richlewis42 / scikit-chem

skchem/vis/mol.py

#! /usr/bin/env python
#
# Copyright (C) 2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD

"""
## skchem.vis.mol

Module for drawing molecules.
"""

from matplotlib import pyplot as plt

The import matplotlib could not be resolved.

from rdkit.Chem.Draw import DrawingOptions, MolToImage

The import rdkit.Chem.Draw could not be resolved.

from matplotlib.widgets import CheckButtons

The import matplotlib.widgets could not be resolved.

from mpl_toolkits.mplot3d import Axes3D  # needed to get 3D

The import mpl_toolkits.mplot3d could not be resolved.

Unused Axes3D imported from mpl_toolkits.mplot3d

import numpy as np

The import numpy could not be resolved.

def draw(mol, quality=1, ax=None):

The name ax does not conform to the argument naming conventions ([a-z_][a-z0-9_]{2,30}$).

    """Draw a molecule on a matplotlib axis.

    Args:
        mol (skchem.Mol):
            The molecule to be drawn.
        quality (int):
            The level of quality.  Higher quality takes more time, but will
            look better (so long as matplotlib's savefig.dpi is high enough).
        ax (plt.Axes or None):
            An existing axis on which to draw the molecule.

    Returns:
        plt.AxesImage:
            A matplotlib AxesImage object with the molecule drawn.
    """

    if not ax:
        ax = plt.gca()
    ax.grid('off')
    ax.axis('off')

    opts = DrawingOptions()
    opts.dotsPerAngstrom *= quality
    opts.atomLabelFontSize *= quality
    opts.bondLineWidth *= quality

    size = 300 * quality

    img, canvas, drawer = MolToImage(mol, size=(size, size), options=opts,

The variable drawer seems to be unused.

                                     returnCanvas=True)
    canvas.flush()
    return ax.imshow(img, extent=(0, 1, 0, 1))


def _plot_sphere(pos=(0, 0, 0), radius=1., ax=None, **kwargs):

The name ax does not conform to the argument naming conventions ([a-z_][a-z0-9_]{2,30}$).

    """ Plot a sphere.

    Args:
        pos tuple[float]:
            the centre of the sphere.
        radius (bool):
            The radius of the sphere.
        ax (plt.axes):
            The axes to draw the sphere on (defaults to current axis).

    Note:
        Keyword args are passed to Axes3D.plot_surface.
    """

    if ax is None:
        ax = plt.gca()

    u, v = np.mgrid[0:2 * np.pi:100j], np.mgrid[0:np.pi:100j]

The name u does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

The name v does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

Slice index is not an int, None, or instance with __index__

    x = 2 * radius * np.outer(np.cos(u), np.sin(v)) + pos[0]

The name x does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

    y = 2 * radius * np.outer(np.sin(u), np.sin(v)) + pos[1]

The name y does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

    z = 2 * radius * np.outer(np.ones(np.size(u)), np.cos(v)) + pos[2]

The name z does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

    return ax.plot_surface(x, y, z, **kwargs)


_skchem_mpl3d_check = None

The name _skchem_mpl3d_check does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

def draw_3d(m, conformer_id=-1, label_atoms=None):

The name m does not conform to the argument naming conventions ([a-z_][a-z0-9_]{2,30}$).

This function exceeds the maximum number of variables (19/15).

The argument label_atoms seems to be unused.

    """ Draw a molecule in three dimensions.

    Args:
        conformer_id (int):
            The id of the conformer to draw.
        label_atoms (bool):
            Whether to label the atoms (this can be toggled in interactive
            mode):

    Returns:
        plt.figure

    Note:
        This works great in the notebook with `%matplotlib notebook`.
    """

    # required to stop widgets getting garbage collected
    global _skchem_mpl3d_check

Usage of the global statement should be avoided.

The name _skchem_mpl3d_check does not conform to the constant naming conventions ((([A-Z_][A-Z0-9_]*)|(__.*__))$).

    fig = plt.figure()
    ax = fig.add_subplot(111, projection='3d')

The name ax does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

    pos = m.conformers[conformer_id].positions

    for i, j in m.bonds.atom_idxs:
        ax.plot(*[(pos[i, d], pos[j, d]) for d in range(3)], c='black',
                zorder=1)

    for atom, p in zip(m.atoms, pos):

The name p does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

       _plot_sphere(p, radius=0.25 * atom.covalent_radius, ax=ax,

The indentation here looks off. 8 spaces were expected, but 7 were found.

                    color=atom.hexcode, linewidth=0, zorder=10)
    x, y, z = p + 0.2

The name x does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

The name y does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

The name z does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

The loop variable p might not be defined here.

    labels = [ax.text(x, y, z, i, visible=False) for i, p in enumerate(pos)]

    # set limits
    lo, hi = min(pos.flatten()) - 1, max(

The name lo does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

The name hi does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

        pos.flatten()) + 1.5  # 1.5 angstrom outside bording box
    ax.set_xlim(lo, hi)
    ax.set_ylim(lo, hi)
    ax.set_zlim(lo, hi)
    ax.set_aspect('equal')

    ax.set_xlabel('x')
    ax.set_ylabel('y')
    ax.set_zlabel('z')

    rax = plt.axes([0.15, 0.1, 0.1, 0.15])

    _skchem_mpl3d_check = CheckButtons(rax, ('show labels', 'show axes'),
                                       (False, True))

    def toggle(label):

This function should have a docstring.

        if label == 'show labels':
            for l in labels:

The name l does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

                l.set_visible(not l.get_visible())

        if label == 'show axes':
            ax._axis3don = not ax._axis3don  # easiest way

It seems like _axis3don was declared protected and should not be accessed from this context.

        plt.draw()

    _skchem_mpl3d_check.on_clicked(toggle)

    return ax