def do_state(self,state): cmd=self.cmd if cmd.get("sculpting")=="on": names = cmd.get_names("all_objects") if (bump_name in names) and (obj_name in names): cmd.update(bump_name,obj_name) if self.bump_scores: state = cmd.get_state() print(' Rotamer %d/%d, strain=%.2f' % (state, cmd.count_states(obj_name), self.bump_scores[state - 1]))
def do_state(self,state): cmd=self.cmd if cmd.get("sculpting")=="on": names = cmd.get_names("all_objects") if (bump_name in names) and (obj_name in names): cmd.update(bump_name,obj_name) if self.bump_scores: print(' Rotamer %d/%d, strain=%.2f' % (state, cmd.count_states(obj_name), self.bump_scores[state - 1])) # update hbonds (polar contacts) cmd.delete(tmp_hbonds) cmd.distance(tmp_hbonds, "?{}".format(obj_name), "(byobj ?{}) and not ?{}".format(src_sele, src_sele), mode=2, state1=state, state2=1)
def join_states(name, selection='all', discrete=-1, zoom=0, quiet=1): ''' DESCRIPTION The reverse of split_states ARGUMENTS name = string: name of object to create or modify selection = string: atoms to include in the new object discrete = -2: match atoms by sequence alignment discrete = -1: Assume identical input objects (matching all atom identifiers) but also check for missing atoms and only include atoms that are present in all input objects {default} discrete = 0: Assume identical input objects discrete = 1: Input object may be (totally) different ''' discrete, quiet = int(discrete), int(quiet) if discrete == -2: _assert_package_import() from .selecting import wait_for aln_obj = cmd.get_unused_name('_') models = cmd.get_object_list('(' + selection + ')') for i in range(len(models)): if discrete == -1 and i > 0: cmd.remove('(%s) and not (alt A+ and (%s) in (%s))' % (name, name, models[i])) cmd.create(name, '(%s) in (%s)' % (models[i], name), 1, i + 1, 0, 0, quiet) elif discrete == -2 and i > 0: cmd.align(models[i], name, cycles=0, transform=0, object=aln_obj) wait_for(aln_obj) cmd.remove('(%s) and not (%s)' % (name, aln_obj)) cmd.create(name, name, 1, i + 1, 0, 0, quiet) cmd.update(name, '(%s) and (%s)' % (models[i], aln_obj), i + 1, 1, 0, quiet) cmd.delete(aln_obj) else: cmd.create(name, models[i], 1, i + 1, discrete == 1, 0, quiet) if int(zoom): cmd.zoom(name, state=0)
def join_states(name, selection="all", discrete=-1, zoom=0, quiet=1): """ DESCRIPTION The reverse of split_states ARGUMENTS name = string: name of object to create or modify selection = string: atoms to include in the new object discrete = -2: match atoms by sequence alignment discrete = -1: Assume identical input objects (matching all atom identifiers) but also check for missing atoms and only include atoms that are present in all input objects {default} discrete = 0: Assume identical input objects discrete = 1: Input object may be (totally) different """ discrete, quiet = int(discrete), int(quiet) if discrete == -2: from .selecting import wait_for aln_obj = cmd.get_unused_name("_") models = cmd.get_object_list("(" + selection + ")") for i in range(len(models)): if discrete == -1 and i > 0: cmd.remove("(%s) and not (alt A+ and (%s) in (%s))" % (name, name, models[i])) cmd.create(name, "(%s) in (%s)" % (models[i], name), 1, i + 1, 0, 0, quiet) elif discrete == -2 and i > 0: cmd.align(models[i], name, cycles=0, transform=0, object=aln_obj) wait_for(aln_obj) cmd.remove("(%s) and not (%s)" % (name, aln_obj)) cmd.create(name, name, 1, i + 1, 0, 0, quiet) cmd.update(name, "(%s) and (%s)" % (models[i], aln_obj), i + 1, 1, 0, quiet) cmd.delete(aln_obj) else: cmd.create(name, models[i], 1, i + 1, discrete == 1, 0, quiet) if int(zoom): cmd.zoom(name, state=0)
