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]
