def get_names(type='public_objects',
enabled_only=0,
selection="",
_self=cmd):
'''
DESCRIPTION
"get_names" returns a list of object and/or selection names.
PYMOL API
cmd.get_names( [string: "objects"|"selections"|"all"|"public_objects"|"public_selections"] )
NOTES
The default behavior is to return only object names.
SEE ALSO
get_type, count_atoms, count_states
'''
selection = selector.process(selection)
r = DEFAULT_ERROR
# this needs to be replaced with a flag & masking scheme...
mode = 1
if type == 'objects':
mode = 1
elif type == 'selections':
mode = 2
elif type == 'all':
mode = 0
elif type == 'public':
mode = 3
elif type == 'public_objects':
mode = 4
elif type == 'public_selections':
mode = 5
elif type == 'public_nongroup_objects':
mode = 6
elif type == 'public_group_objects':
mode = 7
elif type == 'nongroup_objects':
mode = 8
elif type == 'group_objects':
mode = 9
else:
print "Error: unknown type: '%s'" % str(type)
if _raising(-1, _self): raise pymol.CmdException
try:
_self.lock(_self)
r = _cmd.get_names(_self._COb, int(mode), int(enabled_only),
str(selection))
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_names(type='public_objects',enabled_only=0,selection="",_self=cmd):
'''
DESCRIPTION
"get_names" returns a list of object and/or selection names.
PYMOL API
cmd.get_names( [string: "objects"|"selections"|"all"|"public_objects"|"public_selections"] )
NOTES
The default behavior is to return only object names.
SEE ALSO
get_type, count_atoms, count_states
'''
selection = selector.process(selection)
r = DEFAULT_ERROR
# this needs to be replaced with a flag & masking scheme...
mode = 1
if type=='objects':
mode = 1
elif type=='selections':
mode = 2
elif type=='all':
mode = 0
elif type=='public':
mode = 3
elif type=='public_objects':
mode = 4
elif type=='public_selections':
mode = 5
elif type=='public_nongroup_objects':
mode = 6
elif type=='public_group_objects':
mode = 7
elif type=='nongroup_objects':
mode = 8
elif type=='group_objects':
mode = 9
else:
print "Error: unknown type: '%s'"%str(type)
if _raising(-1,_self): raise pymol.CmdException
try:
_self.lock(_self)
r = _cmd.get_names(_self._COb,int(mode),int(enabled_only),str(selection))
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def get_model(selection="(all)", state=1, ref='', ref_state=0, _self=cmd):
'''
DESCRIPTION
"get_model" returns a ChemPy "Indexed" format model from a selection.
PYMOL API
cmd.get_model(string selection [,int state] )
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_model(_self._COb, "(" + str(selection) + ")",
int(state) - 1, str(ref),
int(ref_state) - 1)
if r == None:
r = DEFAULT_ERROR
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_title(object, state, quiet=1, _self=cmd):
'''
DESCRIPTION
"get_title" retrieves a text string to the state of a particular
object which will be displayed when the state is active.
USAGE
set_title object, state
PYMOL API
cmd.set_title(string object, int state, string text)
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_title(_self._COb,str(object),int(state)-1)
if not quiet:
if r!=None:
print " get_title: %s"%r
finally:
_self.unlock(r,_self)
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 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 count_frames(quiet=1, _self=cmd):
'''
DESCRIPTION
"count_frames" returns the number of frames defined for the PyMOL
movie.
USAGE
count_frames
PYMOL API
cmd.count_frames()
SEE ALSO
frame, count_states
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.count_frames(_self._COb)
if not quiet: print " cmd.count_frames: %d frames"%r
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def index(selection="(all)",quiet=1,_self=cmd):
'''
DESCRIPTION
"index" returns a list of tuples corresponding to the
object name and index of the atoms in the selection.
PYMOL API
list = cmd.index(string selection="(all)")
NOTE
Atom indices are fragile and will change as atoms are added
or deleted. Whenever possible, use integral atom identifiers
instead of indices.
