neurosnap.structure.interaction_report module

Data models and reports for structural interactions and coordination centers.

class neurosnap.structure.interaction_report.AtomReference(atom_index, chain_id, res_id, ins_code, res_name, atom_name, element)

Bases: object

A reference to a specific atom in a Structure with copied metadata.

atom_index: int

atom_name: str

chain_id: str

element: str

ins_code: str

res_id: int

res_name: str

class neurosnap.structure.interaction_report.CoordinationCenterRecord(center_id, metal_atom_index, entity, chain, res_id, ins_code, res_name, atom_name, element, coordination_number, donor_atom_indices, donor_elements, geometry=None, geometry_deviation_deg=None, evidence='distance_cutoff', rule_set='default', rule_version='1', model_id=1)

Bases: object

The exact fields representing a metal coordination center.

atom_name: str

center_id: str

chain: str

coordination_number: int

donor_atom_indices: Sequence[int]

donor_elements: Sequence[str]

element: str

entity: str

evidence: str = 'distance_cutoff'

geometry: Optional[str] = None

geometry_deviation_deg: Optional[float] = None

ins_code: str

metal_atom_index: int

model_id: int = 1

res_id: int

res_name: str

rule_set: str = 'default'

rule_version: str = '1'

class neurosnap.structure.interaction_report.InteractionEntity(name, atom_indices, rdkit_mol=None)

Bases: object

Representation of a molecular entity participating in interactions.

class neurosnap.structure.interaction_report.InteractionRecord(interaction_id, interaction_type, evidence, entity1, atom_index1, chain1, res_id1, ins_code1, res_name1, atom_name1, element1, role1, entity2, atom_index2, chain2, res_id2, ins_code2, res_name2, atom_name2, element2, role2, distance_a=None, angle_deg=None, vdw_gap_a=None, source='geometric_rules', rule_set='default', rule_version='1', model_id=1, details=None)

Bases: object

The exact fields representing a detected structural interaction.

angle_deg: Optional[float] = None

atom_index1: int

atom_index2: int

atom_name1: str

atom_name2: str

chain1: str

chain2: str

details: Optional[dict] = None

distance_a: Optional[float] = None

element1: str

element2: str

entity1: str

entity2: str

evidence: str

ins_code1: str

ins_code2: str

interaction_id: str

interaction_type: str

model_id: int = 1

res_id1: int

res_id2: int

res_name1: str

res_name2: str

role1: str

role2: str

rule_set: str = 'default'

rule_version: str = '1'

source: str = 'geometric_rules'

vdw_gap_a: Optional[float] = None

class neurosnap.structure.interaction_report.InteractionReport(records, coordination_centers, metadata=None)

Bases: object

Immutable collection of structural interaction records and coordination centers.

coordination_centers_dataframe()

Convert coordination centers to a pandas DataFrame with the expected columns.

Return type:

DataFrame

filter(*, interaction_types=None, entities=None, chains=None, record_indices=None, predicate=None)

Filter interactions and return a new InteractionReport with relevant coordination centers.

Return type:

InteractionReport

to_csv(**kwargs)

Export the interaction records DataFrame as a CSV string.

Return type:

str

to_dataframe()

Convert interaction records to a pandas DataFrame with the expected columns.

Return type:

DataFrame

to_json(indent=None)

Export the report in record-oriented JSON format with deterministic key order.

Return type:

str