def setAtomsDictionary(self, atoms=None, pdbfile=None): """ set reference to the atoms dictionary atoms = dictionary with atom objects to make the protein from, i.e. atoms[chainID][resName] """ if atoms != None: self.atoms = atoms elif pdbfile != None: self.atoms = pdb.readPDB(filename=pdbfile) else: pka_print("need either an atoms dictionary or pdbfile to create a protein") sys.exit(9) return
def setAtomsDictionary(self, atoms=None, pdbfile=None): """ set reference to the atoms dictionary atoms = dictionary with atom objects to make the protein from, i.e. atoms[chainID][resName] """ if atoms != None: self.atoms = atoms elif pdbfile != None: self.atoms = pdb.readPDB(filename=pdbfile) else: pka_print( "need either an atoms dictionary or pdbfile to create a protein" ) sys.exit(9) return
print('Created ligand residue %s with %2d atoms'%(self, len(self.atoms))) return def __str__(self): return '%s-%4d'%(self.resName,self.resNumb) if __name__ == '__main__': if len(sys.argv)<2: sys.exit(0) protonator = protonate.Protonate() print(sys.argv[1]) atoms = pdb.readPDB(sys.argv[1],tags=["ATOM","HETATM"]) my_ligand = ligand(atoms) #assign sybyl names protonator.remove_all_hydrogen_atoms_from_ligand(my_ligand) my_ligand.assign_atom_names() my_ligand.writePDB('before_ligand_protonation.pdb') #convert to propka input names # for atom in my_ligand.atoms: # temp = atom.name # temp = temp.replace('.','')
if __name__ == '__main__': # If called directly, set up protein bond dictionary import protein, pdb, sys,os arguments = sys.argv if len(arguments) != 2: pka_print('Usage: bonds.py <pdb_file>') sys.exit(0) filename = arguments[1] if not os.path.isfile(filename): pka_print('Error: Could not find \"%s\"'%filename) sys.exit(1) pdblist = pdb.readPDB(filename) my_protein = protein.Protein(pdblist,'test.pdb') for chain in my_protein.chains: for residue in chain.residues: residue.atoms = [atom for atom in residue.atoms if atom.get_element() != 'H'] b = bondmaker() #b.protein_bonds = {} atoms = b.find_bonds_for_protein_by_distance(my_protein) # b.generate_protein_bond_dictionary(atoms) #file = open(b.data_file_name,'wb') #pickle.dump(b.protein_bonds, file) #file.close()
(self, len(self.atoms))) return def __str__(self): return '%s-%4d' % (self.resName, self.resNumb) if __name__ == '__main__': if len(sys.argv) < 2: sys.exit(0) protonator = protonate.Protonate() pka_print(sys.argv[1]) atoms = pdb.readPDB(sys.argv[1], tags=["ATOM", "HETATM"]) my_ligand = ligand(atoms) #assign sybyl names protonator.remove_all_hydrogen_atoms_from_ligand(my_ligand) my_ligand.assign_atom_names() my_ligand.writePDB('before_ligand_protonation.pdb') #convert to propka input names # for atom in my_ligand.atoms: # temp = atom.name # temp = temp.replace('.','') # if len(temp)>3: # temp = temp[0:3]