/usr/lib/python2.7/dist-packages/pymol/preset.py is in pymol 1.8.4.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information.
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-*
#-*
#-*
#Z* -------------------------------------------------------------------
cmd = __import__("sys").modules["pymol.cmd"]
from . import util
import traceback
polar_contacts_suffix = "_pol_conts"
default_polar_contacts = "polar_contacts"
tmp_sele = "_p_tmp"
prot_and_dna_sele = "(resn ALA+CYS+CYX+ASP+GLU+PHE+GLY+HIS+HID+HIE+HIP+HISE+HISD+HISP+ILE+LYS+LEU+MET+MSE+ASN+PRO+GLN+ARG+SER+THR+VAL+TRP+TYR+A+C+T+G+U+DA+DC+DT+DG+DU+DI)"
wat_sele = "(resn WAT,H2O,HOH,TIP)"
ion_sele = "(resn CA,HG,K,NA,ZN,MG,CL)"
solv_sele = "("+wat_sele+"|"+ion_sele+")"
lig_excl = "(resn MSE)"
lig_sele = "((hetatm or not "+prot_and_dna_sele+") and not ("+solv_sele+"|"+ion_sele+"|"+lig_excl+"))"
lig_and_solv_sele = "("+lig_sele+"|"+solv_sele+")"
def get_sname_oname_dname(selection, _self=cmd):
'''
Get a named selection, object names and a distance (polar contacts) name
'''
_self.select(tmp_sele, selection)
if selection not in _self.get_object_list():
selection = ' '.join(_self.get_object_list(tmp_sele))
if selection and ' ' not in selection:
dname = selection + polar_contacts_suffix
else:
dname = default_polar_contacts
return tmp_sele, selection, dname
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, selection, dname = get_sname_oname_dname(selection, _self=cmd)
cmd.cartoon("auto",s)
cmd.hide("everything",s)
cmd.set("two_sided_lighting",0) # global
cmd.unset("transparency",s)
cmd.unset("surface_quality", selection)
cmd.unset("surface_type",selection)
cmd.unset("sphere_scale",s)
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)
if polar_contacts == None:
polar_contacts = dname
if polar_contacts in cmd.get_names('objects'):
cmd.delete(polar_contacts)
return s, selection, dname
def simple(selection="(all)",_self=cmd):
cmd=_self
s, selection = _prepare(selection, _self=cmd)[:2]
util.cbc(s,_self=cmd)
cmd.show("ribbon",s)
cmd.show("lines","(byres (("+s+" & r. CYS+CYX & n. SG) & bound_to ("+s+" & r. CYS+CYX & n. SG))) & n. CA+CB+SG")
# try to show what covalent ligands are connected to...
cmd.show("sticks","("+lig_sele+" and ("+s+")) extend 2")
cmd.show("sticks","byres (("+lig_sele+" and ("+s+") and not resn ACE+NAC+NME+NH2) extend 1)")
cmd.hide("sticks","("+s+") and ((not rep sticks) extend 1)")
cmd.show("sticks","("+lig_sele+" and ("+s+")) extend 2")
# color by atom if lines or sticks are shown
util.cnc("(( rep lines or rep sticks or ("+lig_and_solv_sele+")) and ("+s+"))",_self=cmd)
cmd.show("nonbonded","("+lig_and_solv_sele+" and ("+s+"))")
cmd.show("lines","("+lig_and_solv_sele+" and ("+s+"))")
cmd.delete(s)
def simple_no_solv(selection="(all)",_self=cmd):
cmd=_self
simple(selection,_self=_self)
s, selection = get_sname_oname_dname(selection, _self=_self)[:2]
cmd.hide("nonbonded","("+solv_sele+" and "+s+")")
cmd.delete(s)
def ligands(selection="(all)",_self=cmd):
cmd=_self
try:
s, selection, polar_contacts = _prepare(selection, _self=cmd)
host = "_preset_host"
solvent = "_preset_solvent"
near_solvent = "_preset_solvent"
lig = "_preset_lig"
cmd.select(host,s+" and "+prot_and_dna_sele)
cmd.select(solvent,s+" and "+solv_sele)
cmd.select(lig,s+" and "+lig_sele)
cmd.select(near_solvent,s+" and ("+solvent+" within 4 of "+lig+")")
util.chainbow(host,_self=cmd)
util.cbc(lig,_self=cmd)
util.cbac("(("+s+") and not elem C)",_self=cmd)
