Molecular Interaction Data Structures#
Data structures for representing different types of molecular interactions with comprehensive geometric and chemical information.
Module Overview#
Molecular interaction classes for HBAT analysis.
This module defines the data structures for representing different types of molecular interactions including hydrogen bonds, halogen bonds, π interactions, and cooperativity chains.
This module provides dataclass-based representations for molecular interactions detected in protein and nucleic acid structures. Each interaction type captures specific geometric parameters and provides validation methods.
- class hbat.core.interactions.MolecularInteraction[source]#
Bases:
ABCBase class for all molecular interactions.
This abstract base class defines the unified interface for all types of molecular interactions analyzed by HBAT, including hydrogen bonds, halogen bonds, and π interactions.
All interactions have the following core components: - Donor: The electron/proton donor (atom or virtual atom) - Acceptor: The electron/proton acceptor (atom or virtual atom) - Interaction: The mediating atom/point (e.g., hydrogen, π center) - Geometry: Distances and angles defining the interaction - Bonding: The interaction atom must be bonded to the donor atom
Bonding Requirements: - For H-bonds: Hydrogen must be covalently bonded to the donor - For X-bonds: Halogen is covalently bonded to donor carbon - For X-H…π interactions: Hydrogen must be covalently bonded to the donor - For π-π stacking (future): No bonding requirement - uses centroid distances
- abstractmethod get_interaction() Atom | NPVec3D[source]#
Get the interaction mediating atom or point.
- abstractmethod get_donor_residue() str[source]#
Get the donor residue identifier.
- Returns:
String identifier for the donor residue
- Return type:
- abstractmethod get_acceptor_residue() str[source]#
Get the acceptor residue identifier.
- Returns:
String identifier for the acceptor residue
- Return type:
- abstractmethod get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- abstractmethod get_donor_interaction_distance() float[source]#
Get the donor to interaction distance.
- Returns:
Distance from donor to interaction point in Angstroms
- Return type:
- abstractmethod get_donor_acceptor_distance() float[source]#
Get the donor to acceptor distance.
- Returns:
Distance from donor to acceptor in Angstroms
- Return type:
- abstractmethod get_donor_interaction_acceptor_angle() float[source]#
Get the donor-interaction-acceptor angle.
- Returns:
Angle in radians
- Return type:
- abstractmethod is_donor_interaction_bonded() bool[source]#
Check if the interaction atom is bonded to the donor atom.
This is a fundamental requirement for most molecular interactions (except π-π stacking which will be implemented separately).
- Returns:
True if donor and interaction atom are bonded
- Return type:
- property donor_interaction_acceptor_angle: float#
Property accessor for donor-interaction-acceptor angle.
- get_donor_atom() Atom | None[source]#
Get the donor atom if it’s an Atom instance.
- Returns:
The donor atom if it’s an Atom, None otherwise
- Return type:
Optional[Atom]
- get_acceptor_atom() Atom | None[source]#
Get the acceptor atom if it’s an Atom instance.
- Returns:
The acceptor atom if it’s an Atom, None otherwise
- Return type:
Optional[Atom]
- class hbat.core.interactions.HydrogenBond(_donor: Atom, hydrogen: Atom, _acceptor: Atom, distance: float, angle: float, _donor_acceptor_distance: float, bond_type: str, _donor_residue: str, _acceptor_residue: str)[source]#
Bases:
MolecularInteractionRepresents a hydrogen bond interaction.
This class stores all information about a detected hydrogen bond, including the participating atoms, geometric parameters, and classification information.
- Parameters:
donor (Atom) – The hydrogen bond donor atom
hydrogen (Atom) – The hydrogen atom in the bond
acceptor (Atom) – The hydrogen bond acceptor atom
distance (float) – H…A distance in Angstroms
angle (float) – D-H…A angle in radians
donor_acceptor_distance (float) – D…A distance in Angstroms
bond_type (str) – Classification of the hydrogen bond type
donor_residue (str) – Identifier for donor residue
acceptor_residue (str) – Identifier for acceptor residue
- __init__(_donor: Atom, hydrogen: Atom, _acceptor: Atom, distance: float, angle: float, _donor_acceptor_distance: float, bond_type: str, _donor_residue: str, _acceptor_residue: str)[source]#
- property distance: float#
Legacy property for interaction distance.
