/usr/share/pdb2pqr/pdb2pka/NEWligand_topology.py is in pdb2pqr 2.1.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# $Id$
# PC 2005/09/23
# Get ligand topologies
#
import numpy
#from sets import Set
from ligandclean.trial_templates import *
from ligandclean.lookuptable import *
try:
from substruct import Algorithms
except ImportError:
txt = "Cannot import Algorithms, this may be the result of disabling pdb2pka at configure stage!"
raise ImportError, txt
from types import *
def length(vector):
# This function returns the length of vector
import math
sum=0.0
for value in vector:
sum=sum+math.pow(value,2)
return math.sqrt(sum)
class get_ligand_topology:
### PC
#
# here we need to check if we have MOL2 file, then guess_atom_types
# are not necessary
#
def __init__(self,lines,MOL2FLAG):
#
# Given the atoms, this routine tells you everything you want to know about
# the ligand
#
#
# Store the atoms
#
if MOL2FLAG == False:
self.atoms={}
import string
for line in lines:
split=string.split(line)
name=split[0]
self.atoms[name]={'coords':numpy.array([float(split[1]),float(split[2]),float(split[3])])}
self.atoms[name]['bonds']=[]
#
# Get the likely types from names
#
trivial_types=['N','O','C','H']
for atom in self.atoms.keys():
if atom[0] in trivial_types:
if atom[0]!='H': # Get rid of all the hydrogens
self.atoms[atom]['type']=atom[0]
self.atoms[atom]['sybylType']='Unknown'
#
# Get the bonds
# First approximation: Anything closer than 2.0 A is bonded
#
self.dists={}
for atom1 in self.atoms.keys():
self.dists[atom1]={}
for atom2 in self.atoms.keys():
if atom1==atom2:
continue
#
# Calculate the distance
#
self.dists[atom1][atom2]=length(self.atoms[atom1]['coords']-self.atoms[atom2]['coords'])
if self.dists[atom1][atom2]<2.0:
self.atoms[atom1]['bonds'].append(atom2)
#
# Count number of bonds to non-H atoms and guess atom type
#
bond_lengths={'C-C':[1.5,0.2]}
#
# Get the torsion angles
#
atoms=self.atoms.keys()
atoms.sort()
for atom in atoms:
self.atoms[atom]['torsions']=self.get_torsions(atom)
#
# Produce the definition lines
#
self.lines=self.create_deflines()
#
# Now we try to guess the atom types
#
self.guess_atom_types()
else:
#
# We have a mol2 file
#
LIG = lines
self.atoms={}
for line in lines:
name = line.name
# self.atoms[name] = name
self.atoms[name] = {'coords': numpy.array([float(line.x),float(line.y),float(line.z)])}
self.atoms[name]['sybylType'] = line.sybylType
#
# we don't have this information when coming from PDB!
self.atoms[name]['lBondedAtoms'] = line.lBondedAtoms
self.atoms[name]['lBonds'] = line.lBonds
###PC
# one bond is lost!
self.atoms[name]['bonds']=[]
for BBonds in line.lBondedAtoms: #line.lBonds:
self.atoms[name]['bonds'].append(BBonds.name)
###PC
# save the atomname & id
self.atoms[name]['atomname'] = name
self.atoms[name]['serial'] = line.serial
#
# USEFUL information
# bonded heavy atoms
self.atoms[name]['nbhvy'] = len([x for x in self.atoms[name]['lBondedAtoms'] if x.sybylType != "H"])
# number of bonds (including hydrogens)
self.atoms[name]['nbds'] = len(self.atoms[name]['lBonds'])
# number of bonded hydrogens
self.atoms[name]['nbhyd'] = self.atoms[name]['nbds']- self.atoms[name]['nbhvy']
# element
self.atoms[name]['ele'] = self.atoms[name]['sybylType'].split('.')[0]
#
# Get the torsion angles
#
atoms=self.atoms.keys()
atoms.sort()
for atom in atoms:
self.atoms[atom]['torsions']=self.get_torsions(atom)
self.lines=self.create_deflines()
#
# we have the sybylType in self.atoms!!!
return
#
# -------
#
def guess_atom_types(self):
#
# Phase I
# Loop over all atoms and count number of bonds
# + determine their likely order (e.g. single, double, or triple)
#
ambs={}
atoms=self.atoms.keys()
for atom_name in atoms:
bonds=self.atoms[atom_name]['bonds']
atype=self.atoms[atom_name]['type']
numbonds=0
aromatic=None
for bonded_atom in bonds:
#
# Get the bond order from the distance
#
bond_order=self.get_bond_order(atom_name,bonded_atom)
if bond_order<4:
numbonds=numbonds+bond_order
else:
