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Jimmy Charnley Kromann
2012-11-15 17:47:47 +01:00
parent 57be97bf6b
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Source/protonate.py Executable file
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#!/usr/bin/python
from Source.vector_algebra import *
import Source.bonds, Source.pdb, Source.atom
class Protonate:
""" Protonates atoms using VSEPR theory """
def __init__(self, verbose=False):
self.verbose=verbose
self.valence_electrons = {'H': 1,
'He':2,
'Li':1,
'Be':2,
'B': 3,
'C': 4,
'N': 5,
'O': 6,
'F': 7,
'Ne':8,
'Na':1,
'Mg':2,
'Al':3,
'Si':4,
'P': 5,
'S': 6,
'Cl':7,
'Ar':8,
'K': 1,
'Ca':2,
'Sc':2,
'Ti':2,
'Va':2,
'Cr':1,
'Mn':2,
'Fe':2,
'Co':2,
'Ni':2,
'Cu':1,
'Zn':2,
'Ga':3,
'Ge':4,
'As':5,
'Se':6,
'Br':7,
'Kr':8}
self.standard_charges= {'ARG-NH1':1.0,
'ASP-OD2':-1.0,
'GLU-OE2':-1.0,
'HIS-ND1':1.0,
'LYS-NZ':1.0,
'N+':1.0,
'C-':-1.0}
self.sybyl_charges = {'N.pl3':+1,
'N.3':+1,
'N.4':+1,
'N.ar':+1,
'O.co2-':-1}
self.bond_lengths = {'C':1.09,
'N':1.01,
'O':0.96,
'F':0.92,
'Cl':1.27,
'Br':1.41,
'I':1.61,
'S':1.35}
# protonation_methods[steric_number] = method
self.protonation_methods = {4:self.tetrahedral,
3:self.trigonal}
return
def protonate(self, molecules):
""" Will protonate all atoms in the molecular container """
self.display('----- Protonation started -----')
# Remove all currently present hydrogen atoms
self.remove_all_hydrogen_atoms(molecules)
# protonate all atoms
for name in molecules.conformation_names:
non_H_atoms = molecules.conformations[name].get_non_hydrogen_atoms()
for atom in non_H_atoms:
self.protonate_atom(atom)
# fix hydrogen names
#self.set_proton_names(non_H_atoms)
return
def remove_all_hydrogen_atoms(self, molecular_container):
for name in molecular_container.conformation_names:
molecular_container.conformations[name].atoms = molecular_container.conformations[name].get_non_hydrogen_atoms()
return
def set_charge(self, atom):
# atom is a protein atom
if atom.type=='atom':
key = '%3s-%s'%(atom.resName, atom.name)
if atom.terminal:
self.display(atom.terminal)
key=atom.terminal
if key in list(self.standard_charges.keys()):
atom.charge = self.standard_charges[key]
self.display('Charge', atom, atom.charge)
atom.charge_set = True
# atom is a ligand atom
elif atom.type=='hetatm':
if atom.sybyl_type in list(self.sybyl_charges.keys()):
atom.charge = self.sybyl_charges[atom.sybyl_type]
atom.sybyl_type = atom.sybyl_type.replace('-','')
atom.charge_set = True
return
def protonate_atom(self, atom):
if atom.is_protonated: return
if atom.element == 'H': return
self.set_charge(atom)
self.set_number_of_protons_to_add(atom)
self.set_steric_number_and_lone_pairs(atom)
self.add_protons(atom)
atom.is_protonated = True
return
def set_proton_names(self, heavy_atoms):
for heavy_atom in heavy_atoms:
i = 1
for bonded in heavy_atom.bonded_atoms:
if bonded.element == 'H':
bonded.name+='%d'%i
i+=1
return
def set_number_of_protons_to_add(self, atom):
self.display('*'*10)
self.display('Setting number of protons to add for',atom)
atom.number_of_protons_to_add = 8
self.display(' %4d'%8)
atom.number_of_protons_to_add -= self.valence_electrons[atom.element]
self.display('Valence eletrons: %4d'%-self.valence_electrons[atom.element])
atom.number_of_protons_to_add -= len(atom.bonded_atoms)
self.display('Number of bonds: %4d'%- len(atom.bonded_atoms))
atom.number_of_protons_to_add -= atom.number_of_pi_electrons_in_double_and_triple_bonds
self.display('Pi electrons: %4d'%-atom.number_of_pi_electrons_in_double_and_triple_bonds)
atom.number_of_protons_to_add += int(atom.charge)
self.display('Charge: %4.1f'%atom.charge)
self.display('-'*10)
