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