aromatic=1
self.atoms[atom_name]['sum_bondorder']=numbonds
self.atoms[atom_name]['aromatic']=aromatic
#
# ok, now we have info on all atoms.
# Solve ambiguities starting with the simplest case
#
valences={'C':4,'O':2,'N':3}
for atom in self.atoms:
print atom, self.atoms[atom]
#
# ok, now it gets hairy
#
print
print 'Guessing sybyl atom types'
for atom in self.atoms.keys():
stype=None
at=self.atoms[atom]
#
# Get the precalculated characteristics
#
number_of_bonds=len(at['bonds'])
sum_of_bondorder=at['sum_bondorder']
if at['type']=='C':
#
# Carbon
#
#
# Table or sum of bond-order, number of atoms bound to
#
C_types={5:{3:'C.2'}} # Carboxylic acid typically
C_types[4]={4:'C.3',3:'C.2',2:'C.2'} # sum of bondorder is 4
C_types[3]={3:'C.3',2:'C.2'}
C_types[2]={2:'C.3',1:'C.2'}
C_types[1]={1:'C.3'}
#
# Get the bond order
#
stype=C_types[sum_of_bondorder][number_of_bonds]
elif at['type']=='O':
#
# OXYGEN
#
# Table or sum of bond-order, number of atoms bound to
#
O_types={2:{2:'O.3',1:'O.2'},1:{1:'O.3'}}
stype=O_types[sum_of_bondorder][number_of_bonds]
else:
pass
self.atoms[atom]['sybylType']=stype
#print atom,stype
#
# Do some postchecks
# - right now only for Carboxylic acids
#
for atom in self.atoms.keys():
at=self.atoms[atom]
if at['sybylType']=='C.2':
#
# See if we have two oxygens bound + an extra bond
#
if len(at['bonds'])==3:
Os=[]
for bound_atom_name in at['bonds']:
bound_atom=self.atoms[bound_atom_name]
if bound_atom['sybylType']=='O.2':
Os.append(bound_atom_name)
#
# If we had two O.2s, then change their hybridisation to O.3
#
if len(Os)==2:
for O in Os:
self.atoms[O]['sybylType']='O.3'
#
# All Done
#
atoms=self.atoms.keys()
atoms.sort()
print '\nFinal Sybyl type results'
for atom in atoms:
print atom,self.atoms[atom]['sybylType']
return
#
# --------
#
def get_bond_order(self,atom1,atom2):
#
# Get the bond order
#
# Bond lengths from
# http://www.chem.swin.edu.au/modules/mod2/bondlen.html
# We should get a better reference
#
# Returns:
# 1: single bond, 2: double bond, 3: triple bond, 4: aromatic
#
#
at1=self.atoms[atom1]
at2=self.atoms[atom2]
bond_props={'C-C':[1.54,1],'C=C':[1.34,2],'CtC':[1.20,3],'CaC':[1.40,4],
'C-O':[1.43,1],'C=O':[1.21,2],
'C-N':[1.47,1],'C=N':[1.25,2],'CtN':[1.16,3],'CaN':[1.34,4],
'NaN':[1.35,4]}
dist=length(at1['coords']-at2['coords'])
tps=[at1['type'],at2['type']]
tps.sort() # To agree with dictionary layout
best_fit=2.00
best_type=None
for bond in bond_props.keys():
if bond[0]==tps[0] and bond[-1]==tps[1]:
if abs(dist-bond_props[bond][0])<best_fit:
best_fit=abs(dist-bond_props[bond][0])
best_type=bond
#
# convert to bond order
#
return bond_props[best_type][1]
#
# ----
#
def get_torsions(self,start_atom):
#
# Get the torsion angles that start with this atom
#
#print '---------------------'
#print 'Starting atom',start_atom
possible_torsions=[]
for bonded1 in self.atoms[start_atom]['bonds']:
for bonded2 in self.atoms[bonded1]['bonds']:
if bonded2==start_atom:
continue
for end_atom in self.atoms[bonded2]['bonds']:
if end_atom==bonded1:
continue
#
# Add the torsion
#
possible_torsions.append([start_atom,bonded1,bonded2,end_atom])
#
# Filter the torsions
#
#
# commented out by Paul 010206
# print 'Jens has to write the stuff for filtering torsions..\n'
return possible_torsions
#
# ---------
#
def create_deflines(self):
#
# Make the lines for the pdb2pqr definition
#
self.numbers={}
atoms=self.atoms.keys()
atoms.sort()
number=0
for atom in atoms:
number=number+1
self.numbers[atom]=number
#
# Produce the lines
#
lines=[]
for atom in atoms:
lines.append('%s %.2f %.2f %.2f' %(atom,self.atoms[atom]['coords'][0],
