vmol 3.0rc6

v -- A simple X11 molecular viewer

vmol: v – python binding

This package allows to

• run v from python scripts and receive its output without calling subprocesses and
• facilitate installation (especially if it is a dependency).

Inspired by @aligfellow's xyzrender.

Requirements

• X11
• numpy
• cclib (optional, to read formats without native support)

Installation

PyPI has the wheels for CPython 10 through 14 @ manylinux. See install-other.md for other ways to build and install.

pip install vmol[all]       #  install cclib to parse unsupported file formats and open them with vmol2

pip install vmol            #  base version

pip install --no-deps vmol  #  vmol script and "capture the output" will work, 
                            #  but "pass a structure" feature won't work without numpy

For macOS, an X11 server like XQuartz is required:

brew install --cask xquartz

Usage

Scripts

The package provides two scripts to run from the command line

• vmol, a simple wrapper around v
• vmol2, a wrapper aroung v to view the file formats that are not supported natively (needs cclib (i.e., vmol[all] or vmol[cclib]))

Both have the same CLI interface as the original v (see the reference).

Native formats (xyz / Priroda):

vmol ../mol/MOL_3525.xyz cell:8.93,0.0,0.0,4.2,8.9,0.0,0.48,2.32,10
python -m vmol../mol/periodic.in bonds:0

Unsupported quantum-chemical outputs, e.g., Orca:

vmol2 ../mol/CEHZOF_1_SPE.out
python -m vmol.vmol2 ../mol/AJALIH_5_SPE.out

or Gaussian:

vmol2 mol/Cat1_TSOA_CfA_Cf0.log vib:0  #  geometry optimization
vmol2 mol/Cat1_TSOA_CfA_Cf0.log        #  normal modes (default for files containing both)

Library

Import the wrapper instance:

>>> from vmol import vmol

It provides the two wrapper functions capture and run along with the path to the shared library so, loaded library lib, and function namespace f.

>>> [*filter(lambda x: not str.startswith(x, '_'), dir(vmol))]
['capture', 'f', 'lib', 'run', 'so']

The shared library is automatically searched for in the current and installation directories:

>>> vmol.so
/home/xe/soft/miniconda3/lib/python3.13/site-packages/vmol/v.cpython-313-x86_64-linux-gnu.so

One can use a custom .so file by setting the attribute

>>> vmol.so = '../v.so'

or the VMOL_SO_PATH environment variable:

export VMOL_SO_PATH=`readlink -m ../v.so`

1. Simple wrapper

Analogous to running vmol script:

from vmol import vmol
vmol.run(['../mol/MOL_3525.xyz', 'cell:8.93,0.0,0.0,4.2,8.9,0.0,0.48,2.32,10'])

The arguments are the same as the CLI ones and should be an array of strings.

2. Capture the output

See example 1.

from vmol import vmol
out = vmol.capture(args=['../mol/MOL_3525.xyz', 'cell:8.93,0.0,0.0,4.2,8.9,0.0,0.48,2.32,10'])
# look at the molecule, press `x`/`z`/`p` to produce an output, close with `q`/`esc`
print(out)

The arguments args are the same as the CLI ones and should be an array of strings.

The return code can be captured as well:

ret, out = vmol.capture(args=['../mol/MOL_3525.xyz', 'cell:8.93,0.0,0.0,4.2,8.9,0.0,0.48,2.32,10'], return_code=True)

Headless mode also works:

>>> vmol.capture(args=['../mol/S8.qm.out', 'gui:0', 'com:.'])
'D8h'
>>> vmol.capture(args=['../mol/S8.qm.out', 'gui:0', 'com:.', 'frame:-1'])
'D4d'

Tell the viewer to automatically print the coordinates before exit:

>>> out = vmol.capture(args=['../mol/rotation1.in', 'exitcom:z'])
>>> print(out)

3. Pass a structure

One can pass a structure (or several structures) as an argument. See example 2.

from vmol import vmol
name = 'HF molecule'
q = [1, 'F']
r = [[0,0,0],[0.9,0,0]]
out = vmol.capture(mols={'q': q, 'r': r, 'name': name}, args=['shell:0.6,0.7'])
# look at the molecule, press `x`/`z`/`p` to produce an output, close with `q`/`esc`
print(out)

Without capturing the output:

vmol.run(args=['shell:0.6,0.7'], mols={'q': [1, 'F'], 'r': [[0,0,0],[0.9,0,0]], 'name': 'hydrogen fluoride'})

ASE Atoms (or anything with .numbers and .positions) are also supported:

import ase.io
mols = ase.io.read('../mol/mol0002.xyz', index=':')
out = vmol.capture(mols=mols)

File formats which are not supported natively can be read with cclib and passed (see example and vmol2 source).

One can also pass normal modes data with

from vmol import vmol
CO2 = {'q': [8, 6, 8], 'r': [(x,0,0) for x in [-1.16, 0, 1.16]], name='CO2'}
sym_stretch  = {'freq': [1480], 'ints': [0], 'mass': [16], 'disp': [[(dx,0,0) for dx in [-1, 0, 1]]]}
vmol.run(mols=CO2, vib=sym_stretch)

Press insert to play the animation. (See example and vmol2 source for more details.)