librestraints: functions related to restraints

haddock.libs.librestraints.active_passive_to_ambig(active1, passive1, active2, passive2, segid1='A', segid2='B')

Convert active and passive residues to Ambiguous Interaction Restraints

Parameters:

• active1 (list) – List of active residue numbers of the first segid

• passive1 (list) – List of passive residue numbers of the first segid

• passive2 (list) – List of passive residue numbers of the second segid

• active2 (list) – List of active residue numbers of the second segid

• active2 (list) – List of passive residue numbers of the second segid

• segid1 (string) – Segid to use for the first model

• segid2 (string) – Segid to use for the second model

haddock.libs.librestraints.build_restraints(bodies)

Generates distance restraints to maintain the relative orientation of the different bodies during the simulations.

Generates two unique restraints per pair of bodies.

Each restraint is created using two random atoms on each body and using their exact euclidean distance as target distance.

haddock.libs.librestraints.calc_euclidean(i, j)

haddock.libs.librestraints.check_parenthesis(file)

haddock.libs.librestraints.generate_tbl(atom_lst, restraints)

Makes a list of TBL-formatted restraints.

Parameters:

• atom_lst (list) – List of atoms in the form (chain, resi, aname, coords)

• restraints (list) – List of restraints in the form (res_i, res_j)

haddock.libs.librestraints.get_bodies(atom_lst, prot_threshold=4.0, dna_threshold=7.5)

Determines gaps in an atom list following simple distance based criteria. Returns continuous fragments.

haddock.libs.librestraints.get_surface_resids(structure, cutoff=15)

Calls freesasa using its Python API and returns per-residue accessibilities.

haddock.libs.librestraints.parse_actpass_file(actpass_file)

Parse actpass file

Parameters:

actpass_file (str or Path) – path to actpass_file

Returns:

• active (list) – list of active residues

• passive (list) – list of passive residues

haddock.libs.librestraints.passive_from_active_raw(structure, active, chain_id=None, surface=None, radius=6.5)

Get the passive residues.

Parameters:

• structure (str) – path to the PDB file

• active (list) – List of active residues

• chain_id (str) – Chain ID

• surface (list) – List of surface residues.

• radius (float) – Radius from active residues

haddock.libs.librestraints.read_structure(pdbf, exclude=None)

Reads a PDB file and returns a list of parsed atoms

haddock.libs.librestraints.validate_tbldata(restraints, pcs=False)