def test_update(self): # 3 states cmd.fragment('gly', 'm1') cmd.create('m1', 'm1', 1, 2) cmd.create('m1', 'm1', 1, 3) # second object, 90 degree rotates cmd.copy('m2', 'm1') cmd.rotate('x', 90, '(m2)', state=0) # reference coordsets cs = cmd.get_coordset cs1 = cs('m1', 1) cs2 = cs('m2', 1) # m2/3 will change (pre-check) self.assertArrayEqual(cs2, cs('m2', 3)) self.assertArrayNotEqual(cs1, cs('m2', 3)) # update explicit state cmd.update('m2', 'm1', 3, 2) # m2/3 has changed self.assertArrayEqual(cs1, cs('m2', 3)) self.assertArrayNotEqual(cs2, cs('m2', 3)) # these haven't changed self.assertArrayEqual(cs2, cs('m2', 1)) self.assertArrayEqual(cs2, cs('m2', 2)) # reset m2/3 cmd.load_coordset(cs2, 'm2', 3) self.assertArrayEqual(cs2, cs('m2', 3)) # update all states cmd.update('m2', 'm1', 0, 0) self.assertArrayEqual(cs1, cs('m2', 1)) self.assertArrayEqual(cs1, cs('m2', 2)) self.assertArrayEqual(cs1, cs('m2', 3))
def do_state(self, state): cmd = self.cmd if cmd.get("sculpting") == "on": names = cmd.get_names("all_objects") if (bump_name in names) and (obj_name in names): cmd.update(bump_name, obj_name)
def apply(self): cmd = self.cmd pymol = cmd._pymol if self.status == 1: # find the name of the object which contains the selection new_name = None obj_list = cmd.get_names("objects") for a in obj_list: if cmd.get_type(a) == "object:molecule": if cmd.count_atoms("(%s and %s)" % (a, src_sele)): new_name = a break src_frame = cmd.get_state() if new_name == None: print " Mutagenesis: object not found." else: auto_zoom = cmd.get_setting_text("auto_zoom") cmd.set("auto_zoom", "0", quiet=1) if self.lib_mode != "current": # create copy w/o residue cmd.create(tmp_obj1, "(%s and not %s)" % (new_name, src_sele)) # remove existing c-cap in copy (if any) cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)" % (tmp_obj1, src_sele)) # remove existing n-cap in copy (if any) cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)" % (tmp_obj1, src_sele)) # save copy for bonded atom reference cmd.create(tmp_obj3, new_name) # transfer the selection to copy cmd.select(src_sele, "(%s in %s)" % (tmp_obj3, src_sele)) # create copy with mutant in correct frame cmd.create(tmp_obj2, obj_name, src_frame, 1) cmd.set_title(tmp_obj2, 1, "") cmd.delete(new_name) # create the merged molecule cmd.create(new_name, "(%s or %s)" % (tmp_obj1, tmp_obj2), 1) # only one state in merged object... # now connect them cmd.select(mut_sele, "(byres (%s like %s))" % (new_name, src_sele)) # bond N+0 to C-1 if (cmd.select(tmp_sele1, "(name C and (%s in (neighbor %s)))" % (new_name, src_sele)) == 1) and ( cmd.select(tmp_sele2, "((%s in %s) and n;N)" % (mut_sele, tmp_obj2)) == 1 ): cmd.bond(tmp_sele1, tmp_sele2) cmd.set_geometry(tmp_sele1, 3, 3) # make amide planer cmd.set_geometry(tmp_sele2, 3, 3) # make amide planer # bond C+0 to N+1 if (cmd.select(tmp_sele1, "(name N and (%s in (neighbor %s)))" % (new_name, src_sele)) == 1) and ( cmd.select(tmp_sele2, "((%s in %s) and n;C)" % (mut_sele, tmp_obj2)) == 1 ): cmd.bond(tmp_sele1, tmp_sele2) cmd.set_geometry(tmp_sele1, 3, 3) # make amide planer cmd.set_geometry(tmp_sele2, 3, 3) # make amide planer cmd.delete(tmp_sele1) cmd.delete(tmp_sele2) # fix N-H hydrogen position (if any exists) cmd.h_fix("(name N and bound_to (%s in %s and n;H))" % (new_name, tmp_obj2)) # now transfer selection back to the modified object cmd.delete(tmp_obj1) cmd.delete(tmp_obj2) cmd.delete(tmp_obj3) self.clear() # and return to frame 1 cmd.frame(1) cmd.refresh_wizard() else: # create copy with conformation in correct state