def _prepare(selection, polar_contacts=None, _self=cmd): cmd = _self # this function should undo everything that is done by any preset function in this module # (except for coloring) s = tmp_sele cmd.select(s, selection) cmd.cartoon("auto", s) cmd.hide("everything", s) cmd.set("two_sided_lighting", 0) # global cmd.unset("transparency", s) cmd.unset("dot_normals", s) cmd.unset("mesh_normals", s) cmd.unset("surface_quality", s) cmd.unset("surface_type", selection) cmd.unset("sphere_scale", selection) cmd.unset_bond("stick_radius", s, s) cmd.unset_bond("stick_color", s, s) cmd.unset("cartoon_highlight_color", selection) cmd.unset("cartoon_fancy_helices", selection) cmd.unset("cartoon_smooth_loops", selection) cmd.unset("cartoon_flat_sheets", selection) cmd.unset("cartoon_side_chain_helper", selection) cmd.unset("mesh_normals", s) cmd.unset("dot_normals", s) if polar_contacts == None: polar_contacts = _get_polar_contacts_name(s, _self) if polar_contacts in cmd.get_names('objects'): cmd.delete(polar_contacts)
def _prepare(selection,polar_contacts=None,_self=cmd): cmd=_self # this function should undo everything that is done by any preset function in this module # (except for coloring) s = tmp_sele cmd.select(s,selection) cmd.cartoon("auto",s) cmd.hide("everything",s) cmd.set("two_sided_lighting",0) # global cmd.unset("transparency",s) cmd.unset("dot_normals",s) cmd.unset("mesh_normals",s) cmd.unset("surface_quality",s) cmd.unset("surface_type",selection) cmd.unset("sphere_scale",selection) cmd.unset_bond("stick_radius",s,s) cmd.unset_bond("stick_color",s,s) cmd.unset("cartoon_highlight_color",selection) cmd.unset("cartoon_fancy_helices",selection) cmd.unset("cartoon_smooth_loops",selection) cmd.unset("cartoon_flat_sheets",selection) cmd.unset("cartoon_side_chain_helper",selection) cmd.unset("mesh_normals",s) cmd.unset("dot_normals",s) if polar_contacts == None: polar_contacts = _get_polar_contacts_name(s,_self) if polar_contacts in cmd.get_names('objects'): cmd.delete(polar_contacts)
def pretty_solv(selection="(all)", _self=cmd): cmd = _self s = tmp_sele cmd.select(s, selection) polar_contacts = _get_polar_contacts_name(s, _self) _prepare(s, polar_contacts, _self=cmd) cmd.dss(s, preserve=1) cmd.cartoon("auto", s) cmd.show("cartoon", s) cmd.show("sticks", "(" + lig_sele + " and (" + s + "))") cmd.show("nb_spheres", "((" + lig_sele + "|resn hoh+wat+h2o) and (" + s + "))") util.cbc("(" + lig_sele + " and (" + s + "))", _self=cmd) util.cbac("(" + lig_sele + " and (" + s + ") and not elem c)", _self=cmd) cmd.spectrum("count", selection="(elem c and (" + s + ") and not " + lig_sele + ")") cmd.set("cartoon_highlight_color", -1, selection) cmd.set("cartoon_fancy_helices", 0, selection) cmd.set("cartoon_smooth_loops", 0, selection) cmd.set("cartoon_flat_sheets", 1, selection) cmd.set("cartoon_side_chain_helper", 0, selection) if polar_contacts in cmd.get_names(): cmd.disable(polar_contacts) if cmd.count_atoms(s): cmd.zoom(s)
