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 = 3.5

HB_ANGLE_CUTOFF = 120.0

HB_DA_DISTANCE = 4.0

XB_DISTANCE_CUTOFF = 4.0

XB_ANGLE_CUTOFF = 120.0

PI_DISTANCE_CUTOFF = 4.5

PI_ANGLE_CUTOFF = 90.0

COVALENT_CUTOFF_FACTOR = 0.6

ANALYSIS_MODE = 'complete'

MAX_BOND_DISTANCE = 2.5

MIN_BOND_DISTANCE = 0.5

FIX_PDB_ENABLED = True

FIX_PDB_METHOD = 'openbabel'

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 = 3.5, hb_angle_cutoff: float = 120.0, hb_donor_acceptor_cutoff: float = 4.0, xb_distance_cutoff: float = 4.0, xb_angle_cutoff: float = 120.0, pi_distance_cutoff: float = 4.5, pi_angle_cutoff: float = 90.0, covalent_cutoff_factor: float = 0.6, analysis_mode: str = 'complete', fix_pdb_enabled: bool = True, fix_pdb_method: str = 'openbabel', 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)

Bases: object

Parameters for molecular interaction analysis.

This class contains all configurable parameters used during molecular interaction analysis, including distance cutoffs, angle thresholds, and analysis modes.

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)

• 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)

hb_distance_cutoff: float = 3.5

hb_angle_cutoff: float = 120.0

hb_donor_acceptor_cutoff: float = 4.0

xb_distance_cutoff: float = 4.0

xb_angle_cutoff: float = 120.0

pi_distance_cutoff: float = 4.5

pi_angle_cutoff: float = 90.0

covalent_cutoff_factor: float = 0.6

analysis_mode: str = 'complete'

fix_pdb_enabled: bool = True

fix_pdb_method: str = 'openbabel'

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

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]

__init__(hb_distance_cutoff: float = 3.5, hb_angle_cutoff: float = 120.0, hb_donor_acceptor_cutoff: float = 4.0, xb_distance_cutoff: float = 4.0, xb_angle_cutoff: float = 120.0, pi_distance_cutoff: float = 4.5, pi_angle_cutoff: float = 90.0, covalent_cutoff_factor: float = 0.6, analysis_mode: str = 'complete', fix_pdb_enabled: bool = True, fix_pdb_method: str = 'openbabel', 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) → None

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']

Classes

Parameters Default Values

class hbat.constants.parameters.ParametersDefault

Bases: object

Default values for molecular interaction analysis parameters.

HB_DISTANCE_CUTOFF = 3.5

HB_ANGLE_CUTOFF = 120.0

HB_DA_DISTANCE = 4.0

XB_DISTANCE_CUTOFF = 4.0

XB_ANGLE_CUTOFF = 120.0

PI_DISTANCE_CUTOFF = 4.5

PI_ANGLE_CUTOFF = 90.0

COVALENT_CUTOFF_FACTOR = 0.6

ANALYSIS_MODE = 'complete'

MAX_BOND_DISTANCE = 2.5

MIN_BOND_DISTANCE = 0.5

FIX_PDB_ENABLED = True

FIX_PDB_METHOD = 'openbabel'

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

Analysis Parameters

class hbat.constants.parameters.AnalysisParameters(hb_distance_cutoff: float = 3.5, hb_angle_cutoff: float = 120.0, hb_donor_acceptor_cutoff: float = 4.0, xb_distance_cutoff: float = 4.0, xb_angle_cutoff: float = 120.0, pi_distance_cutoff: float = 4.5, pi_angle_cutoff: float = 90.0, covalent_cutoff_factor: float = 0.6, analysis_mode: str = 'complete', fix_pdb_enabled: bool = True, fix_pdb_method: str = 'openbabel', 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)

Bases: object

Parameters for molecular interaction analysis.

This class contains all configurable parameters used during molecular interaction analysis, including distance cutoffs, angle thresholds, and analysis modes.

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)

• 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)

hb_distance_cutoff: float = 3.5

hb_angle_cutoff: float = 120.0

hb_donor_acceptor_cutoff: float = 4.0

xb_distance_cutoff: float = 4.0

xb_angle_cutoff: float = 120.0

pi_distance_cutoff: float = 4.5

pi_angle_cutoff: float = 90.0

covalent_cutoff_factor: float = 0.6

analysis_mode: str = 'complete'

fix_pdb_enabled: bool = True

fix_pdb_method: str = 'openbabel'

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

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]

__init__(hb_distance_cutoff: float = 3.5, hb_angle_cutoff: float = 120.0, hb_donor_acceptor_cutoff: float = 4.0, xb_distance_cutoff: float = 4.0, xb_angle_cutoff: float = 120.0, pi_distance_cutoff: float = 4.5, pi_angle_cutoff: float = 90.0, covalent_cutoff_factor: float = 0.6, analysis_mode: str = 'complete', fix_pdb_enabled: bool = True, fix_pdb_method: str = 'openbabel', 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) → None

Parameter Validation Ranges

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

PDB Fixing Modes

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']

Analysis Modes

class hbat.constants.parameters.AnalysisModes

Bases: object

Available analysis modes.

COMPLETE = 'complete'

LOCAL = 'local'

ALL_MODES = ['complete', 'local']

Bond Detection Methods

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']