Analysis Parameters

Contains analysis parameters, default values, and validation ranges for molecular interaction analysis.

Module Overview

Analysis parameters for HBAT molecular interaction analysis.

This module contains the AnalysisParameters class that defines all configurable parameters for hydrogen bond, halogen bond, and π interaction analysis.

class hbat.constants.parameters.ParametersDefault

Bases: object

Default values for molecular interaction analysis parameters.

HB_DISTANCE_CUTOFF = 2.5

HB_ANGLE_CUTOFF = 120.0

HB_DA_DISTANCE = 3.5

WHB_DISTANCE_CUTOFF = 3.6

WHB_ANGLE_CUTOFF = 150.0

WHB_DA_DISTANCE = 3.5

XB_DISTANCE_CUTOFF = 3.9

XB_ANGLE_CUTOFF = 150.0

PI_DISTANCE_CUTOFF = 3.5

PI_ANGLE_CUTOFF = 110.0

PI_CCL_DISTANCE_CUTOFF = 3.5

PI_CCL_ANGLE_CUTOFF = 145

PI_CBR_DISTANCE_CUTOFF = 3.5

PI_CBR_ANGLE_CUTOFF = 155

PI_CI_DISTANCE_CUTOFF = 3.6

PI_CI_ANGLE_CUTOFF = 165.0

PI_CH_DISTANCE_CUTOFF = 3.5

PI_CH_ANGLE_CUTOFF = 110.0

PI_NH_DISTANCE_CUTOFF = 3.2

PI_NH_ANGLE_CUTOFF = 115.0

PI_OH_DISTANCE_CUTOFF = 3.0

PI_OH_ANGLE_CUTOFF = 115.0

PI_SH_DISTANCE_CUTOFF = 3.8

PI_SH_ANGLE_CUTOFF = 105.0

COVALENT_CUTOFF_FACTOR = 0.85

ANALYSIS_MODE = 'complete'

MAX_BOND_DISTANCE = 2.5

MIN_BOND_DISTANCE = 0.5

FIX_PDB_ENABLED = True

FIX_PDB_METHOD = 'pdbfixer'

FIX_PDB_ADD_HYDROGENS = True

FIX_PDB_ADD_HEAVY_ATOMS = False

FIX_PDB_REPLACE_NONSTANDARD = False

FIX_PDB_REMOVE_HETEROGENS = False

FIX_PDB_KEEP_WATER = True

class hbat.constants.parameters.AnalysisParameters(hb_distance_cutoff: float = 2.5, hb_angle_cutoff: float = 120.0, hb_donor_acceptor_cutoff: float = 3.5, whb_distance_cutoff: float = 3.6, whb_angle_cutoff: float = 150.0, whb_donor_acceptor_cutoff: float = 3.5, xb_distance_cutoff: float = 3.9, xb_angle_cutoff: float = 150.0, pi_distance_cutoff: float = 3.5, pi_angle_cutoff: float = 110.0, pi_ccl_distance_cutoff: float = 3.5, pi_ccl_angle_cutoff: float = 145, pi_cbr_distance_cutoff: float = 3.5, pi_cbr_angle_cutoff: float = 155, pi_ci_distance_cutoff: float = 3.6, pi_ci_angle_cutoff: float = 165.0, pi_ch_distance_cutoff: float = 3.5, pi_ch_angle_cutoff: float = 110.0, pi_nh_distance_cutoff: float = 3.2, pi_nh_angle_cutoff: float = 115.0, pi_oh_distance_cutoff: float = 3.0, pi_oh_angle_cutoff: float = 115.0, pi_sh_distance_cutoff: float = 3.8, pi_sh_angle_cutoff: float = 105.0, covalent_cutoff_factor: float = 0.85, analysis_mode: str = 'complete', fix_pdb_enabled: bool = True, fix_pdb_method: str = 'pdbfixer', fix_pdb_add_hydrogens: bool = True, fix_pdb_add_heavy_atoms: bool = False, fix_pdb_replace_nonstandard: bool = False, fix_pdb_remove_heterogens: bool = False, fix_pdb_keep_water: bool = True, **kwargs)

Bases: object

Parameters for comprehensive molecular interaction analysis.

This class contains all configurable parameters for detecting and analyzing molecular interactions in protein structures. Supports multiple interaction types with subtype-specific parameters.

