qp.structure.missing

Build missing residues and atoms using Modeller

Usage:

>>> from qp.structure import missing
>>> pdb = "1lnh"

# Parse PDB file, filling in missing residues
>>> residues = missing.get_residues("path/to/PDB.pdb")

# Write alignment file
>>> missing.write_alignment(
...     residues,
...     pdb,
...     "path/to/PDB.pdb",
...     "path/to/ALI.ali"
... )
>P1;1lnh (template from original PDB file)
structureX:1lnh.pdb:FIRST:@ END::::::
--------GHKIKGTVVLMRKNVLDVNSVTSV-------------TLDTLTAFLGRSVSLQLISAT...
>P1;1lnh_fill (full sequence)
sequence:::::::::
MLGGLLHRGHKIKGTVVLMRKNVLDVNSVTSVGGIIGQGLDLVGSTLDTLTAFLGRSVSLQLISAT...

# Run Modeller with the given alignment file
>>> missing.build_model(
...     residues,
...     pdb,
...     "path/to/PDB.pdb",
...     "path/to/ALI.ali",
...     "path/to/OUT.pdb"
... )

Optimization level (optimize argument in missing.build_model):

• 0. No optimization. Missing coordinates filled in using Modeller’s topology library.

• 1. Optimize missing residues and residues with missing atoms only. (Default)

• 2. Optimize the entire structure. Hetero atoms are included but treated as rigid bodies.

Note

Non-standard residues (substrates, cofactors, and other HETATM entries) are preserved as rigid bodies by Modeller and any missing atoms in these residues will not be modeled. A warning is emitted listing the non-standard residues encountered during parsing.

Functions

build_model	Run Modeller to build missing residues and atoms.
clean_termini	Remove unresolve amino acids from the N- and C-termini.
define_residues	Access a look up table of standard and non-standard amino acids.
delete_clashes	Delete residues with clashes from a PDB file and rewrite the PDB file.
fix_numbering	Handles insertion codes from Modeller.
get_chain_order	Get the order of chains in a PDB file.
get_residues	Extract residues from a PDB file, including missing residue annotations.
transfer_numbering	Transfer residue numbers and chain IDs from template to built model.
write_alignment	Write a Modeller alignment file for filling missing residues.