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.index(_self._COb,"("+str(selection)+")",0) # 0 = default mode
finally:
_self.unlock(r,_self)
if not quiet:
if is_list(r):
if len(r):
for a in r:
print " cmd.index: (%s`%d)"%(a[0],a[1])
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 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_extent(selection="(all)", state=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"get_extent" returns the minimum and maximum XYZ coordinates of a
selection as an array:
[ [ min-X , min-Y , min-Z ],[ max-X, max-Y , max-Z ]]
PYMOL API
cmd.get_extent(string selection="(all)", state=0 )
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_min_max(_self._COb, str(selection), int(state) - 1)
finally:
_self.unlock(r, _self)
if not r:
if _self._raising(_self=_self): raise pymol.CmdException
elif not quiet:
print " cmd.extent: min: [%8.3f,%8.3f,%8.3f]" % (r[0][0], r[0][1],
r[0][2])
print " cmd.extent: max: [%8.3f,%8.3f,%8.3f]" % (r[1][0], r[1][1],
r[1][2])
if _raising(r, _self): raise pymol.CmdException
return r
def find_pairs(selection1,
selection2,
state1=1,
state2=1,
cutoff=3.5,
mode=0,
angle=45,
_self=cmd):
'''
DESCRIPTION
"find_pairs" is currently undocumented.
'''
# preprocess selection
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.find_pairs(_self._COb, "(" + str(selection1) + ")",
"(" + str(selection2) + ")",
int(state1) - 1,
int(state2) - 1, int(mode), float(cutoff),
float(angle))
# 0 = default mode
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def index(selection="(all)", quiet=1, _self=cmd):
'''
DESCRIPTION
"index" returns a list of tuples corresponding to the
object name and index of the atoms in the selection.
PYMOL API
list = cmd.index(string selection="(all)")
NOTE
Atom indices are fragile and will change as atoms are added
or deleted. Whenever possible, use integral atom identifiers
instead of indices.
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.index(_self._COb, "(" + str(selection) + ")",
0) # 0 = default mode
finally:
_self.unlock(r, _self)
if not quiet:
if is_list(r):
if len(r):
for a in r:
print " cmd.index: (%s`%d)" % (a[0], a[1])
if _raising(r, _self): raise pymol.CmdException
return r
def count_atoms(selection="(all)", quiet=1, state=0, domain='', _self=cmd):
'''
DESCRIPTION
"count_atoms" returns a count of atoms in a selection.
USAGE
count_atoms (selection)
PYMOL API
cmd.count_atoms(string selection)
'''
r = DEFAULT_ERROR
# preprocess selection
selection = selector.process(selection)
#
try:
_self.lock(_self)
r = _cmd.select(_self._COb, "_count_tmp",
"(" + str(selection) + ")", 1,
int(state) - 1, str(domain))
_cmd.delete(_self._COb, "_count_tmp")
finally:
_self.unlock(r, _self)
if not quiet: print " count_atoms: %d atoms" % r
if _raising(r, _self): raise pymol.CmdException
return r
def get_movie_length(quiet=1, images=-1, _self=cmd):
'''
DESCRIPTION
"get_movie_length" returns the number of frames explicitly defined
in the movie, not including molecular states.
PYMOL API
cmd.count_frames()
SEE ALSO
frame, count_states, count_frames
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_movie_length(_self._COb)
if r < 0:
if images == 0:
r = 0
elif images < 0:
r = -r
if images == 1:
if r > 0:
r = 0
if r >= 0 and not quiet:
print " cmd.get_movie_length: %d frames" % r
finally:
_self.unlock(r, _self)
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 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 overlap(selection1,
selection2,
state1=1,
state2=1,
adjust=0.0,
quiet=1,
_self=cmd):
'''
DESCRIPTION
"overlap" is an unsupported command that may have something to do
with measuring the total amount of van der Waals overlap between
two selections.
NOTES
For best performance, use the smaller molecule as selection 1.