self.atoms[atom]['coords'][1],
self.atoms[atom]['coords'][2]))
#
# Bonds
#
bonds=''
for atom in atoms:
for bond in self.atoms[atom]['bonds']:
start_num=self.numbers[atom]
end_num=self.numbers[bond]
#
# Only write bonds one way (small number -> big number)
#
if end_num>start_num:
bonds=bonds+'%d %d ' %(start_num,end_num)
lines.append(bonds)
#
# Torsions
#
tors=''
written=0
for atom in atoms:
for torsion in self.atoms[atom]['torsions']:
atom1=self.numbers[torsion[0]]
atom2=self.numbers[torsion[1]]
atom3=self.numbers[torsion[2]]
atom4=self.numbers[torsion[3]]
if atom1<atom2 and atom2<atom3 and atom4<atom4:
tors=tors+'%d %d %d %d ' %(atom1,atom2,atom3,atom4)
written=written+1
lines.append('%d %s' %(written,tors))
return lines
#
# ---------
#
def ring_detection(self,start_atom,already_visited=[],level=0):
if start_atom in already_visited and len(already_visited) >= 2:
if start_atom==already_visited[-2]:
return []
if already_visited[0]!=start_atom:
return []
return already_visited+[start_atom]
#
return_lists=[]
for bonded_atom in self.atoms[start_atom]['bonds']:
this_list=already_visited[:]+[start_atom]
this_list=self.ring_detection(bonded_atom,this_list,level+1)
if this_list!=[]:# and len(this_list)>1:
return_lists.append(this_list)
return return_lists
#
# ------
#
def get_items(self,item):
#
# Reformat the lists of lists of lists of ... that we get from the ring detection
#
if type(item) is ListType:
real_list=[]
for sub_item in item:
if not type(sub_item) is ListType:
real_list.append(sub_item)
else:
self.get_items(sub_item)
#
# If we got something in the real_list then add it to the biglist
#
if real_list!=[]:
self.biglist.append(real_list)
return
else:
raise 'this should not happen'
#
# -----
#
def assignRingAttribute(self,ring,atoms,current_atom):
if self.atoms[current_atom]['in_ring'] != 0:
self.atoms[current_atom]['in_ring'] += +1
else:
self.atoms[current_atom]['in_ring'] = 1
return
def find_titratable_groups(self):
"""#
# Look for simple substructures that would be titratable groups in the ligand
#"""
atoms=self.atoms.keys()
#
# ring detection (including deleting redundancies & sorting issues)
ring_list = []
tmp=[]
for atom in self.atoms.keys():
temp_ring_list = []
tmp.append(self.ring_detection(atom))
#
# Get just a single list of lists
self.biglist=[]
self.get_items(tmp)
# bigList = self.biglist
ring_list=self.biglist
sorted_ring_list = []
for rring in ring_list:
rring = rring[:-1]
rring.sort()
sorted_ring_list.append(rring)
sorted_ring_list.sort()
#
# delete ring redundancies - only if ring present
if len(sorted_ring_list) > 0:
last = (sorted_ring_list)[-1]
for i in range(len(sorted_ring_list)-2,-1,-1):
if last == sorted_ring_list[i]:
del sorted_ring_list[i]
else:
last = sorted_ring_list[i]
#print "# overall rings (including potentially fused rings) :", len(sorted_ring_list)
#
#
# assigning ring attribute for every ring atom
for at in self.atoms.keys():
self.atoms[at]['in_ring'] = 0
for rring in sorted_ring_list:
for current_atom in rring:
self.assignRingAttribute(rring,atoms,current_atom)
# new attribute for each ring atom: appending the complete ring
# atom names to which the atom belongs
for atom in atoms:
at = self.atoms[atom]
at['ring_list'] = []
non_fused_counter = 0
for rring in sorted_ring_list:
already_detected_false = False
for atom in rring:
at = self.atoms[atom]
if already_detected_false == False and at['in_ring'] == 1:
non_fused_counter += 1
already_detected_false = True
at = self.atoms[atom]
if at['ring_list'] == []:
at['ring_list'] = [rring]
elif rring not in at['ring_list']:
at['ring_list'].append(rring)
