De-lint ligand.py.
This commit is contained in:
Nathan Baker
427
propka/ligand.py
427
propka/ligand.py
@@ -1,16 +1,9 @@
|
||||
#!/usr/bin/python
|
||||
|
||||
from __future__ import division
|
||||
from __future__ import print_function
|
||||
|
||||
import sys
|
||||
|
||||
import propka.calculations
|
||||
from propka.vector_algebra import *
|
||||
from propka.lib import info, warning
|
||||
"""Ligand classes and functions."""
|
||||
from propka.calculations import squared_distance
|
||||
from propka.vector_algebra import vector
|
||||
|
||||
|
||||
all_sybyl_types = [
|
||||
ALL_SYBYL_TYPES = [
|
||||
'C.3', # carbon sp3
|
||||
'H', # hydrogen
|
||||
'C.2', # carbon sp2
|
||||
@@ -66,344 +59,272 @@ all_sybyl_types = [
|
||||
'Sn'] # tin
|
||||
|
||||
|
||||
#propka_input_types = ['1P','1N','2P','2N']
|
||||
#for type in all_sybyl_types:
|
||||
# temp = type.replace('.','')
|
||||
# if len(temp)>3:
|
||||
# temp = temp[0:3]
|
||||
# propka_input_types.append(temp)
|
||||
#
|
||||
#for t in propka_input_types:
|
||||
# print (t)
|
||||
|
||||
|
||||
propka_input_types = [
|
||||
'1P',
|
||||
'1N',
|
||||
'2P',
|
||||
'2N',
|
||||
'C3',
|
||||
'H',
|
||||
'C2',
|
||||
'Hsp',
|
||||
'C1',
|
||||
'Ht3',
|
||||
'Car',
|
||||
'LP',
|
||||
'Cca',
|
||||
'Du',
|
||||
'N3',
|
||||
'DuC',
|
||||
'N2',
|
||||
'Any',
|
||||
'N1',
|
||||
'Hal',
|
||||
'Nar',
|
||||
'Het',
|
||||
'Nam',
|
||||
'Hev',
|
||||
'Npl',
|
||||
'Li',
|
||||
'N4',
|
||||
'Na',
|
||||
'O3',
|
||||
'Mg',
|
||||
'O2',
|
||||
'Al',
|
||||
'Oco',
|
||||
'Si',
|
||||
'Osp',
|
||||
'K',
|
||||
'Ot3',
|
||||
'Ca',
|
||||
'S3',
|
||||
'Crt',
|
||||
'S2',
|
||||
'Cro',
|
||||
'SO',
|
||||
'Mn',
|
||||
'SO2',
|
||||
'Fe',
|
||||
'P3',
|
||||
'Coo',
|
||||
'F',
|
||||
'Cu',
|
||||
'Cl',
|
||||
'Zn',
|
||||
'Br',
|
||||
'Se',
|
||||
'I',
|
||||
'Mo',
|
||||
'Sn']
|
||||
|
||||
|
||||
max_C_double_bond = 1.3
|
||||
max_C_triple_bond = 1.2
|
||||
|
||||
max_C_double_bond_squared = max_C_double_bond*max_C_double_bond
|
||||
max_C_triple_bond_squared = max_C_triple_bond*max_C_triple_bond
|
||||
|
||||
|
||||
PROPKA_INPUT_TYPES = ['1P', '1N', '2P', '2N', 'C3', 'H', 'C2', 'Hsp', 'C1',
|
||||
'Ht3', 'Car', 'LP', 'Cca', 'Du', 'N3', 'DuC', 'N2',
|
||||
'Any', 'N1', 'Hal', 'Nar', 'Het', 'Nam', 'Hev', 'Npl',
|
||||
'Li', 'N4', 'Na', 'O3', 'Mg', 'O2', 'Al', 'Oco', 'Si',
|
||||
'Osp', 'K', 'Ot3', 'Ca', 'S3', 'Crt', 'S2', 'Cro', 'SO',
|
||||
'Mn', 'SO2', 'Fe', 'P3', 'Coo', 'F', 'Cu', 'Cl', 'Zn',
|
||||
'Br', 'Se', 'I', 'Mo', 'Sn']
|
||||
|
||||
|
||||
MAX_C_DOUBLE_BOND = 1.3
|
||||
MAX_C_TRIPLE_BOND = 1.2
|
||||
MAX_C_DOUBLE_BOND_SQUARED = MAX_C_DOUBLE_BOND*MAX_C_DOUBLE_BOND
|
||||
MAX_C_TRIPLE_BOND_SQUARED = MAX_C_TRIPLE_BOND*MAX_C_TRIPLE_BOND
|
||||
PLANARITY_MARGIN = 0.20
|
||||
|
||||
|
||||
def assign_sybyl_type(atom):
|
||||
"""Assign Sybyl type to atom.
