " +
("( %6.1f, %6.1f )" % r[a]) + "'%(resn+'-'+resi+':')")
_self.feedback('pop')
elif _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: can't compute phi_psi"
if _raising(r, _self): raise pymol.CmdException
return r
def get_version(quiet=1,_self=cmd):
'''
DESCRIPTION
"get_version" returns a tuple of length six containing text,
floating point, and integer representations of the current PyMOL
version number, build date as unix timestamp, GIT SHA and SVN
code revision so far available.
PYMOL API
cmd.get_version(int quiet)
'''
# get_version doesn't need the _COb and doesn't require a lock
r = _cmd.get_version()
if _raising(r,_self):
raise pymol.CmdException
else:
quiet = int(quiet)
if quiet < 1 and _feedback(fb_module.cmd, fb_mask.results, _self):
import re
p = pymol.get_version_message(r)
print re.sub(r'^', ' ', p, re.M)
if quiet < 0:
if r[3]:
print ' build date:', time.strftime('%c %Z', time.localtime(r[3]))
if r[4]:
print ' git sha:', r[4]
return r
def get_color_tuple(name,mode=0,_self=cmd):
name=str(name)
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_color(_self._COb,name,mode)
if r==None:
if _feedback(fb_module.cmd,fb_mask.errors,_self):
print "cmd-Error: Unknown color '%s'."%name
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def get_color_tuple(name, mode=0, _self=cmd):
name = str(name)
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_color(_self._COb, name, mode)
if r == None:
if _feedback(fb_module.cmd, fb_mask.errors, _self):
print "cmd-Error: Unknown color '%s'." % name
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_type(name,quiet=1,_self=cmd):
'''
DESCRIPTION
"get_type" returns a string describing the named object or
selection or the string "nonexistent" if the name in unknown.
PYMOL API
cmd.get_type(string object-name)
NOTES
Possible return values are
"object:molecule"
"object:map"
"object:mesh"
"object:slice"
"object:surface"
"object:measurement"
"object:cgo"
"object:group"
"object:volume"
"selection"
SEE ALSO
get_names
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_type(_self._COb,str(name))
finally:
_self.unlock(r,_self)
if is_error(r):
if not quiet and _feedback(fb_module.cmd,fb_mask.errors,_self):
print "Cmd-Error: unrecognized name."
elif not quiet:
print r
if _raising(r,_self): raise pymol.CmdException
return r
def get_type(name, quiet=1, _self=cmd):
'''
DESCRIPTION
"get_type" returns a string describing the named object or
selection or the string "nonexistent" if the name in unknown.
PYMOL API
cmd.get_type(string object-name)
NOTES
Possible return values are
"object:molecule"
"object:map"
"object:mesh"
"object:slice"
"object:surface"
"object:measurement"
"object:cgo"
"object:group"
"object:volume"
"selection"
SEE ALSO
get_names
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_type(_self._COb, str(name))
finally:
_self.unlock(r, _self)
if is_error(r):
if not quiet and _feedback(fb_module.cmd, fb_mask.errors, _self):
print "Cmd-Error: unrecognized name."
elif not quiet:
print r
if _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 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