'''
# preprocess selections
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.overlap(_self._COb, str(selection1), str(selection2),
int(state1) - 1,
int(state2) - 1, float(adjust))
if not quiet: print " cmd.overlap: %5.3f Angstroms." % r
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def overlap(selection1, selection2, state1=1, state2=1, adjust=0.0, quiet=1, _self=cmd):
'''
DESCRIPTION
"overlap" is an unsupported command that may have something to do
with measuring the total amount of van der Waals overlap between
two selections.
NOTES
For best performance, use the smaller molecule as selection 1.
'''
# preprocess selections
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.overlap(_self._COb,str(selection1),str(selection2),
int(state1)-1,int(state2)-1,
float(adjust))
if not quiet: print " cmd.overlap: %5.3f Angstroms."%r
finally:
_self.unlock(r,_self)
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 (%2.3f) %d" % r
return r
def count_atoms(selection="(all)",quiet=1,state=0,domain='',_self=cmd):
'''
DESCRIPTION
"count_atoms" returns a count of atoms in a selection.
USAGE
count_atoms (selection)
PYMOL API
cmd.count_atoms(string selection)
'''
r = DEFAULT_ERROR
# preprocess selection
selection = selector.process(selection)
#
try:
_self.lock(_self)
r = _cmd.select(_self._COb,"_count_tmp","("+str(selection)+")",1,int(state)-1,str(domain))
_cmd.delete(_self._COb,"_count_tmp")
finally:
_self.unlock(r,_self)
if not quiet: print " count_atoms: %d atoms"%r
if _raising(r,_self): raise pymol.CmdException
return r
def get_symmetry(selection="(all)",quiet=1,_self=cmd):
'''
DESCRIPTION
"get_symmetry" can be used to obtain the crystal
and spacegroup parameters for a molecule
(FUTURE - map object - FUTURE)
USAGE
get_symmetry object-name-or-selection
PYMOL API
cmd.get_symmetry(string selection)
'''
r = DEFAULT_ERROR
selection = selector.process(selection)
try:
_self.lock(_self)
r = _cmd.get_symmetry(_self._COb,str(selection))
if not quiet:
if(is_list(r)):
if(len(r)):
print " get_symmetry: A = %7.3f B = %7.3f C = %7.3f"%tuple(r[0:3])
print " get_symmetry: Alpha = %7.3f Beta = %7.3f Gamma = %7.3f"%tuple(r[3:6])
print " get_symmetry: SpaceGroup = %s"%r[6]
else:
print " get_symmetry: No symmetry defined."
finally:
_self.unlock(r,_self)
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_title(object, state, quiet=1, _self=cmd):
'''
DESCRIPTION
"get_title" retrieves a text string to the state of a particular
object which will be displayed when the state is active.
USAGE
set_title object, state
PYMOL API
cmd.set_title(string object, int state, string text)
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_title(_self._COb, str(object), int(state) - 1)
if not quiet:
if r != None:
print " get_title: %s" % r
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def count_frames(quiet=1, _self=cmd):
'''
DESCRIPTION
"count_frames" returns the number of frames defined for the PyMOL
movie.
USAGE
count_frames
PYMOL API
cmd.count_frames()
SEE ALSO
frame, count_states
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.count_frames(_self._COb)
if not quiet: print " cmd.count_frames: %d frames" % r
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_movie_length(quiet=1, images=-1, _self=cmd):
'''
DESCRIPTION
"get_movie_length" returns the number of frames explicitly defined
in the movie, not including molecular states.