|
||||
|
||||
Args:
|
||||
atom: atom to assign
|
||||
"""
|
||||
# check if we already have assigned a name to this atom
|
||||
if atom.sybyl_assigned:
|
||||
#info(atom.name,'already assigned')
|
||||
return
|
||||
|
||||
# find some properties of the atom
|
||||
ring_atoms = is_ring_member(atom)
|
||||
aromatic = is_aromatic_ring(ring_atoms)
|
||||
planar = is_planar(atom)
|
||||
bonded_elements = {}
|
||||
for i in range(len(atom.bonded_atoms)):
|
||||
bonded_elements[i]=atom.bonded_atoms[i].element
|
||||
|
||||
|
||||
|
||||
for i, bonded_atom in enumerate(atom.bonded_atoms):
|
||||
bonded_elements[i] = bonded_atom.element
|
||||
# Aromatic carbon/nitrogen
|
||||
if aromatic:
|
||||
for ra in ring_atoms:
|
||||
if ra.element in ['C','N']:
|
||||
set_type(ra, ra.element+'.ar')
|
||||
for ring_atom in ring_atoms:
|
||||
if ring_atom.element in ['C', 'N']:
|
||||
set_type(ring_atom, ring_atom.element+'.ar')
|
||||
return
|
||||
|
||||
# check for amide
|
||||
if atom.element in ['O','N','C']:
|
||||
O=None
|
||||
N=None
|
||||
C=None
|
||||
if atom.element in ['O', 'N', 'C']:
|
||||
o_atom = None
|
||||
n_atom = None
|
||||
c_atom = None
|
||||
# oxygen, nitrogen
|
||||
if atom.element in ['O','N']:
|
||||
for b in atom.get_bonded_elements('C'):
|
||||
for bb in b.bonded_atoms:
|
||||
if (bb.element =='N' and atom.element == 'O'):
|
||||
O=atom
|
||||
C=b
|
||||
N=bb
|
||||
elif (bb.element =='O' and atom.element == 'N'):
|
||||
N=atom
|
||||
C=b
|
||||
O=bb
|
||||
if atom.element in ['O', 'N']:
|
||||
for bonded_elem in atom.get_bonded_elements('C'):
|
||||
for bonded_atom in bonded_elem.bonded_atoms:
|
||||
if (bonded_atom.element == 'N' and atom.element == 'O'):
|
||||
o_atom = atom
|
||||
c_atom = bonded_elem
|
||||
n_atom = bonded_atom
|
||||
elif (bonded_atom.element == 'O' and atom.element == 'N'):
|
||||
n_atom = atom
|
||||
c_atom = bonded_elem
|
||||
o_atom = bonded_atom
|
||||
# carbon
|
||||
if atom.element == 'C':
|
||||
nitrogens = atom.get_bonded_elements('N')
|
||||
oxygens = atom.get_bonded_elements('O')
|
||||
if len(nitrogens)==1 and len(oxygens)==1:
|
||||
C = atom
|
||||
N = nitrogens[0]
|
||||
O = oxygens[0]
|
||||
|
||||
|
||||
if C and N and O:
|
||||
if len(nitrogens) == 1 and len(oxygens) == 1:
|
||||
c_atom = atom
|
||||
n_atom = nitrogens[0]
|
||||
o_atom = oxygens[0]
|
||||
if c_atom and n_atom and o_atom:
|
||||
# make sure that the Nitrogen is not aromatic and that it has two heavy atom bonds
|
||||
if not is_aromatic_ring(is_ring_member(N)) and len(N.get_bonded_heavy_atoms())==2:
|
||||
set_type(N,'N.am')
|
||||
set_type(C,'C.2')
|
||||
set_type(O,'O.2')
|
||||
if not is_aromatic_ring(is_ring_member(n_atom)) \
