API documentation¶

class psfgen.PsfGen(output=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, case_sensitive=False)¶

A Psf generator object. Represents the state of a single molecular system, with its own set of loaded topologies, residue and/or atom aliases, segments, and coordinates.

add_segment(segid, first='none', last='none', pdbfile=None, auto_angles=True, auto_dihedrals=True, residues=None, mutate=None)¶

Adds a new segment to the internal molecule state.

Parameters:

segid (str) – Name/ID of the new segment
first (str) – Patch to apply to first residue in segment, or None for topology file default setting
last (str) – Patch to apply to last residue in segment, or None for topology file in default setting
pdbfile (str) – PDB file to read residue information from, or None to create an empty segment
auto_angles (bool) – If angles should be autogenerated.
auto_dihedrals (bool) – If dihedrals should be autogenerated.
residues (list of 2 or 3-tuple) – (resid, residue, [chain]) of residues to append to the end of the segment. Chain can be None or unset in this tuple to use the current chain.
mutate (list of 2 tuple) – (resid, resname) of residues to alter. The given residue IDs will be set to the given residue name.

alias_atom(resname, top_atomname, pdb_atomname)¶

Set a correspondence between an atom name in a specific residue in a PDB file and in the defined topologies.

Parameters:	resname (str) – Residue name in which to make alias top_atomname (str) – Atom name in the topology file pdb_atomname (str) – Equivalent atom name in PDB file

alias_residue(top_resname, pdb_resname)¶

Set a correspondence between a residue name in a PDB file and in the defined topologies. The topology residue names should be treated as the canonical set here.

Parameters:	top_resname (str) – Resname in topology file pdb_resname (str) – Equivalent resname in PDB files

case_sensitive¶: Determines whether or not residue and other names have case sensitivity. Defaults to False. Can only be changed before reading in any topology files.

delete_atoms(segid, resid=None, atomname=None)¶

Deletes atoms from the molecule, with options for increasing specificity. As many atoms as match the passed options will be deleted, so for example if only segid is present, an entire segment will be removed.

Parameters:	segid (str) – Segment ID of atom(s) to delete resid (str or int) – Residue ID of atom(s) to delete, or None to delete entire matching segment atomname (str) – Atom name to delete, or None to delete entire matching segment or residue

get_atom_indices(segid, resid)¶

Obtains atom indices/IDs in a given residue

Parameters:	segid (str) – Segment ID to query resid (str or int) – Residue ID to query
Returns:	(list of int) – Atom IDs in residue

get_atom_names(segid, resid)¶

Obtains atom names in a given residue

Parameters:	segid (str) – Segment ID to query resid (str or int) – Residue ID to query
Returns:	(list of str) – Atom names in residue

get_charges(segid, resid)¶

Obtains atom charges in a given residue

Parameters:	segid (str) – Segment ID to query resid (str or int) – Residue ID to query
Returns:	(list of float) – Atom charges in residue

get_coordinates(segid, resid)¶

Obtains atom coordinates in a given residue

Parameters:	segid (str) – Segment ID to query resid (str or int) – Residue ID to query
Returns:	(list of 3-tuple) – (x,y,z) position of all atoms in residue

get_first(segid)¶

Get the name of the patch applied to the beginning of a given segment

Parameters:	segid (str) – Segment ID to query
Returns:	(str) – Patch name, or None

get_last(segid)¶

Get the name of the patch applied to the end of a given segment

Parameters:	segid (str) – Segment ID to query
Returns:	(str) – Patch name, or None

get_masses(segid, resid)¶

Obtains atom masses in a given residue

Parameters:	segid (str) – Segment ID to query resid (str or int) – Residue ID to query
Returns:	(list of float) – Atom masses in residue

get_patches(list_defaults=True, list_all=False)¶

Obtain information about available or applied patches in the current system state.

Parameters:	list_defaults (bool) – If True, default patches will be listed too. Otherwise only explicitly applied patches will be shown. Defaults to True list_all (bool) – List all available patches, not just applied ones. For psfgen internal reasons, “NONE”, “None”, and “none” will appear in this list.
Returns:	(list of 3-tuple) – (patchname, segid, resid) of all applied patches

get_resids(segid)¶

Obtain all currently defined resids in a given segment

Parameters:	segid (str) – Segment ID to query
Returns:	(list of str) – All defined resids in given segment

get_residue_types()¶

Get all defined residues

Returns:	(list of str) – Defined residue types from current topologies

get_resname(segid, resid)¶

Obtains the residue name given a resid and segment

Parameters:	segid (str) – Segment ID to query resid (str or int) – Residue ID to query
Returns:	(str) – Residue name

get_segids()¶

Obtain all the currently defined segment IDs.

Returns:	(list of str) – All defined segids in current molecule

get_topologies()¶

Get all loaded topology files

Returns:	(list of str) – Filenames that have been loaded

get_velocities(segid, resid)¶

Obtains atom velocities in a given residue, if set

Parameters:	segid (str) – Segment ID to query resid (str or int) – Residue ID to query
Returns:	(list of 3-tuple) – (vx,vy,vz) velocities of all atoms in residue

guess_coords()¶: Sets unset coordinates using geometric assumptions

patch(patchname, targets)¶

Applies a patch to the molecule.