Hydrogen Bonds (Classical): - Strong N-H···O, O-H···O, N-H···N interactions - Default: 2.5Å H···A distance, 120° D-H···A angle

Weak Hydrogen Bonds (C-H···O): - Carbon-hydrogen donor interactions with oxygen acceptors - Default: 3.6Å H···A distance, 150° D-H···A angle - Important in protein-ligand binding and aromatic interactions

Halogen Bonds: - C-X···A interactions where X is Cl, Br, I - Default: 3.9Å X···A distance, 150° C-X···A angle (updated default)

π Interactions (Multiple Subtypes): - Hydrogen-π: C-H···π, N-H···π, O-H···π, S-H···π - Halogen-π: C-Cl···π, C-Br···π, C-I···π - Each subtype has optimized distance/angle cutoffs

Parameters:

• hb_distance_cutoff (float) – Maximum H…A distance for hydrogen bonds (Å)

• hb_angle_cutoff (float) – Minimum D-H…A angle for hydrogen bonds (degrees)

• hb_donor_acceptor_cutoff (float) – Maximum D…A distance for hydrogen bonds (Å)

• whb_distance_cutoff (float) – Maximum H…A distance for weak hydrogen bonds (Å)

• whb_angle_cutoff (float) – Minimum D-H…A angle for weak hydrogen bonds (degrees)

• whb_donor_acceptor_cutoff (float) – Maximum D…A distance for weak hydrogen bonds (Å)

• xb_distance_cutoff (float) – Maximum X…A distance for halogen bonds (Å)

• xb_angle_cutoff (float) – Minimum C-X…A angle for halogen bonds (degrees, default: 150°)

• pi_distance_cutoff (float) – Maximum H…π distance for π interactions (Å, legacy)

• pi_angle_cutoff (float) – Minimum D-H…π angle for π interactions (degrees, legacy)

• pi_ccl_distance_cutoff (float) – Maximum C-Cl…π distance for halogen-π interactions (Å)

• pi_ccl_angle_cutoff (float) – Minimum C-Cl…π angle for halogen-π interactions (degrees)

• pi_cbr_distance_cutoff (float) – Maximum C-Br…π distance for halogen-π interactions (Å)

• pi_cbr_angle_cutoff (float) – Minimum C-Br…π angle for halogen-π interactions (degrees)

• pi_ci_distance_cutoff (float) – Maximum C-I…π distance for halogen-π interactions (Å)

• pi_ci_angle_cutoff (float) – Minimum C-I…π angle for halogen-π interactions (degrees)

• pi_ch_distance_cutoff (float) – Maximum C-H…π distance for hydrogen-π interactions (Å)

• pi_ch_angle_cutoff (float) – Minimum C-H…π angle for hydrogen-π interactions (degrees)

• pi_nh_distance_cutoff (float) – Maximum N-H…π distance for hydrogen-π interactions (Å)

• pi_nh_angle_cutoff (float) – Minimum N-H…π angle for hydrogen-π interactions (degrees)

• pi_oh_distance_cutoff (float) – Maximum O-H…π distance for hydrogen-π interactions (Å)

• pi_oh_angle_cutoff (float) – Minimum O-H…π angle for hydrogen-π interactions (degrees)

• pi_sh_distance_cutoff (float) – Maximum S-H…π distance for hydrogen-π interactions (Å)

• pi_sh_angle_cutoff (float) – Minimum S-H…π angle for hydrogen-π interactions (degrees)

• covalent_cutoff_factor (float) – Factor for covalent bond detection

• analysis_mode (str) – Analysis mode (‘local’ or ‘global’)

• fix_pdb_enabled (bool) – Enable PDB structure fixing

• fix_pdb_method (str) – PDB fixing method (‘openbabel’ or ‘pdbfixer’)

• fix_pdb_add_hydrogens (bool) – Add missing hydrogen atoms (both methods)

• fix_pdb_add_heavy_atoms (bool) – Add missing heavy atoms (PDBFixer only)

• fix_pdb_replace_nonstandard (bool) – Replace nonstandard residues (PDBFixer only)

• fix_pdb_remove_heterogens (bool) – Remove heterogens (PDBFixer only)

• fix_pdb_keep_water (bool) – Keep water when removing heterogens (PDBFixer only)

__init__(hb_distance_cutoff: float = 2.5, hb_angle_cutoff: float = 120.0, hb_donor_acceptor_cutoff: float = 3.5, whb_distance_cutoff: float = 3.6, whb_angle_cutoff: float = 150.0, whb_donor_acceptor_cutoff: float = 3.5, xb_distance_cutoff: float = 3.9, xb_angle_cutoff: float = 150.0, pi_distance_cutoff: float = 3.5, pi_angle_cutoff: float = 110.0, pi_ccl_distance_cutoff: float = 3.5, pi_ccl_angle_cutoff: float = 145, pi_cbr_distance_cutoff: float = 3.5, pi_cbr_angle_cutoff: float = 155, pi_ci_distance_cutoff: float = 3.6, pi_ci_angle_cutoff: float = 165.0, pi_ch_distance_cutoff: float = 3.5, pi_ch_angle_cutoff: float = 110.0, pi_nh_distance_cutoff: float = 3.2, pi_nh_angle_cutoff: float = 115.0, pi_oh_distance_cutoff: float = 3.0, pi_oh_angle_cutoff: float = 115.0, pi_sh_distance_cutoff: float = 3.8, pi_sh_angle_cutoff: float = 105.0, covalent_cutoff_factor: float = 0.85, analysis_mode: str = 'complete', fix_pdb_enabled: bool = True, fix_pdb_method: str = 'pdbfixer', fix_pdb_add_hydrogens: bool = True, fix_pdb_add_heavy_atoms: bool = False, fix_pdb_replace_nonstandard: bool = False, fix_pdb_remove_heterogens: bool = False, fix_pdb_keep_water: bool = True, **kwargs)

Initialize analysis parameters.

