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
