def testResidueCopying(self):
smi = "C[C@@H](C(=O)N[C@@H](CS)C(=O)O)N" # H-Ala-Cys-OH
mol = pybel.readstring("smi", smi).OBMol
ob.cvar.chainsparser.PerceiveChains(mol)
mol.SetChainsPerceived()
residues = list(ob.OBResidueIter(mol))
self.assertEqual(len(residues), 2)
# Copy just the Cys N
bv = self.createBitVec(mol.NumAtoms() + 1, (5, ))
nmol = ob.OBMol()
mol.CopySubstructure(nmol, bv)
self.assertEqual(len(list(ob.OBResidueIter(nmol))), 1)
pdb = pybel.Molecule(nmol).write("pdb")
atoms = [line for line in pdb.split("\n") if line.startswith("ATOM")]
self.assertEqual(len(atoms), 1)
cysN = "ATOM 1 N CYS A 2"
self.assertTrue(atoms[0].startswith(cysN))
# Copy the Cys N and Ca
bv = self.createBitVec(mol.NumAtoms() + 1, (5, 6))
nmol.Clear()
mol.CopySubstructure(nmol, bv)
self.assertEqual(len(list(ob.OBResidueIter(nmol))), 1)
pdb = pybel.Molecule(nmol).write("pdb")
atoms = [line for line in pdb.split("\n") if line.startswith("ATOM")]
self.assertEqual(len(atoms), 2)
self.assertTrue(atoms[0].startswith(cysN))
cysCa = "ATOM 2 CA CYS A 2"
self.assertTrue(atoms[1].startswith(cysCa))
# Copy the Ala C and Cys N
bv = self.createBitVec(mol.NumAtoms() + 1, (3, 5))
nmol.Clear()
mol.CopySubstructure(nmol, bv)
self.assertEqual(len(list(ob.OBResidueIter(nmol))), 2)
pdb = pybel.Molecule(nmol).write("pdb")
atoms = [line for line in pdb.split("\n") if line.startswith("ATOM")]
self.assertEqual(len(atoms), 2)
alaC = "ATOM 1 C ALA A 1"
self.assertTrue(atoms[0].startswith(alaC))
cysN = "ATOM 2 N CYS A 2"
self.assertTrue(atoms[1].startswith(cysN))
def GetAtomByID(protein, residueNumber, name):
"""
Returns the OBAtom object given the AtomID (PDB Columns 13-16),
the protein name (ace2 or spike), and the residue number
"""
for res in ob.OBResidueIter(protein):
if res.GetNum() == residueNumber:
for atom in ob.OBResidueAtomIter(res):
if res.GetAtomID(atom) == name:
return atom
def GetResidueMolecule(protein, residueNumber):
"""
Gets the OBMol object corresponding to a residue number on ACE2 protein or Spike protein
protein: 'ace2' or 'spike'
residueNumber: The residue Number
returns: The OBMol object representing the molecule
"""
resMol = ob.OBMol()
for res in ob.OBResidueIter(protein):
if res.GetNum() == residueNumber:
for atom in ob.OBResidueAtomIter(res):
resMol.AddAtom(atom)
break
return resMol
def rna_coords_atom_index_dict(structure):
"""For the debug/detail mode only; creates a dictionary or nucleic acid's atoms' coords with their atom ids as values
:param structure: nucleic acid structure object
:type structure: pybel.Molecule
:return: dictionary indexed by nucleic acid's atoms' coords, with their atom ids as values
:rtype: dict
"""
dictionary = {}
for residue in openbabel.OBResidueIter(structure.OBMol):
if residue.GetNumAtoms() > 3:
for atom in openbabel.OBResidueAtomIter(residue):
dictionary[(
atom.GetX(), atom.GetY(),
atom.GetZ())] = atom.GetResidue().GetAtomID(atom).strip()
return dictionary
def printAtomNames(mol):
for res in openbabel.OBResidueIter(mol):
for atom in openbabel.OBResidueAtomIter(res):
name = res.GetAtomID(atom)
print(name)
def calculateIFPPlants(self, ligands, flex_proteins, ligand_atom_group):
pose_num = len(ligands)
self.flex_residues = [residue.GetName() for residue in ob.OBResidueIter(flex_proteins[0])]
self.full_bits_list = [self.full_bitstring.copy() for i in range(pose_num)]
self.simp_bits_list = [self.simp_bitstring.copy() for i in range(pose_num)]
self.full_nobb_list = [self.full_nobb_bitstring.copy() for i in range(pose_num)]
possible_interactions = []
for x, y in zip(self.interactions, ligand_atom_group['interactions']):
