OverlayMol

Overlay and align molecular structures for comparison and analysis.

Installation

pip

pip install -q git+https://github.com/kangmg/OverlayMol.git

git clone

git clone https://github.com/kangmg/OverlayMol.git
cd OverlayMol
pip install .

Overlay Diagram

!wget -q https://raw.githubusercontent.com/kangmg/OverlayMol/main/examples/DA.xyz -O DA.xyz

from overlaymol import OverlayMolecules

# config molecules to overlay
DA = OverlayMolecules()
DA.set_molecules('./DA.xyz')

# check default parameters
display(DA.parameters)

# change parameter options
DA.parameters.legend = True
DA.parameters.atom_scaler = 300
DA.parameters.bond_scaler = 8200000
DA.parameters.alpha_bonds = 1
DA.parameters.alpha_atoms = 1


# plot overlay diagram
DA.plot_overlay()

Traj animation

!wget -q https://raw.githubusercontent.com/kangmg/aimDIAS/main/examples/wittig.xyz -O wittig.xyz

from overlaymol import OverlayMolecules

# config molecules to overlay
wittig = OverlayMolecules()
wittig.set_molecules('./wittig.xyz')

# check default parameters
display(wittig.parameters)

# change parameter options
wittig.parameters.colorby = 'molecule'
wittig.parameters.superimpose_option = 'aa'

# plot traj animation
wittig.plot_animation()

Low level API

!wget -q https://github.com/kangmg/OverlayMol/blob/main/examples/sn2.xyz

from overlaymol import open_xyz_files, plotly_overlay, superimpose

# config molecules to overlay
molecules_jsons = open_xyz_files('./sn2.xyz')

# superimpose
superimposed_molecules_json = superimpose(molecules_jsons)

# plot overlay diagram
plotly_overlay(
    xyz_format_jsons=superimposed_molecules_json, 
    colorby='atom',
    bgcolor='navy')