schrodinger.rdkit.alignment module

schrodinger.rdkit.alignment.transform_conformer(conformer: rdkit.Chem.rdchem.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.

Parameters

• conformer – a conformer with nonzero coordinates

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

schrodinger.rdkit.alignment.get_height(conformer: rdkit.Chem.rdchem.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: rdkit.Chem.rdchem.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: rdkit.Chem.rdchem.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

schrodinger.rdkit.alignment.generate_min_height_coords(mol: rdkit.Chem.rdchem.Mol)

Clear the existing conformers of the input Mol object and generate one such that its height (greatest y-axis distance between two points) is minimized to some extent.

Parameters

mol – input RDKit molecule object

schrodinger.rdkit.alignment.align_to_template(mol, template_mol)

Align a 2D Mol object against a similar template.

Parameters

• mol (rdchem.Mol) – the Mol to be aligned

• template_mol (rdchem.Mol) – the template

Returns

the RMSD of the aligned structures

Return type

float