def b_factor_putty(selection="(name ca or name p)",_self=cmd): cmd=_self s = tmp_sele cmd.select(s,selection) _prepare(s,_self=cmd) cmd.select(s,"(name ca or name p) and ("+selection+")") cmd.show("cartoon",s) cmd.set("cartoon_flat_sheets",0,selection) cmd.cartoon("putty",s) cmd.spectrum("b",selection=s)
def b_factor_putty(selection="(name ca or name p)", _self=cmd): cmd = _self s = tmp_sele cmd.select(s, selection) _prepare(s, _self=cmd) cmd.select(s, "(name ca or name p) and (" + selection + ")") cmd.show("cartoon", s) cmd.set("cartoon_flat_sheets", 0, selection) cmd.cartoon("putty", s) cmd.spectrum("b", selection=s)
def pretty_solv(selection="(all)",_self=cmd): cmd=_self s = tmp_sele cmd.select(s,selection) polar_contacts = _get_polar_contacts_name(s,_self) _prepare(s,polar_contacts,_self=cmd) cmd.dss(s,preserve=1) cmd.cartoon("auto",s) cmd.show("cartoon",s) cmd.show("sticks","("+lig_sele+" and ("+s+"))") cmd.show("nb_spheres","(("+lig_sele+"|resn hoh+wat+h2o) and ("+s+"))") util.cbc("("+lig_sele+" and ("+s+"))",_self=cmd) util.cbac("("+lig_sele+" and ("+s+") and not elem c)",_self=cmd) cmd.spectrum("count",selection="(elem c and ("+s+") and not "+lig_sele+")") cmd.set("cartoon_highlight_color",-1,selection) cmd.set("cartoon_fancy_helices",0,selection) cmd.set("cartoon_smooth_loops",0,selection) cmd.set("cartoon_flat_sheets",1,selection) cmd.set("cartoon_side_chain_helper",0,selection) if polar_contacts in cmd.get_names(): cmd.disable(polar_contacts) if cmd.count_atoms(s): cmd.zoom(s)
def ss(selection="(name ca and alt '',A)",state=1,_self=cmd): pymol=_self._pymol cmd=_self # NOT THREAD SAFE print ' util.ss: WARNING: This is not a "correct" secondary structure' print ' util.ss: assignment algorithm! Please use only as a last resort.' cmd.feedback("push") cmd.feedback("disable","executive","actions") ss_pref = "_sss" sss1 = ss_pref+"1" cnt = cmd.select(sss1,"((byres ("+selection+")) and name ca and not het)") print " util.ss: initiating secondary structure assignment on %d residues."%cnt cas = cmd.index(sss1) if not len(cas): return # set cartoon mode to auto over the selection cmd.cartoon("auto",sss1) print " util.ss: extracting sequence and relationships..." # get CA list res_list = [] pymol._ss = pymol.Scratch_Storage() pymol._ss.res_list = res_list cmd.iterate(sss1,'_ss.res_list.append((model,index))') # generate atom-to-residue conversion dictionaries ca_dict = {} n_dict = {} o_dict = {} scr_dict = {} # scr = segment,chain,resi pymol._ss.n_dict = n_dict pymol._ss.o_dict = o_dict pymol._ss.scr_dict = scr_dict pymol._ss.ca_dict = ca_dict cmd.iterate(sss1, '_ss.scr_dict[(model,index)]=(segi,chain,resi)') # CA's cmd.iterate("((byres "+sss1+") and n;n)" ,'_ss.scr_dict[(model,index)]=(segi,chain,resi)') # N's cmd.iterate("((byres "+sss1+") and n;o)", '_ss.scr_dict[(model,index)]=(segi,chain,resi)') # O's cmd.iterate(sss1, '_ss.ca_dict[(segi,chain,resi)] = (model,index)') cmd.iterate("((byres "+sss1+") and n;n)", '_ss.n_dict[(segi,chain,resi)] = (model,index)') cmd.iterate("((byres "+sss1+") and n;o)", '_ss.o_dict[(segi,chain,resi)] = (model,index)') scr_dict[None]=None o_dict[None]=None n_dict[None]=None ca_dict[None]=None # create special version of cas with gaps gap = [None,None,None,None] # gap large enough to distinguish i+4 interations from gaps last = None for a in res_list: if last!