Merge pull request #101 from evanfeinberg/complex_tutorial

  hyd_conversion.SetInAndOutFormats(str(input_format), str("pdb"))

  mol = openbabel.OBMol()

  hyd_conversion.ReadFile(mol, str(input_file))

  # AddHydrogens(polaronly, correctForPH, pH)

  mol.AddHydrogens(True, True, 7.4)

  # AddHydrogens(not-polaronly, correctForPH, pH)

  mol.AddHydrogens(False, True, 7.4)

  hyd_conversion.WriteFile(mol, str(hyd_output))

  if verbose:

import tempfile

import os

import mdtraj as md

import numpy as np

def combine_mdtraj(protein, ligand):

  chain = protein.topology.add_chain()

  residue = protein.topology.add_residue("LIG", chain, resSeq=1)

  for atom in ligand.topology.atoms:

      protein.topology.add_atom(atom.name, atom.element, residue)

  protein.xyz = np.hstack([protein.xyz, ligand.xyz])

  protein.topology.create_standard_bonds()

  return protein

def visualize_complex(complex_mdtraj):

  ligand_atoms = [a.index for a in complex_mdtraj.topology.atoms if "LIG" in str(a.residue)]

  binding_pocket_atoms = md.compute_neighbors(complex_mdtraj, 0.5, ligand_atoms)[0]

  binding_pocket_residues = list(set([complex_mdtraj.topology.atom(a).residue.resSeq for a in binding_pocket_atoms]))

  binding_pocket_residues = [str(r) for r in binding_pocket_residues]

  binding_pocket_residues = " or ".join(binding_pocket_residues)

  traj = nglview.MDTrajTrajectory( complex_mdtraj ) # load file from RCSB PDB

  ngltraj = nglview.NGLWidget( traj )

  ngltraj.representations = [

  { "type": "cartoon", "params": {

  "sele": "protein", "color": "residueindex"

  } },

  { "type": "licorice", "params": {

  "sele": "(not hydrogen) and (resi (%s))" %  binding_pocket_residues

  } },

  { "type": "ball+stick", "params": {

  "sele": "resn LIG"

  } }

  ]

  return ngltraj

def convert_lines_to_mdtraj(molecule_lines):

  tempdir = tempfile.mkdtemp()

  molecule_file = os.path.join(tempdir, "molecule.pdb")

  with open(molecule_file, "wb") as f:

    f.writelines(molecule_lines)

  molecule_mdtraj = md.load(molecule_file)

  return molecule_mdtraj

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