is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| mutagenesis.py (pymol-v1.8.6.0.tar.bz2) | : | mutagenesis.py (pymol-v2.1.0.tar.bz2) |
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| | |
| skipping to change at line 48 | | skipping to change at line 48 |
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| } | | } |
| | |
| class Mutagenesis(Wizard): | | class Mutagenesis(Wizard): |
| | |
| count = 0 | | count = 0 |
| cutoff = 3.5 | | cutoff = 3.5 |
| | |
| def __init__(self,_self=cmd): | | def __init__(self,_self=cmd): |
| Wizard.__init__(self,_self) | | Wizard.__init__(self,_self) |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| | |
| if self.cmd.get_movie_length() > 0: | | if self.cmd.get_movie_length() > 0: |
| raise pymol.wizarding.WizardError('Mutagenesis Wizard cannot be used
with Movie') | | raise pymol.wizarding.WizardError('Mutagenesis Wizard cannot be used
with Movie') |
| | |
| cmd.unpick() | | cmd.unpick() |
| | |
| self.stored = pymol.Scratch_Storage() | | self.stored = pymol.Scratch_Storage() |
| self.space = {'stored': self.stored} | | self.space = {'stored': self.stored} |
| | |
| self.bump_scores = [] | | self.bump_scores = [] |
| | |
| skipping to change at line 230 | | skipping to change at line 229 |
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| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def load_library(self): | | def load_library(self): |
| if self.dep == 'dep': | | if self.dep == 'dep': |
| if not hasattr(self,'dep_library'): | | if not hasattr(self,'dep_library'): |
| self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+ | | self.dep_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+ |
| "/chempy/sidechains/sc_bb_dep.pkl") | | "/chempy/sidechains/sc_bb_dep.pkl") |
| | |
| def set_mode(self,mode): | | def set_mode(self,mode): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if mode in self.modes: | | if mode in self.modes: |
| self.mode = mode | | self.mode = mode |
| if self.status==1: | | if self.status==1: |
| self.do_library() | | self.do_library() |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def set_rep(self,rep): | | def set_rep(self,rep): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if rep in self.reps: | | if rep in self.reps: |
| self.rep=rep | | self.rep=rep |
| cmd.hide("("+obj_name+")") | | cmd.hide("("+obj_name+")") |
| cmd.show('lines',obj_name) # always show lines | | cmd.show('lines',obj_name) # always show lines |
| cmd.show(self.rep,obj_name) | | cmd.show(self.rep,obj_name) |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def set_c_cap(self,c_cap): | | def set_c_cap(self,c_cap): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if c_cap in self.c_caps: | | if c_cap in self.c_caps: |
| self.c_cap=c_cap | | self.c_cap=c_cap |
| if self.status==1: | | if self.status==1: |
| self.do_library() | | self.do_library() |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def set_n_cap(self,n_cap): | | def set_n_cap(self,n_cap): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if n_cap in self.n_caps: | | if n_cap in self.n_caps: |
| self.n_cap=n_cap | | self.n_cap=n_cap |
| if self.status==1: | | if self.status==1: |
| self.do_library() | | self.do_library() |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def set_hyd(self,hyd): | | def set_hyd(self,hyd): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if hyd in self.hyds: | | if hyd in self.hyds: |
| self.hyd=hyd | | self.hyd=hyd |
| if self.status==1: | | if self.status==1: |
| self.do_library() | | self.do_library() |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def set_dep(self,value): | | def set_dep(self,value): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if value!=self.dep: | | if value!=self.dep: |
| self.dep = value | | self.dep = value |
| self.load_library() | | self.load_library() |
| if src_sele in cmd.get_names("all"): | | if src_sele in cmd.get_names("all"): |
