parmed.charmm.CharmmCrdFile

class parmed.charmm.CharmmCrdFile(fname)

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

Parameters

fnamestr

Name of the restart file to parse

Attributes

natomint

Number of atoms in the system

resnamelist of str

List of all residue names in the system

coordinatesnp.ndarray with shape (1, natom, 3)

Atomic coordinates in a numpy array

positionsnatom x 3 distance Quantity

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

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)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(fname)	Initialize self.
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)