def fit(mobile,
target,
mobile_state=0,
target_state=0,
quiet=1,
matchmaker=0,
cutoff=2.0,
cycles=0,
object=None,
_self=cmd):
'''
DESCRIPTION
"fit" superimposes the model in the first selection on to the model
in the second selection.
USAGE
fit mobile, target
EXAMPLES
fit protA, protB
NOTES
Only matching atoms in both selections will be used for the fit.
Since atoms are matched based on all of their identifiers
(including segment and chain identifiers), this command is only
helpful when comparing very similar structures.
SEE ALSO
align, super, pair_fit, rms, rms_cur, intra_fit, intra_rms, intra_rms_cur
'''
r = DEFAULT_ERROR
a = str(mobile)
b = str(target)
# preprocess selections
a = selector.process(a)
b = selector.process(b)
#
if object == None: object = ''
if int(matchmaker) == 0:
sele1 = "((%s) in (%s))" % (str(a), str(b))
sele2 = "((%s) in (%s))" % (str(b), str(a))
else:
sele1 = str(a)
sele2 = str(b)
try:
_self.lock(_self)
r = _cmd.fit(_self._COb, sele1, sele2, 2,
int(mobile_state) - 1,
int(target_state) - 1, int(quiet), int(matchmaker),
float(cutoff), int(cycles), str(object))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
def expfit(a,b,_self=cmd): # Huh?
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.fit(_self._COb,a,b,2)
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def expfit(a, b, _self=cmd): # Huh?
r = DEFAULT_ERROR
try:
_self.lock(_self)
r = _cmd.fit(_self._COb, a, b, 2)
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
def rms(mobile,
target,
mobile_state=0,
target_state=0,
quiet=1,
matchmaker=0,
cutoff=2.0,
cycles=0,
object=None,
_self=cmd):
'''
DESCRIPTION
"rms" computes a RMS fit between two atom selections, but does not
tranform the models after performing the fit.
USAGE
rms (selection), (target-selection)
EXAMPLES
fit ( mutant and name ca ), ( wildtype and name ca )
SEE ALSO
fit, rms_cur, intra_fit, intra_rms, intra_rms_cur, pair_fit
'''
r = DEFAULT_ERROR
a = str(mobile)
b = str(target)
# preprocess selections
a = selector.process(a)
b = selector.process(b)
#
if object == None: object = ''
if int(matchmaker) == 0:
sele1 = "((%s) in (%s))" % (str(a), str(b))
sele2 = "((%s) in (%s))" % (str(b), str(a))
else:
sele1 = str(a)
sele2 = str(b)
try:
_self.lock(_self)
r = _cmd.fit(_self._COb, sele1, sele2, 1,
int(mobile_state) - 1,
int(target_state) - 1, int(quiet), int(matchmaker),
float(cutoff), int(cycles), str(object))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
def fit(mobile, target, mobile_state=0, target_state=0,
quiet=1, matchmaker=0, cutoff=2.0, cycles=0, object=None, _self=cmd):
'''
DESCRIPTION
"fit" superimposes the model in the first selection on to the model
in the second selection.
USAGE
fit mobile, target
EXAMPLES
fit protA, protB
NOTES
Only matching atoms in both selections will be used for the fit.
Since atoms are matched based on all of their identifiers
(including segment and chain identifiers), this command is only
helpful when comparing very similar structures.
SEE ALSO
align, super, pair_fit, rms, rms_cur, intra_fit, intra_rms, intra_rms_cur
'''
r = DEFAULT_ERROR
a=str(mobile)
b=str(target)
# preprocess selections
a = selector.process(a)
b = selector.process(b)
#
if object==None: object=''
if int(matchmaker)==0:
sele1 = "((%s) in (%s))" % (str(a),str(b))
sele2 = "((%s) in (%s))" % (str(b),str(a))
else:
sele1 = str(a)
sele2 = str(b)
try:
_self.lock(_self)
r = _cmd.fit(_self._COb,sele1,sele2,2,
int(mobile_state)-1,int(target_state)-1,
int(quiet),int(matchmaker),float(cutoff),
int(cycles),str(object))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def rms_cur(mobile,
target,
mobile_state=0,
target_state=0,
quiet=1,
matchmaker=0,
cutoff=2.0,
cycles=0,
object=None,
_self=cmd):
'''
DESCRIPTION
"rms_cur" computes the RMS difference between two atom
selections without performing any fitting.
USAGE
rms_cur (selection), (selection)
SEE ALSO
fit, rms, intra_fit, intra_rms, intra_rms_cur, pair_fit
'''
r = DEFAULT_ERROR
a = str(mobile)
b = str(target)
# preprocess selections
a = selector.process(a)
b = selector.process(b)
#
if object == None: object = ''
if int(matchmaker) == 0:
sele1 = "((%s) in (%s))" % (str(a), str(b))
sele2 = "((%s) in (%s))" % (str(b), str(a))
else:
sele1 = str(a)
sele2 = str(b)
try:
_self.lock(_self)
r = _cmd.fit(_self._COb, sele1, sele2, 0,
int(mobile_state) - 1,
int(target_state) - 1, int(quiet), int(matchmaker),
float(cutoff), int(cycles), str(object))
finally:
_self.unlock(r, _self)
if _self._raising(r, _self): raise pymol.CmdException
return r
def rms(mobile, target, mobile_state=0, target_state=0, quiet=1,
matchmaker=0, cutoff=2.0, cycles=0, object=None, _self=cmd):
'''
DESCRIPTION
"rms" computes a RMS fit between two atom selections, but does not
tranform the models after performing the fit.
USAGE
rms (selection), (target-selection)
EXAMPLES
fit ( mutant and name ca ), ( wildtype and name ca )
SEE ALSO
fit, rms_cur, intra_fit, intra_rms, intra_rms_cur, pair_fit
'''
r = DEFAULT_ERROR
a=str(mobile)
b=str(target)
# preprocess selections
a = selector.process(a)
b = selector.process(b)
#
if object==None: object=''
if int(matchmaker)==0:
sele1 = "((%s) in (%s))" % (str(a),str(b))
sele2 = "((%s) in (%s))" % (str(b),str(a))
else:
sele1 = str(a)
sele2 = str(b)
try:
_self.lock(_self)
r = _cmd.fit(_self._COb,sele1,sele2,1,
int(mobile_state)-1,int(target_state)-1,
int(quiet),int(matchmaker),float(cutoff),
int(cycles),str(object))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
def rms_cur(mobile, target, mobile_state=0, target_state=0,
quiet=1, matchmaker=0, cutoff=2.0, cycles=0,
object=None, _self=cmd):
'''
DESCRIPTION
"rms_cur" computes the RMS difference between two atom
selections without performing any fitting.
USAGE
rms_cur (selection), (selection)
SEE ALSO
fit, rms, intra_fit, intra_rms, intra_rms_cur, pair_fit
'''
r = DEFAULT_ERROR
a=str(mobile)
b=str(target)
# preprocess selections
a = selector.process(a)
b = selector.process(b)
#
if object==None: object=''
if int(matchmaker)==0:
sele1 = "((%s) in (%s))" % (str(a),str(b))
sele2 = "((%s) in (%s))" % (str(b),str(a))
else:
sele1 = str(a)
sele2 = str(b)
try:
_self.lock(_self)
r = _cmd.fit(_self._COb,sele1,sele2,0,
int(mobile_state)-1,int(target_state)-1,
int(quiet),int(matchmaker),float(cutoff),
int(cycles),str(object))
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise pymol.CmdException
return r