| self.do_library() | | self.do_library() |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def get_panel(self): | | def get_panel(self): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if int(cmd.get("mouse_selection_mode")!=1): | | if int(cmd.get("mouse_selection_mode")!=1): |
| cmd.set("mouse_selection_mode",1) | | cmd.set("mouse_selection_mode",1) |
| if self.mode == 'current': | | if self.mode == 'current': |
| label = 'No Mutation' | | label = 'No Mutation' |
| else: | | else: |
| label = 'Mutate to '+self.mode_label[self.mode] | | label = 'Mutate to '+self.mode_label[self.mode] |
| return [ | | return [ |
| [ 1, 'Mutagenesis',''], | | [ 1, 'Mutagenesis',''], |
| [ 3, label,'mode'], | | [ 3, label,'mode'], |
| [ 3, 'N-Cap: '+self.n_cap_name[self.n_cap],'n_cap'], | | [ 3, 'N-Cap: '+self.n_cap_name[self.n_cap],'n_cap'], |
| | |
| skipping to change at line 311 | | skipping to change at line 303 |
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| [ 2, 'Apply' , 'cmd.get_wizard().apply()'], | | [ 2, 'Apply' , 'cmd.get_wizard().apply()'], |
| [ 2, 'Clear' , 'cmd.get_wizard().clear()'], | | [ 2, 'Clear' , 'cmd.get_wizard().clear()'], |
| [ 2, 'Done','cmd.set_wizard()'], | | [ 2, 'Done','cmd.set_wizard()'], |
| ] | | ] |
| | |
| def get_event_mask(self): | | def get_event_mask(self): |
| return Wizard.event_mask_pick + Wizard.event_mask_select + Wizard.event_
mask_state | | return Wizard.event_mask_pick + Wizard.event_mask_select + Wizard.event_
mask_state |
| | |
| def cleanup(self): | | def cleanup(self): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| global default_mode,default_rep,default_dep,default_hyd | | global default_mode,default_rep,default_dep,default_hyd |
| global default_n_cap, default_c_cap | | global default_n_cap, default_c_cap |
| default_mode = self.mode | | default_mode = self.mode |
| default_rep = self.rep | | default_rep = self.rep |
| default_dep = self.dep | | default_dep = self.dep |
| default_hyd = self.hyd | | default_hyd = self.hyd |
| default_n_cap = self.n_cap | | default_n_cap = self.n_cap |
| default_c_cap = self.c_cap | | default_c_cap = self.c_cap |
| cmd.set("mouse_selection_mode",self.selection_mode) # restore selection
mode | | cmd.set("mouse_selection_mode",self.selection_mode) # restore selection
mode |
| self.clear() | | self.clear() |
| | |
| def clear(self): | | def clear(self): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| self.status=0 | | self.status=0 |
| self.bump_scores = [] | | self.bump_scores = [] |
| cmd.delete(tmp_obj2) | | cmd.delete(tmp_obj2) |
| cmd.delete(mut_sele) | | cmd.delete(mut_sele) |
| cmd.delete(src_sele) | | cmd.delete(src_sele) |
| cmd.delete(obj_name) | | cmd.delete(obj_name) |
| cmd.delete(bump_name) | | cmd.delete(bump_name) |
| cmd.delete("_seeker_hilight") | | cmd.delete("_seeker_hilight") |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| | |
| def apply(self): | | def apply(self): |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if self.status==1: | | if self.status==1: |
| # find the name of the object which contains the selection | | # find the name of the object which contains the selection |
| src_frame = cmd.get_state() | | src_frame = cmd.get_state() |
| try: | | try: |
| new_name = cmd.get_object_list(src_sele)[0] | | new_name = cmd.get_object_list(src_sele)[0] |
| except IndexError: | | except IndexError: |
| print(" Mutagenesis: object not found.") | | print(" Mutagenesis: object not found.") |
| return | | return |
| | |
| if True: | | if True: |
| | |
| skipping to change at line 476 | | skipping to change at line 465 |
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| # use N-terminal fragment | | # use N-terminal fragment |
| frag_type ="NT_"+frag_type | | frag_type ="NT_"+frag_type |
| if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'): | | if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'): |
| if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))
) & !resn NME+NHH"% | | if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))
) & !resn NME+NHH"% |
