binana.interactions package

This module contains functions that return information about various types of interactions between a protein receptor and a small-molecule ligand.

binana.interactions.get_active_site_flexibility(ligand, receptor, cutoff=None)[source]

Categorizes ligand-adjacent receptor atoms as belonging to a sidechain or backbone, as well as an alpha helix, beta sheet, or other secondary structure. Output is formatted like this:

{

    'counts': {
        'SIDECHAIN_OTHER': 136,
        'SIDECHAIN_BETA': 72,
        'BACKBONE_OTHER': 7,
        'BACKBONE_BETA': 3,
        'SIDECHAIN_ALPHA': 18
    },
    'mols': {
        'alpha_helix': <binana._structure.mol.Mol instance at 0x7feb20438170>,
        'beta_sheet': <binana._structure.mol.Mol instance at 0x7feb204381b8>,
        'side_chain': <binana._structure.mol.Mol instance at 0x7feb20438368>,
        'other_2nd_structure': <binana._structure.mol.Mol instance at 0x7feb20438248>,
        'back_bone': <binana._structure.mol.Mol instance at 0x7feb20438320>
    }
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • cutoff (float, optional) – The distance cutoff. Defaults to ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF.

Returns

Contains the atom tallies (“counts”), as well as a list of binana._structure.mol.Mol objects (“mols”), each with the participating atoms that belong to alpha helixes, beta sheets, and other, respectively.

Return type

dict

binana.interactions.get_all_interactions(ligand, receptor, closest_dist_cutoff=None, close_dist_cutoff=None, electrostatic_dist_cutoff=None, active_site_flexibility_dist_cutoff=None, hydrophobic_dist_cutoff=None, hydrogen_bond_dist_cutoff=None, hydrogen_halogen_bond_angle_cutoff=None, halogen_bond_dist_cutoff=None, pi_pi_general_dist_cutoff=None, pi_stacking_angle_tol=None, t_stacking_angle_tol=None, t_stacking_closest_dist_cutoff=None, cation_pi_dist_cutoff=None, salt_bridge_dist_cutoff=None, metal_coordination_dist_cutoff=None, pi_padding=None)[source]

A single function to identify and characterize all BINANA-supported protein/ligand interactions. Output is formatted like this:

{
    "closest": ...,
    "close": ...,
    "electrostatic_energies": ...,
    "active_site_flexibility": ...,
    "hydrophobics": ...,
    "hydrogen_bonds": ...,
    "halogen_bonds": ...,
    "ligand_atom_types": ...,
    "pi_pi": ...,
    "cat_pi": ...,
    "salt_bridges": ...,
    "metal_coordinations": ...,
}

where each … is a dictionary containing the corresponding interaction information (see the output of the other functions in this module).

Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • closest_dist_cutoff (float, optional) – The closest-atom distance cutoff. Defaults to CLOSE_CONTACTS_DIST1_CUTOFF.

  • close_dist_cutoff (float, optional) – The close-atom distance cutoff. Defaults to CLOSE_CONTACTS_DIST2_CUTOFF.

  • electrostatic_dist_cutoff (float, optional) – The electrostatic distance cutoff. Defaults to ELECTROSTATIC_DIST_CUTOFF.

  • active_site_flexibility_dist_cutoff (float, optional) – The active-site-flexibility distance cutoff. Defaults to ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF.

  • hydrophobic_dist_cutoff (float, optional) – The hydrophobic distance cutoff. Defaults to HYDROPHOBIC_DIST_CUTOFF.

  • hydrogen_bond_dist_cutoff (float, optional) – The hydrogen-bond distance cutoff. Defaults to HYDROGEN_BOND_DIST_CUTOFF.

  • hydrogen_halogen_bond_angle_cutoff (float, optional) – The hydrogen- and halogen-bond angle cutoff. Defaults to HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF.

  • halogen_bond_dist_cutoff (float, optional) – The halogen-bond distance cutoff. Defaults to HALOGEN_BOND_DIST_CUTOFF.

