Source code for schrodinger.rdkit.alignment

from math import ceil

import numpy
from rdkit.Chem import Conformer
from rdkit.Chem import rdMolTransforms
from scipy.spatial.transform import Rotation


[docs]def transform_conformer(conformer: Conformer, matrix: numpy.ndarray):
    """
    Apply a 3x3 transformational matrix to the coordinates of the conformer.

    This is a convenience function that fits the 3x3 matrix into a 4x4 matrix to
    include the extra translational dimension required by `TransformConformer`.

    :param conformer: a conformer with nonzero coordinates
    :param matrix: a 3x3 matrix to transform the conformer coordinates
    """
    mat_with_translation = numpy.identity(4)
    for idx, col in enumerate(matrix):
        mat_with_translation[idx][:3] = col
    rdMolTransforms.TransformConformer(conformer, mat_with_translation)


[docs]def get_height(conformer: Conformer) -> float:
    """
    :param conformer: a conformer with nonzero coordinates
    :return: the maximum y-axis distance between positions of the conformer
    """
    pos = conformer.GetPositions()
    return pos[:, 1].max() - pos[:, 1].min()


[docs]def rotate_2D(conformer: Conformer, rot_angle: float):
    """
    Rotate a conformer clockwise around the z axis.

    :param conformer: a conformer with nonzero coordinates
    :param rot_angle: the angle at which to rotate the conformer (clockwise in
            around the z axis, in degrees)
    """
    rot = Rotation.from_euler(seq='z', angles=rot_angle, degrees=True)
    transform_conformer(conformer, rot.as_matrix())


[docs]def align_horizontally(conformer: Conformer):
    """
    Rotate the specified conformer to minimize its height.

    :param conformer: a conformer with nonzero coordinates
    :note: this optimization is performed over a limited number of possible
            angles in order to preserve aesthetically-pleasing bond angles
            generated for this conformer by `Chem.rdCoordGen`
    """
    degrees_per_rotation = 30
    max_rotation_count = ceil(90 / degrees_per_rotation) + 1
    conf_copy = Conformer(conformer)

    min_height = get_height(conf_copy)
    min_height_angle = 0
    for rotation_count in range(1, max_rotation_count):
        rotate_2D(conf_copy, rot_angle=degrees_per_rotation)
        height = get_height(conf_copy)
        if height < min_height:
            min_height = height
            min_height_angle = rotation_count * degrees_per_rotation

    rotate_2D(conformer, rot_angle=min_height_angle)