self.display(atom.number_of_protons_to_add)
return
def set_steric_number_and_lone_pairs(self, atom):
# If we already did this, there is no reason to do it again
if atom.steric_number_and_lone_pairs_set:
return
self.display('='*10)
self.display('Setting steric number and lone pairs for',atom)
# costumly set the N backbone atoms up for peptide bond trigonal planer shape
#if atom.name == 'N' and len(atom.bonded_atoms) == 2:
# atom.steric_number = 3
# atom.number_of_lone_pairs = 0
# self.display 'Peptide bond: steric number is %d and number of lone pairs is %s'%(atom.steric_number,
# atom.number_of_lone_pairs)
# return
atom.steric_number = 0
self.display('%65s: %4d'%('Valence electrons',self.valence_electrons[atom.element]))
atom.steric_number += self.valence_electrons[atom.element]
self.display('%65s: %4d'%('Number of bonds',len(atom.bonded_atoms)))
atom.steric_number += len(atom.bonded_atoms)
self.display('%65s: %4d'%('Number of hydrogen atoms to add',atom.number_of_protons_to_add))
atom.steric_number += atom.number_of_protons_to_add
self.display('%65s: %4d'%('Number of pi-electrons in double and triple bonds(-)',atom.number_of_pi_electrons_in_double_and_triple_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_double_and_triple_bonds
self.display('%65s: %4d'%('Number of pi-electrons in conjugated double and triple bonds(-)',atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds))
atom.steric_number -= atom.number_of_pi_electrons_in_conjugate_double_and_triple_bonds
self.display('%65s: %4d'%('Number of donated co-ordinated bonds',0))
atom.steric_number += 0
self.display('%65s: %4.1f'%('Charge(-)',atom.charge))
atom.steric_number -= atom.charge
atom.steric_number = math.floor(atom.steric_number/2.0)
atom.number_of_lone_pairs = atom.steric_number - len(atom.bonded_atoms) - atom.number_of_protons_to_add
self.display('-'*70)
self.display('%65s: %4d'%('Steric number',atom.steric_number))
self.display('%65s: %4d'%('Number of lone pairs',atom.number_of_lone_pairs))
atom.steric_number_and_lone_pairs_set = True
return
def add_protons(self, atom):
# decide which method to use
self.display('PROTONATING',atom)
if atom.steric_number in list(self.protonation_methods.keys()):
self.protonation_methods[atom.steric_number](atom)
else:
print('Warning: Do not have a method for protonating',atom,'(steric number: %d)'%atom.steric_number)
return
def trigonal(self, atom):
self.display('TRIGONAL - %d bonded atoms'%(len(atom.bonded_atoms)))
rot_angle = math.radians(120.0)
c = vector(atom1 = atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
a = vector(atom1 = atom, atom2 = atom.bonded_atoms[0])
# use plane of bonded trigonal atom - e.g. arg
self.set_steric_number_and_lone_pairs(atom.bonded_atoms[0])
if atom.bonded_atoms[0].steric_number == 3 and len(atom.bonded_atoms[0].bonded_atoms)>1:
# use other atoms bonded to the neighbour to establish the plane, if possible
other_atom_indices = []
for i in range(len(atom.bonded_atoms[0].bonded_atoms)):
if atom.bonded_atoms[0].bonded_atoms[i] != atom:
other_atom_indices.append(i)
v1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0])
v2 = vector(atom1 = atom.bonded_atoms[0],
atom2 = atom.bonded_atoms[0].bonded_atoms[other_atom_indices[0]])
axis = v1**v2
# this is a trick to make sure that the order of atoms doesn't influence
# the final postions of added protons
if len(other_atom_indices)>1:
v3 = vector(atom1 = atom.bonded_atoms[0],
atom2 = atom.bonded_atoms[0].bonded_atoms[other_atom_indices[1]])
axis2 = v1**v3
if axis * axis2>0:
axis = axis+axis2
else:
axis = axis-axis2
else:
axis = a.orthogonal()
a = rotate_vector_around_an_axis(rot_angle, axis, a)
a = self.set_bond_distance(a, atom.element)