Parameters:

• hb_distance_cutoff (float) – Maximum H…A distance for hydrogen bonds (Å)

• hb_angle_cutoff (float) – Minimum D-H…A angle for hydrogen bonds (degrees)

• hb_donor_acceptor_cutoff (float) – Maximum D…A distance for hydrogen bonds (Å)

• whb_distance_cutoff (float) – Maximum H…A distance for weak hydrogen bonds (Å)

• whb_angle_cutoff (float) – Minimum D-H…A angle for weak hydrogen bonds (degrees)

• whb_donor_acceptor_cutoff (float) – Maximum D…A distance for weak hydrogen bonds (Å)

• xb_distance_cutoff (float) – Maximum X…A distance for halogen bonds (Å)

• xb_angle_cutoff (float) – Minimum C-X…A angle for halogen bonds (degrees)

• pi_distance_cutoff (float) – Maximum H…π distance for π interactions (Å)

• pi_angle_cutoff (float) – Minimum D-H…π angle for π interactions (degrees)

• covalent_cutoff_factor (float) – Factor for covalent bond detection

• analysis_mode (str) – Analysis mode (‘local’ or ‘global’)

• fix_pdb_enabled (bool) – Enable PDB structure fixing

• fix_pdb_method (str) – PDB fixing method (‘openbabel’ or ‘pdbfixer’)

• fix_pdb_add_hydrogens (bool) – Add missing hydrogen atoms (both methods)

• fix_pdb_add_heavy_atoms (bool) – Add missing heavy atoms (PDBFixer only)

• fix_pdb_replace_nonstandard (bool) – Replace nonstandard residues (PDBFixer only)

• fix_pdb_remove_heterogens (bool) – Remove heterogens (PDBFixer only)

• fix_pdb_keep_water (bool) – Keep water when removing heterogens (PDBFixer only)

• kwargs (dict) – Additional parameters (for future extensibility)

__repr__() → str

Return string representation of the parameters object.

Returns:

String representation showing all parameters

Return type:

str

__eq__(other) → bool

Compare two AnalysisParameters objects for equality.

Parameters:

other (AnalysisParameters) – Other AnalysisParameters object to compare

Returns:

True if all parameters are equal

Return type:

bool

__hash__() → int

Return hash of the parameters object for use in sets/dicts.

Returns:

Hash value based on all parameters

Return type:

int

to_dict() → dict

Convert parameters to dictionary format.

Returns:

Dictionary representation of all parameters

Return type:

dict

classmethod from_dict(data: dict) → AnalysisParameters

Create AnalysisParameters object from dictionary.

Parameters:

data (dict) – Dictionary containing parameter values

Returns:

New AnalysisParameters object

Return type:

AnalysisParameters

validate() → List[str]

Validate parameter values and return list of validation errors.

Checks all parameter values for validity and logical consistency. Returns a list of validation error messages, empty list if all valid.

Returns:

List of validation error messages

Return type:

List[str]

class hbat.constants.parameters.ParameterRanges

Bases: object

Valid ranges for analysis parameters.

MIN_DISTANCE = 0.5

MAX_DISTANCE = 6

MIN_ANGLE = 0.0

MAX_ANGLE = 180.0

MIN_COVALENT_FACTOR = 0.0

MAX_COVALENT_FACTOR = 1.0

class hbat.constants.parameters.PDBFixingModes

Bases: object

Available PDB structure fixing modes.

OPENBABEL = 'openbabel'

PDBFIXER = 'pdbfixer'

ALL_METHODS = ['openbabel', 'pdbfixer']

ADD_HYDROGENS = 'add_hydrogens'

ADD_HEAVY_ATOMS = 'add_heavy_atoms'

REPLACE_NONSTANDARD = 'replace_nonstandard'

REMOVE_HETEROGENS = 'remove_heterogens'

OPENBABEL_OPERATIONS = ['add_hydrogens']

PDBFIXER_OPERATIONS = ['add_hydrogens', 'add_heavy_atoms', 'replace_nonstandard', 'remove_heterogens']

class hbat.constants.parameters.AnalysisModes

Bases: object

Available analysis modes.

COMPLETE = 'complete'

LOCAL = 'local'

ALL_MODES = ['complete', 'local']

class hbat.constants.parameters.BondDetectionMethods

Bases: object

Available bond detection methods.

CONECT_RECORDS = 'conect_records'

RESIDUE_LOOKUP = 'residue_lookup'

DISTANCE_BASED = 'distance_based'

ALL_METHODS = ['conect_records', 'residue_lookup', 'distance_based']