|
||||
and len(n_atom.get_bonded_heavy_atoms()) == 2:
|
||||
set_type(n_atom, 'N.am')
|
||||
set_type(c_atom, 'C.2')
|
||||
set_type(o_atom, 'O.2')
|
||||
return
|
||||
|
||||
|
||||
if atom.element=='C':
|
||||
if atom.element == 'C':
|
||||
# check for carboxyl
|
||||
if len(atom.bonded_atoms)==3 and list(bonded_elements.values()).count('O')==2:
|
||||
i1 = list(bonded_elements.values()).index('O')
|
||||
i2 = list(bonded_elements.values()).index('O',i1+1)
|
||||
if len(atom.bonded_atoms[i1].bonded_atoms)==1 and len(atom.bonded_atoms[i2].bonded_atoms)==1:
|
||||
set_type(atom.bonded_atoms[i1],'O.co2-')
|
||||
set_type(atom.bonded_atoms[i2],'O.co2')
|
||||
set_type(atom,'C.2')
|
||||
if len(atom.bonded_atoms) == 3 and list(bonded_elements.values()).count('O') == 2:
|
||||
index1 = list(bonded_elements.values()).index('O')
|
||||
index2 = list(bonded_elements.values()).index('O', index1+1)
|
||||
if len(atom.bonded_atoms[index1].bonded_atoms) == 1 \
|
||||
and len(atom.bonded_atoms[index2].bonded_atoms) == 1:
|
||||
set_type(atom.bonded_atoms[index1], 'O.co2-')
|
||||
set_type(atom.bonded_atoms[index2], 'O.co2')
|
||||
set_type(atom, 'C.2')
|
||||
return
|
||||
|
||||
|
||||
|
||||
# sp carbon
|
||||
if len(atom.bonded_atoms)<=2:
|
||||
for b in atom.bonded_atoms:
|
||||
if propka.calculations.squared_distance(atom, b) < max_C_triple_bond_squared:
|
||||
set_type(atom,'C.1')
|
||||
set_type(b,b.element+'.1')
|
||||
if len(atom.bonded_atoms) <= 2:
|
||||
for bonded_atom in atom.bonded_atoms:
|
||||
if squared_distance(atom, bonded_atom) < MAX_C_TRIPLE_BOND_SQUARED:
|
||||
set_type(atom, 'C.1')
|
||||
set_type(bonded_atom, bonded_atom.element + '.1')
|
||||
if atom.sybyl_assigned:
|
||||
return
|
||||
|
||||
# sp2 carbon
|
||||
if planar:
|
||||
set_type(atom,'C.2')
|
||||
set_type(atom, 'C.2')
|
||||
# check for N.pl3
|
||||
for b in atom.bonded_atoms:
|
||||
if b.element=='N':
|
||||
if len(b.bonded_atoms)<3 or is_planar(b):
|
||||
set_type(b,'N.pl3')
|
||||
for bonded_atom in atom.bonded_atoms:
|
||||
if bonded_atom.element == 'N':
|
||||
if len(bonded_atom.bonded_atoms) < 3 \
|
||||
or is_planar(bonded_atom):
|
||||
set_type(bonded_atom, 'N.pl3')
|
||||
return
|
||||
|
||||
# sp3 carbon
|
||||
set_type(atom, 'C.3')
|
||||
return
|
||||
|
||||
# Nitrogen
|
||||
if atom.element == 'N':
|
||||
# check for planar N
|
||||
if len(atom.bonded_atoms)==1:
|
||||
if len(atom.bonded_atoms) == 1:
|
||||
if is_planar(atom.bonded_atoms[0]):
|
||||
set_type(atom,'N.pl3')
|
||||
set_type(atom, 'N.pl3')
|
||||
return
|
||||
|
||||
if planar:
|
||||
set_type(atom,'N.pl3')
|
||||
set_type(atom, 'N.pl3')
|
||||
return
|
||||
|
||||
set_type(atom,'N.3')