=None: if(cmd.count_atoms( "((neighbor(neighbor(neighbor (%s`%d)))) and (%s`%d))"% (last[0],last[1],a[0],a[1]),quiet=1)==0): gap.extend([None,None,None,None]) gap.append(a) last = a gap.extend([None,None,None,None]) print " util.ss: analyzing phi/psi angles (slow)..." # generate reverse-lookup for gap indices ss = {} c = 0 gap_idx = {} for a in gap: gap_idx[a] = c c = c + 1 # secondary structure database... ss = {} ss[None]=None # make decisions based on phi/psi for a in cas: ss[a] = 'L' # default phipsi = cmd.get_phipsi(sss1,state) for a in phipsi.keys(): (phi,psi) = phipsi[a] # print scr_dict[a],(phi,psi) if (phi!=None) and (psi!=None): if ((phi<-45) and (phi>-160) and (psi<-170) or (psi>10)): # beta? ss[a] = 's' elif ((phi<-45) and (phi>-160) and (psi>-80) and (psi<-25)): # helix? ss[a] = 'H' print " util.ss: finding hydrogen bonds..." # find all pairwise hydrogen bonds and make note of them in dict hb = cmd.find_pairs("((byres "+sss1+") and n;n)", "((byres "+sss1+") and n;o)",mode=1, cutoff=3.7,angle=55, state1=state,state2=state) hb_dict = {} # [((N-atom) (O-atom))] = 1 n_hb_dict = {} # [(N-atom)] = [(O-atom),...] o_hb_dict = {} # [(O-atom)] = [(N-atom),...] for a in hb: # cmd.dist("(%s`%d)"%a[0],"(%s`%d)"%a[1]) hb_dict[a] = 1 n = a[0] o = a[1] if not n_hb_dict.has_key(n): n_hb_dict[n]=[] if not o_hb_dict.has_key(o): o_hb_dict[o]=[] n_hb_dict[n].append(o) o_hb_dict[o].append(n) # check to insure that all helical residues have at least an i +/- 4 # hydrogen bond for c in xrange(4,len(gap)-4): a = gap[c] if ss[a]=='H': aN = n_dict[scr_dict[a]] aO = o_dict[scr_dict[a]] am4O = o_dict[scr_dict[gap[c-4]]] ap4N = n_dict[scr_dict[gap[c+4]]] if not hb_dict.has_key((aN,am4O)): if not hb_dict.has_key((ap4N,aO)): ss[a]='L' print " util.ss: verifying beta sheets..." # check to insure that all beta residues have proper interactions rep_dict = {} repeat = 1 while repeat: repeat = 0 c = 4 cc = len(gap)-4 while c<cc: a1 = gap[c] if (ss[a1] in ['s','S']) and not rep_dict.has_key(a1): rep_dict[a1] = 1 valid = 0 scr_a1 = scr_dict[a1] # look for antiparallel 2:2 H-bonds (NH-O=C + C=O-HN) n_a1_atom = n_dict[scr_a1] o_a1_atom = o_dict[scr_a1] if (n_hb_dict.has_key(n_a1_atom) and o_hb_dict.has_key(o_a1_atom)): for n_hb_atom in n_hb_dict[n_a1_atom]: for o_hb_atom in o_hb_dict[o_a1_atom]: n_hb_scr = scr_dict[n_hb_atom] o_hb_scr = scr_dict[o_hb_atom] if o_hb_scr == n_hb_scr: b1 = ca_dict[o_hb_scr] if abs(c-gap_idx[b1])>2: ss[b1] = 'S' ss[a1] = 'S' valid = 1 # look for antiparallel offset HB (i,i+2,j,j-2) a3 = gap[c+2] if (a3!