- Returns:
Donor-interaction distance for backward compatibility
- Return type:
- property angle: float#
Legacy property for interaction angle.
- Returns:
Donor-interaction-acceptor angle for backward compatibility
- Return type:
- get_donor_residue() str[source]#
Get the donor residue identifier.
- Returns:
String identifier for the donor residue
- Return type:
- get_acceptor_residue() str[source]#
Get the acceptor residue identifier.
- Returns:
String identifier for the acceptor residue
- Return type:
- get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- is_donor_interaction_bonded() bool[source]#
Check if hydrogen is bonded to donor.
For hydrogen bonds, the hydrogen must be covalently bonded to the donor atom. This method assumes the bond has been validated during creation.
- Returns:
True (assumes validation was done during creation)
- Return type:
- class hbat.core.interactions.HalogenBond(halogen: Atom, _acceptor: Atom, distance: float, angle: float, bond_type: str, _halogen_residue: str, _acceptor_residue: str)[source]#
Bases:
MolecularInteractionRepresents a halogen bond interaction.
This class stores information about a detected halogen bond, where a halogen atom acts as an electron acceptor.
- Parameters:
halogen (Atom) – The halogen atom (F, Cl, Br, I)
acceptor (Atom) – The electron donor/acceptor atom
distance (float) – X…A distance in Angstroms
angle (float) – C-X…A angle in radians
bond_type (str) – Classification of the halogen bond type
halogen_residue (str) – Identifier for halogen-containing residue
acceptor_residue (str) – Identifier for acceptor residue
- __init__(halogen: Atom, _acceptor: Atom, distance: float, angle: float, bond_type: str, _halogen_residue: str, _acceptor_residue: str)[source]#
- property distance: float#
Legacy property for interaction distance.
- Returns:
Donor-interaction distance for backward compatibility
- Return type:
- property angle: float#
Legacy property for interaction angle.
- Returns:
Donor-interaction-acceptor angle for backward compatibility
- Return type:
- get_donor_residue() str[source]#
Get the donor residue identifier.
- Returns:
String identifier for the donor residue
- Return type:
- get_acceptor_residue() str[source]#
Get the acceptor residue identifier.
- Returns:
String identifier for the acceptor residue
- Return type:
- get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- get_donor_interaction_distance() float[source]#
Distance from donor to interaction point (0 for halogen bonds).
- is_donor_interaction_bonded() bool[source]#
Check if halogen is bonded to donor carbon.
For halogen bonds, the halogen atom must be covalently bonded to a carbon atom. The halogen serves as both the donor and interaction point.
- Returns:
True (assumes validation was done during creation)
- Return type:
- class hbat.core.interactions.PiInteraction(_donor: Atom, hydrogen: Atom, pi_center: NPVec3D, distance: float, angle: float, _donor_residue: str, _pi_residue: str)[source]#
Bases:
MolecularInteractionRepresents an X-H…π interaction.
This class stores information about a detected X-H…π interaction, where a hydrogen bond donor interacts with an aromatic π system.
- Parameters:
donor (Atom) – The hydrogen bond donor atom
hydrogen (Atom) – The hydrogen atom
pi_center (NPVec3D) – Center of the aromatic π system
distance (float) – H…π distance in Angstroms
angle (float) – D-H…π angle in radians
donor_residue (str) – Identifier for donor residue
pi_residue (str) – Identifier for π-containing residue
- __init__(_donor: Atom, hydrogen: Atom, pi_center: NPVec3D, distance: float, angle: float, _donor_residue: str, _pi_residue: str)[source]#
- property distance: float#
Legacy property for interaction distance.
- Returns:
Donor-interaction distance for backward compatibility
- Return type:
- property angle: float#
Legacy property for interaction angle.
- Returns:
Donor-interaction-acceptor angle for backward compatibility
- Return type:
- get_donor_residue() str[source]#
Get the donor residue identifier.
- Returns:
String identifier for the donor residue
- Return type:
- get_acceptor_residue() str[source]#
Get the acceptor residue identifier.
- Returns:
String identifier for the acceptor residue
- Return type:
- get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- is_donor_interaction_bonded() bool[source]#
Check if hydrogen is bonded to donor.
For X-H…π interactions, the hydrogen must be covalently bonded to the donor atom.
- Returns:
True (assumes validation was done during creation)
- Return type:
- property donor_acceptor_properties: str#
Get the donor-acceptor property description.
