def find_pairs(selection1, selection2, state1=1, state2=1, cutoff=3.5, mode=0, angle=45, _self=cmd): ''' DESCRIPTION "find_pairs" is currently undocumented. ''' # preprocess selection selection1 = selector.process(selection1) selection2 = selector.process(selection2) # r = DEFAULT_ERROR try: _self.lock(_self) r = _cmd.find_pairs(_self._COb, "(" + str(selection1) + ")", "(" + str(selection2) + ")", int(state1) - 1, int(state2) - 1, int(mode), float(cutoff), float(angle)) # 0 = default mode finally: _self.unlock(r, _self) if _raising(r, _self): raise pymol.CmdException return r
def find_pairs(selection1, selection2, state1=1, state2=1, cutoff=3.5, mode=0, angle=45, _self=cmd): ''' DESCRIPTION API only function. Returns a list of atom pairs. Atoms are represented as (model,index) tuples. Can be restricted to hydrogen-bonding-like contacts. WARNING: Only checks atom orientation, not atom type (so would hydrogen bond between carbons for example), so make sure to provide appropriate atom selections. ARGUMENTS selection1, selection2 = string: atom selections state1, state2 = integer: state-index (only positive values allowed) {default: 1} cutoff = float: distance cutoff {default: 3.5} mode = integer: if mode=1, do coarse hydrogen bonding assessment {default: 0} angle = float: hydrogen bond angle cutoff, only if mode=1 {default: 45.0} NOTE Although this does a similar job like "distance", it uses a completely different routine and the "mode" argument has different meanings! ''' # preprocess selection selection1 = selector.process(selection1) selection2 = selector.process(selection2) # r = DEFAULT_ERROR try: _self.lock(_self) r = _cmd.find_pairs(_self._COb, "(" + str(selection1) + ")", "(" + str(selection2) + ")", int(state1) - 1, int(state2) - 1, int(mode), float(cutoff), float(angle)) # 0 = default mode finally: _self.unlock(r, _self) if _raising(r, _self): raise pymol.CmdException return r
def find_pairs(selection1,selection2,state1=1,state2=1,cutoff=3.5,mode=0,angle=45,_self=cmd): ''' DESCRIPTION API only function. Returns a list of atom pairs. Atoms are represented as (model,index) tuples. Can be restricted to hydrogen-bonding-like contacts. WARNING: Only checks atom orientation, not atom type (so would hydrogen bond between carbons for example), so make sure to provide appropriate atom selections. ARGUMENTS selection1, selection2 = string: atom selections state1, state2 = integer: state-index (only positive values allowed) {default: 1} cutoff = float: distance cutoff {default: 3.5} mode = integer: if mode=1, do coarse hydrogen bonding assessment {default: 0} angle = float: hydrogen bond angle cutoff, only if mode=1 {default: 45.0} NOTE Although this does a similar job like "distance", it uses a completely different routine and the "mode" argument has different meanings! ''' # preprocess selection selection1 = selector.process(selection1) selection2 = selector.process(selection2) # r = DEFAULT_ERROR try: _self.lock(_self) r = _cmd.find_pairs(_self._COb,"("+str(selection1)+")", "("+str(selection2)+")", int(state1)-1,int(state2)-1, int(mode),float(cutoff),float(angle)) # 0 = default mode finally: _self.unlock(r,_self) if _raising(r,_self): raise pymol.CmdException return r
def find_pairs(selection1,selection2,state1=1,state2=1,cutoff=3.5,mode=0,angle=45,_self=cmd): ''' DESCRIPTION "find_pairs" is currently undocumented. ''' # preprocess selection selection1 = selector.process(selection1) selection2 = selector.process(selection2) # r = DEFAULT_ERROR try: _self.lock(_self) r = _cmd.find_pairs(_self._COb,"("+str(selection1)+")", "("+str(selection2)+")", int(state1)-1,int(state2)-1, int(mode),float(cutoff),float(angle)) # 0 = default mode finally: _self.unlock(r,_self) if _raising(r,_self): raise pymol.CmdException return r