def _get_polar_contacts_name(s,_self=cmd):
cmd=_self
list = cmd.get_object_list(s)
if list!=None and (len(list)==1):
return list[0]+polar_contacts_suffix
else:
return default_polar_contacts
def _get_polar_contacts_name(s, _self=cmd):
cmd = _self
list = cmd.get_object_list(s)
if list != None and (len(list) == 1):
return list[0] + polar_contacts_suffix
else:
return default_polar_contacts
def get_selection_state(selection):
'''
DESCRIPTION
Returns the effective object state for all objects in given selection.
Raises exception if objects are in different states.
'''
state_set = set(map(get_object_state,
cmd.get_object_list('(' + selection + ')')))
if len(state_set) != 1:
if len(state_set) == 0:
return 1
raise pymol.CmdException('Selection spans multiple object states')
return state_set.pop()
def get_selection_state(selection):
'''
DESCRIPTION
Returns the effective object state for all objects in given selection.
Raises exception if objects are in different states.
'''
state_set = set(
map(get_object_state, cmd.get_object_list('(' + selection + ')')))
if len(state_set) != 1:
if len(state_set) == 0:
return 1
raise pymol.CmdException('Selection spans multiple object states')
return state_set.pop()
def cealign(target,
mobile,
target_state=1,
mobile_state=1,
quiet=1,
guide=1,
d0=3.0,
d1=4.0,
window=8,
gap_max=30,
transform=1,
object=None,
_self=cmd):
'''
DESCRIPTION
"cealign" aligns two proteins using the CE algorithm.
USAGE
cealign target, mobile [, target_state [, mobile_state [, quiet [,
guide [, d0 [, d1 [, window [, gap_max, [, transform ]]]]]]]]]
NOTES
If "guide" is set PyMOL will align using only alpha carbons, which is the
default behavior. Otherwise, PyMOL will use all atoms. If "quiet" is set
to -1, PyMOL will print the rotation matrix as well.
Reference: Shindyalov IN, Bourne PE (1998) Protein structure alignment by
incremental combinatorial extension (CE) of the optimal path. Protein
Engineering 11(9) 739-747.
EXAMPLES
cealign protA////CA, protB////CA
# fetch two proteins and align them
fetch 1rlw 1rsy, async=0
cealign 1rlw, 1rsy
SEE ALSO
align, pair_fit, fit, rms, rms_cur, intra_rms, intra_rms_cur, super
'''
quiet = int(quiet)
window = int(window)
guide = "" if int(guide) == 0 else "and guide"
mobile = "(%s) %s" % (mobile, guide)
target = "(%s) %s" % (target, guide)
# handle PyMOL's macro /// notation
mobile = selector.process(mobile)
target = selector.process(target)
# make the lists for holding coordinates and IDs
mod1 = _self.get_model(target, state=target_state)
mod2 = _self.get_model(mobile, state=mobile_state)
sel1 = mod1.get_coord_list()
sel2 = mod2.get_coord_list()
ids1 = [a.id for a in mod1.atom]
ids2 = [a.id for a in mod2.atom]
if len(sel1) < 2 * window:
print "CEalign-Error: Your target selection is too short."
raise pymol.CmdException
if len(sel2) < 2 * window:
print "CEalign-Error: Your mobile selection is too short."
raise pymol.CmdException
if window < 3:
print "CEalign-Error: window size must be an integer greater than 2."
raise pymol.CmdException
if int(gap_max) < 0:
print "CEalign-Error: gap_max must be a positive integer."
raise pymol.CmdException
r = DEFAULT_ERROR
try:
_self.lock(_self)
# call the C function
r = _cmd.cealign(_self._COb, sel1, sel2, float(d0), float(d1),
int(window), int(gap_max))
(aliLen, RMSD, rotMat, i1, i2) = r
if quiet == -1:
import pprint
print "RMSD %f over %i residues" % (float(RMSD), int(aliLen))
print "TTT Matrix:"
pprint.pprint(rotMat)
elif quiet == 0:
print "RMSD %f over %i residues" % (float(RMSD), int(aliLen))
if int(transform):
for model in cmd.get_object_list("(" + mobile + ")"):
_self.transform_object(model, rotMat, state=0)
if object is not None:
obj1 = cmd.get_object_list("(" + target + ")")
obj2 = cmd.get_object_list("(" + mobile + ")")
if len(obj1) > 1 or len(obj2) > 1:
print ' CEalign-Error: selection spans multiple' + \
' objects, cannot create alignment object'
raise pymol.CmdException
tmp1 = _self.get_unused_name('_1')
tmp2 = _self.get_unused_name('_2')
_self.select_list(
tmp1, obj1[0],
[ids1[j] for i in i1 for j in range(i, i + window)])
_self.select_list(
tmp2, obj2[0],
[ids2[j] for i in i2 for j in range(i, i + window)])
_self.rms_cur(tmp1,
tmp2,
cycles=0,
matchmaker=4,
object=object)
_self.delete(tmp1)
_self.delete(tmp2)
except SystemError:
# findBest might return NULL, which raises SystemError
print " CEalign-Error: alignment failed"
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return ({
"alignment_length": aliLen,
"RMSD": RMSD,
"rotation_matrix": rotMat
})
def cealign(target, mobile, target_state=1, mobile_state=1, quiet=1,
guide=1, d0=3.0, d1=4.0, window=8, gap_max=30, transform=1,
object=None, _self=cmd):
'''
DESCRIPTION
"cealign" aligns two proteins using the CE algorithm.