cmd.create(tmp_obj2, obj_name, src_frame, 1) # remove existing c-cap in copy (if any) cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)" % (new_name, src_sele)) cmd.remove("(%s) and name OXT" % src_sele) # remove existing n-cap in copy (if any) cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)" % (new_name, src_sele)) # save existing conformation on undo stack # cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele)) cmd.push_undo("(" + src_sele + ")") # modify the conformation cmd.update(new_name, tmp_obj2) # cmd.unpick() cmd.delete(tmp_obj2) self.clear() # and return to frame 1 cmd.frame(1) cmd.refresh_wizard() cmd.set("auto_zoom", auto_zoom, quiet=1)
def apply(self): cmd=self.cmd if self.status==1: # find the name of the object which contains the selection src_frame = cmd.get_state() try: new_name = cmd.get_object_list(src_sele)[0] except IndexError: print(" Mutagenesis: object not found.") return if True: auto_zoom = cmd.get_setting_text('auto_zoom') cmd.set('auto_zoom',"0",quiet=1) if self.lib_mode!="current": # create copy with mutant in correct frame state = cmd.get_object_state(new_name) cmd.create(tmp_obj2, obj_name, src_frame, state) cmd.set_title(tmp_obj2, state, '') cmd.color(self.stored.identifiers[4], "?%s & elem C" % tmp_obj2) cmd.alter(tmp_obj2, 'ID = -1') # select backbone connection atoms cmd.select(tmp_sele1, 'neighbor ?%s' % (src_sele), 0) # remove residue and neighboring c-cap/n-cap (if any) cmd.remove("?%s | byres (?%s & " "(name N & resn NME+NHH | name C & resn ACE))" % (src_sele, tmp_sele1)) # create the merged molecule cmd.create(new_name, "?%s | ?%s" % (new_name, tmp_obj2), state, state) # now connect them cmd.select(tmp_sele2, '/%s/%s/%s/%s' % ((new_name,) + self.stored.identifiers[:3])) cmd.bond('?%s & name C' % (tmp_sele1), '?%s & name N' % (tmp_sele2), quiet=1) cmd.bond('?%s & name N' % (tmp_sele1), '?%s & name C' % (tmp_sele2), quiet=1) cmd.set_geometry('(?%s | ?%s) & name C+N' % (tmp_sele1, tmp_sele2), 3, 3) # make amide planer # fix N-H hydrogen position (if any exists) cmd.h_fix('?%s & name N' % (tmp_sele2)) # delete temporary objects/selections cmd.delete(tmp_sele1) cmd.delete(tmp_sele2) cmd.delete(tmp_obj2) self.clear() # and return to frame 1 cmd.frame(1) cmd.refresh_wizard() else: # create copy with conformation in correct state cmd.create(tmp_obj2,obj_name,src_frame,1) # remove existing c-cap in copy (if any) cmd.remove("byres (name N and (%s in (neighbor %s)) and resn NME+NHH)"% (new_name,src_sele)) cmd.remove("(%s) and name OXT"%src_sele) # remove existing n-cap in copy (if any) cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ACE)"% (new_name,src_sele)) # save existing conformation on undo stack # cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele)) cmd.push_undo("("+src_sele+")") # modify the conformation cmd.update(new_name,tmp_obj2) # cmd.unpick() cmd.delete(tmp_obj2) self.clear() # and return to frame 1 cmd.frame(1) cmd.refresh_wizard() cmd.set('auto_zoom',auto_zoom,quiet=1)
def peptide_rebuild(name, selection='all', cycles=1000, state=1, quiet=1): ''' DESCRIPTION Rebuild the peptide from selection. All atoms which are present in selection will be kept fixed, while atoms missing in selection are placed by sculpting. USAGE peptide_rebuild name [, selection [, cycles [, state ]]] SEE ALSO stub2ala, add_missing_atoms, peptide_rebuild_modeller ''' from chempy import fragments, feedback, models cycles, state, quiet = int(cycles), int(state), int(quiet) # suppress feedback for model merging feedback['actions'] = False # work with named selection