|
||||
set_type(atom, 'N.3')
|
||||
return
|
||||
|
||||
# Oxygen
|
||||
if atom.element == 'O':
|
||||
set_type(atom,'O.3')
|
||||
|
||||
set_type(atom, 'O.3')
|
||||
if len(atom.bonded_atoms) == 1:
|
||||
# check for carboxyl
|
||||
if atom.bonded_atoms[0].element == 'C':
|
||||
the_carbon = atom.bonded_atoms[0]
|
||||
if len(the_carbon.bonded_atoms)==3 and the_carbon.count_bonded_elements('O')==2:
|
||||
[O1,O2] = the_carbon.get_bonded_elements('O')
|
||||
|
||||
if len(O1.bonded_atoms)==1 and len(O2.bonded_atoms)==1:
|
||||
set_type(O1,'O.co2-')
|
||||
set_type(O2,'O.co2')
|
||||
set_type(the_carbon,'C.2')
|
||||
if len(the_carbon.bonded_atoms) == 3 \
|
||||
and the_carbon.count_bonded_elements('O') == 2:
|
||||
[oxy1, oxy2] = the_carbon.get_bonded_elements('O')
|
||||
if len(oxy1.bonded_atoms) == 1 and len(oxy2.bonded_atoms) == 1:
|
||||
set_type(oxy1, 'O.co2-')
|
||||
set_type(oxy2, 'O.co2')
|
||||
set_type(the_carbon, 'C.2')
|
||||
return
|
||||
|
||||
# check for X=O
|
||||
if propka.calculations.squared_distance(atom, atom.bonded_atoms[0]) < max_C_double_bond_squared:
|
||||
set_type(atom,'O.2')
|
||||
if atom.bonded_atoms[0].element=='C':
|
||||
set_type(atom.bonded_atoms[0],'C.2')
|
||||
if squared_distance(atom, atom.bonded_atoms[0]) < MAX_C_DOUBLE_BOND_SQUARED:
|
||||
set_type(atom, 'O.2')
|
||||
if atom.bonded_atoms[0].element == 'C':
|
||||
set_type(atom.bonded_atoms[0], 'C.2')
|
||||
return
|
||||
|
||||
|
||||
# Sulphur
|
||||
if atom.element == 'S':
|
||||
# check for SO2
|
||||
if list(bonded_elements.values()).count('O')==2:
|
||||
i1 = list(bonded_elements.values()).index('O')
|
||||
i2 = list(bonded_elements.values()).index('O',i1+1)
|
||||
set_type(atom.bonded_atoms[i1],'O.2')
|
||||
set_type(atom.bonded_atoms[i2],'O.2')
|
||||
set_type(atom,'S.o2')
|
||||
if list(bonded_elements.values()).count('O') == 2:
|
||||
index1 = list(bonded_elements.values()).index('O')
|
||||
index2 = list(bonded_elements.values()).index('O', index1+1)
|
||||
set_type(atom.bonded_atoms[index1], 'O.2')
|
||||
set_type(atom.bonded_atoms[index2], 'O.2')
|
||||
set_type(atom, 'S.o2')
|
||||
return
|
||||
|
||||
# check for SO4
|
||||
if list(bonded_elements.values()).count('O')==4:
|
||||
no_O2 = 0
|
||||
if list(bonded_elements.values()).count('O') == 4:
|
||||
no_o2 = 0
|
||||
for i in range(len(atom.bonded_atoms)):
|
||||
if len(atom.bonded_atoms[i].bonded_atoms)==1 and no_O2<2:
|
||||
set_type(atom.bonded_atoms[i],'O.2')
|
||||
no_O2+=1
|
||||
if len(atom.bonded_atoms[i].bonded_atoms) == 1 and no_o2 < 2:
|
||||
set_type(atom.bonded_atoms[i], 'O.2')
|
||||
no_o2 += 1
|
||||
else:
|
||||
set_type(atom.bonded_atoms[i],'O.3')
|
||||