cmd.hide("everything",s)
cmd.show("ribbon",host)
cmd.show("lines","("+s+" and byres ("+host+" within 5 of "+lig+"))")
cmd.show("sticks",lig)
cmd.show("sticks",solvent+" and neighbor "+lig)
cmd.show("lines","("+s+" and (rep lines extend 1) and "+lig+")")
if cmd.count_atoms(lig):
cmd.dist(polar_contacts,host+"|"+near_solvent,lig+"|"+near_solvent,
mode=2,quiet=1,label=0,reset=1) # hbonds
if polar_contacts in cmd.get_names():
cmd.enable(polar_contacts)
cmd.hide("labels",polar_contacts)
cmd.show("dashes",polar_contacts)
else:
cmd.delete(polar_contacts)
cmd.show("nonbonded",lig+"|"+host+"|"+near_solvent)
if cmd.count_atoms(lig):
cmd.zoom(lig,3, animate=1)
cmd.delete(host)
cmd.delete(solvent)
cmd.delete(near_solvent)
cmd.delete(lig)
except:
traceback.print_exc()
cmd.delete(s)
def ball_and_stick(selection="(all)",mode=1,_self=cmd):
cmd=_self
s, selection = _prepare(selection, _self=cmd)[:2]
if mode == 1:
cmd.hide("everything",s)
cmd.set_bond("stick_color","white",s,s)
cmd.set_bond("stick_radius","0.14",s,s)
cmd.set("sphere_scale","0.25",s)
cmd.show("sticks",s)
cmd.show("spheres",s)
elif mode == 2:
cmd.hide("everything",s)
cmd.set_bond("stick_color","white",s,s)
cmd.set_bond("stick_radius","-0.14",s,s)
cmd.set("stick_ball","1")
cmd.set("stick_ball_ratio",-1.0)
cmd.set("stick_ball_color","atomic")
cmd.show("sticks",s)
cmd.delete(s)
def b_factor_putty(selection="(name CA+P)",_self=cmd):
cmd=_self
s, selection = _prepare(selection, _self=cmd)[:2]
cmd.select(s,"(name CA+P) and ("+selection+")")
cmd.show("cartoon",s)
cmd.set("cartoon_flat_sheets",0,selection)
cmd.cartoon("putty",s)
cmd.spectrum("b",selection=s)
cmd.delete(s)
def ligand_cartoon(selection="(all)",_self=cmd):
cmd=_self
s, selection = ligand_sites(selection, _self)[:2]
cmd.set("cartoon_side_chain_helper",1,selection)
cmd.show("cartoon","rep ribbon")
cmd.hide("ribbon")
cmd.hide("surface")
cmd.delete(s)
def ligand_sites(selection="(all)",_self=cmd):
cmd=_self
try:
s, selection, polar_contacts = _prepare(selection, _self=cmd)
host = "_preset_host"
solvent = "_preset_solvent"
near_solvent = "_preset_solvent"
lig = "_preset_lig"
cmd.select(host,s+" and "+prot_and_dna_sele)
cmd.select(solvent,s+" and "+solv_sele)
cmd.select(lig,s+" and "+lig_sele)
cmd.select(near_solvent,s+" and ("+solvent+" within 4 of "+lig+")")
cmd.flag("ignore",host,"clear")
cmd.flag("ignore",lig+"|"+solvent,"set")
util.chainbow(host,_self=cmd)
util.cbc(lig,_self=cmd)
util.cbac("(("+s+") and not elem C)",_self=cmd)
cmd.hide("everything",s)
cmd.show("ribbon",host)
cmd.show("lines","("+s+" and byres ("+host+" within 5 of "+lig+"))")
cmd.show("surface","("+s+" and ((rep lines expand 4) within 6 of "+lig+"))")
cmd.set("two_sided_lighting",1) # global setting
cmd.set("transparency",0,s)
cmd.set("surface_quality",0, selection)
cmd.show("sticks",lig)
cmd.show("sticks",solvent+" and neighbor "+lig)
cmd.show("lines","("+s+" and (rep lines extend 1) and "+lig+")")
if cmd.count_atoms(lig):
cmd.dist(polar_contacts,host+"|"+near_solvent,lig+"|"+near_solvent,mode=2,quiet=1,label=0,reset=1) # hbonds
if polar_contacts in cmd.get_names():
cmd.enable(polar_contacts)
cmd.hide("labels",polar_contacts)
cmd.show("dashes",polar_contacts)
else:
cmd.delete(polar_contacts)
cmd.show("nb_spheres",lig+"|"+host+"|"+near_solvent)
if cmd.count_atoms(lig):
cmd.zoom(lig,3, animate=1)
cmd.delete(host)
cmd.delete(solvent)
cmd.delete(near_solvent)
cmd.delete(lig)
finally:
pass
return s, selection, polar_contacts