| (src_sele,src_sele))): | | (src_sele,src_sele))): |
| # use C-terminal fragment | | # use C-terminal fragment |
| frag_type ="CT_"+frag_type | | frag_type ="CT_"+frag_type |
| if rot_type[0:3] in [ 'NT_', 'CT_' ]: | | if rot_type[0:3] in [ 'NT_', 'CT_' ]: |
| rot_type = rot_type[3:] | | rot_type = rot_type[3:] |
| rot_type = _rot_type_xref.get(rot_type, rot_type) | | rot_type = _rot_type_xref.get(rot_type, rot_type) |
|
| cmd.fragment(frag_type.lower(), frag_name) | | cmd.fragment(frag_type.lower(), frag_name, origin=0) |
| # trim off hydrogens | | # trim off hydrogens |
| if (self.hyd == 'none'): | | if (self.hyd == 'none'): |
| cmd.remove("("+frag_name+" and hydro)") | | cmd.remove("("+frag_name+" and hydro)") |
| elif (self.hyd == 'auto'): | | elif (self.hyd == 'auto'): |
| if cmd.count_atoms("("+src_sele+") and hydro")==0: | | if cmd.count_atoms("("+src_sele+") and hydro")==0: |
| cmd.remove("("+frag_name+" and hydro)") | | cmd.remove("("+frag_name+" and hydro)") |
| # copy identifying information | | # copy identifying information |
| cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, c
hain, resi, ss, color)", space=self.space) | | cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, c
hain, resi, ss, color)", space=self.space) |
| cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.ident
ifiers[:4]", space=self.space) | | cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.ident
ifiers[:4]", space=self.space) |
| # move the fragment | | # move the fragment |
| | |
| skipping to change at line 694 | | skipping to change at line 683 |
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| if (bump_name in names) and (obj_name in names): | | if (bump_name in names) and (obj_name in names): |
| cmd.update(bump_name,obj_name) | | cmd.update(bump_name,obj_name) |
| if self.bump_scores: | | if self.bump_scores: |
| state = cmd.get_state() | | state = cmd.get_state() |
| print(' Rotamer %d/%d, strain=%.2f' % (state, | | print(' Rotamer %d/%d, strain=%.2f' % (state, |
| cmd.count_states(obj_name), self.bump_scores[state - 1])) | | cmd.count_states(obj_name), self.bump_scores[state - 1])) |
| | |
| def do_select(self,selection): | | def do_select(self,selection): |
| print("Selected!") | | print("Selected!") |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if (obj_name in cmd.get_names()): | | if (obj_name in cmd.get_names()): |
| if cmd.count_atoms("(%s) and (%s)"%(obj_name,selection)): | | if cmd.count_atoms("(%s) and (%s)"%(obj_name,selection)): |
| cmd.deselect() | | cmd.deselect() |
| return 1 | | return 1 |
| if self.status!=0: | | if self.status!=0: |
| cmd.delete(obj_name) | | cmd.delete(obj_name) |
| cmd.select(src_sele,selection) | | cmd.select(src_sele,selection) |
| cmd.unpick() | | cmd.unpick() |
| cmd.enable(src_sele) | | cmd.enable(src_sele) |
| self.status = 1 | | self.status = 1 |
| self.error = None | | self.error = None |
| self.do_library() | | self.do_library() |
| cmd.delete(selection) | | cmd.delete(selection) |
| cmd.refresh_wizard() | | cmd.refresh_wizard() |
| cmd.deselect() | | cmd.deselect() |
| return 1 | | return 1 |
| | |
| def do_pick(self,bondFlag): | | def do_pick(self,bondFlag): |
| print("Picked!") | | print("Picked!") |
| cmd=self.cmd | | cmd=self.cmd |
|
| pymol=cmd._pymol | | |
| if bondFlag: | | if bondFlag: |
| self.error = "Error: please select an atom, not a bond." | | self.error = "Error: please select an atom, not a bond." |
| print(self.error) | | print(self.error) |
| else: | | else: |
| if self.status!=0: | | if self.status!=0: |
| cmd.delete(obj_name) | | cmd.delete(obj_name) |
| cmd.select(src_sele,"(byres pk1)") | | cmd.select(src_sele,"(byres pk1)") |
| cmd.unpick() | | cmd.unpick() |
| cmd.enable(src_sele) | | cmd.enable(src_sele) |
| self.status = 1 | | self.status = 1 |
| | | |
| End of changes. 14 change blocks. |
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| 14 lines changed or deleted | | 1 lines changed or added |
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