=None): scr_a3 = scr_dict[a3] o_a1_atom = o_dict[scr_a1] n_a3_atom = n_dict[scr_a3] if (n_hb_dict.has_key(n_a3_atom) and o_hb_dict.has_key(o_a1_atom)): for n_hb_atom in n_hb_dict[n_a3_atom]: for o_hb_atom in o_hb_dict[o_a1_atom]: n_hb_scr = scr_dict[n_hb_atom] o_hb_scr = scr_dict[o_hb_atom] b1 = ca_dict[o_hb_scr] if b1!=None: b1_i = gap_idx[b1] if abs(c-b1_i)>2: # no turns! b3 = gap[b1_i-2] if b3!=None: b3_scr = scr_dict[b3] if b3_scr == n_hb_scr: a2 = gap[c+1] b2 = gap[gap_idx[b1]-1] ss[b1] = 'S' ss[b3] = 'S' ss[a1] = 'S' ss[a3] = 'S' if ss[a2]=='L': ss[a2] = 's' if ss[b2]=='L': ss[b2] = 's' valid = 1 # look for antiparallel offset HB (i,i-2,j,j+2) a3 = gap[c-2] if (a3!=None): scr_a3 = scr_dict[a3] n_a1_atom = n_dict[scr_a1] o_a3_atom = o_dict[scr_a3] if (n_hb_dict.has_key(n_a1_atom) and o_hb_dict.has_key(o_a3_atom)): for n_hb_atom in n_hb_dict[n_a1_atom]: for o_hb_atom in o_hb_dict[o_a3_atom]: n_hb_scr = scr_dict[n_hb_atom] o_hb_scr = scr_dict[o_hb_atom] b1 = ca_dict[o_hb_scr] if b1!=None: b1_i = gap_idx[b1] if abs(c-b1_i)>2: # no turns! b3 = gap[b1_i-2] if b3!=None: b3_scr = scr_dict[b3] if b3_scr == n_hb_scr: a2 = gap[c-1] b2 = gap[gap_idx[b1]-1] ss[b1] = 'S' ss[b3] = 'S' ss[a1] = 'S' ss[a3] = 'S' if ss[a2]=='L': ss[a2] = 's' if ss[b2]=='L': ss[b2] = 's' valid = 1 # look for parallel 1:3 HB (i,j-1,j+1) n_a1_atom = n_dict[scr_a1] o_a1_atom = o_dict[scr_a1] if (n_hb_dict.has_key(n_a1_atom) and o_hb_dict.has_key(o_a1_atom)): for n_hb_atom in n_hb_dict[n_a1_atom]: for o_hb_atom in o_hb_dict[o_a1_atom]: n_hb_scr = scr_dict[n_hb_atom] o_hb_scr = scr_dict[o_hb_atom] b0 = ca_dict[n_hb_scr] if b0!=None: b2 = gap[gap_idx[b0]+2] if b2!=None: b2_scr = scr_dict[b2] if b2_scr == o_hb_scr: b1 = gap[gap_idx[b0]+1] ss[a1] = 'S' ss[b0] = 'S' if ss[b1]=='L': ss[b1]='s' ss[b2] = 'S' valid = 1 repeat = 1 if not valid: ss[a1] = 'L' c = c + 1 # automatically fill 1 residue gaps in helices and well-defined sheets c = 4 cc = len(gap)-6 while c<cc: a1 = gap[c] a3 = gap[c+2] ss_a1 = ss[a1] ss_a3 = ss[a3] if (ss_a1==ss_a3) and (ss_a1 in ['S','H']): a2 = gap[c+1] ss[a2] = ss_a1 c = c + 1 # remove singleton sheet residues c = 4 cc = len(gap)-4 while c<cc: a0 = gap[c-1] a1 = gap[c] a2 = gap[c+1] if ss[a1] in ['s','S']: if ((not ss[a0] in ['s','S']) and (not ss[a2] in ['s','S'])): ss[a1] = 'L' c = c + 1 # remove sheet residues which aren't next to another sheet c = 4 cc = len(gap)-4 while c<cc: a1 = gap[c] if ss[a1]=='S': a1 = gap[c] scr_a1 = scr_dict[a1] # look for hydrogen bonds to another sheet n_a1_atom = n_dict[scr_a1] o_a1_atom = o_dict[scr_a1] certain = 0 if n_hb_dict.has_key(n_a1_atom): for n_hb_atom in n_hb_dict[n_a1_atom]: n_hb_ca_atom=ca_dict[scr_dict[n_hb_atom]] if ss[n_hb_ca_atom]=='S': certain = 1 break if o_hb_dict.has_key(o_a1_atom): for o_hb_atom in o_hb_dict[o_a1_atom]: o_hb_ca_atom=ca_dict[scr_dict[o_hb_atom]] if ss[o_hb_ca_atom]=='S': certain = 1 break if not certain: ss[a1] = 's' c = c + 1 # remove questionable sheet residues c = 4 cc = len(gap)-4 while c<cc: a0 = gap[c-1] a1 = gap[c] a2 = gap[c+1] if ss[a1]=='s': if (not ((ss[a0]=='S') and (ss[a2]=='S'))): ss[a1] = 'L' c = c + 1 # extend helices if hydrogen bonding requirements are met rep_dict = {} repeat = 1 while repeat: repeat = 0 c = 4 cc = len(gap)-4 while c<cc: a = gap[c] if not rep_dict.has_key(a): if ss[gap[c+1]]=='H': rep_dict[a] = 1 if ss[a]!