def align(mobile,
target,
cutoff=2.0,
cycles=5,
gap=-10.0,
extend=-0.5,
max_gap=50,
object=None,
matrix="BLOSUM62",
mobile_state=0,
target_state=0,
quiet=1,
max_skip=0,
transform=1,
reset=0,
_self=cmd):
'''
DESCRIPTION
"align" performs a sequence alignment followed by a structural
superposition, and then carries out zero or more cycles of
refinement in order to reject outliers.
USAGE
align mobile, target [, object=name ]
ARGUMENTS
mobile = string: atom selection for mobile atoms
target = string: atom selection for target atoms
object = string: name of alignment object to create
NOTES
If object is specified, then align will create an object which
indicates paired atoms and supports visualization of the alignment
in the sequence viewer.
EXAMPLE
align protA////CA, protB////CA, object=alnAB
SEE ALSO
super, pair_fit, fit, rms, rms_cur, intra_rms, intra_rms_cur
'''
r = DEFAULT_ERROR
mobile = selector.process(mobile)
target = selector.process(target)
matrix = str(matrix)
if matrix.lower() in ['none', '']:
mfile = ''
elif os.path.exists(matrix):
mfile = matrix
else:
mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/" + matrix)
if object == None: object = ''
# delete existing alignment object (if asked to reset it)
try:
_self.lock(_self)
r = _cmd.align(_self._COb, mobile,
"(" + target + ")", float(cutoff), int(cycles),
float(gap), float(extend), int(max_gap),
str(object), str(mfile),
int(mobile_state) - 1,
int(target_state) - 1, int(quiet), int(max_skip),
int(transform), int(reset), -1.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0, 0.0)
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
def align(mobile, target, cutoff=2.0, cycles=5, gap=-10.0,
extend=-0.5, max_gap=50, object=None,
matrix="BLOSUM62", mobile_state=0, target_state=0,
quiet=1, max_skip=0, transform=1, reset=0, _self=cmd):
'''
DESCRIPTION
"align" performs a sequence alignment followed by a structural
superposition, and then carries out zero or more cycles of
refinement in order to reject outliers.
USAGE
align mobile, target [, object=name ]
ARGUMENTS
mobile = string: atom selection for mobile atoms
target = string: atom selection for target atoms
object = string: name of alignment object to create
NOTES
If object is specified, then align will create an object which
indicates paired atoms and supports visualization of the alignment
in the sequence viewer.
EXAMPLE
align protA////CA, protB////CA, object=alnAB
SEE ALSO
super, pair_fit, fit, rms, rms_cur, intra_rms, intra_rms_cur
'''
r = DEFAULT_ERROR
mobile = selector.process(mobile)
target = selector.process(target)
matrix = str(matrix)
if string.lower(matrix)=='none':
matrix=''
if len(matrix):
mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
else:
mfile = ''
if object==None: object=''
# delete existing alignment object (if asked to reset it)
try:
_self.lock(_self)
r = _cmd.align(_self._COb,mobile,"("+target+")",
float(cutoff),int(cycles),float(gap),
float(extend),int(max_gap),str(object),str(mfile),
int(mobile_state)-1,int(target_state)-1,
int(quiet),int(max_skip),int(transform),int(reset),
-1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0, 0.0)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def super(mobile,
target,
cutoff=2.0,
cycles=5,
gap=-1.5,
extend=-0.7,
max_gap=50,
object=None,
matrix="BLOSUM62",
mobile_state=0,
target_state=0,
quiet=1,
max_skip=0,
transform=1,
reset=0,
seq=0.0,
radius=12.0,
scale=17.0,
base=0.65,
coord=0.0,
expect=6.0,
window=3,
ante=-1.0,
_self=cmd):
'''
DESCRIPTION
NOTE: This feature is experimental and unsupported.
"super" performs a residue-based pairwise alignment followed by a
structural superposition, and then carries out zero or more cycles
of refinement in order to reject outliers.
USAGE
super mobile, target [, object=name ]
NOTES
By adjusting various parameters, the nature of the initial
alignment can be modified to include or exclude various factors
including sequence similarity, main chain path, secondary &
tertiary structure, and current coordinates.
EXAMPLE
super protA////CA, protB////CA, object=supeAB
SEE ALSO
align, pair_fit, fit, rms, rms_cur, intra_rms, intra_rms_cur
'''
r = DEFAULT_ERROR
mobile = selector.process(mobile)
target = selector.process(target)
if object == None: object = ''
matrix = str(matrix)
if matrix.lower() in ['none', '']:
mfile = ''
elif os.path.exists(matrix):
mfile = matrix
else:
mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/" + matrix)
# delete existing alignment object (if asked to reset it)
try:
_self.lock(_self)
r = _cmd.align(_self._COb, mobile,
"(" + target + ")", float(cutoff), int(cycles),
float(gap), float(extend), int(max_gap),
str(object), str(mfile),
int(mobile_state) - 1,
int(target_state) - 1, int(quiet), int(max_skip),
int(transform), int(reset), float(seq),
float(radius), float(scale), float(base),
float(coord), float(expect), int(window),
float(ante))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
def super(mobile, target, cutoff=2.0, cycles=5,
gap=-1.5, extend=-0.7, max_gap=50, object=None,
matrix="BLOSUM62", mobile_state=0, target_state=0,
quiet=1, max_skip=0, transform=1, reset=0,
seq=0.0, radius=12.0, scale=17.0, base=0.65,
coord=0.0, expect=6.0, window=3, ante=-1.0,
_self=cmd):
'''
DESCRIPTION
NOTE: This feature is experimental and unsupported.
"super" performs a residue-based pairwise alignment followed by a
structural superposition, and then carries out zero or more cycles
of refinement in order to reject outliers.
USAGE
super mobile, target [, object=name ]
NOTES
By adjusting various parameters, the nature of the initial
alignment can be modified to include or exclude various factors
including sequence similarity, main chain path, secondary &
tertiary structure, and current coordinates.
EXAMPLE
super protA////CA, protB////CA, object=supeAB
SEE ALSO
align, pair_fit, fit, rms, rms_cur, intra_rms, intra_rms_cur
'''
r = DEFAULT_ERROR
mobile = selector.process(mobile)
target = selector.process(target)
if object==None: object=''
matrix = str(matrix)
if string.lower(matrix)=='none':
matrix=''
if len(matrix):
mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
else:
mfile = ''
# delete existing alignment object (if asked to reset it)
try:
_self.lock(_self)
r = _cmd.align(_self._COb,mobile,"("+target+")",float(cutoff),
int(cycles),float(gap),float(extend),int(max_gap),
str(object),str(mfile),
int(mobile_state)-1,int(target_state)-1,
int(quiet),int(max_skip),int(transform),
int(reset),float(seq),
float(radius),float(scale),float(base),
float(coord),float(expect),int(window),
float(ante))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