#print "# non-fused rings :", non_fused_counter
## LET'S START THE MATCHING...
def match(t,l):
class Node:
def __init__(self, idx1, idx2):
self.at_idx1 = idx1
self.at_idx2 = idx2
nodes = []
for ligand_atoms in l:
self.atoms[ligand_atoms]['alreadyvisited'] = False
for ligand_atoms in l:
for template_atoms in t:
if templates[current_template][template_atoms]['sybylType'] == self.atoms[ligand_atoms]['sybylType']:
matched_type = Node(ligand_atoms,template_atoms)
nodes.append(matched_type)
#print "matching ", self.atoms[ligand_atoms]['sybylType'], self.atoms[ligand_atoms]['atomname']
else:
pass
if len(nodes) != 0:
AtomNameListList = []
for i in nodes:
for j in nodes:
AtomNameList = []
# the O.co2 atoms of the ligand can only match ONCE on EACH template O.co2 template atom
if i.at_idx1 == j.at_idx1 and (i.at_idx2 == j.at_idx2) and (self.atoms[i.at_idx1]['sybylType'] != "O.co2"):
AtomNameList.append(i.at_idx1)
AtomNameList.append(i.at_idx2)
AtomNameListList.append(AtomNameList)
elif i.at_idx1 == j.at_idx1 and (i.at_idx2 == j.at_idx2) \
and (self.atoms[i.at_idx1]['sybylType'] == "O.co2")\
and (self.atoms[i.at_idx1]['alreadyvisited'] != True)\
and (templates[current_template][i.at_idx2]['alreadyvisited'] != True):
AtomNameList.append(i.at_idx1)
AtomNameList.append(i.at_idx2)
self.atoms[i.at_idx1]['alreadyvisited'] = True
templates[current_template][i.at_idx2]['alreadyvisited'] = True
AtomNameListList.append(AtomNameList)
# AGL must be a 2-D integer array, this fixes the bug with NumPy. --Yong Huang
AGL = numpy.zeros((len(AtomNameListList),len(AtomNameListList)))
if str(AGL[0,0]) != '0':
AGL = numpy.zeros((len(AtomNameListList),len(AtomNameListList)), numpy.int)
daseinecounter = 0
dasanderecounter = 0
# what again are these counters counting?
for daseine in AtomNameListList:
dasanderecounter = 0
for dasandere in AtomNameListList:
if (daseine[0] == dasandere[0]) and (daseine[1] == dasandere[1]):
AGL[daseinecounter][dasanderecounter] = 1
# bonded
elif dasandere[0] in self.atoms[daseine[0]]['bonds'] and\
dasandere[1] in templates[current_template][daseine[1]]['neighbours']:
AGL[daseinecounter][dasanderecounter] = 1
# non-bonded atoms in template must also be non-bonded in the ligand
elif dasandere[0] not in self.atoms[daseine[0]]['bonds'] and\
dasandere[1] not in templates[current_template][daseine[1]]['neighbours']:
AGL[daseinecounter][dasanderecounter] = 1
dasanderecounter += 1
daseinecounter += 1
allcliques = Algorithms.find_cliques(AGL)
return allcliques,AtomNameListList,current_template
else:
return [],[],None
# Looping over the entries of the template entries
AllCliqueList = []
dictCounter = 0
dict_of_matched_lig_fragments = {}
matched_lig_template = []
for current_template in templates.keys():
#print "MATCHING", current_template
#print "######## ########"
output = match(templates[current_template],atoms)
for ee in output[0]:
templateDoubleCounter = 0
templateList = []
ligList = []
goodList = []
for cliq_ee in ee:
templateList.append(output[1][cliq_ee][1])
ligList.append(output[1][cliq_ee][0])
temp_templateList = list(set(templateList))
matchedLigAtoms =[]
temptemp = []
if len(temp_templateList) == len(ligList) and (len(ee) == len(templates[current_template].keys())):
for xxee in ee:
# output[1][xxee] => maching pair of ligand and template atoms
# temporary depostion
temptemp.append(output[1][xxee])
matchedLigAtoms.append(output[1][xxee][0])
AllCliqueList.append(matchedLigAtoms)
dict_of_matched_lig_fragments[dictCounter] = {}
dict_of_matched_lig_fragments[dictCounter]['matchedligatoms'] = matchedLigAtoms
dict_of_matched_lig_fragments[dictCounter]['templatename'] = current_template
dict_of_matched_lig_fragments[dictCounter]['type'] = templates_attributes[output[2]]['type']
dict_of_matched_lig_fragments[dictCounter]['modelpka'] = templates_attributes[output[2]]['modelpka']
#print "ligList",ligList
#print "dict",templates_attributes[output[2]]['titratableatoms']
#
# detection of titratable atoms by comparison with template_dict
deposit_list = []
# that's for the hydrogen injection
# in the template library, STANDARD are being used
deposit_template_list = []
dict={}
for looping_template in templates_attributes[output[2]]['titratableatoms']:
for looping_lig in output[1]:
#print looping_lig
if looping_lig[1] == looping_template and (looping_lig in temptemp) :
deposit_list.append(looping_lig[0])
deposit_template_list.append(looping_lig[1])
dict[looping_lig[1]]=looping_lig[0]
#print "tt", looping_lig[1]," ll ", looping_lig[0],looping_lig
dict_of_matched_lig_fragments[dictCounter]['titratableatoms']=deposit_list
dict_of_matched_lig_fragments[dictCounter]['matching_atoms']=dict
dictCounter += 1
#if len(AllCliqueList) == 0:
