import cmd
from cmd import _cmd, is_tuple
from chempy import Storage,Atom,Bond
from chempy.models import Indexed
from pymol import util
import re
import string
from chempy import cex
CEX=cex
00036 class CEXpyParser(CEX.CEXsmilesParser):
def __init__(self):
self.model = Indexed()
self.atomN = 0
def MakeAtom(self, atnum):
at = Atom()
at.index = self.atomN
self.atomN = self.atomN+1
at.symbol = CEX.CEXsmilesParser.num2sym(self,atnum)
self.model.atom.append(at)
return at
def MakeBond(self,at1, at2, bo):
bnd = Bond()
bnd.index = [ at1.index, at2.index ]
bnd.order = bo
self.model.bond.append(bnd)
def SetFormalCharge(self, atom, charge):
atom.formal_charge = charge
def SetHcount(self, atom, count):
pass
def SetAtomicMass(self, atom, mass):
pass
def readcex(file,*args):
import os.path
standardResidues = ("ALA", "ARG", "ASP", "ASN", "ASX", "CYS", "GLY", "GLU",
"GLN", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", "PRO",
"SER", "THR", "TYR", "TRP", "VAL", "HID", "HIE")
def childprop(tag, tree,_self=cmd):
try:
p = CEX.selectChildren(tree,tag)[0].value
if p[0] == '"': p = p[1:-1]
list = map(string.strip,string.split(p,";"))
return list
except IndexError:
return None
f = open(file,"r")
cs = CEX.CEXstream(f)
modelname = os.path.splitext(os.path.basename(file))[0]
if len(args) > 0: modelname = args[0]
while 1:
tree = CEX.readTree(cs)
if not tree: break
if tree.name == "$MOL":
smiles = tree.value
confs = CEX.selectChildren(tree,"XYZ")
try:
name = CEX.selectProperty(tree,"/NAM").value
except AttributeError:
name = ""
anames = childprop("ANAM", tree)
atypes = childprop("ATYPE", tree)
resnos = childprop("RESNO", tree)
resnames = childprop("RESNA", tree)
chains = childprop("CHAIN", tree)
occups = childprop("OCCUP", tree)
bvals = childprop("BVAL", tree)
pcharges = childprop("PCHARGE", tree)
rads = childprop("RAD", tree)
ligsites = childprop("SCORE", tree)
clusters = childprop("CLUSTER", tree)
parser = CEXpyParser()
try:
parser.parse(smiles)
except CEX.CEXsmilesError, data:
print data
break
parser.model.molecule.title = name
for at in parser.model.atom:
i = at.index
if anames: at.name = anames[i]
if resnames:
at.resn = resnames[i]
if at.resn in standardResidues: at.hetatm = 0
if resnos:
at.resi = resnos[i]
at.resi_number = int(resnos[i])
if chains: at.chain = chains[i]
if bvals: at.b = bvals[i]
if occups: at.q = occups[i]
if rads: at.vdw = rads[i]
if atypes: at.text_type = atypes[i]
if pcharges:
chg = pcharges[i]
if chg == "": chg = 0.0
at.partial_charge = float(chg)
if clusters:
at.resi = clusters[i]
at.resi_number = int(clusters[i])
if ligsites: at.b = ligsites[i]
for conf in confs:
if conf.value[0] == '"':
conf.value = conf.value[1:-1]
xyz = map(lambda x:string.split(x,","),string.split(conf.value,";"))
for at in parser.model.atom:
i = at.index
at.coord = [ float(xyz[i][0]), float(xyz[i][1]), float(xyz[i][2]) ]
cmd.load_model(parser.model,modelname,discrete=1,finish=0)
else:
pass
_cmd.finish_object(_self._COb,modelname)
f.close()
def colorbyB(selection="spheres",first=7,last=3):
cols = [(0.,0.,1.),(.5,.5,1.),(.8,.8,1.),(1.,1.,1.),
(1.,.9,.9),(1.,.6,.6),(1.,0.,0.)]
