ljmartin

def setBasicNitrogens(mol):
    nitrogens = [i[0] for i in mol.GetSubstructMatches(Chem.MolFromSmarts('N'))]
    for nidx in nitrogens:
        atom = mol.GetAtomWithIdx(nidx)
        if atom.GetIsAromatic():
            continue
        bonds = atom.GetBonds()
        conj = any([b.GetIsConjugated() for b in bonds])
        if conj:
            continue

ljmartin

ljmartin

ljmartin

ljmartin

<ForceField>
 <AtomTypes>
  <Type name="metha-C" class="O" element="C" mass="16.04"/>
 </AtomTypes>
 <Residues>
  <Residue name="UME">
   <Atom name="C" type="metha-C"/>
  </Residue>
 </Residues>
 <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">

ljmartin

ljmartin

ljmartin

prot_dons = np.array(pocket.GetSubstructMatches(HDonorSmarts)).flatten()
prot_accs = np.array(pocket.GetSubstructMatches(HAcceptorSmarts)).flatten()


lig_dons = np.array(ligand.GetSubstructMatches(HDonorSmarts)).flatten()
lig_accs = np.array(ligand.GetSubstructMatches(HAcceptorSmarts)).flatten()

def unit_vector(vector):
    """ Returns the unit vector of the vector.  """
    return vector / np.linalg.norm(vector)

ljmartin

ljmartin