='H': # N-terminal end aO = o_dict[scr_dict[a]] ap4N = n_dict[scr_dict[gap[c+4]]] ap3N = n_dict[scr_dict[gap[c+3]]] if hb_dict.has_key((ap4N,aO)) or hb_dict.has_key((ap3N,aO)): ss[a]='H' repeat = 1 c = c - 5 if c<4: c=4 if ss[gap[c-1]]=='H': a = gap[c] if ss[a]!='H': # C-terminal end rep_dict[a] = 1 aN = n_dict[scr_dict[a]] am4O = o_dict[scr_dict[gap[c-4]]] am3O = o_dict[scr_dict[gap[c-3]]] if hb_dict.has_key((aN,am4O)) or hb_dict.has_key((aN,am3O)): ss[a]='H' repeat = 1 c = c - 5 if c<4: c=4 c = c + 1 # remove doubleton helices c = 4 cc = len(gap)-5 while c<cc: a0 = gap[c-1] a1 = gap[c] a2 = gap[c+1] a3 = gap[c+2] ss_a0 = ss[gap[c-1]] ss_a1 = ss[gap[c]] ss_a2 = ss[gap[c+1]] ss_a3 = ss[gap[c+2]] if ss_a1=='H': if (ss_a2==ss_a1) and (ss_a0!=ss_a2) and (ss_a2!=ss_a3): ss[a1] = 'L' ss[a2] = 'L' c = c + 1 # remove totally unreasonable helix and sheet residues c = 4 cc = len(gap)-5 while c<cc: a1 = gap[c] ss_a1 = ss[gap[c]] if ss_a1=='H': if phipsi.has_key(a1): (phi,psi) = phipsi[a1] if (phi>0) and (phi<150): ss[a1] = 'L' elif((psi<-120) or (psi>140)): ss[a1] = 'L' elif ss_a1 in ['S','s']: if phipsi.has_key(a1): (phi,psi) = phipsi[a1] if (phi>45) and (phi<160): ss[a1] = 'L' # if (psi<-30) and (psi>-150): if (psi<-65) and (psi>-150): ss[a1] = 'L' c = c + 1 for x in range(1,3): # remove singleton sheet residues c = 4 cc = len(gap)-4 while c<cc: a0 = gap[c-1] a1 = gap[c] a2 = gap[c+1] if ss[a1] in ['s','S']: if ((not ss[a0] in ['s','S']) and (not ss[a2] in ['s','S'])): ss[a1] = 'L' c = c + 1 # remove sheet residues which aren't next to another sheet c = 4 cc = len(gap)-4 while c<cc: a1 = gap[c] if ss[a1]=='S': a1 = gap[c] scr_a1 = scr_dict[a1] # look for hydrogen bonds to another sheet n_a1_atom = n_dict[scr_a1] o_a1_atom = o_dict[scr_a1] certain = 0 if n_hb_dict.has_key(n_a1_atom): for n_hb_atom in n_hb_dict[n_a1_atom]: n_hb_ca_atom=ca_dict[scr_dict[n_hb_atom]] if ss[n_hb_ca_atom]=='S': certain = 1 break if o_hb_dict.has_key(o_a1_atom): for o_hb_atom in o_hb_dict[o_a1_atom]: o_hb_ca_atom=ca_dict[scr_dict[o_hb_atom]] if ss[o_hb_ca_atom]=='S': certain = 1 break if not certain: ss[a1] = 's' c = c + 1 # remove questionable sheet residues c = 4 cc = len(gap)-4 while c<cc: a0 = gap[c-1] a1 = gap[c] a2 = gap[c+1] if ss[a1]=='s': if (not ((ss[a0]=='S') and (ss[a2]=='S'))): ss[a1] = 'L' c = c + 1 # lst = ss.keys() # lst.sort() # for a in lst: print scr_dict[a],ss[a] # assign protein for a in cas: if ss[a]=='s': ss[a]='S' cmd.alter(sss1,"ss ='L'") for a in cas: if ss[a]!='L': cmd.alter("(%s`%d)"%a,"ss='%s'"%ss[a]) cmd.feedback("pop") del pymol._ss # IMPORTANT cmd.delete(sss1) cmd.rebuild(selection,'cartoon') # # print conn_hash.keys() print " util.ss: assignment complete."