|
||||
set_type(atom,'S.3')
|
||||
|
||||
|
||||
set_type(atom.bonded_atoms[i], 'O.3')
|
||||
set_type(atom, 'S.3')
|
||||
return
|
||||
|
||||
|
||||
# Phosphorus
|
||||
if atom.element == 'P':
|
||||
set_type(atom,'P.3')
|
||||
|
||||
set_type(atom, 'P.3')
|
||||
# check for phosphate group
|
||||
bonded_oxygens = atom.get_bonded_elements('O')
|
||||
for o in bonded_oxygens: set_type(o,'O.3')
|
||||
# if len(bonded_oxygens)>=3:
|
||||
# # find oxygens only bonded to current phosphorus
|
||||
# bonded_oxygens_1 = [o for o in bonded_oxygens if len(o.get_bonded_heavy_atoms())==1]
|
||||
# # find the closest oxygen ...
|
||||
# closest_oxygen = min(bonded_oxygens_1,
|
||||
# key= lambda o:propka.calculations.squared_distance(atom,o))
|
||||
# # ... and set it to O.2
|
||||
# set_type(closest_oxygen,'O.2')
|
||||
|
||||
for o_atom in bonded_oxygens:
|
||||
set_type(o_atom, 'O.3')
|
||||
return
|
||||
|
||||
|
||||
|
||||
element = atom.element.capitalize()
|
||||
set_type(atom,element)
|
||||
# info('Using element as type for %s'%atom.element)
|
||||
|
||||
return
|
||||
set_type(atom, element)
|
||||
|
||||
|
||||
def is_ring_member(atom):
|
||||
return identify_ring(atom,atom,0,[])
|
||||
"""Determine if atom is a member of a ring.
|
||||
|
||||
Args:
|
||||
atom: atom to test
|
||||
Returns:
|
||||
list of atoms
|
||||
"""
|
||||
return identify_ring(atom, atom, 0, [])
|
||||
|
||||
|
||||
def identify_ring(this_atom, original_atom, number, past_atoms):
|
||||
number+=1
|
||||
past_atoms=past_atoms+[this_atom]
|
||||
"""Identify the atoms in a ring
|
||||
|
||||
Args:
|
||||
this_atom: atom to test
|
||||
original_atom: some other atom
|
||||
number: number of atoms
|
||||
past_atoms: atoms that have already been found
|
||||
Returns:
|
||||
list of atoms
|
||||
"""
|
||||
number += 1
|
||||
past_atoms = past_atoms + [this_atom]
|
||||
return_atoms = []
|
||||
if number > 10:
|
||||
return return_atoms
|
||||
|
||||
for atom in this_atom.get_bonded_heavy_atoms():
|
||||
if atom == original_atom and number>2:
|
||||
if atom == original_atom and number > 2:
|
||||
return past_atoms
|
||||
|
||||
if atom not in past_atoms:
|
||||
these_return_atoms = identify_ring(atom, original_atom, number, past_atoms)
|
||||
these_return_atoms = identify_ring(atom, original_atom, number,
|
||||
past_atoms)
|
||||
if len(these_return_atoms) > 0:
|
||||
if len(return_atoms)>len(these_return_atoms) or len(return_atoms)==0:
|
||||
if len(return_atoms) > len(these_return_atoms) \
|
||||
or len(return_atoms) == 0:
|
||||
return_atoms = these_return_atoms
|
||||
|
||||
return return_atoms
|
||||
|
||||
|
||||
def set_type(atom, type_):
|
||||
"""Set atom type..
