parmed.charmm.CharmmCrdFile

class parmed.charmm.CharmmCrdFile(fname)[source]

Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc.

Parameters:

fname : str

Name of the restart file to parse

Attributes

positions Atomic coordinates with units attached to them with the shape (natom, 3)
natom (int) Number of atoms in the system
resname (list of str) List of all residue names in the system
coordinates (np.ndarray with shape (1, natom, 3)) Atomic coordinates in a numpy array

Methods

id_format(filename) Identifies the file type as a CHARMM coordinate file
write(struct, dest) Writes a CHARMM coordinate file from a structure
__init__(fname)[source]

Methods

__init__(fname)
id_format(filename) Identifies the file type as a CHARMM coordinate file
write(struct, dest) Writes a CHARMM coordinate file from a structure

Attributes

box
coordinates
positions Atomic coordinates with units attached to them with the shape (natom, 3)
static id_format(filename)[source]

Identifies the file type as a CHARMM coordinate file

Parameters:

filename : str

Name of the file to check format for

Returns:

is_fmt : bool

True if it is a CHARMM coordinate file

positions

Atomic coordinates with units attached to them with the shape (natom, 3)

static write(struct, dest)[source]

Writes a CHARMM coordinate file from a structure

Parameters:

struct : parmed.structure.Structure

The input structure to write the CHARMM coordinate file from

dest : str or file-like object

The file name or file object to write the coordinate file to