Interactions

Feature: protein interaction feature

class hippo.feature.Feature(id: int, family: str, target: Target, chain_name: str, residue_name: str, residue_number: int, atom_names: str)[source]

Pharmocophoric feature in a protein

id

Database ID

Type:: int

family

Feature family

Type:: str

chain_name

Protein chain name/letter

Type:: str

residue_name

Protein residue name

Type:: str

residue_number

Protein residue number

Type:: int

atom_names

Protein atom names (whitespace-delimited)

Type:: str

repr(self) → str[source]: ANSI Formatted string representation

str(self) → str[source]: Unformatted string representation

property backbone: bool: Are any of the atoms referenced by this feature on the backbone?

property chain_res_name_number_str: str: Return a string representation of the feature

property res_name_number_family_str: str: Return a string representation of the feature

property res_name_number_str: str: Return a string representation of the feature

property res_number_name_tuple: str: Return a tuple representation of the feature

property sidechain: bool: Are any of the atoms referenced by this feature on the sidechain?

Interaction: between atom(s) on a Pose and a Feature

class hippo.interaction.Interaction(db: Database, id: int, feature_id: int, pose_id: int, type: str, family: str, atom_ids: str, prot_coord: str, lig_coord: str, distance: float, angle: float, energy: float | None, table: str = 'interaction')[source]

A Interaction represents an interaction between an rdkit Feature on a Pose and a Feature on the protein Target.

Attention

Interaction objects should not be created directly. Instead use Pose.interactions(), or PoseSet.interactions() methods.

Interaction initialisation

repr(self) → str[source]: ANSI Formatted string representation

str(self) → str[source]: Plain string representation

property angle: float | None: Returns the interaction angle (only defined for π-stacking and π-cation interactions)

property atom_ids: list[int]: Returns the indices of atoms making up the ligand feature

property db: Database: Returns a pointer to the parent database

property description: str: One line description of this interaction

property distance: float: Returns the euclidian distance of the interaction

property energy: float | None: Returns the interaction energy, if defined

property family: str: The Feature family

property family_str: str: String of the two feature families

property feature: Feature: Returns the associated Feature’s object

property feature_id: int: Returns the associated Feature’s database ID

property id: int: Returns the interaction’s database ID

property lig_coord: list[float]: Returns the cartesian position of the ligand feature

property pose: Pose: Returns the associated Pose’s object

property pose_id: int: Returns the associated Pose’s database ID

property prot_coord: list[float]: Returns the cartesian position of the protein Feature

property residue_name: str: Returns the associated Feature’s residue name

property residue_number: int: Returns the associated Feature’s residue number

summary() → None[source]: Print a summary of this interaction’s properties

property table: str: Returns the name of the Database table

property type: str: Interaction type string

InteractionTable: All Interactions

class hippo.iset.InteractionTable(db: Database, table: str = 'interaction')[source]

Class representing all Interaction objects in the ‘interaction’ table of the Database.

Attention

InteractionTable objects should not be created directly. Instead use the HIPPO.interactions() property.

InteractionTable initialisation

len(self) → int[source]: The total number of interactions

repr(self) → str[source]: ANSI formatted command-line representation

str(self) → str[source]: Unformatted command-line representation

property db: Database: Returns the associated Database

property df: pandas.DataFrame

DataFrame representation of the interactions

Returns:: a pandas.Dataframe of the interactions

property table: str: Returns the name of the Database table

InteractionSet: Subset of interactions

class hippo.iset.InteractionSet(db: Database, indices: list = None, table: str = 'interaction')[source]

Class representing a subset of the Interaction objects in the ‘interaction’ table of the Database.

Attention

InteractionSet objects should not be created directly. Instead use Pose.interactions(), or PoseSet.interactions() methods.

InteractionSet initialisation

self[key] → Interaction | InteractionSet[source]: Get interaction or subsets thereof from this set

iter(self)[source]: Iterate through interactions in this set

len(self) → int[source]: The number of interactions in this set

repr(self) → str[source]: ANSI formatted command-line representation

str(self) → str[source]: Unformatted command-line representation

classmethod all(db: Database, table: str = 'interaction') → InteractionSet[source]

Construct a InteractionSet for all interactions in the table.

Returns:: an InteractionSet

property avg_num_interaction_type_residue_pairs_per_pose: list[tuple]: Get a list of (residue_number, chain_name) tuples

property avg_num_interactions_per_feature: float: Average number of interactions formed with each protein Feature

property avg_num_interactions_per_pose: list[tuple]: Get a list of (residue_number, chain_name) tuples

property avg_num_residues_per_pose: list[tuple]: Get a list of (residue_number, chain_name) tuples

property classic_fingerprint: dict: Classic HIPPO fingerprint dictionary, mapping protein Feature ID’s to the number of corresponding ligand features (from any Pose)

property db: Database: The associated HIPPO Database

property df: pandas.DataFrame

DataFrame representation of the interactions

Returns:: a pandas.Dataframe of the interactions

classmethod from_pose(pose: Pose | PoseSet, table: str = 'interaction') → InteractionSet[source]

Construct a InteractionSet from one or more poses.

Parameters:: pose – a Pose or PoseSet object
Returns:: an InteractionSet

classmethod from_residue(db: Database, residue_number: int, chain: None | str = None, target: Target | int = 1) → InteractionSet[source]

Get the set of interactions for a given residue number (and chain)

Parameters:

db – HIPPO Database
residue_number – the residue number
chain – the chain name / letter, defaults to any chain
target – the protein Target object or ID, defaults to first target in database

Returns:

a InteractionSet object

get_classic_fingerprint() → dict[source]: Classic HIPPO fingerprint dictionary, mapping protein Feature ID’s to the number of corresponding ligand features (from any Pose)

property ids: list[int]: Returns the ids of interactions in this set

property indices: list[int]: Returns the ids of interactions in this set

property num_features: int: Count the funmber of protein :class:`.Feature`s with which interactions are formed

property per_feature_count_hirsch: float: A measure for how evenly protein :class:`.Feature`s are being interacted with

property residue_number_chain_pairs: list[tuple]: Get a list of (residue_number, chain_name) tuples

resolve(debug: bool = False, commit: bool = True) → InteractionSet[source]

Resolve into predicted key interactions. In place modification.

Parameters:

debug – Increased verbosity for debugging (Default value = False)
commit – commit the changes (Default value = True)

Returns:

a filtered InteractionSet

property str_ids: str: Return an SQL formatted tuple string of the Interaction IDs

summary(families: bool = False) → None[source]: Print a summary of this InteractionSet

property table: str: Get the name of the database table

property type_residue_number_chain_triples: list[tuple]: Get a list of (interaction_type, residue_number, chain_name) tuples

property types: list[str]: Returns the ids of interactions in this set