- Returns:
Property description string
- Return type:
- class hbat.core.interactions.CooperativityChain(interactions: List[HydrogenBond | HalogenBond | PiInteraction], chain_length: int, chain_type: str)[source]#
Bases:
MolecularInteractionRepresents a chain of cooperative molecular interactions.
This class represents a series of linked molecular interactions where the acceptor of one interaction acts as the donor of the next, creating cooperative effects.
- Parameters:
interactions (List[Union[HydrogenBond, HalogenBond, PiInteraction]]) – List of interactions in the chain
chain_length (int) – Number of interactions in the chain
chain_type (str) – Description of the interaction types in the chain
- __init__(interactions: List[HydrogenBond | HalogenBond | PiInteraction], chain_length: int, chain_type: str)[source]#
- get_interaction() Atom | NPVec3D[source]#
Get the center point of the chain (middle interaction point).
- get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- get_donor_interaction_distance() float[source]#
Get the distance from chain start to middle interaction.
Base Classes#
MolecularInteraction#
- class hbat.core.interactions.MolecularInteraction[source]#
Bases:
ABCBase class for all molecular interactions.
This abstract base class defines the unified interface for all types of molecular interactions analyzed by HBAT, including hydrogen bonds, halogen bonds, and π interactions.
All interactions have the following core components: - Donor: The electron/proton donor (atom or virtual atom) - Acceptor: The electron/proton acceptor (atom or virtual atom) - Interaction: The mediating atom/point (e.g., hydrogen, π center) - Geometry: Distances and angles defining the interaction - Bonding: The interaction atom must be bonded to the donor atom
Bonding Requirements: - For H-bonds: Hydrogen must be covalently bonded to the donor - For X-bonds: Halogen is covalently bonded to donor carbon - For X-H…π interactions: Hydrogen must be covalently bonded to the donor - For π-π stacking (future): No bonding requirement - uses centroid distances
Abstract base class defining the common interface for all molecular interactions.
Common Properties:
Interaction Type: Classification of the interaction
Participating Atoms: Atoms involved in the interaction
Geometric Parameters: Distance, angle, and orientation measurements
Energy Estimation: Approximate interaction strength
Validation Methods: Quality assessment and filtering
- abstractmethod get_interaction() Atom | NPVec3D[source]#
Get the interaction mediating atom or point.
- abstractmethod get_donor_residue() str[source]#
Get the donor residue identifier.
- Returns:
String identifier for the donor residue
- Return type:
- abstractmethod get_acceptor_residue() str[source]#
Get the acceptor residue identifier.
- Returns:
String identifier for the acceptor residue
- Return type:
- abstractmethod get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- abstractmethod get_donor_interaction_distance() float[source]#
Get the donor to interaction distance.
- Returns:
Distance from donor to interaction point in Angstroms
- Return type:
- abstractmethod get_donor_acceptor_distance() float[source]#
Get the donor to acceptor distance.
- Returns:
Distance from donor to acceptor in Angstroms
- Return type:
- abstractmethod get_donor_interaction_acceptor_angle() float[source]#
Get the donor-interaction-acceptor angle.
- Returns:
Angle in radians
- Return type:
- abstractmethod is_donor_interaction_bonded() bool[source]#
Check if the interaction atom is bonded to the donor atom.
This is a fundamental requirement for most molecular interactions (except π-π stacking which will be implemented separately).
- Returns:
True if donor and interaction atom are bonded
- Return type:
- property donor_interaction_acceptor_angle: float#
Property accessor for donor-interaction-acceptor angle.
- get_donor_atom() Atom | None[source]#
Get the donor atom if it’s an Atom instance.
- Returns:
The donor atom if it’s an Atom, None otherwise
- Return type:
Optional[Atom]
- get_acceptor_atom() Atom | None[source]#
Get the acceptor atom if it’s an Atom instance.
- Returns:
The acceptor atom if it’s an Atom, None otherwise
- Return type:
Optional[Atom]
Specific Interaction Types#
Hydrogen Bonds#
- class hbat.core.interactions.HydrogenBond(_donor: Atom, hydrogen: Atom, _acceptor: Atom, distance: float, angle: float, _donor_acceptor_distance: float, bond_type: str, _donor_residue: str, _acceptor_residue: str)[source]#
Bases:
MolecularInteractionRepresents a hydrogen bond interaction.
