Crate haddock_restraints

Main library crate for haddock-restraints

Structs

Air

Represents the Air (Ambiguous Interaction Restraints) structure.

AsaValues

Represents the Accessible Surface Area (ASA) values for a residue.

Bead

ExtendedAtom

Represents an atom with additional solvent accessible surface area (SASA) information.

ExtendedRes

Represents a residue with extended SASA information.

Gap

Represents two residues in a protein chain.

Interactor

Represents an interactor in a molecular system.

Pair

PassiveResidues

Constants

REL_ASA

Functions

calculate_geometric_center

calculate_sasa

Calculates the Solvent Accessible Surface Area (SASA) for a given PDB structure.

collect_residues

Collects residue numbers from a vector of Interactors.

create_iter_body_gaps

Creates a list of gaps between different bodies in a protein structure.

filter_unique_by_atom_j

Filters a vector of Gap elements, retaining only the unique elements based on the atom_j value.

find_bodies

Identifies separate bodies within a protein structure based on CA atom distances.

find_furthest_selections

format_atom_string

Formats a string representing atom names for use in constraints.

format_distance_string

Formats a distance string based on target, lower, and upper bounds.

gaps_around_ligand

Finds pairs of atoms between a ligand and nearby protein residues within a certain distance.

gen_tbl

Generates a table of Ambiguous Interaction Restraints (AIRs) based on input data.

generate_grid_beads

generate_z_restraints

get_atoms_from_resnumbers

get_chains_in_contact

Identifies pairs of chains in a PDB structure that are in contact with each other.

get_closest_residue_pairs

Finds the closest residue pairs between different protein chains within a specified distance cutoff.

get_residues

Retrieves specific residues from a PDB structure based on their serial numbers.

get_true_interface

Identifies the true interface residues between chains in a PDB structure.

list_interface

Lists the interface residues for each chain in a protein structure.

load_pdb

Loads a PDB structure from a file path

load_pdb_from_content

Loads a PDB structure from string content

neighbor_search

Performs a neighbor search for residues within a specified radius of target residues.

process_pdb_contents

Processes raw PDB content by removing remarks and padding lines

read_json_file

Reads and processes a JSON file containing Interactor data.

restraint_bodies

Generates distance restraints between non-contiguous bodies in a protein structure.

true_interface

Analyzes the true interface of a protein structure and generates Ambiguous Interaction Restraints (AIRs).

unambig_ti

Generates Unambiguous Topological Interactions (TIs) from a protein structure.

write_beads_pdb

write_string_to_file