namedsele = cmd.get_unused_name('_') cmd.select(namedsele, selection, 0) identifiers = [] cmd.iterate(namedsele + ' and polymer and guide and alt +A', 'identifiers.append([segi,chain,resi,resv,resn])', space=locals()) model = models.Indexed() for (segi,chain,resi,resv,resn) in identifiers: try: fname = resn.lower() if resn != 'MSE' else 'met' frag = fragments.get(fname) except IOError: print(' Warning: unknown residue: ' + resn) continue for a in frag.atom: a.segi = segi a.chain = chain a.resi = resi a.resi_number = resv a.resn = resn model.merge(frag) if not quiet: print(' Loading model...') cmd.load_model(model, name, 1, zoom=0) if cmd.get_setting_boolean('auto_remove_hydrogens'): cmd.remove(name + ' and hydro') cmd.protect(name + ' in ' + namedsele) cmd.sculpt_activate(name) cmd.update(name, namedsele, 1, state) cmd.delete(namedsele) if not quiet: print(' Sculpting...') cmd.set('sculpt_field_mask', 0x003, name) # bonds and angles only cmd.sculpt_iterate(name, 1, int(cycles / 4)) cmd.set('sculpt_field_mask', 0x09F, name) # local + torsions cmd.sculpt_iterate(name, 1, int(cycles / 4)) cmd.set('sculpt_field_mask', 0x0FF, name) # ... + vdw cmd.sculpt_iterate(name, 1, int(cycles / 2)) cmd.sculpt_deactivate(name) cmd.deprotect(name) cmd.unset('sculpt_field_mask', name) if not quiet: print(' Connecting peptide...') pairs = cmd.find_pairs(name + ' and name C', name + ' and name N', 1, 1, 2.0) for pair in pairs: cmd.bond(*pair) cmd.h_fix(name) if not quiet: print(' peptide_rebuild: done')
def peptide_rebuild(name, selection='all', cycles=1000, state=1, quiet=1): ''' DESCRIPTION Rebuild the peptide from selection. All atoms which are present in selection will be kept fixed, while atoms missing in selection are placed by sculpting. USAGE peptide_rebuild name [, selection [, cycles [, state ]]] SEE ALSO stub2ala, add_missing_atoms, peptide_rebuild_modeller ''' from chempy import fragments, feedback, models cycles, state, quiet = int(cycles), int(state), int(quiet) # suppress feedback for model merging feedback['actions'] = False # work with named selection namedsele = cmd.get_unused_name('_') cmd.select(namedsele, selection, 0) identifiers = [] cmd.iterate(namedsele + ' and polymer and guide and alt +A', 'identifiers.append([segi,chain,resi,resv,resn])', space=locals()) model = models.Indexed() for (segi,chain,resi,resv,resn) in identifiers: try: fname = resn.lower() if resn != 'MSE' else 'met' frag = fragments.get(fname) except IOError: print(' Warning: unknown residue:', resn) continue for a in frag.atom: a.segi = segi a.chain = chain a.resi = resi a.resi_number = resv a.resn = resn model.merge(frag) if not quiet: print(' Loading model...') cmd.load_model(model, name, 1, zoom=0) if cmd.get_setting_boolean('auto_remove_hydrogens'): cmd.remove(name + ' and hydro') cmd.protect(name + ' in ' + namedsele) cmd.sculpt_activate(name) cmd.update(name, namedsele, 1, state) cmd.delete(namedsele) if not quiet: print(' Sculpting...') cmd.set('sculpt_field_mask', 0x003, name) # bonds and angles only cmd.sculpt_iterate(name, 1, int(cycles / 4)) cmd.set('sculpt_field_mask', 0x09F, name) # local + torsions cmd.sculpt_iterate(name, 1, int(cycles / 4)) cmd.set('sculpt_field_mask', 0x0FF, name) # ... + vdw cmd.sculpt_iterate(name, 1, int(cycles / 2)) cmd.sculpt_deactivate(name) cmd.deprotect(name) cmd.unset('sculpt_field_mask', name) if not quiet: print(' Connecting peptide...') pairs = cmd.find_pairs(name + ' and name C', name + ' and name N', 1, 1, 2.0) for pair in pairs: cmd.bond(*pair) cmd.h_fix(name) if not quiet: print(' peptide_rebuild: done')
