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.
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 |