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mesh

molecule_to_meshes(molecule, **kwargs)

Convert the provided molecule into a list of trimesh Meshes representing the molecule either as van der Waals spheres or as a CPK representation.

Parameters:

Name Type Description Default
molecule Molecule

The molecule to represent

 required
kwargs dict

Optional Keyword arguments

 {}

Returns:

Name Type Description
list

a list of meshes representing atoms and (optionally) bonds
Source code in chmpy/util/mesh.py 
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def molecule_to_meshes(molecule, **kwargs):
    """
    Convert the provided molecule into a list
    of trimesh Meshes representing the molecule
    either as van der Waals spheres or as a CPK
    representation.

    Args:
        molecule (Molecule): The molecule to represent
        kwargs (dict): Optional Keyword arguments

    Returns:
        list: a list of meshes representing atoms and (optionally) bonds
    """

    from trimesh.creation import icosphere, cylinder
    import numpy as np

    representation = kwargs.get("representation", "ball_stick")
    base_sphere = icosphere(subdivisions=3)
    n_points = len(base_sphere.vertices)
    meshes = {}
    for i, (el, pos) in enumerate(molecule):
        m = base_sphere.copy()
        m.apply_scale(getattr(el, f"{representation}_radius"))
        m.apply_translation(pos)
        m.visual.vertex_colors = np.repeat([el.color], n_points, axis=0)
        meshes[f"atom_{molecule.labels[i]}"] = m
    if representation == "ball_stick":
        bond_thickness = 0.12
        for i, (a, b, d) in enumerate(molecule.unique_bonds):
            x1 = molecule.positions[a]
            x3 = molecule.positions[b]
            cyl = cylinder(bond_thickness, d, segment=(x1, x3))
            cyl.visual.vertex_colors = np.repeat(
                [
                    (100, 100, 100, 255),
                ],
                cyl.vertices.shape[0],
                axis=0,
            )
            bond_label = f"bond_{molecule.labels[a]}_{molecule.labels[b]}"
            meshes[bond_label] = cyl
    return meshes

save_mesh(mesh, filename)

Save the given Trimesh to a file.

Parameters:

Name Type Description Default
mesh Trimesh

The mesh to save.

 required
filename str

The path to the destination file.

 required
Source code in chmpy/util/mesh.py 
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def save_mesh(mesh, filename):
    """
    Save the given Trimesh to a file.

    Args:
        mesh (trimesh.Trimesh): The mesh to save.
        filename (str): The path to the destination file.
    """
    ext = filename.split(".")[-1]
    with open(filename, "wb") as f:
        mesh.export(f, ext)

    LOG.debug("Saved mesh %s to %s", mesh, filename)