  • pi_pi_general_dist_cutoff (float, optional) – The distance cutoff used for all pi-pi interactions (stacking and T-shaped). Defaults to PI_PI_INTERACTING_DIST_CUTOFF.

  • pi_stacking_angle_tol (float, optional) – The angle tolerance for the pi-pi stacking interactions. Defaults to PI_STACKING_ANGLE_TOLERANCE.

  • t_stacking_angle_tol (float, optional) – The angle tolerance for the T-shaped interactions. Defaults to T_STACKING_ANGLE_TOLERANCE.

  • t_stacking_closest_dist_cutoff (float, optional) – The T-stacking_closest distance cutoff. Defaults to T_STACKING_CLOSEST_DIST_CUTOFF.

  • cation_pi_dist_cutoff (float, optional) – The cation-pi distance cutoff. Defaults to CATION_PI_DIST_CUTOFF.

  • salt_bridge_dist_cutoff (float, optional) – The salt-bridge distance cutoff. Defaults to SALT_BRIDGE_DIST_CUTOFF.

  • metal_coordination_dist_cutoff (float, optional) – The metal-coordination distance cutoff. Defaults to METAL_COORDINATION_DIST_CUTOFF.

  • pi_padding (float, optional) – The amount by which the radius of each pi ring should be artificially expanded, to be sure to catch the interactions. Defaults to PI_PADDING_DIST.

Returns

Contains the atom tallies (“counts”), binana._structure.mol.Mol objects with the participating atoms (“mol”), and labels to use in the log file (“labels”), for every BINANA interaction type.

Return type

dict

binana.interactions.get_cation_pi(ligand, receptor, cutoff=None, pi_padding=None)[source]

Identifies and counts the number of pi-cation interactions between the protein and ligand. Output is formatted like this:

{
    'counts': {
        'PI-CATION_LIGAND-CHARGED_BETA': 2,
        'PI-CATION_LIGAND-CHARGED_OTHER': 2,
        'PI-CATION_RECEPTOR-CHARGED_OTHER': 1
    },
    'labels': [
        (
            '[A:CHT(1):N1(2) / A:CHT(1):C5(1) / A:CHT(1):C6(3) / A:CHT(1):C6(4) / A:CHT(1):C7(9)]',
            '[A:TRP(43):CG(28) / A:TRP(43):CD1(29) / A:TRP(43):NE1(31) / A:TRP(43):CE2(32) / A:TRP(43):CD2(30)]',
            {'distance': 4.403228947034208}
        ),
        (
            '[A:CHT(1):N1(2) / A:CHT(1):C5(1) / A:CHT(1):C6(3) / A:CHT(1):C6(4) / A:CHT(1):C7(9)]',
            '[A:TRP(43):CE2(32) / A:TRP(43):CD2(30) / A:TRP(43):CE3(33) / A:TRP(43):CZ3(35) / A:TRP(43):CH2(36) / A:TRP(43):CZ2(34)]',
            {'distance': 3.608228947034208}
        )
    ],
    'mol': <binana._structure.mol.Mol instance at 0x7feb20488128>
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • cutoff (float, optional) – The distance cutoff. Defaults to CATION_PI_DIST_CUTOFF.

  • pi_padding (float, optional) – The amount by which the radius of each pi ring should be artificially expanded, to be sure to catch the interactions. Defaults to PI_PADDING_DIST.

Returns

Contains the atom tallies (“counts”), the binana._structure.mol.Mol object with the participating atoms (“mol”), and the labels to use in the log file (“labels”).

Return type

dict

binana.interactions.get_close(ligand, receptor, cutoff=None)[source]

Identifies and counts the number of close protein/ligand contacts. Output is formatted like this:

{
    'counts': {
        'C_C': 5,
        'A_OA': 29,
        'HD_NA': 1,
        'HD_N': 6
    },
    'labels': [
        (
            'A:CHT(1):C5(1)',
            'A:TRP(43):CD2(30)',
            {'distance': 4.403228947034208}
        ),
        (
            'A:CHT(1):C5(1)',
            'A:TRP(43):CE2(32)',
            {'distance': 3.923228947034208}
        ),
        (
            'A:CHT(1):C5(1)',
            'A:TRP(43):CE3(33)',
            {'distance': 4.123228947034208}
        )
    ],
    'mol': <binana._structure.mol.Mol instance at 0x7feb203ce3f8>
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • cutoff (float, optional) – The distance cutoff. Defaults to CLOSE_CONTACTS_DIST2_CUTOFF.