PYMOL API
cmd.count_frames()
SEE ALSO
frame, count_states, count_frames
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_movie_length(_self._COb)
if r<0:
if images==0:
r = 0
elif images<0:
r = -r
if images == 1:
if r>0:
r = 0
if r>=0 and not quiet:
print " cmd.get_movie_length: %d frames"%r
finally:
_self.unlock(r,_self)
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 get_extent(selection="(all)",state=0,quiet=1,_self=cmd):
'''
DESCRIPTION
"get_extent" returns the minimum and maximum XYZ coordinates of a
selection as an array:
[ [ min-X , min-Y , min-Z ],[ max-X, max-Y , max-Z ]]
PYMOL API
cmd.get_extent(string selection="(all)", state=0 )
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_min_max(_self._COb,str(selection),int(state)-1)
finally:
_self.unlock(r,_self)
if not r:
if _self._raising(_self=_self): raise pymol.CmdException
elif not quiet:
print " cmd.extent: min: [%8.3f,%8.3f,%8.3f]"%(r[0][0],r[0][1],r[0][2])
print " cmd.extent: max: [%8.3f,%8.3f,%8.3f]"%(r[1][0],r[1][1],r[1][2])
if _raising(r,_self): raise pymol.CmdException
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_legal_name(name,_self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_legal_name(_self._COb,str(name))
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def get_renderer(_self=cmd): #
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_renderer(_self._COb)
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_color_index(color, _self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_color(_self._COb, str(color), 3)
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_legal_name(name, _self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_legal_name(_self._COb, str(name))
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_renderer(_self=cmd): #
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_renderer(_self._COb)
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def get_color_index(color,_self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_color(_self._COb,str(color),3)
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def get_color_indices(all=0, _self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
if all:
r = _cmd.get_color(_self._COb, '', 2)
else:
r = _cmd.get_color(_self._COb, '', 1)
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_color_indices(all=0,_self=cmd):
r = DEFAULT_ERROR
try:
_self.lock(_self)
if all:
r = _cmd.get_color(_self._COb,'',2)
else:
r = _cmd.get_color(_self._COb,'',1)
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def get_phipsi(selection="(name ca)",state=-1,_self=cmd):
# preprocess selections
selection = selector.process(selection)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_phipsi(_self._COb,"("+str(selection)+")",int(state)-1)
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def find_pairs(selection1,
selection2,
state1=1,
state2=1,
cutoff=3.5,
mode=0,
angle=45,
_self=cmd):
'''
DESCRIPTION
API only function. Returns a list of atom pairs. Atoms are represented as
(model,index) tuples.
Can be restricted to hydrogen-bonding-like contacts. WARNING: Only checks
atom orientation, not atom type (so would hydrogen bond between carbons for
example), so make sure to provide appropriate atom selections.
ARGUMENTS
selection1, selection2 = string: atom selections
state1, state2 = integer: state-index (only positive values allowed) {default: 1}
cutoff = float: distance cutoff {default: 3.5}
mode = integer: if mode=1, do coarse hydrogen bonding assessment {default: 0}
angle = float: hydrogen bond angle cutoff, only if mode=1 {default: 45.0}
NOTE
Although this does a similar job like "distance", it uses a completely
different routine and the "mode" argument has different meanings!
'''
# preprocess selection
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.find_pairs(_self._COb, "(" + str(selection1) + ")",
"(" + str(selection2) + ")",
int(state1) - 1,
int(state2) - 1, int(mode), float(cutoff),
float(angle))
# 0 = default mode
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_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_phipsi(selection="(name ca)", state=-1, _self=cmd):
# preprocess selections
selection = selector.process(selection)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_phipsi(_self._COb, "(" + str(selection) + ")",
int(state) - 1)
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_dihedral(atom1="pk1",
atom2="pk2",
atom3="pk3",
atom4="pk4",
state=-1,
quiet=1,
_self=cmd):
'''
DESCRIPTION
"get_dihedral" returns the dihedral angle between four atoms. By
default, the coordinates used are from the current state, however
an alternate state identifier can be provided.
By convention, positive dihedral angles are right-handed
(looking down the atom2-atom3 axis).
USAGE
get_dihedral atom1, atom2, atom3, atom4 [,state ]
EXAMPLES
get_dihedral 4/n,4/c,4/ca,4/cb
get_dihedral 4/n,4/c,4/ca,4/cb,state=4
PYMOL API
cmd.get_dihedral(atom1,atom2,atom3,atom4,state=-1)
'''
# preprocess selections
atom1 = selector.process(atom1)
atom2 = selector.process(atom2)
atom3 = selector.process(atom3)
atom4 = selector.process(atom4)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_dihe(_self._COb, str(atom1), str(atom2), str(atom3),
str(atom4),
int(state) - 1)
finally:
_self.unlock(r, _self)
if _raising(r, _self):
raise pymol.CmdException
elif not quiet:
print " cmd.get_dihedral: %5.3f degrees." % r
return r
def export_dots(object, state, _self=cmd):
'''
DESCRIPTION
"export_dots" is an old unsupported command that may have
something to do with returning the coordinates of the dot
representation back to the Python layer.
