schrodinger.protein.protassign.unsatisfied_donors module¶
Module containing functions to detect unsatisfied H-bond donors.
TODO consider moving some of this functionality into schrodinger.structutils package.
- schrodinger.protein.protassign.unsatisfied_donors.get_bulk_solvent_accessible_atoms(st, radius=2.5, radius2=3.0, spacing=0.5, include_water=False)¶
Return bulk solvent accessible atoms.
Bulk solvent accessible atoms are determined by creating a grid and setting occupied voxels to 1 using a fixed radius for each atom and then checking if any non-occupied voxels are present within a slightly larger radius.
- Parameters
st (Structure) – Structure to determine bulk solvent accessible atoms. The atom property BULK_SOLVENT_ACCESSIBLE_PROPERTY will be set for each atom.
radius (float) – Initial radius
radius2 (float) –
spacing (float) – Spacing of grid. Lower spacing makes the calculation more accurate but requires more compute time and memory.
include_water (bool) – Whether to keep waters or not when calculating bulk solvent accessible atoms.
- Returns
List of atom indices that are bulk solvent accessible
- Return type
List[int]
- schrodinger.protein.protassign.unsatisfied_donors.get_unsatisfied_donors(st, include_bsa=True)¶
Return unsatisfied buried donors