# print
# print
# print "NOTHING CLIQUED."
# print
# print
#
# AVOID REDUNDANCIES FROM HERE ON
counter = 0
NonRedundantCliques = []
# looping over all entries of maximum_cliques
if len(AllCliqueList) > 1:
for xxxx in AllCliqueList:
if counter < len(AllCliqueList):
internalCounter = counter
# comparison of an individual clique with all other cliques
for comparing in range(internalCounter,len(AllCliqueList)):
# do not compare a clique with itself
if xxxx != AllCliqueList[internalCounter]:
if len(set(xxxx).intersection(set(AllCliqueList[internalCounter]))) > 0:
if len(xxxx) >= len(AllCliqueList[internalCounter]) and xxxx not in NonRedundantCliques: # >= INSTEAD of >
# piperidine case!
# avoid that subset is added to this list
if len(NonRedundantCliques) != 0:
# loop over all entries
for possiblyredundantentries in NonRedundantCliques:
if set(possiblyredundantentries).issubset(set(xxxx)):
print NonRedundantCliques
NonRedundantCliques.remove(possiblyredundantentries)
NonRedundantCliques.append(xxxx)
print NonRedundantCliques
elif set(xxxx).issubset(set(possiblyredundantentries)):
#print "found subset which is not added to the list"
pass
else:
NonRedundantCliques.append(xxxx)
# the other way around
elif len(AllCliqueList[internalCounter]) >= len(xxxx) and AllCliqueList[internalCounter] not in NonRedundantCliques:
if len(NonRedundantCliques) != 0:
for possiblyredundantentries in NonRedundantCliques:
if set(possiblyredundantentries).issubset(set(AllCliqueList[internalCounter])):
NonRedundantCliques.remove(possiblyredundantentries)
NonRedundantCliques.append(AllCliqueList[internalCounter])
elif set(AllCliqueList[internalCounter]).issubset(set(possiblyredundantentries)):
#print "found subset which is not added to the list"
pass
else:
NonRedundantCliques.append(AllCliqueList[internalCounter])
#
# how to adoid, that the actual matching (pair of ligand and template atoms) is not lost?
internalCounter += 1
counter += 1
# if we only find one titratable group
elif len(AllCliqueList) == 1:
NonRedundantCliques = AllCliqueList
# redundancies should be removed now...
#
for allCl in dict_of_matched_lig_fragments:
if dict_of_matched_lig_fragments[allCl]['matchedligatoms'] == NonRedundantCliques[0]:
print "WE MATCHED", dict_of_matched_lig_fragments[allCl]['templatename']
print "matchedligatoms : ", dict_of_matched_lig_fragments[allCl]['matchedligatoms']
print "type : ", dict_of_matched_lig_fragments[allCl]['type']
print "modelpka : ", dict_of_matched_lig_fragments[allCl]['modelpka']
print "titratableatoms : ", dict_of_matched_lig_fragments[allCl]['titratableatoms']
print "matching atoms : ", dict_of_matched_lig_fragments[allCl]['matching_atoms']
# re-run matching to get mutiple titratable sites?
# TJD: This is to resolve the bug fix when allCl is None
if dict_of_matched_lig_fragments != {}:
print dict_of_matched_lig_fragments[allCl]
return dict_of_matched_lig_fragments[allCl]
else:
return {}
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