def convert_db2_to_mol2(db2mols):
allmol2s = []
# loop over each molecule
for mol in db2mols:
# loop over each conformer in the molcule
mol2mols = []
for conf in mol.conformer_list:
#print conf.seglist
# the conformer is defined as a set of segement of the molecule
mol2atomlist = []
residue_list = {}
for segint in conf.seglist:
segment = mol.seg_list[segint - 1]
print segment.num, segment.start, segment.stop
# the segement point to a bunch of coordenates, we know what atom the coordenate coresponds to.
#print segment.start,segment.stop, range(segment.start,segment.stop)
for coordint in range(segment.start, segment.stop + 1):
coord = mol.coord_list[coordint - 1]
print coord.num, coord.atomnum, coord.segnum, coord.X, coord.Y, coord.Z
tempatom = mol.atom_list[coord.atomnum - 1]
#X,Y,Z,Q,type,name,num,resnum,resname):
res_num = 1
resname = "lig"
mol2atom = mol2.atom(coord.X, coord.Y, coord.Z, tempatom.Q,
tempatom.type, tempatom.name,
tempatom.num, res_num, resname)
if residue_list.has_key(res_num):
residue_list[res_num].append(mol2atom)
else:
residue_list[res_num] = [mol2atom]
#residue_list[res_num] = [tempatom]
mol2atomlist.append(mol2atom)
mol2bondlist = []
for bond in mol.bond_list:
#,a1_num,a2_num,num,type
mol2bond = mol2.bond(bond.a1_num, bond.a2_num, bond.num,
bond.type)
mol2bondlist.append(mol2bond)
mol2mol = mol2.Mol("", "", mol2atomlist, mol2bondlist,
residue_list)
mol2mols.append(mol2mol)
allmol2s.append(mol2mols)
#exit()
#return allmol2s
return allmol2s
for j, mol_3 in enumerate(mol_3list):
print "molecule %d" % (j)
#mol_3_new = copy.deepcopy(mol_3)
atomlist = []
for i, move in enumerate(maping):
#print i,move,maping[i]
atom = mol_3.atom_list[move]
atom.num = i + 1
atomlist.append(atom)
#mol_3_new.atom_list = atomlist
#bondlist = copy.deepcopy(mol_2.bond_list)
bondlist = mol_2.bond_list
header = mol_3.header
name = mol_3.name
residuelist = mol_3.residue_list
mol_3_new = mol2.Mol(header, name, atomlist, bondlist, residuelist)
print mol_3.header, mol_3_new.header
# for bond in mol_3_new.bond_list:
# print bond.a1_num, bond.a2_num, bond.num, bond.type
# print atomlist[bond.a1_num-1].num, atomlist[bond.a2_num-1].num, bond.num, bond.type
if j == 0:
mol2.write_mol2(mol_3_new, outfile)
else:
mol2.append_mol2(mol_3_new, outfile)
#print len(mol_list)
#mol = mol2.remove_hydrogens( mol_list[0] )
#mol2.write_mol2(mol,outfile)
def combine_q_and_remove_hydrogens(m):
atom_list = []
bond_list = []
#residue_list = {}
atom_keep_dict = {}
# proceed with only bonds containing 1 heavy atom and 1 hydrogen atom
# check if it is a polar hydrogen ( if so continue)
# add hydrogen charge to that of the heavy atom
for bond_id in range(len(m.bond_list)):
#retain_bond = True
bond = m.bond_list[bond_id]
a1 = m.atom_list[bond.a1_num - 1]
a2 = m.atom_list[bond.a2_num - 1]
#print (a2.type, a1.type)
if (a1.heavy_atom and a2.heavy_atom):
bond_list.append(bond)
atom_keep_dict[bond.a1_num - 1] = True
atom_keep_dict[bond.a2_num - 1] = True
continue
# Atoms down here are always hydrogen
elif (a1.heavy_atom):
if (a1.type in polar_heavy):
print("polar ", a2.type, a1.type)
bond_list.append(bond)
atom_keep_dict[bond.a1_num - 1] = True
atom_keep_dict[bond.a2_num - 1] = True
continue
print bond.a1_num, bond.a1_num, m.atom_list[
bond.a1_num - 1].Q, m.atom_list[bond.a2_num - 1].Q
m.atom_list[bond.a1_num -
1].Q = m.atom_list[bond.a1_num -
1].Q + m.atom_list[bond.a2_num -
1].Q
m.atom_list[bond.a2_num - 1].Q = 0
atom_keep_dict[bond.a1_num - 1] = True
atom_keep_dict[bond.a2_num - 1] = False
elif (a2.heavy_atom):
if (a2.type in polar_heavy):
print(a2.type, a1.type)
bond_list.append(bond)
atom_keep_dict[bond.a1_num - 1] = True
atom_keep_dict[bond.a2_num - 1] = True
continue
print bond.a1_num, bond.a1_num, m.atom_list[
bond.a1_num - 1].Q, m.atom_list[bond.a2_num - 1].Q
m.atom_list[bond.a2_num -
1].Q = m.atom_list[bond.a2_num -
1].Q + m.atom_list[bond.a1_num -
1].Q
m.atom_list[bond.a1_num - 1].Q = 0
atom_keep_dict[bond.a2_num - 1] = True
atom_keep_dict[bond.a1_num - 1] = False // hydrogen
for atom_id in range(len(m.atom_list)):
if (atom_keep_dict[atom_id]):
atom_list.append(m.atom_list[atom_id])
# Assuming that residue list does not change
m2 = mol2.Mol(m.header, m.name, atom_list, bond_list, m.residue_list)
#return data
return m2