Usage

The easiest way to use CineMol is to use the functions from the cinemol.api module.

This module provides a high-level API for drawing SVGs of molecular structures.

Using the Python API

from cinemol.parsers import parse_sdf
from cinemol.api import Style, Look, draw_molecule

# Parse atoms and bonds from an SDF file ...
with open("path/to/your/molecule.sdf", "r") as f:
    sdf_str = f.read()

atoms, bonds = parse_sdf(sdf_str)

# ... or create your own atom and bond objects.
atoms = [
    Atom(
        index=0,
        symbol="C",
        coordinates=(0.0, 0.0, 0.0)
    ),
    Atom(
        index=1,
        symbol="N",
        coordinates=(1.0, 0.0, 0.0)
    )
]
bonds = [
    Bond(
        start_index=0,
        end_index=1,
        order=3
    )
]

# Draw molecule to SVG string.
svg = draw_molecule(
    atoms=atoms,
    bonds=bonds,
    style=Style.Tube,  # See cinemol.api.Style for more options.
    look=Look.Glossy,  # See cinemol.api.Look for more options.
    resolution=100,
    scale=10.0
)

svg_str = svg.to_svg()

Fine-grained control

See Scene in cinemol.model module if you want direct access to the drawing scene. The scene can be given various objects for drawing (e.g., ModelSphere, ModelCylinder, ModelWire). The draw_molecule() function is a convenience function on top of Scene that creates a scene, adds the molecule to the scene, and draws the scene to an SVG string.

Examples:

  1. Highlighted amino acids in daptomycin conformer (examples/draw_substructure_highlights.py)

  2. Three aligned conformers of benzylphenol (examples/draw_superimposed_conformers.py)

  3. Wireframe model of lysozome 9LYZ with space-filling model of bound ligand trisaccharide NAM-NAG-NAM (examples/draw_protein_with_ligands.py)