possible_interactions.append(1) if x & y else possible_interactions.append(0)
for ligand, flex, full, full_nobb, simp in \
zip(ligands, flex_proteins, self.full_bits_list, self.full_nobb_list, self.simp_bits_list):
interaction_flags = [0, 0, 0, 0, 0, 0, 0]
if possible_interactions[0]:
for ligand_id in ligand_atom_group['hydrophobic']:
ligand_atom = ligand.GetAtomById(ligand_id)
for atom in self.atomGroup['hydrophobic']:
distance = ligand_atom.GetDistance(atom)
if distance <= HYDROPHOBIC:
if self.simplified:
simp |= self.hydrophobic[self.AA_name]['bitarray']
if self.full:
full |= bitarray('1000000')
if self.full_nobb:
full_nobb |= bitarray('1000000')
interaction_flags[0] = 1
break
if interaction_flags[0]:
break
if possible_interactions[1]:
for path in ligand_atom_group['rings']:
path3 = path[:3]
path3atoms = []
for i in path3:
path3atoms.append(ligand.GetAtom(i))
for ligand_id in path:
for atom in self.atomGroup['aromatic']:
distance = ligand.GetAtom(ligand_id).GetDistance(atom)
if distance <= AROMATIC:
ligCross, ligModulus = getCrossModulus(path3atoms)
dot = np.dot(self.cross, ligCross)
cos_angle = dot / self.modulus / ligModulus
ring_angle = np.arccos(cos_angle) * 180 / np.pi
if (AROMATIC_ANGLE_LOW >= ring_angle) or (AROMATIC_ANGLE_HIGH <= ring_angle):
if self.simplified:
simp |= self.aromatic[self.AA_name]['bitarrayF2F']
if self.full:
full |= bitarray('0100000')
if self.full_nobb:
full_nobb |= bitarray('0100000')
interaction_flags[1] = 1
else:
if self.simplified:
simp |= self.aromatic[self.AA_name]['bitarrayE2F']
if self.full:
full |= bitarray('0010000')
if self.full_nobb:
full_nobb |= bitarray('0010000')
interaction_flags[2] = 1
break
if interaction_flags[1] | interaction_flags[2]:
break
if interaction_flags[1] & interaction_flags[2]:
break
if possible_interactions[2]:
for ligand_id in ligand_atom_group['h_accept']:
ligand_atom = ligand.GetAtomById(ligand_id)
for atom, h_list in zip(self.atomGroup['h_donor'], self.atomGroup['h_donorh']):
distance = ligand_atom.GetDistance(atom)
if distance <= HBOND:
angle_flag = 0
if self.res_name in self.flex_residues:
for flex_atom in ob.OBMolAtomIter(flex):
if (flex_atom.GetAtomicNum() == 1) & (flex_atom.GetResidue().GetName() == self.res_name):
angle = atom.GetAngle(flex_atom, ligand_atom)
if angle > HBOND_ANGLE:
angle_flag = 1
break
else:
for hydrogen in h_list:
angle = atom.GetAngle(hydrogen, ligand_atom)
if angle > HBOND_ANGLE:
angle_flag = 1
break
if angle_flag:
if self.simplified:
simp |= self.h_donor[self.AA_name]['bitarray']
if self.full:
full |= bitarray('0001000')
if self.full_nobb:
full_nobb |= bitarray('0001000')
interaction_flags[3] = 1
break
if interaction_flags[3]:
break
if possible_interactions[3]:
for ligand_id, h_list in zip(ligand_atom_group['h_donor'], ligand_atom_group['h_donorh']):
ligand_atom = ligand.GetAtomById(ligand_id)
for atom in self.atomGroup['h_accept']:
distance = ligand_atom.GetDistance(atom)
if distance <= HBOND:
angle_flag = 0
for h in h_list:
hydrogen = ligand.GetAtomById(h)
angle = ligand_atom.GetAngle(hydrogen, atom)
if angle > HBOND_ANGLE:
angle_flag = 1
break
if angle_flag:
if self.simplified:
simp |= self.h_accept[self.AA_name]['bitarray']
if self.full:
full |= bitarray('0000100')
if self.full_nobb:
full_nobb |= bitarray('0000100')
interaction_flags[4] = 1
if interaction_flags[4]:
break
if possible_interactions[4]:
for ligand_id in ligand_atom_group['negative']:
ligand_atom = ligand.GetAtomById(ligand_id)
for atom in self.atomGroup['positive']:
distance = ligand_atom.GetDistance(atom)
if distance <= ELECTROSTATIC:
if self.simplified:
simp |= self.positive[self.AA_name]['bitarray']
if self.full:
full |= bitarray('0000010')
if self.full_nobb:
full_nobb |= bitarray('0000010')
interaction_flags[5] = 1
break
if interaction_flags[5]:
break
if possible_interactions[5]:
for ligand_id in ligand_atom_group['positive']:
ligand_atom = ligand.GetAtomById(ligand_id)
for atom in self.atomGroup['negative']:
distance = ligand_atom.GetDistance(atom)
if distance <= ELECTROSTATIC:
if self.simplified:
simp |= self.negative[self.AA_name]['bitarray']
if self.full:
full |= bitarray('0000001')
if self.full_nobb:
full_nobb |= bitarray('0000001')
interaction_flags[6] = 1
break
if interaction_flags[6]:
break
if self.full:
if ligand_atom_group['interactions'][0]:
for ligand_id in ligand_atom_group['hydrophobic']:
ligand_atom = ligand.GetAtomById(ligand_id)
bb_atom = self.heavyatoms[1]
distance = ligand_atom.GetDistance(bb_atom)
if distance <= HYDROPHOBIC:
full |= bitarray('1000000')
break
notPRO = False if self.AA_name == 'PRO' else True
if ligand_atom_group['interactions'][3] & notPRO:
for ligand_id in ligand_atom_group['h_accept']:
bb_atom = self.heavyatoms[0]
ligand_atom = ligand.GetAtomById(ligand_id)
distance = ligand_atom.GetDistance(bb_atom)
if distance <= HBOND:
hydrogen = self.hydrogens[0]
angle = bb_atom.GetAngle(hydrogen, ligand_atom)
if angle > HBOND_ANGLE:
full |= bitarray('0001000')
break
if ligand_atom_group['interactions'][2]:
for ligand_id, h_list in zip(ligand_atom_group['h_donor'], ligand_atom_group['h_donorh']):
ligand_atom = ligand.GetAtomById(ligand_id)
bb_atom = self.heavyatoms[3]
distance = ligand_atom.GetDistance(bb_atom)
if distance <= HBOND:
angle_flag = 0
for h in h_list:
hydrogen = ligand.GetAtomById(h)
angle = ligand_atom.GetAngle(hydrogen, bb_atom)
if angle > HBOND_ANGLE:
angle_flag = 1
break
if angle_flag:
full |= bitarray('0000100')
break
print(mssg)
print('#' * len(mssg))
if fingerprint == 'SIMPLE' or fingerprint == 'PBS':
# Read all ligands
ligands_mols = list(pybel.readfile(extension_ligand, filename_ligand))
# Create ligands all atoms (except hydrogens) dictionary
ligands_all_atoms = find_ligands_all_atoms(ligands_mols)
# Fill the RESULTS dictionary of keys - ligand ids and values - lists of 0
for ligand_name in ligands_all_atoms.keys():
RESULTS[ligand_name] = [0] * RNA_LENGTH * FUNCTIONS[fingerprint]
for residue in openbabel.OBResidueIter(
structure.OBMol): # Loop over all RNA residues
RNA_residues.append(
str(residue.GetNum()) + ':' + str(residue.GetChain()))
RNA_nucleotides.append(str(residue.GetName()))
for ligand_name, ligand_atoms in ligands_all_atoms.items():
centroid_ligand = centroid(ligand_atoms)
if fingerprint == 'SIMPLE':
result = calculate_SIMPLE(residue, ligand_name,
ligand_atoms, centroid_ligand)
if result[-1] != 0:
assign_interactions_results(result, RESULTS,
RNA_LENGTH,
len(RNA_residues) - 1,
newfile = open(F'{pdb_code}_{chain_letter}.pdb', 'w+')
for i in range(len(lines)):
line = lines[i]
if line[0:6] == "ATOM " and line[16:17] != 'B':
if line[21:22] == chain_letter:
newfile.write(line)
newfile.close()
obconv.ReadFile(protein, F'{pdb_code}_{chain_letter}.pdb')
os.chdir('/Users/andyjiang/Documents/sherrill/CCProtein/')
for res in ob.OBResidueIter(protein):
mol = Cap(protein, res.GetNum())
print(res.GetNum(), GetCharge(mol), mol.NumAtoms())
obconv.WriteFile(
mol, F"{pdb_code}/{pdb_code}_{chain_letter}_{res.GetNum()}_capped.xyz")
resFile = open(
F"{pdb_code}/{pdb_code}_{chain_letter}_{res.GetNum()}_capped.xyz", "r")
resLines = resFile.readlines()
resFile.close()
newResFile = open(
F"{pdb_code}/{pdb_code}_{chain_letter}_{res.GetNum()}_capped.xyz", "w")
newResFile.write(resLines[0])
newResFile.write(F'{GetCharge(mol)} 1\n')