schrodinger.structutils.interactions.hbond module¶
Module for identifying hydrogen and halogen bond interactions.
Copyright Schrodinger, LLC. All rights reserved.
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schrodinger.structutils.interactions.hbond.
get_maestro_params
(interaction_type)¶ Gets current Maestro preference values. Use like:
- try:
- params = get_maestro_params(hbonds.HYDROGEN_BONDS)
- except schrodinger.MaestroNotAvailableError:
- params = get_default_params(hbonds.HYDROGEN_BONDS)
pairs = get_donor_acceptor_bonds(params, st1, atoms1, st2, atoms2)
This attempts to read all current Maestro defaults. However, there is no current way to gaurantee that it is complete or exhaustive.
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schrodinger.structutils.interactions.hbond.
get_default_params
(interaction_type)¶ Get query parameters for an interaction type.
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schrodinger.structutils.interactions.hbond.
get_hydrogen_bonds
(st, atoms1=None, st2=None, atoms2=None, max_dist=None, min_donor_angle=None, min_acceptor_angle=None, max_acceptor_angle=None, honor_pbc=True)¶ Return hydrogen bonds meeting the specified threshold criteria. See get_interactions for details on how structure and atom set parameters are interpreted. Any threshold not specified will default to the Maestro preferences threshold.
Parameters: - st (
structure.Structure
) – Structure containing the two atom sets. - atoms1 – First set of atom indices to check within st. If not specified, all atoms will be used.
- st2 (
structure.Structure
or None) – Structure containing the atoms specified in atoms2. If None, st will be used for both sets. - atoms2 (list of ints or
structure._StructureAtom
objects or None) – Second set of atom indices to check within st. If not specified, all atoms will be used. - max_dist (float) – Maximum allowable bond distance. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- min_donor_angle (float) – Minimum allowable donor angle. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- min_acceptor_angle (float) – Minimum allowable acceptor angle. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- max_acceptor_angle (float) – Maximum allowable acceptor angle. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- honor_pbc (bool) – Honor Periodic Boundary Conditions, if defined as properties in the structure, and if st is equal to st2. Default is True.
Returns: A list of (donor atom object, acceptor atom object) for each hydrogen bond between the subsets of atoms.
Return type: list of (
structure._StructureAtom
,structure._StructureAtom
) tuples- st (
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schrodinger.structutils.interactions.hbond.
get_halogen_bonds
(st, atoms1=None, st2=None, atoms2=None, max_dist=None, min_donor_angle=None, min_acceptor_angle=None, max_acceptor_angle=None, honor_pbc=True)¶ Return halogen bonds meeting the specified threshold criteria. See get_interactions for details on how structure and atom set parameters are interpreted. Any threshold not specified will default to the Maestro preferences threshold.
Parameters: - st (
structure.Structure
) – Structure containing the two atom sets. - atoms1 – First set of atom indices to check within st. If not specified, all atoms will be used.
- st2 (
structure.Structure
or None) – Structure containing the atoms specified in atoms2. If None, st will be used for both sets. - atoms2 (list of ints or
structure._StructureAtom
objects or None) – Second set of atom indices to check within st. If not specified, all atoms will be used. - max_dist (float) – Maximum allowable bond distance. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- min_donor_angle (float) – Minimum allowable donor angle. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- min_acceptor_angle (float) – Minimum allowable acceptor angle. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- max_acceptor_angle (float) – Maximum allowable acceptor angle. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- honor_pbc (bool) – Honor Periodic Boundary Conditions, if defined as properties in the structure, and if st is equal to st2. Default is True.
Returns: A list of (donor atom object, acceptor atom object) for each halogen bond between the subsets of atoms.
Return type: list of (
structure._StructureAtom
,structure._StructureAtom
) tuples- st (
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schrodinger.structutils.interactions.hbond.
get_aromatic_hydrogen_bonds
(st, atoms1=None, st2=None, atoms2=None, max_dist=None, min_donor_angle=None, min_acceptor_angle=None, max_acceptor_angle=None, honor_pbc=True)¶ Return aromatic hydrogen bonds meeting the specified threshold criteria. See get_interactions for details on how structure and atom set parameters are interpreted. Any threshold not specified will default to the Maestro preferences threshold.
Parameters: - st (
structure.Structure
) – Structure containing the two atom sets. - atoms1 – First set of atom indices to check within st. If not specified, all atoms will be used.
- st2 (
structure.Structure
or None) – Structure containing the atoms specified in atoms2. If None, st will be used for both sets. - atoms2 (list of ints or
structure._StructureAtom
objects or None) – Second set of atom indices to check within st. If not specified, all atoms will be used. - max_dist (float) – Maximum allowable bond distance. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- min_donor_angle (float) – Minimum allowable donor angle. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- min_acceptor_angle (float) – Minimum allowable acceptor angle. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- max_acceptor_angle (float) – Maximum allowable acceptor angle. If not specified, the Maestro preference default value will be used. (Not the current user setting).
- honor_pbc (bool) – Honor Periodic Boundary Conditions, if defined as properties in the structure, and if st is equal to st2. Default is True.
Returns: A list of (donor atom object, acceptor atom object) for each hydrogen bond between the subsets of atoms.
Return type: list of (
structure._StructureAtom
,structure._StructureAtom
) tuples- st (
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schrodinger.structutils.interactions.hbond.
get_donor_acceptor_bonds
(params, st, atoms1=None, st2=None, atoms2=None, honor_pbc=True)¶ Get the requested type of interactions
Parameters: - params (list(schrodinger.infra.structure.AtomQueryParams)) – Parameters for accepting a donor/acceptor pair.
- st (
structure.Structure
) – Structure containing the two atom sets. - atoms1 – First set of atom indices to check within st. If not specified, all atoms will be used.
- st2 (
structure.Structure
or None) – Structure containing the atoms specified in atoms2. If None, st will be used for both sets. - atoms2 (list of ints or
structure._StructureAtom
objects or None) – Second set of atom indices to check within st. If not specified, all atoms will be used. - honor_pbc (bool) – Honor Periodic Boundary Conditions, if defined as properties in the structure, and if st is equal to st2. Default is True.
Returns: A list of (donor atom object, acceptor atom object) for each hydrogen bond between the subsets of atoms.
Return type: list of (
structure._StructureAtom
,structure._StructureAtom
) tuples