parmed.charmm.CharmmPsfFile¶

class parmed.charmm.CharmmPsfFile(**kwargs)[source]¶

A chemical Structure instantiated from CHARMM files.

Parameters

psf_namestr, optional: Name of the PSF file (it must exist)

Raises

IOErrorIf file psf_name does not exist
CharmmPsfErrorIf any parsing errors are encountered

Attributes

box
box_vectors: 3, 3-element tuple of unit cell vectors that are Quantity objects of
combining_rule
coordinates
positions: A list of 3-element Quantity tuples of dimension length representing the atomic positions for every atom in the system.
topology: The OpenMM Topology object.
velocities: A (natom, 3)-shape numpy array with atomic velocities for every atom in
view: Returns an indexable object that can be indexed like a standard

Methods

`add_atom`(atom, resname, resnum[, chain, …])	Adds a new atom to the Structure, adding a new residue to residues if it has a different name or number as the last residue added and adding it to the atoms list.
`add_atom_to_residue`(atom, residue)	Adds a new atom to the Structure at the end if the given residue
`assign_bonds`(*reslibs)	Assigns bonds to all atoms based on the provided residue template libraries.
`clear_cmap`()	Clear the cmap list to prevent any CMAP parameters from being used
`copy`(cls[, split_dihedrals])	Makes a copy of the current structure as an instance of a specified subclass
`createSystem`([params])	Creates an OpenMM System object from the CHARMM PSF file.
`from_structure`(struct[, copy])	Instantiates a CharmmPsfFile from an input Structure instance.
`get_box`([frame])	In some cases, multiple conformations may be stored in the Structure.
`get_coordinates`([frame])	In some cases, multiple conformations may be stored in the Structure.
`has_NBFIX`()	Returns whether or not any pairs of atom types have their LJ interactions modified by an NBFIX definition
`is_changed`()	Determines if any of the topology has changed for this structure
`join_dihedrals`()	Joins multi-term torsions into a single term and makes all of the parameters DihedralTypeList instances.
`load_dataframe`(df)	Loads atomic properties from an input DataFrame
`load_parameters`(parmset[, copy_parameters])	Loads parameters from a parameter set that was loaded via CHARMM RTF, PAR, and STR files.
`omm_add_constraints`(system, constraints, …)	Adds constraints to a given system
`omm_angle_force`([constraints, …])	Creates an OpenMM HarmonicAngleForce object (or AmoebaAngleForce if the angles are for an Amoeba-parametrized system)
`omm_bond_force`([constraints, rigidWater, …])	Creates an OpenMM Bond Force object (or AmoebaBondForce if the bonds are for an Amoeba-parametrized system)
`omm_cmap_force`()	Creates the OpenMM CMAP torsion force
`omm_dihedral_force`([split])	Creates the OpenMM PeriodicTorsionForce modeling dihedrals
`omm_gbsa_force`(implicitSolvent[, …])	Creates a Generalized Born force for running implicit solvent calculations
`omm_improper_force`()	Creates the OpenMM improper torsion force (quadratic bias)
`omm_nonbonded_force`([nonbondedMethod, …])	Creates the OpenMM NonbondedForce instance
`omm_out_of_plane_bend_force`()	Creates the Amoeba out-of-plane bend force
`omm_pi_torsion_force`()	Creates the Amoeba pi-torsion force
`omm_rb_torsion_force`()	Creates the OpenMM RBTorsionForce for Ryckaert-Bellemans torsions
`omm_set_virtual_sites`(system)	Sets the virtual sites in a given OpenMM System object from the extra points defined in this system
`omm_stretch_bend_force`()	Create the OpenMM Amoeba stretch-bend force for this system
`omm_torsion_torsion_force`()	Create the OpenMM Amoeba coupled-torsion (CMAP) force
`omm_trigonal_angle_force`()	Creates the Amoeba trigonal-angle force
`omm_urey_bradley_force`()	Creates the OpenMM Urey-Bradley force
`prune_empty_terms`()	Looks through all of the topological lists and gets rid of terms in which at least one of the atoms is None or has an idx attribute set to -1 (indicating that it has been removed from the atoms atom list)
`save`(fname[, format, overwrite])	Saves the current Structure in the requested file format.
`split`()	Split the current Structure into separate Structure instances for each unique molecule.
`strip`(selection)	Deletes a subset of the atoms corresponding to an atom-based selection.
`to_dataframe`()	Generates a DataFrame from the current Structure’s atomic properties
`unchange`()	Toggles all lists so that they do not indicate any changes
`update_dihedral_exclusions`()	Nonbonded exclusions and exceptions have the following priority:
`visualize`(args, *kwargs)	Use nglview for visualization.
`write_cif`(dest[, renumber, coordinates, …])	Write a PDB file from the current Structure instance
`write_pdb`(dest[, renumber, coordinates, …])	Write a PDB file from a Structure instance
`write_psf`(dest[, vmd])	Writes a PSF file from the stored molecule

