qp.structure.missing.build_model

qp.structure.missing.build_model(residues, pdb, path, ali, out, optimize=1)[source]

Run Modeller to build missing residues and atoms.

Constructs a complete model by filling in missing residues and atoms using Modeller’s homology modeling capabilities. The level of structure optimization can be controlled.

Parameters:

  • residues (list of list) – Residues separated by chain, as returned by get_residues().

  • pdb (str) – PDB code (must match the alignment file identifiers).

  • path (str) – Path to the template PDB file.

  • ali (str) – Path to the Modeller alignment file.

  • out (str) – Path to the output PDB file.

  • optimize (int, optional) – Optimization level (default 1):

    • 0: No optimization; coordinates from topology library only.

    • 1: Optimize only missing residues and residues with missing atoms.

    • 2: Optimize the entire structure (heteroatoms as rigid bodies).

Notes

The output PDB file will have residue numbering transferred from the template. Modeller intermediate files are cleaned up automatically.