schrodinger.rdkit.alignment module

schrodinger.rdkit.alignment.transform_conformer(conformer: Conformer, matrix: 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.

Parameters:

• conformer – a conformer with nonzero coordinates

• matrix – a 3x3 matrix to transform the conformer coordinates

schrodinger.rdkit.alignment.get_height(conformer: Conformer) → float

Parameters:

conformer – a conformer with nonzero coordinates

Returns:

the maximum y-axis distance between positions of the conformer

schrodinger.rdkit.alignment.rotate_2D(conformer: Conformer, rot_angle: float)

Rotate a conformer clockwise around the z axis.

Parameters:

• conformer – a conformer with nonzero coordinates

• rot_angle – the angle at which to rotate the conformer (clockwise in around the z axis, in degrees)

schrodinger.rdkit.alignment.align_horizontally(conformer: Conformer)

Rotate the specified conformer to minimize its height.

Parameters:

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