Molecule

Methods to interact with molecule, including loading data, querying molecule attributes, working with volumetric data, or setting its visibility in the render window.

Basic functionality

cancel	Cancel background loading of files for given molid
delete	Delete a molecule
delframe	Delete a frame or frame(s) from a loaded molecule
dupframe	Duplicate a frame.
exists	Check if a molecule ID is valid
listall	List all valid molecule IDs
load	Load a molecule from a file.
new	Create a new molecule, with optional number of ‘empty’ atoms
num	Get the number of loaded molecules
read	Read coordinate data into an existing molecule
rename	Change the name of a molecule
write	Write coordinate and topology data from a loaded molecule to a file
ssrecalc	Recalculate secondary structure for molecule

Typically for molecular dynamics simulation trajectories, a topology file will be loaded, then a trajectory file will be read in to it in a way that blocks program execution until all frames are done loading. This code snippit does this, then saves the last frame as a PDB file.

from vmd import molecule

molid = molecule.load("parm7", "system.prmtop")
molecule.read(molid, "netcdf", "simulation.nc", skip=5, waitfor=-1)
last_frame = molecule.numframes - 1
molecule.write(molid, "pdb", "last_frame.pdb", first=last_frame)

VMD has the concept of the “top” molecule, which is the default molecule for all operations unless otherwise specified.

get_top	Get the ID of the top molecule
set_top	Set the top molecule

Querying loaded molecules

Depending on the information available in the input molecule files, these fields may or may not be populated.

get_accessions	Get database accession codes associated with files loaded into a molecule
get_databases	Get databases associated with files loaded into a molecule
get_periodic	Get the periodic cell layout
get_physical_time	Get the physical time value for a frame, if set
get_remarks	Get remarks associated with files loaded into a molecule
set_periodic	Set the periodic cell layout for a particular frame.
set_physical_time	Set the physical time value for a frame

These attributes are always available:

get_filenames	Get list of all files loaded into a molecule
get_filetypes	Get file types loaded into a molecule
get_frame	Get the current frame
get_visible	Get if a molecule is visible
name	Get name of a given molecule
numatoms	Get number of atoms in a given molecule
numframes	Get the number of loaded frames in a molecule
set_frame	Set the frame of a molecule
set_visible	Set the visiblity of a molecule

Working with volumetric data

add_volumetric	Add a new volumetric dataset to a molecule
delete_volumetric	Delete a volumetric dataset from a molecule
get_volumetric	Obtain a volumetric dataset loaded into a molecule
num_volumetric	Get the number of volumetric datasets loaded into a molecule