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