self.add_proton(atom, c+a)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
a1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1 = atom, atom2 = atom.bonded_atoms[1]).rescale(1.0)
new_a = -a1 - a2
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c+new_a)
return
def tetrahedral(self, atom):
self.display('TETRAHEDRAL - %d bonded atoms'%(len(atom.bonded_atoms)))
rot_angle = math.radians(109.5)
# sanity check
# if atom.number_of_protons_to_add + len(atom.bonded_atoms) != 4:
# self.display 'Error: Attempting tetrahedral structure with %d bonds'%(atom.number_of_protons_to_add +
# len(atom.bonded_atoms))
c = vector(atom1 = atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
a = vector(atom1 = atom, atom2 = atom.bonded_atoms[0])
axis = a.orthogonal()
a = rotate_vector_around_an_axis(rot_angle, axis, a)
a = self.set_bond_distance(a, atom.element)
self.add_proton(atom, c+a)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
a1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1 = atom, atom2 = atom.bonded_atoms[1]).rescale(1.0)
axis = a1 + a2
new_a = rotate_vector_around_an_axis(math.radians(90), axis, -a1)
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c+new_a)
# 3 bonds
if len(atom.bonded_atoms) == 3 and atom.number_of_protons_to_add > 0:
a1 = vector(atom1 = atom, atom2 = atom.bonded_atoms[0]).rescale(1.0)
a2 = vector(atom1 = atom, atom2 = atom.bonded_atoms[1]).rescale(1.0)
a3 = vector(atom1 = atom, atom2 = atom.bonded_atoms[2]).rescale(1.0)
new_a = -a1-a2-a3
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, c+new_a)
return
def add_proton(self, atom, position):
# Create the new proton
new_H = Source.atom.Atom()
new_H.setProperty(numb = None,
name = 'H%s'%atom.name[1:],
resName = atom.resName,
chainID = atom.chainID,
resNumb = atom.resNumb,
x = round(position.x,3), # round of to three digimal points
y = round(position.y,3), # to avoid round-off differences
z = round(position.z,3), # when input file
occ = None,
beta = None)
new_H.element = 'H'
new_H.type = atom.type
new_H.bonded_atoms = [atom]
new_H.charge = 0
new_H.steric_number = 0
new_H.number_of_lone_pairs = 0
new_H.number_of_protons_to_add = 0
new_H.number_of_pi_electrons_in_double_and_triple_bonds = 0
new_H.is_protonates = True
atom.bonded_atoms.append(new_H)
atom.number_of_protons_to_add -=1
atom.conformation_container.add_atom(new_H)
# update names of all protons on this atom
new_H.residue_label = "%-3s%4d%2s" % (new_H.name,new_H.resNumb, new_H.chainID)
no_protons = atom.count_bonded_elements('H')
if no_protons > 1:
i = 1
for proton in atom.get_bonded_elements('H'):
proton.name = 'H%s%d'%(atom.name[1:],i)
proton.residue_label = "%-3s%4d%2s" % (proton.name,proton.resNumb, proton.chainID)
i+=1
self.display('added',new_H, 'to',atom)
return
def set_bond_distance(self, a, element):
d = 1.0
if element in list(self.bond_lengths.keys()):
d = self.bond_lengths[element]
else:
print('WARNING: Bond length for %s not found, using the standard value of %f'%(element, d))
a = a.rescale(d)
return a
def display(self,*text):
if self.verbose:
s = ''
for t in text:
s+='%s '%t
print(s)
return
if __name__ == '__main__':
import protein, pdb, sys,os
arguments = sys.argv
if len(arguments) != 2:
print('Usage: protonate.py <pdb_file>')
sys.exit(0)
filename = arguments[1]
if not os.path.isfile(filename):
print('Error: Could not find \"%s\"'%filename)
sys.exit(1)
p = Protonate()
pdblist = pdb.readPDB(filename)
my_protein = protein.Protein(pdblist,'test.pdb')
p.remove_all_hydrogen_atoms_from_protein(my_protein)
my_protein.writePDB('before_protonation.pdb')
p.protonate_protein(my_protein)
## write out protonated file
my_protein.writePDB('protonated.pdb')