schrodinger.rdkit.alignment module¶
- schrodinger.rdkit.alignment.transform_conformer(conformer: rdkit.Chem.rdchem.Conformer, matrix: numpy.ndarray)[source]¶
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[source]¶
- 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)[source]¶
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)[source]¶
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)[source]¶
Clear the existing conformers of the input
Molobject 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