def do_state(self,state): cmd=self.cmd if cmd.get("sculpting")=="on": names = cmd.get_names("all_objects") if (bump_name in names) and (obj_name in names): cmd.update(bump_name,obj_name)
def apply(self): cmd=self.cmd pymol=cmd._pymol if self.status==1: # find the name of the object which contains the selection new_name = None obj_list = cmd.get_names('objects') for a in obj_list: if cmd.get_type(a)=="object:molecule": if cmd.count_atoms("(%s and %s)"%(a,src_sele)): new_name = a break src_frame = cmd.get_state() if new_name==None: print " Mutagenesis: object not found." else: auto_zoom = cmd.get_setting_text('auto_zoom') cmd.set('auto_zoom',"0",quiet=1) if self.lib_mode!="current": # create copy w/o residue cmd.create(tmp_obj1,"(%s and not %s)"%(new_name,src_sele)) # remove existing c-cap in copy (if any) cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)"% (tmp_obj1,src_sele)) # remove existing n-cap in copy (if any) cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)"% (tmp_obj1,src_sele)) # save copy for bonded atom reference cmd.create(tmp_obj3,new_name) # transfer the selection to copy cmd.select(src_sele,"(%s in %s)"%(tmp_obj3,src_sele)) # create copy with mutant in correct frame cmd.create(tmp_obj2,obj_name,src_frame,1) cmd.set_title(tmp_obj2,1,'') cmd.delete(new_name) # create the merged molecule cmd.create(new_name,"(%s or %s)"%(tmp_obj1,tmp_obj2),1) # only one state in merged object... # now connect them cmd.select(mut_sele,"(byres (%s like %s))"%(new_name,src_sele)) # bond N+0 to C-1 if ((cmd.select(tmp_sele1, "(name C and (%s in (neighbor %s)))"% (new_name,src_sele)) == 1) and (cmd.select(tmp_sele2, "((%s in %s) and n;N)"% (mut_sele,tmp_obj2)) == 1)): cmd.bond(tmp_sele1,tmp_sele2) cmd.set_geometry(tmp_sele1,3,3) # make amide planer cmd.set_geometry(tmp_sele2,3,3) # make amide planer # bond C+0 to N+1 if ((cmd.select(tmp_sele1, "(name N and (%s in (neighbor %s)))"% (new_name,src_sele)) == 1) and (cmd.select(tmp_sele2,"((%s in %s) and n;C)"% (mut_sele,tmp_obj2)) == 1)): cmd.bond(tmp_sele1,tmp_sele2) cmd.set_geometry(tmp_sele1,3,3) # make amide planer cmd.set_geometry(tmp_sele2,3,3) # make amide planer cmd.delete(tmp_sele1) cmd.delete(tmp_sele2) # fix N-H hydrogen position (if any exists) cmd.h_fix("(name N and bound_to (%s in %s and n;H))"%(new_name,tmp_obj2)) # now transfer selection back to the modified object cmd.delete(tmp_obj1) cmd.delete(tmp_obj2) cmd.delete(tmp_obj3) self.clear() # and return to frame 1 cmd.frame(1) cmd.refresh_wizard() else: # create copy with conformation in correct state cmd.create(tmp_obj2,obj_name,src_frame,1) # remove existing c-cap in copy (if any) cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)"% (new_name,src_sele)) cmd.remove("(%s) and name OXT"%src_sele) # remove existing n-cap in copy (if any) cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)"% (new_name,src_sele)) # save existing conformation on undo stack # cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele)) cmd.push_undo("("+src_sele+")") # modify the conformation cmd.update(new_name,tmp_obj2) # cmd.unpick() cmd.delete(tmp_obj2) self.clear() # and return to frame 1 cmd.frame(1) cmd.refresh_wizard() cmd.set('auto_zoom',auto_zoom,quiet=1)
# This script gets a copy of the coordinates in Python, # rotates the object about the Z axis, and then # updates the coordinates in the original object. from pymol import cmd model = cmd.get_model("pept") for a in model.atom: a.coord=[ -a.coord[1], a.coord[0], a.coord[2]] cmd.load_model(model,"tmp") cmd.update("pept","tmp") cmd.delete("tmp")