def get_positions_from_pdbfile(filename): """ Reads the positions from a PDB file. :param filename: Path to the file where we will read PDB coordinates. :type filename: str :returns: - positions ( `Quantity() <https://docs.openmm.org/development/api-python/generated/simtk.unit.quantity.Quantity.html>`_ ( np.array( [cgmodel.num_beads,3] ), simtk.unit ) ) - Positions for the particles in the PDB file. """ pdb_mm_obj = PDBFile(filename) positions = pdb_mm_obj.getPositions() return positions
def read_pdbfile(cgmodel, filename): """ Reads the positions and topology from a PDB file. :param cgmodel: CGModel() class object :type cgmodel: class :param filename: Path to the file where we will read PDB coordinates. :type filename: str :returns: - cgmodel - A CGModel() class object with the positions and topology from the PDB file that was read. """ pdb_mm_obj = PDBFile(filename) cgmodel.positions = pdb_mm_obj.getPositions() cgmodel.topology = pdb_mm_obj.getTopology() return cgmodel