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.export_dots(_self._COb, object, int(state) - 1)
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_collada(version=2, _self=cmd):
'''
DESCRIPTION
"get_collada" returns a COLLADA string representing the content
currently displayed.
PYMOL API
cmd.get_collada()
'''
r = DEFAULT_ERROR
with _self.lockcm:
r = _cmd.get_collada(_self._COb,int(version))
if _raising(r,_self): raise pymol.CmdException
return r
def get_object_matrix(object, state=1, _self=cmd):
'''
DESCRIPTION
"get_object_matrix" is an unsupported command that may have
something to do with querying the transformation matrices
associated with an object
'''
r = DEFAULT_ERROR
object = str(object)
try:
_self.lock(_self)
r = _cmd.get_object_matrix(_self._COb, str(object), int(state) - 1)
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_object_matrix(object,state=1,_self=cmd):
'''
DESCRIPTION
"get_object_matrix" is an unsupported command that may have
something to do with querying the transformation matrices
associated with an object
'''
r = DEFAULT_ERROR
object = str(object)
try:
_self.lock(_self)
r = _cmd.get_object_matrix(_self._COb,str(object), int(state)-1)
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def export_dots(object,state,_self=cmd):
'''
DESCRIPTION
"export_dots" is an old unsupported command that may have
something to do with returning the coordinates of the dot
representation back to the Python layer.
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.export_dots(_self._COb,object,int(state)-1)
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def paste(_self=cmd): # INTERNAL
r=DEFAULT_SUCCESS
lst = []
if hasattr(pymol,"machine_get_clipboard"):
lst = pymol.machine_get_clipboard()
if len(lst):
new_lst = []
for a in lst:
while len(a):
if ord(a[-1])>32:
break
else:
a=a[:-1]
if len(a):
new_lst.append(a)
r = _cmd.paste(_self._COb,new_lst)
if _raising(r,_self): raise pymol.CmdException
return r
def get_angle(atom1="pk1",
atom2="pk2",
atom3="pk3",
state=-1,
quiet=1,
_self=cmd):
'''
DESCRIPTION
"get_angle" returns the angle between three atoms. By default, the
coordinates used are from the current state, however an alternate
state identifier can be provided.
USAGE
get_angle atom1, atom2, atom3, [,state ]
EXAMPLES
get_angle 4/n,4/c,4/ca
get_angle 4/n,4/c,4/ca,state=4
PYMOL API
cmd.get_angle(atom1="pk1",atom2="pk2",atom3="pk3",state=-1)
'''
# preprocess selections
atom1 = selector.process(atom1)
atom2 = selector.process(atom2)
atom3 = selector.process(atom3)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_angle(_self._COb, str(atom1), str(atom2), str(atom3),
int(state) - 1)
finally:
_self.unlock(r, _self)
if _raising(r, _self):
raise pymol.CmdException
elif not quiet:
print " cmd.get_angle: %5.3f degrees." % r
return r
def find_pairs(selection1,selection2,state1=1,state2=1,cutoff=3.5,mode=0,angle=45,_self=cmd):
'''
DESCRIPTION
API only function. Returns a list of atom pairs. Atoms are represented as
(model,index) tuples.
Can be restricted to hydrogen-bonding-like contacts. WARNING: Only checks
atom orientation, not atom type (so would hydrogen bond between carbons for
example), so make sure to provide appropriate atom selections.
ARGUMENTS
selection1, selection2 = string: atom selections
state1, state2 = integer: state-index (only positive values allowed) {default: 1}
cutoff = float: distance cutoff {default: 3.5}
mode = integer: if mode=1, do coarse hydrogen bonding assessment {default: 0}
angle = float: hydrogen bond angle cutoff, only if mode=1 {default: 45.0}
NOTE
Although this does a similar job like "distance", it uses a completely
different routine and the "mode" argument has different meanings!