Returns

Contains the atom tallies (“counts”), a binana._structure.mol.Mol object with the participating atoms (“mol”), and the labels to use in the log file (“labels”).

Return type

dict

binana.interactions.get_closest(ligand, receptor, cutoff=None)[source]

Identifies and counts the number of closest (very close) protein/ligand contacts. Output is formatted like this:

{
    'counts': {
        'HD_OA': 8,
        'A_OA': 3
    },
    'labels': [
        (
            'A:CHT(1):C9(7)',
            'A:TRP(205):CB(467)',
            {'distance': 4.403228947034208}
        ),
        (
            'A:CHT(1):O2(8)',
            'A:TRP(205):CG(468)',
            {'distance': 3.923228947034208}
        )
    'mol': <binana._structure.mol.Mol instance at 0x7feb20290908>
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • cutoff (float, optional) – The distance cutoff. Defaults to CLOSE_CONTACTS_DIST1_CUTOFF.

Returns

Contains the atom tallies (“counts”), a binana._structure.mol.Mol object with the participating atoms (“mol”), and the labels to use in the log file (“labels”).

Return type

dict

binana.interactions.get_electrostatic_energies(ligand, receptor, cutoff=None)[source]

Calculates and tallies the electrostatic energies between receptor and ligand atoms that come within a given distance of each other. Output is formatted like this:

{
    'counts': {
        'C_C': 49372.61585423234,
        'A_OA': -311243.9243779809
    }
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • cutoff (float, optional) – The distance cutoff. Defaults to ELECTROSTATIC_DIST_CUTOFF.

Returns

Contains the tallies (“counts”) of the energies by atom-type pair.

Return type

dict

binana.interactions.get_halogen_bonds(ligand, receptor, dist_cutoff=None, angle_cutoff=None)[source]

Identifies and counts the number of halogen bonds between the protein and ligand. Output is formatted like this:

{
    'counts': {
        'HDONOR_RECEPTOR_SIDECHAIN_OTHER': 1,
        'HDONOR_LIGAND_SIDECHAIN_OTHER': 2
    },
    'labels': [
        ('A:CHT(1):N1(14)', 'A:CHT(1):H1(16)', 'A:ASP(157):OD2(285)', 'LIGAND'),
        ('A:CHT(1):O6(22)', 'A:ASN(156):2HD2(276)', 'A:ASN(156):ND2(274)', 'RECEPTOR'),
        ('A:CHT(1):O6(22)', 'A:CHT(1):HO6(23)', 'A:ASP(157):OD1(284)', 'LIGAND')
    ],
    'mol': <binana._structure.mol.Mol instance at 0x7feb20478518>
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • dist_cutoff (float, optional) – The distance cutoff. Defaults to HALOGEN_BOND_DIST_CUTOFF.

  • angle_cutoff (float, optional) – The angle cutoff. Defaults to HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF.

Returns

Contains the atom tallies (“counts”), a binana._structure.mol.Mol object with the participating atoms (“mol”), and the labels to use in the log file (“labels”).