This class stores all information about a detected hydrogen bond, including the participating atoms, geometric parameters, and classification information.
- Parameters:
donor (Atom) – The hydrogen bond donor atom
hydrogen (Atom) – The hydrogen atom in the bond
acceptor (Atom) – The hydrogen bond acceptor atom
distance (float) – H…A distance in Angstroms
angle (float) – D-H…A angle in radians
donor_acceptor_distance (float) – D…A distance in Angstroms
bond_type (str) – Classification of the hydrogen bond type
donor_residue (str) – Identifier for donor residue
acceptor_residue (str) – Identifier for acceptor residue
Represents a hydrogen bond with donor-hydrogen-acceptor geometry.
Geometric Parameters:
Distance (D-A): Direct donor to acceptor distance
Distance (H-A): Hydrogen to acceptor distance
Angle (D-H…A): Donor-hydrogen-acceptor angle
Dihedral Angles: Additional geometric descriptors
Chemical Properties:
Donor Atom: Electronegative atom covalently bonded to hydrogen
Hydrogen Atom: Bridging hydrogen with partial positive charge
Acceptor Atom: Electronegative atom with lone electron pairs
Residue Context: Protein/nucleic acid environment
Usage Example:
from hbat.core.interactions import HydrogenBond from hbat.core.pdb_parser import Atom # Create hydrogen bond representation hbond = HydrogenBond( donor=donor_atom, hydrogen=hydrogen_atom, acceptor=acceptor_atom, distance_da=2.8, distance_ha=1.9, angle_dha=165.0, energy=-2.5 ) # Validate interaction if hbond.is_valid(): print(f"Strong hydrogen bond: {hbond.energy:.1f} kcal/mol")
- __init__(_donor: Atom, hydrogen: Atom, _acceptor: Atom, distance: float, angle: float, _donor_acceptor_distance: float, bond_type: str, _donor_residue: str, _acceptor_residue: str)[source]#
- property distance: float#
Legacy property for interaction distance.
- Returns:
Donor-interaction distance for backward compatibility
- Return type:
- property angle: float#
Legacy property for interaction angle.
- Returns:
Donor-interaction-acceptor angle for backward compatibility
- Return type:
- get_donor_residue() str[source]#
Get the donor residue identifier.
- Returns:
String identifier for the donor residue
- Return type:
- get_acceptor_residue() str[source]#
Get the acceptor residue identifier.
- Returns:
String identifier for the acceptor residue
- Return type:
- get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- is_donor_interaction_bonded() bool[source]#
Check if hydrogen is bonded to donor.
For hydrogen bonds, the hydrogen must be covalently bonded to the donor atom. This method assumes the bond has been validated during creation.
- Returns:
True (assumes validation was done during creation)
- Return type:
Halogen Bonds#
- class hbat.core.interactions.HalogenBond(halogen: Atom, _acceptor: Atom, distance: float, angle: float, bond_type: str, _halogen_residue: str, _acceptor_residue: str)[source]#
Bases:
MolecularInteractionRepresents a halogen bond interaction.
This class stores information about a detected halogen bond, where a halogen atom acts as an electron acceptor.
- Parameters:
halogen (Atom) – The halogen atom (F, Cl, Br, I)
acceptor (Atom) – The electron donor/acceptor atom
distance (float) – X…A distance in Angstroms
angle (float) – C-X…A angle in radians
bond_type (str) – Classification of the halogen bond type
halogen_residue (str) – Identifier for halogen-containing residue
acceptor_residue (str) – Identifier for acceptor residue
Represents a halogen bond with carbon-halogen-acceptor geometry and σ-hole directionality.
Geometric Parameters:
Distance (X…A): Halogen to acceptor distance
Angle (C-X…A): Carbon-halogen-acceptor angle
σ-hole Direction: Electrostatic potential direction
Approach Angle: Acceptor approach to σ-hole
Chemical Properties:
Carbon Atom: Atom covalently bonded to halogen
Halogen Atom: Electron-deficient halogen (Cl, Br, I, F)
Acceptor Atom: Electron-rich acceptor (N, O, S)
σ-hole Strength: Depends on halogen polarizability
Usage Example:
from hbat.core.interactions import HalogenBond # Create halogen bond representation xbond = HalogenBond( carbon=carbon_atom, halogen=bromine_atom, acceptor=oxygen_atom, distance_xa=3.2, angle_cxa=172.0, sigma_hole_angle=5.0, energy=-1.8 ) # Check σ-hole directionality if xbond.has_good_directionality(): print(f"Well-directed halogen bond: {xbond.angle_cxa:.1f}°")
- __init__(halogen: Atom, _acceptor: Atom, distance: float, angle: float, bond_type: str, _halogen_residue: str, _acceptor_residue: str)[source]#
- property distance: float#
Legacy property for interaction distance.
