Molecules¶

SDF Input¶

The viewer accepts an SDF string and uses COSMolKit for parsing:

from cosmol_viewer import Molecule

sdf = open("ligand.sdf", encoding="utf-8").read()
molecule = Molecule.from_sdf(sdf).centered()

COSMolKit Integration¶

Convert an existing Python cosmolkit.Molecule without crossing through a temporary SDF file. Stored 3D coordinates are preferred; stored 2D coordinates are used next, and 2D coordinates are generated if neither is available.

import cosmolkit as ck
from cosmol_viewer import Molecule

source = (
    ck.Molecule.from_smiles("CC(=O)Nc1ccc(O)cc1")
    .with_hydrogens()
    .with_3d_conformer()
)
molecule = Molecule.from_cosmolkit(source).centered()

Representations¶

ball_and_stick = Molecule.from_sdf(sdf).ball_and_stick()
sticks = Molecule.from_sdf(sdf).stick()
space_filling = Molecule.from_sdf(sdf).sphere()

The stick representation retains double and triple bond separation and renders aromatic bonds as a single stick with an inner aromatic line.

Materials and Outlines¶

All shapes support color(), opacity(), roughness(), and metallic(). Molecules additionally support an imposter-based outline:

molecule = (
    Molecule.from_sdf(sdf)
    .centered()
    .roughness(0.55)
    .metallic(0.0)
    .enable_outline(color="#101010", width=0.04)
)

roughness and metallic use values from 0 to 1. Use disable_outline() or set_outline(False) to remove the outline.