neurosnap.structure.interface module#

Chain-interface analysis helpers for Neurosnap structures.

neurosnap.structure.interface.calculate_bsa(structure, chain_group_1, chain_group_2, *, level='R')[source]#

Calculate buried surface area between two chain groups.

The buried surface area (BSA) is computed as:

(SASA(group 1) + SASA(group 2)) - SASA(complex)

Parameters:

  • structure (Structure) – Input complex as a single-model Structure.

  • chain_group_1 (List[str]) – Chain IDs for the first group.

  • chain_group_2 (List[str]) – Chain IDs for the second group.

  • level (str) – Surface-area aggregation level forwarded to calculate_surface_area().

Return type:

float

Returns:

Buried surface area in Ų.

neurosnap.structure.interface.find_contacts(atoms1, atoms2, cutoff=4.5)[source]#

Identify atom-atom contacts between two atom sets using a distance cutoff.

Parameters:

  • atoms1 (List[Atom]) – First set of atoms.

  • atoms2 (List[Atom]) – Second set of atoms.

  • cutoff (float) – Distance cutoff in Å.

Return type:

List[Tuple[Atom, Atom]]

Returns:

List of (atom1, atom2) pairs within the cutoff distance.

neurosnap.structure.interface.find_interface_contacts(structure, chain1, chain2, *, cutoff=4.5, hydrogens=True)[source]#

Identify atom-atom contacts between two chains using a distance cutoff.

Parameters:

  • structure (Structure) – Input single-model Structure.

  • chain1 (str) – First chain ID.

  • chain2 (str) – Second chain ID.

  • cutoff (float) – Contact cutoff distance in Å.

  • hydrogens (bool) – Whether hydrogen atoms should be included.

Return type:

List[Tuple[Atom, Atom]]

Returns:

List of contacting (atom1, atom2) pairs.

neurosnap.structure.interface.find_interface_residues(structure, chain1, chain2, *, cutoff=4.5, hydrogens=True)[source]#

Identify unique residue-residue contacts between two chains.

Multiple atom-atom contacts between the same residue pair are collapsed into one output pair.

Parameters:

  • structure (Structure) – Input single-model Structure.

  • chain1 (str) – First chain ID.

  • chain2 (str) – Second chain ID.

  • cutoff (float) – Contact cutoff distance in Å.

  • hydrogens (bool) – Whether hydrogen atoms should be included in the contact search.

Return type:

List[Tuple[Residue, Residue]]

Returns:

List of unique contacting (residue1, residue2) pairs.

neurosnap.structure.interface.find_non_interface_hydrophobic_patches(structure, chain_pairs, target_chains=None, *, cutoff_interface=4.5, hydrogens=True, patch_cutoff=6.0, min_patch_area=40.0)[source]#

Identify solvent-exposed hydrophobic patches outside specified interfaces.

Hydrophobic residues are first filtered to remove interface residues and buried residues, then clustered by CA-CA proximity into connected components.

Parameters:

  • structure (Structure) – Input single-model Structure.

  • chain_pairs (Iterable[Tuple[str, str]]) – Iterable of chain-ID pairs whose interfaces should be excluded from patch detection.

  • target_chains (Optional[Iterable[str]]) – Optional chain IDs to search for patches. If None, all chains are considered.

  • cutoff_interface (float) – Distance cutoff in Å used to classify interface contacts.

  • hydrogens (bool) – Whether hydrogen atoms should be included in the interface contact search.

  • patch_cutoff (float) – CA-CA distance cutoff in Å used to connect hydrophobic residues into the same patch.

  • min_patch_area (float) – Minimum summed SASA in Ų required for a connected component to be returned.

Return type:

List[List[Residue]]

Returns:

List of residue lists, where each list represents one hydrophobic patch.