nbins = len(cols)
incr = float(first-last)/nbins
for i in range(nbins):
cname = "_spcol%03d"%i
cmd.set_color(cname,cols[i])
b = first - i*incr
cmd.color(cname,"((%s) and not(b > %f) and b > %f)"%(selection,b,b-incr))
def metaphorics():
cmd.extend("readcex",readcex)
cmd.extend("colorbyB",colorbyB)
def get_context_info():
context_dict= {}
context_list= []
for a in cmd.get_names("all"):
context = None
if a[-6:]=='_water':
context = a[:-6]
if a[-7:]=='_ligand':
context = a[:-7]
if a[-5:]=='_site':
context = a[:-5]
if a[-6:]=='_hbond':
context = a[:-6]
if context!=None:
if not context_dict.has_key(context):
context_list.append(context)
context_dict[context] = [a]
else:
context_dict[context].append(a)
return (context_list,context_dict)
def toggle_labels(mode=-1):
global labels
if mode<0:
labels = not labels
else:
labels = mode
if labels:
cmd.show("labels")
else:
cmd.hide("labels")
def toggle_cgos(mode=-1):
global cgos
if mode<0:
cgos = not cgos
else:
cgos = mode
if cgos:
cmd.show("cgo")
else:
cmd.hide("cgo")
def toggle_ligands(mode=-1):
global ligands
if mode<0:
ligands = not ligands
else:
ligands = mode
if ligands:
cmd.show("sticks",m4x_ligands)
else:
cmd.hide("sticks",m4x_ligands)
def toggle_sites(mode=-1):
global sites
if mode<0:
sites = not sites
else:
sites = mode
if sites:
cmd.show("lines",m4x_sites)
else:
cmd.hide("lines",m4x_sites)
def toggle_waters(mode=-1):
global waters
if mode<0:
waters = not waters
else:
waters = mode
if waters:
cmd.show("nonbonded",m4x_waters)
else:
cmd.hide("nonbonded",m4x_waters)
def toggle_dashes(mode=-1):
global dashes
if mode<0:
dashes = not dashes
else:
dashes = mode
if dashes:
cmd.show("dashes")
else:
cmd.hide("dashes")
def toggle_zooms(mode=-1):
global zooms
if mode<0:
zooms = not zooms
else:
zooms = mode
if zooms:
cmd.zoom(m4x_ligands,2)
else:
cmd.zoom("m4x_aligned")
def setup_contexts(context_info):
(list,dict) = context_info[0:2]
key_list = [
'F1','F2','F3','F4','F5','F6','F7','F8','F9','F10',
'SHFT-F1','SHFT-F2','SHFT-F3','SHFT-F4','SHFT-F5','SHFT-F6','SHFT-F7',
'SHFT-F8','SHFT-F9','SHFT-F10']
doc_list = ["Keys"]
zoom_context = 1
global labels
labels = 1
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_labels)
doc_list.append(key+": Toggle Dist")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,lambda :(cmd.zoom(),toggle_labels(0)))
doc_list.append(key+": Zoom All")
for a in list:
water = a+"_water"
ligand = a+"_ligand"
site = a+"_site"
hbond = a+"_hbond"
name_list = dict[a]
zoom_list = []
if water in name_list:
cmd.show("nonbonded",water)
util.cbac(water)
zoom_list.append(water)
if ligand in name_list:
cmd.show("sticks",ligand)
cmd.hide("cartoon",ligand)
util.cbag(ligand)
zoom_list.append(ligand)
if site in name_list:
cmd.show("sticks",site)
util.cbac(site)
zoom_list.append(site)
cmd.hide("cartoon",site)
cmd.show("sticks","(byres (neighbor ("+site+" and name c))) and name n+ca")
cmd.show("sticks","(byres (neighbor ("+site+" and name n))) and name c+ca+o")
if len(zoom_list):
if len(key_list):
key = key_list.pop(0)
zoom_str = string.join(zoom_list,' or ')
if zoom_context == 1:
zoom_context = zoom_str
elif zoom_context not in (0,1):
zoom_context = 0
cmd.set_key(key,lambda x=zoom_str:(cmd.zoom(x)))
mo = re.search("_([^_]+)$",a)
if mo:
cont_name = mo.groups()[0]
else:
cont_name = a
doc_list.append(key+": Zoom "+cont_name)
if hbond in name_list:
cmd.show("dashes",hbond)
cmd.show("labels",hbond)
cmd.wizard("fedora",doc_list)
if zoom_context not in (0,1):
cmd.zoom(zoom_context)
toggle_labels(0)
cmd.feedback("enable","objectmolecule","results")
cmd.feedback("disable","selector","actions")
cmd.feedback("disable","scene","actions")
cmd.set("internal_feedback",1)
cmd.set("internal_prompt",0)
def setup_alignment_contexts(context_info):
(list,dict) = context_info[0:2]
doc_list = ['\888Legend:']
obj_name_dict = {}
for a in list:
sf = string.find(a,"_")
if sf>=0:
object_name = a[0:sf]
if not obj_name_dict.has_key(object_name):
obj_name_dict[object_name] = 1
col_index = cmd.get_object_color_index(object_name)
if col_index>=0:
col_tup = cmd.get_color_tuple(col_index)
if is_tuple(col_tup):
col_int = map(lambda x:int(x*9+0.49999),col_tup)
col_str = string.join(map(lambda x:chr(ord('0')+x),col_int),'')
doc_list.append("\\"+col_str+object_name+"\\---")
key_list = [
'F1','F2','F3','F4','F5','F6','F7','F8','F9','F10',
'SHFT-F1','SHFT-F2','SHFT-F3','SHFT-F4','SHFT-F5','SHFT-F6','SHFT-F7',
'SHFT-F8','SHFT-F9','SHFT-F10']
doc_list.append("")
doc_list.append("\\888Toggles:")
zoom_context = 1
global labels,ligands,waters,sites,cgos,zooms,dashes
labels = 1
ligands = 1
waters = 1
sites = 1
cgos = 0
zooms = 0
dashes = 1
global m4x_sites,m4x_ligands,m4x_waters
m4x_sites = "m4x_sites"
m4x_ligands = "m4x_ligands"
m4x_waters = "m4x_waters"
cmd.select(m4x_sites,"none")
cmd.select(m4x_ligands,"none")
cmd.select(m4x_waters,"none")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_zooms)
doc_list.append(key+": Zoom")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_sites)
doc_list.append(key+": Sites")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_waters)
doc_list.append(key+": Waters")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_dashes)
doc_list.append(key+": H-Bonds")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_cgos)
doc_list.append(key+": Fits")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_ligands)
doc_list.append(key+": Ligands")
if len(key_list):
key = key_list.pop(0)
cmd.set_key(key,toggle_labels)
doc_list.append(key+": HB-Dists")
for a in list:
include_flag = 0
water = a+"_water"
ligand = a+"_ligand"
site = a+"_site"
hbond = a+"_hbond"
if cmd.count_atoms(site):
if cmd.count_atoms(site+" & m4x_aligned"):
include_flag = 1
if cmd.count_atoms(ligand):
if cmd.count_atoms(ligand+" & m4x_nearby"):
include_flag = 1
if include_flag:
name_list = dict[a]
if water in name_list:
cmd.select(m4x_waters,m4x_waters+"|"+water)
if ligand in name_list:
cmd.select(m4x_ligands,m4x_ligands+"|"+ligand)
if site in name_list:
cmd.select(m4x_sites,m4x_sites+"|"+site+
"|((byres (neighbor ("+site+" and name c))) and name n+ca)"+
"|((byres (neighbor ("+site+" and name n))) and name c+ca+o)")
cmd.wizard("fedora",doc_list)
toggle_cgos(1)
toggle_labels(0)
toggle_dashes(0)
toggle_ligands(1)
toggle_sites(0)
toggle_waters(0)
toggle_cgos(1)
cmd.deselect()
cmd.feedback("enable","objectmolecule","results")
cmd.set("internal_feedback",1)
cmd.set("internal_prompt",0)
cmd.feedback("disable","selector","actions")
cmd.feedback("disable","scene","actions")