schrodinger.application.bioluminate.protein_interaction.calculate module

schrodinger.application.bioluminate.protein_interaction.calculate.calculate_interactions(struct, asl1, asl2, options, progress_callback=None, calc_distances=True, calc_surface_parameters=True)
Calculate residue interactions. Calculated interactions,

  • Neary by residues

  • Hydrogen Bonds

  • Pi Pi

  • Salt bridges

  • Disulfides

  • Steric Clashes

Parameters

  • struct (structure.Structure) – Structure to find interactions in.

  • asl1 (str) – Set1 ASL string.

  • asl2 (str) – Set2 ASL string.

  • options (ProteinInteractionOptions) – Interaction options.

  • progress_callback (function) – Callback for progress updates.

  • calc_distances (bool) – Whether to calculate distances between residues (slow)

  • calc_surface_parameters (bool) – Whether to calculate surface parameters (slow)

Returns

Residue interactions.

Return type

list[ProteinInteraction]

schrodinger.application.bioluminate.protein_interaction.calculate.get_neighboring_atom_distances(struct, group1_atoms, group2_atoms, max_dist)

Return neighbor atoms from group2_atoms for all atoms in group1_atoms within the given threshold.

Parameters

  • struct (structure.Structure) – Structure to which the atoms belong to.

  • group1_atoms (list[int]) – list of atom indices in first group.

  • group2_atoms – List of atom indices in second group.

  • max_dist (float) – Maximum distance of a neighbor.

Returns

Neighbors within the maximum distance.

Return type

dict((structure._StructureAtom, structure._StructureAtom), float))

class schrodinger.application.bioluminate.protein_interaction.calculate.HBOND_TYPE(value)

Bases: enum.Enum

An enumeration.

SS = 1
SB = 2
BS = 3
BB = 4
schrodinger.application.bioluminate.protein_interaction.calculate.check_if_backbone_atom(atom)

Returnt whether the atom is a backbone atom or not. :param atom: Structure atom. :type atom: structure._structureAtom :return: Whether the atom is a backbone atom or not. :rtype: bool

schrodinger.application.bioluminate.protein_interaction.calculate.get_hydrogen_bond_type(atom1, atom2)

Return the hydrogen bond type.

Parameters

  • atom1 (structure._StructureAtom) – Atom of the hydrogen bond.

  • atom2 (structure._structureAtom) – Atom of the hydrogen bond.

Returns

Hydrogen bond type.

Return type

HBOND_TYPE