Return type

dict

binana.interactions.get_hydrogen_bonds(ligand, receptor, dist_cutoff=None, angle_cutoff=None)[source]

Identifies and counts the number of hydrogen bonds between the protein and ligand. Output is formatted like this:

{
    'counts': {
        'HDONOR_RECEPTOR_SIDECHAIN_OTHER': 1,
        'HDONOR_LIGAND_SIDECHAIN_OTHER': 2
    },
    'labels': [
        ('A:CHT(1):N1(14)', 'A:CHT(1):H1(16)', 'A:ASP(157):OD2(285)', 'LIGAND'),
        ('A:CHT(1):O6(22)', 'A:ASN(156):2HD2(276)', 'A:ASN(156):ND2(274)', 'RECEPTOR'),
        ('A:CHT(1):O6(22)', 'A:CHT(1):HO6(23)', 'A:ASP(157):OD1(284)', 'LIGAND')
    ],
    'mol': <binana._structure.mol.Mol instance at 0x7feb20478518>
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • dist_cutoff (float, optional) – The distance cutoff. Defaults to HYDROGEN_BOND_DIST_CUTOFF.

  • angle_cutoff (float, optional) – The angle cutoff. Defaults to HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF.

Returns

Contains the atom tallies (“counts”), a binana._structure.mol.Mol object with the participating atoms (“mol”), and the labels to use in the log file (“labels”).

Return type

dict

binana.interactions.get_hydrophobics(ligand, receptor, cutoff=None)[source]

Identifies and counts the number of hydrophobic (C-C) interactions between the protein and ligand. Output is formatted like this:

{
    'counts': {
        'SIDECHAIN_OTHER': 43,
        'SIDECHAIN_BETA': 29,
        'BACKBONE_OTHER': 2
    },
    'labels': [
        (
            'A:CHT(1):C5(1)',
            'A:TRP(43):CD2(30)',
            {'distance': 4.403228947034208}
        ),
        (
            'A:CHT(1):C5(1)',
            'A:TRP(43):CE2(32)',
            {'distance': 3.923228947034208}
        ),
        (
            'A:CHT(1):C5(1)',
            'A:TRP(43):CE3(33)',
            {'distance': 4.123228947034208}
        )
    ],
    'mol': <binana._structure.mol.Mol instance at 0x7feb000acc68>
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • cutoff (float, optional) – The distance cutoff. Defaults to HYDROPHOBIC_DIST_CUTOFF.

Returns

Contains the atom tallies (“counts”), a binana._structure.mol.Mol object with the participating atoms (“mol”), and the labels to use in the log file (“labels”).

Return type

dict

binana.interactions.get_ligand_atom_types(ligand)[source]

Tallies the ligand atoms by atom type. Output is formatted like this:

{
    'counts': {
        'A': 8,
        'C': 5,
        'HD': 3,
        'OA': 5,
        'N': 2
    }
}
Parameters

ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

Returns

Contains the atom tallies (“counts”).

Return type

dict

binana.interactions.get_metal_coordinations(ligand, receptor, cutoff=None)[source]

Identifies and counts the number of metal-coordination protein/ligand contacts. Output is formatted like this:

{
    'counts': {
        'N_ZN': 3,
        'O_ZN': 2
    },
    'labels': [
        (
            'A:ZN(201):ZN(3059)',
            'A:HIS(97):ND1(1426)',
            {'distance': 1.974986835399159}
        ),
        (
            'A:ZN(201):ZN(3059)',
            'A:HIS(100):NE2(1470)',
            {'distance': 2.0332422383965976}
        )
    ],
    'mol': <binana._structure.mol.Mol instance at 0x7feb20290908>
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • cutoff (float, optional) – The distance cutoff. Defaults to METAL_COORDINATION_DIST_CUTOFF.

Returns

Contains the atom tallies (“counts”), a binana._structure.mol.Mol object with the participating atoms (“mol”), and the labels to use in the log file (“labels”).

Return type

dict

binana.interactions.get_pi_pi(ligand, receptor, pi_pi_general_dist_cutoff=None, pi_stacking_angle_tol=None, t_stacking_angle_tol=None, t_stacking_closest_dist_cutoff=None, pi_padding=None)[source]

Identifies and counts the number of pi-pi stacking and T-shaped interactions between the protein and ligand. Output is formatted like this:

{
    'labels': {
        'T_stacking': [
            (
                '[A:CHT(1):C6(4) / A:CHT(1):C7(5) / A:CHT(1):C8(6) / A:CHT(1):C9(7) / A:CHT(1):O2(8)]',
                '[A:PHE(233):CG(657) / A:PHE(233):CD1(658) / A:PHE(233):CE1(660) / A:PHE(233):CZ(662) / A:PHE(233):CE2(661) / A:PHE(233):CD2(659)]',
                {'distance': 3.2176272313616425, 'angle': 78.66902972009667}
            ),
            (
                '[A:CHT(1):C2(17) / A:CHT(1):O1(18) / A:CHT(1):C5(19) / A:CHT(1):C4(20) / A:CHT(1):C3(21)]',
                '[A:TRP(43):CG(28) / A:TRP(43):CD1(29) / A:TRP(43):NE1(31) / A:TRP(43):CE2(32) / A:TRP(43):CD2(30)]',
                {'distance': 3.8236272313616425, 'angle': 91.23102972009667}
            )
        ],
        'pi_stacking': [
            (
                '[A:CHT(1):C6(4) / A:CHT(1):C7(5) / A:CHT(1):C8(6) / A:CHT(1):C9(7) / A:CHT(1):O2(8)]',
                '[A:TRP(90):CG(100) / A:TRP(90):CD1(101) / A:TRP(90):NE1(103) / A:TRP(90):CE2(104) / A:TRP(90):CD2(102)]',
                {'distance': 4.296775339716984, 'angle': 17.315362614715923}
            ),
            (
                '[A:CHT(1):C6(4) / A:CHT(1):C7(5) / A:CHT(1):C8(6) / A:CHT(1):C9(7) / A:CHT(1):O2(8)]',
                '[A:TRP(90):CE2(104) / A:TRP(90):CD2(102) / A:TRP(90):CE3(105) / A:TRP(90):CZ3(107) / A:TRP(90):CH2(108) / A:TRP(90):CZ2(106)]',
                {'distance': 3.256775339716984, 'angle': 7.323362614715923}
            )
        ]
    },
    'counts': {
        'STACKING_BETA': 2,
        'T-SHAPED_OTHER': 3
    },
    'mols': {
        'T_stacking': <binana._structure.mol.Mol instance at 0x7feb20478fc8>,
        'pi_stacking': <binana._structure.mol.Mol instance at 0x7feb20478f80>
    }
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • pi_pi_general_dist_cutoff (float, optional) – The distance cutoff used for all pi-pi interactions (stacking and T-shaped). Defaults to PI_PI_INTERACTING_DIST_CUTOFF.

  • pi_stacking_angle_tol (float, optional) – The angle tolerance for the pi-pi stacking interactions. Defaults to PI_STACKING_ANGLE_TOLERANCE.

  • t_stacking_angle_tol (float, optional) – The angle tolerance for the T-shaped interactions. Defaults to T_STACKING_ANGLE_TOLERANCE.

  • t_stacking_closest_dist_cutoff (float, optional) – The distance cutoff for T-shaped interactions specifically. Defaults to T_STACKING_CLOSEST_DIST_CUTOFF.

  • pi_padding (float, optional) – The amount by which the radius of each pi ring should be artificially expanded, to be sure to catch the interactions. Defaults to PI_PADDING_DIST.

Returns

Contains the atom tallies (“counts”), the binana._structure.mol.Mol objects with the participating atoms (“mols”), and the labels to use in the log file (“labels”).

Return type

dict

binana.interactions.get_salt_bridges(ligand, receptor, cutoff=None)[source]

Identifies and counts the number of salt-bridge interactions between the protein and ligand. Output is formatted like this:

{
    'counts': {
        'SALT-BRIDGE_OTHER': 1,
        'SALT-BRIDGE_ALPHA': 2
    },
    'labels': [
        (
            '[A:CHT(1):N1(2) / A:CHT(1):C5(1) / A:CHT(1):C6(3) / A:CHT(1):C6(4) / A:CHT(1):C7(9)]',
            '[A:ASP(45):CG(53) / A:ASP(45):OD1(54) / A:ASP(45):OD2(55)]',
            {'distance': 4.403228947034208}
        ),
        (
            '[A:CHT(1):N1(14) / A:CHT(1):C4(13) / A:CHT(1):H2(15) / A:CHT(1):H1(16) / A:CHT(1):C2(17)]',
            '[A:ASP(157):CG(283) / A:ASP(157):OD1(284) / A:ASP(157):OD2(285)]',
            {'distance': 3.608228947034208}
        )
    ],
    'mol': <binana._structure.mol.Mol instance at 0x7feb20494098>
}
Parameters

  • ligand (binana._structure.mol.Mol) – The ligand molecule to analyze.

