utilities.iotools submodule
- cg_openmm.utilities.iotools.get_positions_from_pdbfile(filename)[source]
Reads the positions from a PDB file.
- Parameters
filename (str) – Path to the file where we will read PDB coordinates.
- Returns
positions ( Quantity() ( np.array( [cgmodel.num_beads,3] ), simtk.unit ) ) - Positions for the particles in the PDB file.
- cg_openmm.utilities.iotools.get_topology_from_pdbfile(filename)[source]
Reads the positions from a PDB file.
- Parameters
filename (str) – Path to the file where we will read PDB coordinates.
- Returns
topology ( Topology() ) - OpenMM Topology() object, which stores bonds, angles, and other structural attributes of the coarse grained model
- cg_openmm.utilities.iotools.read_mm_energies(openmm_data_file)[source]
Read the energies from an OpenMM data file.
- Parameters
openmm_data_file (str) – The path to an OpenMM data file (CSV format)
- Returns
energies ( np.array( float * simtk.unit ) ) - An array containing all data in ‘openmm_data_file’
- cg_openmm.utilities.iotools.read_pdbfile(cgmodel, filename)[source]
Reads the positions and topology from a PDB file.
- Parameters
cgmodel (class) – CGModel() class object
filename (str) – Path to the file where we will read PDB coordinates.
- Returns
cgmodel - A CGModel() class object with the positions and topology from the PDB file that was read.
- cg_openmm.utilities.iotools.write_bonds(CGModel, pdb_object)[source]
Writes the bonds from an input CGModel class object to the file object ‘pdb_object’, using PDB ‘CONECT’ syntax.
- Parameters
CGModel (class) – CGModel() class object
pdb_object (file) – File object to which we will write the bond list
- cg_openmm.utilities.iotools.write_pdbfile_without_topology(CGModel, filename, energy=None)[source]
Writes the positions from an input CGModel class object to the file ‘filename’.
- Parameters
CGModel (class) – CGModel() class object
filename (str) – Path to the file where we will write PDB coordinates.
energy – Energy to write to the PDB file, default = None