def ligand_sites_hq(selection="(all)",_self=cmd):
cmd=_self
s, selection = ligand_sites(selection, _self)[:2]
cmd.set("surface_quality","1",selection)
cmd.set("surface_type",0,selection)
cmd.delete(s)
def ligand_sites_trans(selection="(all)",_self=cmd):
cmd=_self
s, selection = ligand_sites(selection, _self)[:2]
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("transparency","0.33",s)
cmd.set("surface_type",0,selection)
cmd.set("surface_quality",0,selection)
cmd.delete(s)
def ligand_sites_trans_hq(selection="(all)",_self=cmd):
cmd=_self
s, selection = ligand_sites(selection, _self)[:2]
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("transparency","0.33",s)
cmd.set("surface_type",0,selection)
cmd.set("surface_quality",1,selection)
cmd.delete(s)
def ligand_sites_mesh(selection="(all)",_self=cmd):
cmd=_self
s, selection = ligand_sites(selection, _self)[:2]
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("surface_type","2",selection)
cmd.set("surface_quality","0",selection)
cmd.delete(s)
def ligand_sites_dots(selection="(all)",_self=cmd):
cmd=_self
s, selection = ligand_sites(selection, _self)[:2]
cmd.show("sticks",s+" and rep lines")
cmd.hide("lines",s+" and rep lines")
cmd.set("surface_type","1",selection)
cmd.set("surface_quality","1",selection)
cmd.delete(s)
def technical(selection="(all)",_self=cmd):
cmd=_self
s, selection, polar_contacts = _prepare(selection, _self=cmd)
util.chainbow(s,_self=cmd)
util.cbc("("+lig_sele+" and ("+s+"))",_self=cmd)
util.cbac("(("+s+") and not elem C)",_self=cmd)
cmd.show("nonbonded",s)
cmd.show("lines","((("+s+") and not "+lig_sele+") extend 1)")
cmd.show("sticks","("+lig_sele+" and ("+s+"))")
cmd.show("ribbon",s)
cmd.dist(polar_contacts,s,s,mode=2,label=0,reset=1) # hbonds
if polar_contacts in cmd.get_names():
cmd.enable(polar_contacts)
cmd.set("dash_width",1.5,polar_contacts)
cmd.hide("labels",polar_contacts)
cmd.show("dashes",polar_contacts)
cmd.show("nonbonded","(("+lig_sele+"|resn HOH+WAT+H2O) and ("+s+"))")
cmd.delete(s)
def pretty_solv(selection="(all)",_self=cmd):
cmd=_self
s, selection = _prepare(selection, _self=cmd)[:2]
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)
cmd.delete(s)
def pretty(selection,_self=cmd):
cmd=_self
pretty_solv(selection,_self)
s, selection = get_sname_oname_dname(selection, _self=_self)[:2]
cmd.hide("nb_spheres","("+s+" and "+lig_sele+"|resn HOH+WAT+H2O)")
cmd.delete(s)
pretty_no_solv = pretty
def pub_solv(selection="(all)",_self=cmd):
cmd=_self
pretty_solv(selection,_self)
s, selection = get_sname_oname_dname(selection, _self=_self)[:2]
cmd.set("cartoon_smooth_loops",1,selection)
cmd.set("cartoon_highlight_color","grey50",selection)
cmd.set("cartoon_fancy_helices",1,selection)
cmd.set("cartoon_flat_sheets",1,selection)
cmd.set("cartoon_side_chain_helper",0,selection)
cmd.delete(s)
def publication(selection="(all)",_self=cmd):
cmd=_self
pub_solv(selection,_self)
s, selection = get_sname_oname_dname(selection, _self=_self)[:2]
cmd.hide("nb_spheres","(("+lig_sele+"|resn HOH+WAT+H2O) and "+s+")")
cmd.delete(s)
pub_no_solv = publication
def default(selection="(all)",_self=cmd):
cmd=_self
s, selection = _prepare(selection, _self=cmd)[:2]
cmd.show("lines",s)
cmd.show("nonbonded",s)
color=cmd.get_object_color_index(selection)
if color<0:
util.cbag(selection,_self=cmd)
else:
util.cnc(selection,_self=cmd)
cmd.color(str(color),"("+s+") and elem C")
cmd.delete(s)
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