- Returns:
Donor-interaction distance for backward compatibility
- Return type:
- property angle: float#
Legacy property for interaction angle.
- Returns:
Donor-interaction-acceptor angle for backward compatibility
- Return type:
- get_donor_residue() str[source]#
Get the donor residue identifier.
- Returns:
String identifier for the donor residue
- Return type:
- get_acceptor_residue() str[source]#
Get the acceptor residue identifier.
- Returns:
String identifier for the acceptor residue
- Return type:
- get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- get_donor_interaction_distance() float[source]#
Distance from donor to interaction point (0 for halogen bonds).
- is_donor_interaction_bonded() bool[source]#
Check if halogen is bonded to donor carbon.
For halogen bonds, the halogen atom must be covalently bonded to a carbon atom. The halogen serves as both the donor and interaction point.
- Returns:
True (assumes validation was done during creation)
- Return type:
π Interactions#
- class hbat.core.interactions.PiInteraction(_donor: Atom, hydrogen: Atom, pi_center: NPVec3D, distance: float, angle: float, _donor_residue: str, _pi_residue: str)[source]#
Bases:
MolecularInteractionRepresents an X-H…π interaction.
This class stores information about a detected X-H…π interaction, where a hydrogen bond donor interacts with an aromatic π system.
- Parameters:
donor (Atom) – The hydrogen bond donor atom
hydrogen (Atom) – The hydrogen atom
pi_center (NPVec3D) – Center of the aromatic π system
distance (float) – H…π distance in Angstroms
angle (float) – D-H…π angle in radians
donor_residue (str) – Identifier for donor residue
pi_residue (str) – Identifier for π-containing residue
Represents π interactions including π-π stacking and X-H…π contacts.
Geometric Parameters:
Centroid Distance: Distance between aromatic ring centers
Ring Angles: Angle between aromatic ring planes
Offset Parameters: Lateral displacement measurements
Approach Geometry: Face-to-face vs. edge-to-face orientation
Interaction Types:
π-π Stacking: Face-to-face aromatic ring interaction
T-shaped π-π: Edge-to-face aromatic contact
X-H…π: Hydrogen bond donor to π system
Cation-π: Positively charged group to π system
Usage Example:
from hbat.core.interactions import PiInteraction # Create π-π stacking interaction pi_interaction = PiInteraction( ring1_residue=phe_residue, ring2_residue=trp_residue, ring1_atoms=["CG", "CD1", "CD2", "CE1", "CE2", "CZ"], ring2_atoms=["CG", "CD1", "NE1", "CE2", "CD2"], centroid_distance=3.8, ring_angle=12.0, offset=1.2, interaction_type="stacking" ) # Classify interaction geometry if pi_interaction.is_stacking(): print("Face-to-face π-π stacking detected") elif pi_interaction.is_t_shaped(): print("Edge-to-face T-shaped contact detected")
- __init__(_donor: Atom, hydrogen: Atom, pi_center: NPVec3D, distance: float, angle: float, _donor_residue: str, _pi_residue: str)[source]#
- property distance: float#
Legacy property for interaction distance.
- Returns:
Donor-interaction distance for backward compatibility
- Return type:
- property angle: float#
Legacy property for interaction angle.
- Returns:
Donor-interaction-acceptor angle for backward compatibility
- Return type:
- get_donor_residue() str[source]#
Get the donor residue identifier.
- Returns:
String identifier for the donor residue
- Return type:
- get_acceptor_residue() str[source]#
Get the acceptor residue identifier.
- Returns:
String identifier for the acceptor residue
- Return type:
- get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- is_donor_interaction_bonded() bool[source]#
Check if hydrogen is bonded to donor.
For X-H…π interactions, the hydrogen must be covalently bonded to the donor atom.
- Returns:
True (assumes validation was done during creation)
- Return type:
- property donor_acceptor_properties: str#
Get the donor-acceptor property description.