|
||||
|
||||
|
||||
def set_type(atom,type):
|
||||
#info(atom, '->',type)
|
||||
atom.sybyl_type = type
|
||||
atom.sybyl_assigned=True
|
||||
return
|
||||
|
||||
|
||||
Args:
|
||||
atom: atom to set
|
||||
type_: type value to set
|
||||
"""
|
||||
atom.sybyl_type = type_
|
||||
atom.sybyl_assigned = True
|
||||
|
||||
|
||||
def is_planar(atom):
|
||||
""" Finds out if atom forms a plane together with its bonded atoms"""
|
||||
atoms = [atom]+atom.bonded_atoms
|
||||
"""Finds out if atom forms a plane together with its bonded atoms.
|
||||
|
||||
Args:
|
||||
atom: atom to test
|
||||
Returns:
|
||||
Boolean
|
||||
"""
|
||||
atoms = [atom] + atom.bonded_atoms
|
||||
return are_atoms_planar(atoms)
|
||||
|
||||
|
||||
def are_atoms_planar(atoms):
|
||||
if len(atoms)==0:
|
||||
return False
|
||||
if len(atoms)<4:
|
||||
return False
|
||||
v1 = vector(atom1=atoms[0], atom2=atoms[1])
|
||||
v2 = vector(atom1=atoms[0], atom2=atoms[2])
|
||||
n = (v1**v2).rescale(1.0)
|
||||
"""Test whether a group of atoms are planar.
|
||||
|
||||
margin = 0.20
|
||||
for b in atoms[3:]:
|
||||
v = vector(atom1=atoms[0], atom2=b).rescale(1.0)
|
||||
#info(atoms[0],abs(v*n) )
|
||||
if abs(v*n)>margin:
|
||||
Args:
|
||||
atoms: list of atoms
|
||||
Returns:
|
||||
Boolean
|
||||
"""
|
||||
if len(atoms) == 0:
|
||||
return False
|
||||
if len(atoms) < 4:
|
||||
return False
|
||||
vec1 = vector(atom1=atoms[0], atom2=atoms[1])
|
||||
vec2 = vector(atom1=atoms[0], atom2=atoms[2])
|
||||
norm = (vec1**vec2).rescale(1.0)
|
||||
margin = PLANARITY_MARGIN
|
||||
for atom in atoms[3:]:
|
||||
vec = vector(atom1=atoms[0], atom2=atom).rescale(1.0)
|
||||
if abs(vec*norm) > margin:
|
||||
return False
|
||||
|
||||
return True
|
||||
|
||||
def is_aromatic_ring(atoms):
|
||||
if len(atoms)<5:
|
||||
return False
|
||||
|
||||
def is_aromatic_ring(atoms):
|
||||
"""Determine whether group of atoms form aromatic ring.
|
||||
|
||||
Args:
|
||||
atoms: list of atoms to test
|
||||
Returns:
|
||||
Boolean
|
||||
"""
|
||||
if len(atoms) < 5:
|
||||
return False
|
||||
for i in range(len(atoms)):
|
||||
if not are_atoms_planar(atoms[i:]+atoms[:i]):
|
||||
return False
|
||||
|
||||
return True
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user