__init__(psf_name=None)[source]¶: Opens and parses a PSF file, then instantiates a CharmmPsfFile instance from the data.

Methods

`__init__`([psf_name])	Opens and parses a PSF file, then instantiates a CharmmPsfFile instance from the data.
`add_atom`(atom, resname, resnum[, chain, …])	Adds a new atom to the Structure, adding a new residue to residues if it has a different name or number as the last residue added and adding it to the atoms list.
`add_atom_to_residue`(atom, residue)	Adds a new atom to the Structure at the end if the given residue
`assign_bonds`(*reslibs)	Assigns bonds to all atoms based on the provided residue template libraries.
`clear_cmap`()	Clear the cmap list to prevent any CMAP parameters from being used
`copy`(cls[, split_dihedrals])	Makes a copy of the current structure as an instance of a specified subclass
`createSystem`([params])	Creates an OpenMM System object from the CHARMM PSF file.
`from_structure`(struct[, copy])	Instantiates a CharmmPsfFile from an input Structure instance.
`get_box`([frame])	In some cases, multiple conformations may be stored in the Structure.
`get_coordinates`([frame])	In some cases, multiple conformations may be stored in the Structure.
`has_NBFIX`()	Returns whether or not any pairs of atom types have their LJ interactions modified by an NBFIX definition
`is_changed`()	Determines if any of the topology has changed for this structure
`join_dihedrals`()	Joins multi-term torsions into a single term and makes all of the parameters DihedralTypeList instances.
`load_dataframe`(df)	Loads atomic properties from an input DataFrame
`load_parameters`(parmset[, copy_parameters])	Loads parameters from a parameter set that was loaded via CHARMM RTF, PAR, and STR files.
`omm_add_constraints`(system, constraints, …)	Adds constraints to a given system
`omm_angle_force`([constraints, …])	Creates an OpenMM HarmonicAngleForce object (or AmoebaAngleForce if the angles are for an Amoeba-parametrized system)
`omm_bond_force`([constraints, rigidWater, …])	Creates an OpenMM Bond Force object (or AmoebaBondForce if the bonds are for an Amoeba-parametrized system)
`omm_cmap_force`()	Creates the OpenMM CMAP torsion force
`omm_dihedral_force`([split])	Creates the OpenMM PeriodicTorsionForce modeling dihedrals
`omm_gbsa_force`(implicitSolvent[, …])	Creates a Generalized Born force for running implicit solvent calculations
`omm_improper_force`()	Creates the OpenMM improper torsion force (quadratic bias)
`omm_nonbonded_force`([nonbondedMethod, …])	Creates the OpenMM NonbondedForce instance
`omm_out_of_plane_bend_force`()	Creates the Amoeba out-of-plane bend force
`omm_pi_torsion_force`()	Creates the Amoeba pi-torsion force
`omm_rb_torsion_force`()	Creates the OpenMM RBTorsionForce for Ryckaert-Bellemans torsions
`omm_set_virtual_sites`(system)	Sets the virtual sites in a given OpenMM System object from the extra points defined in this system
`omm_stretch_bend_force`()	Create the OpenMM Amoeba stretch-bend force for this system
`omm_torsion_torsion_force`()	Create the OpenMM Amoeba coupled-torsion (CMAP) force
`omm_trigonal_angle_force`()	Creates the Amoeba trigonal-angle force
`omm_urey_bradley_force`()	Creates the OpenMM Urey-Bradley force
`prune_empty_terms`()	Looks through all of the topological lists and gets rid of terms in which at least one of the atoms is None or has an idx attribute set to -1 (indicating that it has been removed from the atoms atom list)
`save`(fname[, format, overwrite])	Saves the current Structure in the requested file format.
`split`()	Split the current Structure into separate Structure instances for each unique molecule.
`strip`(selection)	Deletes a subset of the atoms corresponding to an atom-based selection.
`to_dataframe`()	Generates a DataFrame from the current Structure’s atomic properties
`unchange`()	Toggles all lists so that they do not indicate any changes
`update_dihedral_exclusions`()	Nonbonded exclusions and exceptions have the following priority:
`visualize`(args, *kwargs)	Use nglview for visualization.
`write_cif`(dest[, renumber, coordinates, …])	Write a PDB file from the current Structure instance
`write_pdb`(dest[, renumber, coordinates, …])	Write a PDB file from a Structure instance
`write_psf`(dest[, vmd])	Writes a PSF file from the stored molecule

Attributes

`ANGLE_FORCE_GROUP`
`BOND_FORCE_GROUP`
`CMAP_FORCE_GROUP`
`DIHEDRAL_FORCE_GROUP`
`IMPROPER_FORCE_GROUP`
`NONBONDED_FORCE_GROUP`
`OUT_OF_PLANE_BEND_FORCE_GROUP`
`PI_TORSION_FORCE_GROUP`
`RB_TORSION_FORCE_GROUP`
`STRETCH_BEND_FORCE_GROUP`
`TORSION_TORSION_FORCE_GROUP`
`TRIGONAL_ANGLE_FORCE_GROUP`
`UREY_BRADLEY_FORCE_GROUP`
`box`
`box_vectors`	3, 3-element tuple of unit cell vectors that are Quantity objects of dimension length
`combining_rule`
`coordinates`
`positions`	A list of 3-element Quantity tuples of dimension length representing the atomic positions for every atom in the system.
`topology`	The OpenMM Topology object.
`velocities`
`view`	Returns an indexable object that can be indexed like a standard Structure, but returns a view rather than a copy