moleculekit.vmdviewer module

class moleculekit.vmdviewer.VMD(vmd=None, host=None, dispdev='win')

Bases: object

Please do not directly call this class constructor. Use the viewer or getCurrentViewer function instead.

Parameters:

• vmd (str) –

• host (str) –

• dispdev (str) –

close()

completed()

Check if the viewer has been closed

Returns:

comp – Returns True if the VMD viewer has closed

Return type:

bool

copy()

loadMol(mol, name=None)

Load a Molecule object into VMD

Parameters:

• mol (Molecule object) – The Molecule to load into VMD

• name (str) – The name to give to the Molecule

movie_reps()

Adds some default settings and representations for creating movies with Tachyon in VMD

render(outfile, renderer='TachyonInternal', resolution=None, aasamples=None, skylight=None, tachyon=None, convert=None, trim=False)

Renders the current VMD scene into a file.

Parameters:

• outfile (str) – File to which to render image

• renderer (('TachyonInternal', 'tachyon', 'snapshot')) – Which renderer to use

• resolution (tuple) – X,Y resolution of the output image i.e. (1920, 1080). Only used with the renderer=’tachyon’ option.

• aasamples (int) – Number of anti-aliasing samples. Only used with the renderer=’tachyon’ option.

• skylight (float) – Add a skylight. Only used with the renderer=’tachyon’ option.

• tachyon (str) – Path to tachyon renderer executable. Only used with the renderer=’tachyon’ option.

• convert (bool) – Attempts to convert the image to the datatype of the outfile extension

• trim (bool) – Trims the whitespace of the image

rep(mode, sel='resname MOL', color=0)

Modify representations for the top molecule in VMD

Parameters:

• mode (str ('protein', 'ligand')) – If set to ‘protein’, it will show a single conformation of the protein with sequence coloring If set to ‘ligand’, it will show all ligands in the specified color and the protein in teal

• sel (str) – Atom selection string for the ligand mode. See more here

• color (int) – Color for the ligand. Use color numbers of VMD

send(command)

Send a tcl command to VMD

Parameters:

command (str) – The tcl command which to send

moleculekit.vmdviewer.getCurrentViewer(dispdev='win')

Get the handle to the current molecular viewer

Parameters:

dispdev (str, ('win', 'text', 'cave', 'caveforms', 'none')) – Specify the type of graphical display to use. The possible display devices include: win: a standard graphics display window. text: do not provide any graphics display window. cave: use the CAVE virtual environment for display, forms are disabled. caveforms: use the CAVE virtual environment for display and with forms enabled. This is useful with -display machine:0 for remote display of the forms when the CAVE uses the local screen.

Returns:

viewer – Returns a handle to the current viewer

Return type:

VMD object

moleculekit.vmdviewer.getVMDpath(vmd=None)

moleculekit.vmdviewer.viewer(dispdev='win')

Start a new molecular viewer

Returns:

viewer – Returns a handle to a new viewer

Return type:

VMD object