- Returns:
Property description string
- Return type:
Cooperativity Chains#
- class hbat.core.interactions.CooperativityChain(interactions: List[HydrogenBond | HalogenBond | PiInteraction], chain_length: int, chain_type: str)[source]#
Bases:
MolecularInteractionRepresents a chain of cooperative molecular interactions.
This class represents a series of linked molecular interactions where the acceptor of one interaction acts as the donor of the next, creating cooperative effects.
- Parameters:
interactions (List[Union[HydrogenBond, HalogenBond, PiInteraction]]) – List of interactions in the chain
chain_length (int) – Number of interactions in the chain
chain_type (str) – Description of the interaction types in the chain
Represents chains of cooperative molecular interactions where the strength of one interaction influences neighboring interactions.
Chain Properties:
Sequential Connectivity: Ordered list of connected interactions
Chain Length: Number of interactions in the cooperative chain
Cumulative Strength: Total interaction energy with cooperativity effects
Topology: Linear, branched, or cyclic chain organization
Cooperativity Effects:
Enhancement: Neighboring interactions strengthen each other
Anti-cooperativity: Interactions compete and weaken each other
Resonance Assistance: Shared electron delocalization effects
Geometric Constraints: Structural organization influences
Usage Example:
from hbat.core.interactions import CooperativityChain # Create cooperativity chain coop_chain = CooperativityChain( interactions=[hbond1, hbond2, hbond3], chain_type="linear", enhancement_factor=1.15, total_energy=-8.2 ) # Analyze cooperative effects individual_energy = sum(i.energy for i in coop_chain.interactions) cooperative_enhancement = coop_chain.total_energy / individual_energy print(f"Cooperativity enhancement: {cooperative_enhancement:.2f}x")
- __init__(interactions: List[HydrogenBond | HalogenBond | PiInteraction], chain_length: int, chain_type: str)[source]#
- get_interaction() Atom | NPVec3D[source]#
Get the center point of the chain (middle interaction point).
- get_interaction_type() str[source]#
Get the interaction type.
- Returns:
String identifier for the interaction type
- Return type:
- get_donor_interaction_distance() float[source]#
Get the distance from chain start to middle interaction.
Validation and Quality Assessment#
Geometric Validation:
All interaction classes provide validation methods to assess interaction quality:
# Standard validation checks
if interaction.is_valid():
print("Interaction passes geometric criteria")
if interaction.is_strong():
print("Interaction has favorable energy")
quality_score = interaction.get_quality_score()
print(f"Interaction quality: {quality_score:.2f}")
Distance Criteria:
Hydrogen bonds: 2.5-3.5 Å (donor-acceptor)
Halogen bonds: 3.0-4.0 Å (halogen-acceptor)
π interactions: 3.5-5.5 Å (centroid-centroid)
Angular Criteria:
Hydrogen bonds: >120° (D-H…A angle)
Halogen bonds: >150° (C-X…A angle)
π interactions: <30° (ring plane angle for stacking)
Energy Estimation#
Energy Models:
Each interaction type uses empirical energy functions based on geometric parameters:
# Hydrogen bond energy (Lippincott-Schroeder)
energy_hb = -2.0 * exp(-distance/2.0) * cos(angle)**2
# Halogen bond energy (empirical)
energy_xb = -1.5 * (R_vdw/distance)**6 * cos(angle)**4
# π interaction energy (Hunter-Sanders)
energy_pi = -2.5 * exp(-distance/3.5) * orientation_factor
Energy Units:
All energies reported in kcal/mol
Negative values indicate favorable interactions
Typical ranges: -0.5 to -5.0 kcal/mol for most interactions
Data Persistence#
Serialization Support:
All interaction classes support JSON serialization for data storage:
import json
from dataclasses import asdict
# Convert interaction to dictionary
interaction_dict = asdict(hydrogen_bond)
# Save to JSON
with open("interactions.json", "w") as f:
json.dump(interaction_dict, f, indent=2)
Database Integration:
Interaction objects can be easily stored in databases or converted to pandas DataFrames for analysis:
import pandas as pd
# Convert interactions to DataFrame
interaction_data = [asdict(i) for i in interactions]
df = pd.DataFrame(interaction_data)
# Analysis and filtering
strong_hbonds = df[df.energy < -2.0]
print(f"Found {len(strong_hbonds)} strong hydrogen bonds")