'''
# preprocess selection
selection1 = selector.process(selection1)
selection2 = selector.process(selection2)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.find_pairs(_self._COb,"("+str(selection1)+")",
"("+str(selection2)+")",
int(state1)-1,int(state2)-1,
int(mode),float(cutoff),float(angle))
# 0 = default mode
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def get_position(quiet=1, _self=cmd):
'''
DESCRIPTION
"get_position" returns the 3D coordinates of the center of the
viewer window.
'''
try:
_self.lock(_self)
r = _cmd.get_position(_self._COb)
finally:
_self.unlock(r,_self)
if _raising(r,_self):
raise pymol.CmdException
elif not quiet:
print " cmd.get_position: [%8.3f,%8.3f,%8.3f]"%(r[0],r[1],r[2])
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_raw_alignment(name='', active_only=0, _self=cmd):
'''
DESCRIPTION
"get_raw_alignment" returns a list of lists of (object,index)
tuples containing the raw per-atom alignment relationships
PYMOL API
cmd.get_raw_alignment(name)
'''
try:
_self.lock(_self)
r = _cmd.get_raw_alignment(_self._COb, str(name), int(active_only))
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_position(quiet=1, _self=cmd):
'''
DESCRIPTION
"get_position" returns the 3D coordinates of the center of the
viewer window.
'''
try:
_self.lock(_self)
r = _cmd.get_position(_self._COb)
finally:
_self.unlock(r, _self)
if _raising(r, _self):
raise pymol.CmdException
elif not quiet:
print " cmd.get_position: [%8.3f,%8.3f,%8.3f]" % (r[0], r[1], r[2])
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_raw_alignment(name='',active_only=0,_self=cmd):
'''
DESCRIPTION
"get_raw_alignment" returns a list of lists of (object,index)
tuples containing the raw per-atom alignment relationships
PYMOL API
cmd.get_raw_alignment(name)
'''
try:
_self.lock(_self)
r = _cmd.get_raw_alignment(_self._COb,str(name),int(active_only))
finally:
_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException
return r
def get_dihedral(atom1="pk1",atom2="pk2",atom3="pk3",atom4="pk4",state=-1,quiet=1,_self=cmd):
'''
DESCRIPTION
"get_dihedral" returns the dihedral angle between four atoms. By
default, the coordinates used are from the current state, however
an alternate state identifier can be provided.
By convention, positive dihedral angles are right-handed
(looking down the atom2-atom3 axis).
USAGE
get_dihedral atom1, atom2, atom3, atom4 [,state ]
EXAMPLES
get_dihedral 4/n,4/c,4/ca,4/cb
get_dihedral 4/n,4/c,4/ca,4/cb,state=4
PYMOL API
cmd.get_dihedral(atom1,atom2,atom3,atom4,state=-1)
'''
# preprocess selections
atom1 = selector.process(atom1)
atom2 = selector.process(atom2)
atom3 = selector.process(atom3)
atom4 = selector.process(atom4)
#
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_dihe(_self._COb,str(atom1),str(atom2),str(atom3),str(atom4),int(state)-1)
finally:
_self.unlock(r,_self)
if _raising(r,_self):
raise pymol.CmdException
elif not quiet:
print " cmd.get_dihedral: %5.3f degrees."%r
return r
def get_idtf(_self=cmd):
'''
DESCRIPTION
"get_idft" is under development, but should eventually return an
idtf file containing multiple objects and scenes.
PYMOL API
cmd.idtf()
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_idtf(_self._COb)
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r
def get_vrml(version=2, _self=cmd):
'''
DESCRIPTION
"get_vrml" returns a VRML2 string representing the content
currently displayed.
PYMOL API
cmd.get_vrml()
'''
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.get_vrml(_self._COb, int(version))
finally:
_self.unlock(r, _self)
if _raising(r, _self): raise pymol.CmdException
return r