  • receptor (binana._structure.mol.Mol) – The receptor molecule to analyze.

  • cutoff (float, optional) – The distance cutoff. Defaults to SALT_BRIDGE_DIST_CUTOFF.

Returns

Contains the atom tallies (“counts”), the binana._structure.mol.Mol object with the participating atoms (“mol”), and the labels to use in the log file (“labels”).

Return type

dict

Submodules

binana.interactions.default_params module

binana.interactions.default_params.ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF = 4.0

Atom-atom distance cutoff to use when categorizing ligand-adjacent protein atoms according to backbone vs. side chain, as well as alpha helix vs. beta sheet vs. other.

Type

float

binana.interactions.default_params.CATION_PI_DIST_CUTOFF = 6.0

Charged-moiety/ring-center distance cutoff for cation-pi interactions.

Type

float

binana.interactions.default_params.CLOSE_CONTACTS_DIST1_CUTOFF = 2.5

Atom-atom distance cutoff for very-close contacts.

Type

float

binana.interactions.default_params.CLOSE_CONTACTS_DIST2_CUTOFF = 4.0

Atom-atom distance cutoff for close contacts.

Type

float

binana.interactions.default_params.ELECTROSTATIC_DIST_CUTOFF = 4.0

Atom-atom distance cutoff to use when summing electrostatic energies.

Type

float

binana.interactions.default_params.HALOGEN_BOND_DIST_CUTOFF = 5.5

Donor/acceptor distance cutoff for halogen bonds.

Type

float

binana.interactions.default_params.HYDROGEN_BOND_DIST_CUTOFF = 4.0

Donor/acceptor distance cutoff for hydrogen bonds.

Type

float

binana.interactions.default_params.HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF = 40.0

Donor-hydrogen-acceptor or donor-halogen-acceptor angle cutoff, in degrees, for hydrogen and halogen bonds.

Type

float

binana.interactions.default_params.HYDROPHOBIC_DIST_CUTOFF = 4.0

Carbon-carbon distance cutoff for hydrophobics interactions.

Type

float

binana.interactions.default_params.METAL_COORDINATION_DIST_CUTOFF = 3.5

Metal-ligand distance cutoff for metal-coordination interactions.

Type

float

binana.interactions.default_params.PI_PADDING_DIST = 0.75

Aromatic-ring padding. For the purpose of detecting interactions, this value is added to a given atomatic ring’s actual radius.

Type

float

binana.interactions.default_params.PI_PI_INTERACTING_DIST_CUTOFF = 7.5

Ring-center distance cutoff for detecting pi-pi stacking and T-shaped interactions.

Type

float

binana.interactions.default_params.PI_STACKING_ANGLE_TOLERANCE = 30.0

pi-pi stacking angle cutoff, in degrees. The angle between the two vectors normal to the planes of each ring must be at least within this cutoff of parallel.

Type

float

binana.interactions.default_params.SALT_BRIDGE_DIST_CUTOFF = 5.5

Charged-moiety/charged-moiety distance cutoff for salt-bridge interactions.

Type

float

binana.interactions.default_params.T_STACKING_ANGLE_TOLERANCE = 30.0

pi-pi T-shaped angle cutoff, in degrees. The angle between the two vectors normal to the planes of each ring must be at least within this cutoff of perpendicular.

Type

float

binana.interactions.default_params.T_STACKING_CLOSEST_DIST_CUTOFF = 5.0

Atom-atom distance cutoff for detecting pi-pi T-shaped interactions.

Type

float