Bio.PDB.ic_rebuild module¶
Convert XYZ Structure to internal coordinates and back, test result.
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Bio.PDB.ic_rebuild.
structure_rebuild_test
(entity, verbose: bool = False) → Dict¶ Test rebuild PDB structure from internal coordinates.
- Parameters
entity – Biopython Structure, Model or Chain Structure to test
verbose – bool print extra messages
- Returns
dict comparison dict from compare_residues()
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Bio.PDB.ic_rebuild.
report_IC
(entity: Union[Bio.PDB.Structure.Structure, Bio.PDB.Model.Model, Bio.PDB.Chain.Chain, Bio.PDB.Residue.Residue], reportDict: Dict[str, Any] = None, verbose: bool = False) → Dict[str, Any]¶ Generate dict with counts of ic data elements for each entity level.
- reportDict entries are:
idcode : PDB ID
hdr : PDB header lines
mdl : models
chn : chains
res : residue objects
res_e : residues with dihedra and/or hedra
dih : dihedra
hed : hedra
- Parameters
entity (Entity) – Biopython PDB Entity object: S, M, C or R
- Raises
PDBException – if entity level not S, M, C, or R
Exception – if entity does not have .level attribute
- Returns
dict with counts of IC data elements
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Bio.PDB.ic_rebuild.
IC_duplicate
(entity) → Bio.PDB.Structure.Structure¶ Duplicate structure entity with IC data, no atom coordinates.
Employs write_PIC(), read_PIC() with StringIO buffer. Calls atom_to_internal_coordinates() if needed.
- Parameters
entity – Biopython PDB Entity (will fail for Atom)
- Returns
Biopython PDBStructure, no Atom objects
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Bio.PDB.ic_rebuild.
compare_residues
(e0: Union[Bio.PDB.Structure.Structure, Bio.PDB.Model.Model, Bio.PDB.Chain.Chain], e1: Union[Bio.PDB.Structure.Structure, Bio.PDB.Model.Model, Bio.PDB.Chain.Chain], verbose: bool = False) → Dict[str, Any]¶ Compare full IDs and atom coordinates for 2 Biopython PDB entities.
Skip DNA and HETATMs.
- Parameters
e1 (e0,) – Biopython PDB Entity objects (S, M or C) Structures, Models or Chains to be compared
verbose – Bool whether to print mismatch info, default False
- Returns
Dictionary Result counts for Residues, Full ID match Residues, Atoms, Full ID match atoms, and Coordinate match atoms; report string; error status (bool)
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Bio.PDB.ic_rebuild.
write_PDB
(entity: Bio.PDB.Structure.Structure, file: str, pdbid: str = None, chainid: str = None) → None¶ Write PDB file with HEADER and TITLE.