Parameters:	patchname (str) – Name of the patch to apply targets (list of 2 tuple) – (segid, resid) to apply patch to

query_segment(task, segid=None, resid=None)¶

Ask for information about a segment.

Parameters:	task (str) – In [first, last, residue, resids, segids] depending on what information is desired. segid (str) – Segment ID to query resid (str) – Residue ID to query, if task is “residue”
Returns:	(str or list of str) – Requested information

read_coords(filename, segid)¶

Reads in coordinates from a PDB file, matching segment, residue, and atom names to the current segment.

Parameters:	filename (str) – Filename of PDB file to read segid (str) – Segment ID to assign coordinates to

read_psf(filename, pdbfile=None, namdbinfile=None, velnamdbinfile=None)¶

Reads structure information from a PSF file and adds it to the internal molecule state. Can also read insertion codes and coordinates from a PDB file, and/or coordinates from a NAMD binary file, if atoms are in the same order. Can read velocities from a NAMD binary file as well.

The PSF file is read in and also kind of interpreted: topology files in the REMARKS section are loaded, and a new segment is created with the segid specified in the PSF file. Note that if the topology files cannot be found, they will still be listed as “loaded” in the internal PsfGen state.

Parameters:

filename (str) – PSF file to read
pdbfile (str) – PDB file to obtain coordinates, elements, and insertion codes from. Atoms must be in same order as the PSF.
namdbinfile (str) – Binary NAMD file to read coordinates from. Will take priority over coordinates in pdbfile, if specified. Atoms must be in the same order as the PSF.
velnamdbinfile (str) – Binary NAMD file to read velocities from. Atoms must be in the same order as the PSF.

read_topology(filename)¶

Parses a charmm format topology file into current library.

Parameters:	filename (str) – File to parse
Raises:	`FileNotFoundError` – If the file cannot be opened for reading `ValueError` – If an error occurs during parsing

regenerate_angles()¶: Removes angles and regenerates them from bonds. Can be used after patching.

regenerate_dihedrals()¶: Removes dihedrals and regenerates them from angles. Can be used after patching. Usually, you should call regenerate_angles first.

regenerate_resids()¶: Regenerates residue IDs by removing insertion codes and minimially modifying them for uniqueness.

set_atom_name(segid, resid, atomname, new_atomname)¶

Renames an atom

Parameters:	segid (str) – Segment ID of atom to update resid (str or int) – Residue ID of atom to update atomname (str) – Name of atom to update new_atomname (str) – New atom name

set_beta(segid, resid, atomname, beta)¶

Updates the beta-factor of an atom

Parameters:	segid (str) – Segment ID of atom to update resid (str or int) – Residue ID of atom to update atomname (str) – Name of atom to update beta (float) – New beta factor

set_charge(segid, resid, atomname, charge)¶

Updates the charge of an atom

Parameters:	segid (str) – Segment ID of atom to update resid (str or int) – Residue ID of atom to update atomname (str) – Name of atom to update charge (float) – New charge

set_mass(segid, resid, atomname, mass)¶

Updates the mass of an atom

Parameters:	segid (str) – Segment ID of atom to update resid (str or int) – Residue ID of atom to update atomname (str) – Name of atom to update mass (float) – New mass

set_position(segid, resid, atomname, position)¶

Sets the coordinates of a given atom to new values.

Parameters:	segid (str) – Segment ID of atom resid (str or int) – Residue ID of atom atomname (str) – Atom name position (3-tuple or 3-list of double) – New x, y, and z coordinates for atom

set_resname(segid, resid, new_resname)¶

Renames a residue

Parameters:	segid (str) – Segment ID of residue to update resid (str or int) – Residue ID to update new_resname (str) – New residue name

set_segid(segid, new_segid)¶

Renames a segment.

Parameters:	segid (str) – Segment ID to change new_segid (str) – New segment ID

set_velocity(segid, resid, atomname, velocity)¶

Sets the velocity of a given atom to new values

Parameters:	segid (str) – Segment ID of atom resid (str or int) – Residue ID of atom atomname (str) – Atom name velocity (3 membered list or tuple of double) – New vx, vy, vz velocities for atom

write_namdbin(filename, velocity_filename=None)¶

Writes the current molecule state as a NAMD binary file. This file format can only contain coordinate information for each atom. Optionally write velocities to another NAMD binary file.

Parameters:	filename (str) – Filename to write to velocity_filename (str) – If present, filename to write velocities to

write_pdb(filename)¶

Writes the current molecule state out as a pdb file

Parameters:	filename (str) – Filename to write to

write_psf(filename, type='x-plor')¶

Writes the current molecule state out as a psf file

Parameters:	filename (str) – Filename to write to type (str) – Type of psf file to write, in [“charmm”, “x-plor”]