def intra_fit(selection, state=1, quiet=1, mix=0, _self=cmd):
'''
DESCRIPTION
"intra_fit" fits all states of an object to an atom selection
in the specified state. It returns the rms values to python
as an array.
USAGE
intra_fit selection [, state]
ARGUMENTS
selection = string: atoms to fit
state = integer: target state
PYMOL API
cmd.intra_fit( string selection, int state )
EXAMPLES
intra_fit ( name ca )
PYTHON EXAMPLE
from pymol import cmd
rms = cmd.intra_fit("(name ca)",1)
SEE ALSO
fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
state = int(state)
mix = int(mix)
try:
_self.lock(_self)
r = _cmd.intrafit(_self._COb,"("+str(selection)+")",int(state)-1,2,int(quiet),int(mix))
finally:
_self.unlock(r,_self)
if r<0.0:
r = DEFAULT_ERROR
elif not quiet:
st = 1
for a in r:
if a>=0.0:
if mix:
print " cmd.intra_fit: %5.3f in state %d vs mixed target"%(a,st)
else:
print " cmd.intra_fit: %5.3f in state %d vs state %d"%(a,st,state)
st = st + 1
if _self._raising(r,_self): raise pymol.CmdException
return r
def intra_rms(selection, state=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"intra_rms" calculates rms fit values for all states of an object
over an atom selection relative to the indicated state.
Coordinates are left unchanged. The rms values are returned as a
python array.
EXAMPLE
from pymol import cmd
rms = cmd.intra_rms("(name ca)",1)
print rms
PYMOL API
cmd.intra_rms(string selection, int state)
SEE ALSO
fit, rms, rms_cur, intra_fit, intra_rms_cur, pair_fit
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
state = int(state)
try:
_self.lock(_self)
r = _cmd.intrafit(_self._COb, "(" + str(selection) + ")",
int(state) - 1, 1, int(quiet), int(0))
finally:
_self.unlock(r, _self)
if r < 0.0:
r = DEFAULT_ERROR
elif not quiet:
st = 1
for a in r:
if a >= 0.0:
print " cmd.intra_rms: %5.3f in state %d vs state %d" % (
a, st, state)
st = st + 1
if _self._raising(r, _self): raise pymol.CmdException
return r
def intra_rms(selection, state=0, quiet=1, _self=cmd):
'''
DESCRIPTION
"intra_rms" calculates rms fit values for all states of an object
over an atom selection relative to the indicated state.
Coordinates are left unchanged. The rms values are returned as a
python array.
EXAMPLE
from pymol import cmd
rms = cmd.intra_rms("(name ca)",1)
print rms
PYMOL API
cmd.intra_rms(string selection, int state)
SEE ALSO
fit, rms, rms_cur, intra_fit, intra_rms_cur, pair_fit
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
state = int(state)
try:
_self.lock(_self)
r = _cmd.intrafit(_self._COb,"("+str(selection)+")",int(state)-1,1,int(quiet),int(0))
finally:
_self.unlock(r,_self)
if r<0.0:
r = DEFAULT_ERROR
elif not quiet:
st = 1
for a in r:
if a>=0.0:
print " cmd.intra_rms: %5.3f in state %d vs state %d"%(a,st,state)
st = st + 1
if _self._raising(r,_self): raise pymol.CmdException
return r
def intra_fit(selection, state=1, quiet=1, mix=0, _self=cmd):
'''
DESCRIPTION
"intra_fit" fits all states of an object to an atom selection
in the specified state. It returns the rms values to python
as an array.
USAGE
intra_fit selection [, state]
ARGUMENTS
selection = string: atoms to fit
state = integer: target state
PYMOL API
cmd.intra_fit( string selection, int state )
EXAMPLES
intra_fit ( name ca )
PYTHON EXAMPLE
from pymol import cmd
rms = cmd.intra_fit("(name ca)",1)
SEE ALSO
fit, rms, rms_cur, intra_rms, intra_rms_cur, pair_fit
'''
# preprocess selection
selection = selector.process(selection)
#
r = DEFAULT_ERROR
state = int(state)
mix = int(mix)
try:
_self.lock(_self)
r = _cmd.intrafit(_self._COb, "(" + str(selection) + ")",
int(state) - 1, 2, int(quiet), int(mix))
finally:
_self.unlock(r, _self)
if r < 0.0:
r = DEFAULT_ERROR
elif not quiet:
st = 1
for a in r:
if a >= 0.0:
if mix:
print " cmd.intra_fit: %5.3f in state %d vs mixed target" % (
a, st)
else:
print " cmd.intra_fit: %5.3f in state %d vs state %d" % (
a, st, state)
st = st + 1
if _self._raising(r, _self): raise pymol.CmdException
return r