USAGE
cealign target, mobile [, target_state [, mobile_state [, quiet [,
guide [, d0 [, d1 [, window [, gap_max, [, transform ]]]]]]]]]
NOTES
If "guide" is set PyMOL will align using only alpha carbons, which is the
default behavior. Otherwise, PyMOL will use all atoms. If "quiet" is set
to -1, PyMOL will print the rotation matrix as well.
Reference: Shindyalov IN, Bourne PE (1998) Protein structure alignment by
incremental combinatorial extension (CE) of the optimal path. Protein
Engineering 11(9) 739-747.
EXAMPLES
cealign protA////CA, protB////CA
# fetch two proteins and align them
fetch 1rlw 1rsy, async=0
cealign 1rlw, 1rsy
SEE ALSO
align, pair_fit, fit, rms, rms_cur, intra_rms, intra_rms_cur, super
'''
quiet = int(quiet)
window = int(window)
guide = "" if int(guide)==0 else "and guide"
mobile = "(%s) %s" % (mobile,guide)
target = "(%s) %s" % (target,guide)
# handle PyMOL's macro /// notation
mobile = selector.process(mobile)
target = selector.process(target)
# make the lists for holding coordinates and IDs
mod1 = _self.get_model(target, state=target_state)
mod2 = _self.get_model(mobile, state=mobile_state)
sel1 = mod1.get_coord_list()
sel2 = mod2.get_coord_list()
ids1 = [a.id for a in mod1.atom]
ids2 = [a.id for a in mod2.atom]
if len(sel1) < 2 * window:
print "CEalign-Error: Your target selection is too short."
raise pymol.CmdException
if len(sel2) < 2 * window:
print "CEalign-Error: Your mobile selection is too short."
raise pymol.CmdException
if window < 3:
print "CEalign-Error: window size must be an integer greater than 2."
raise pymol.CmdException
if int(gap_max) < 0:
print "CEalign-Error: gap_max must be a positive integer."
raise pymol.CmdException
r = DEFAULT_ERROR
try:
_self.lock(_self)
# call the C function
r = _cmd.cealign( _self._COb, sel1, sel2, float(d0), float(d1), int(window), int(gap_max) )
(aliLen, RMSD, rotMat, i1, i2) = r
if quiet==-1:
import pprint
print "RMSD %f over %i residues" % (float(RMSD), int(aliLen))
print "TTT Matrix:"
pprint.pprint(rotMat)
elif quiet==0:
print "RMSD %f over %i residues" % (float(RMSD), int(aliLen))
if int(transform):
for model in cmd.get_object_list("(" + mobile + ")"):
_self.transform_object(model, rotMat, state=0)
if object is not None:
obj1 = cmd.get_object_list("(" + target + ")")
obj2 = cmd.get_object_list("(" + mobile + ")")
if len(obj1) > 1 or len(obj2) > 1:
print ' CEalign-Error: selection spans multiple' + \
' objects, cannot create alignment object'
raise pymol.CmdException
tmp1 = _self.get_unused_name('_1')
tmp2 = _self.get_unused_name('_2')
_self.select_list(tmp1, obj1[0], [ids1[j] for i in i1 for j in range(i, i+window)])
_self.select_list(tmp2, obj2[0], [ids2[j] for i in i2 for j in range(i, i+window)])
_self.rms_cur(tmp2, tmp1, cycles=0, matchmaker=4, object=object)
_self.delete(tmp1)
_self.delete(tmp2)
except SystemError:
# findBest might return NULL, which raises SystemError
print " CEalign-Error: alignment failed"
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return ( {"alignment_length": aliLen, "RMSD" : RMSD, "rotation_matrix" : rotMat } )
