# {py:mod}`ovo.core.utils.pdb` ```{py:module} ovo.core.utils.pdb ``` ```{autodoc2-docstring} ovo.core.utils.pdb :allowtitles: ``` ## Module Contents ### Classes ````{list-table} :class: autosummary longtable :align: left * - {py:obj}`PDBSegmentSelector ` - ```` ### Functions ````{list-table} :class: autosummary longtable :align: left * - {py:obj}`parse_pdb ` - ```{autodoc2-docstring} ovo.core.utils.pdb.parse_pdb :summary: ``` * - {py:obj}`parse_pdb_lines ` - ```{autodoc2-docstring} ovo.core.utils.pdb.parse_pdb_lines :summary: ``` * - {py:obj}`fix_contigs ` - ```{autodoc2-docstring} ovo.core.utils.pdb.fix_contigs :summary: ``` * - {py:obj}`get_pdb ` - ```{autodoc2-docstring} ovo.core.utils.pdb.get_pdb :summary: ``` * - {py:obj}`detect_glycosylation_sites ` - ```{autodoc2-docstring} ovo.core.utils.pdb.detect_glycosylation_sites :summary: ``` * - {py:obj}`calculate_coords_from_transformed_displacements ` - ```{autodoc2-docstring} ovo.core.utils.pdb.calculate_coords_from_transformed_displacements :summary: ``` * - {py:obj}`add_glycan_to_pdb ` - ```{autodoc2-docstring} ovo.core.utils.pdb.add_glycan_to_pdb :summary: ``` * - {py:obj}`get_atom_coordinates ` - ```{autodoc2-docstring} ovo.core.utils.pdb.get_atom_coordinates :summary: ``` * - {py:obj}`_align_sequences_and_get_indices ` - ```{autodoc2-docstring} ovo.core.utils.pdb._align_sequences_and_get_indices :summary: ``` * - {py:obj}`align_multiple_proteins_pdb ` - ```{autodoc2-docstring} ovo.core.utils.pdb.align_multiple_proteins_pdb :summary: ``` * - {py:obj}`get_aligned_structure_as_string ` - ```{autodoc2-docstring} ovo.core.utils.pdb.get_aligned_structure_as_string :summary: ``` * - {py:obj}`pad_line ` - ```{autodoc2-docstring} ovo.core.utils.pdb.pad_line :summary: ``` * - {py:obj}`pdb_to_mmcif_iter ` - ```{autodoc2-docstring} ovo.core.utils.pdb.pdb_to_mmcif_iter :summary: ``` * - {py:obj}`pdb_to_mmcif ` - ```{autodoc2-docstring} ovo.core.utils.pdb.pdb_to_mmcif :summary: ``` * - {py:obj}`get_sequences_from_pdb_str ` - ```{autodoc2-docstring} ovo.core.utils.pdb.get_sequences_from_pdb_str :summary: ``` * - {py:obj}`get_remark_header ` - ```{autodoc2-docstring} ovo.core.utils.pdb.get_remark_header :summary: ``` * - {py:obj}`get_standardized_remarks_from_pdb_str ` - ```{autodoc2-docstring} ovo.core.utils.pdb.get_standardized_remarks_from_pdb_str :summary: ``` * - {py:obj}`trim_pdb_str ` - ```{autodoc2-docstring} ovo.core.utils.pdb.trim_pdb_str :summary: ``` * - {py:obj}`filter_pdb_str ` - ```{autodoc2-docstring} ovo.core.utils.pdb.filter_pdb_str :summary: ``` ```` ### Data ````{list-table} :class: autosummary longtable :align: left * - {py:obj}`num2aa ` - ```{autodoc2-docstring} ovo.core.utils.pdb.num2aa :summary: ``` * - {py:obj}`aa2num ` - ```{autodoc2-docstring} ovo.core.utils.pdb.aa2num :summary: ``` * - {py:obj}`aa2long ` - ```{autodoc2-docstring} ovo.core.utils.pdb.aa2long :summary: ``` * - {py:obj}`aa3to1 ` - ```{autodoc2-docstring} ovo.core.utils.pdb.aa3to1 :summary: ``` * - {py:obj}`transformed_displacements ` - ```{autodoc2-docstring} ovo.core.utils.pdb.transformed_displacements :summary: ``` * - {py:obj}`REMARK_KEYS ` - ```{autodoc2-docstring} ovo.core.utils.pdb.REMARK_KEYS :summary: ``` ```` ### API ````{py:data} num2aa :canonical: ovo.core.utils.pdb.num2aa :value: > ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLN', 'GLU', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', '... ```{autodoc2-docstring} ovo.core.utils.pdb.num2aa ``` ```` ````{py:data} aa2num :canonical: ovo.core.utils.pdb.aa2num :value: > None ```{autodoc2-docstring} ovo.core.utils.pdb.aa2num ``` ```` ````{py:data} aa2long :canonical: ovo.core.utils.pdb.aa2long :value: > [(' N ', ' CA ', ' C ', ' O ', ' CB ', None, None, None, None, None, None, None, None, None, ' H ... ```{autodoc2-docstring} ovo.core.utils.pdb.aa2long ``` ```` ````{py:data} aa3to1 :canonical: ovo.core.utils.pdb.aa3to1 :value: > None ```{autodoc2-docstring} ovo.core.utils.pdb.aa3to1 ``` ```` ````{py:data} transformed_displacements :canonical: ovo.core.utils.pdb.transformed_displacements :value: > 'array(...)' ```{autodoc2-docstring} ovo.core.utils.pdb.transformed_displacements ``` ```` ````{py:function} parse_pdb(filename, **kwargs) :canonical: ovo.core.utils.pdb.parse_pdb ```{autodoc2-docstring} ovo.core.utils.pdb.parse_pdb ``` ```` ````{py:function} parse_pdb_lines(lines, parse_hetatom=False, ignore_het_h=True) :canonical: ovo.core.utils.pdb.parse_pdb_lines ```{autodoc2-docstring} ovo.core.utils.pdb.parse_pdb_lines ``` ```` ````{py:function} fix_contigs(contigs, parsed_pdb) :canonical: ovo.core.utils.pdb.fix_contigs ```{autodoc2-docstring} ovo.core.utils.pdb.fix_contigs ``` ```` ````{py:function} get_pdb(pdb_code: str) -> bytes :canonical: ovo.core.utils.pdb.get_pdb ```{autodoc2-docstring} ovo.core.utils.pdb.get_pdb ``` ```` `````{py:class} PDBSegmentSelector(segments: list[str]) :canonical: ovo.core.utils.pdb.PDBSegmentSelector Bases: {py:obj}`Bio.PDB.Select` ````{py:method} accept_model(model) :canonical: ovo.core.utils.pdb.PDBSegmentSelector.accept_model ```` ````{py:method} accept_chain(chain) :canonical: ovo.core.utils.pdb.PDBSegmentSelector.accept_chain ```` ````{py:method} accept_residue(residue) :canonical: ovo.core.utils.pdb.PDBSegmentSelector.accept_residue ```` ````{py:method} accept_atom(model) :canonical: ovo.core.utils.pdb.PDBSegmentSelector.accept_atom ```` ````` ````{py:function} detect_glycosylation_sites(atom_ppdb: pandas.DataFrame, chains: list[str] | str | None = None, query_atoms: list[str] | None = None, cyclic: bool = False) -> dict | None :canonical: ovo.core.utils.pdb.detect_glycosylation_sites ```{autodoc2-docstring} ovo.core.utils.pdb.detect_glycosylation_sites ``` ```` ````{py:function} calculate_coords_from_transformed_displacements(P1, P2) -> numpy.ndarray :canonical: ovo.core.utils.pdb.calculate_coords_from_transformed_displacements ```{autodoc2-docstring} ovo.core.utils.pdb.calculate_coords_from_transformed_displacements ``` ```` ````{py:function} add_glycan_to_pdb(pdb_str: str) -> tuple[str, list[str] | None] :canonical: ovo.core.utils.pdb.add_glycan_to_pdb ```{autodoc2-docstring} ovo.core.utils.pdb.add_glycan_to_pdb ``` ```` ````{py:function} get_atom_coordinates(structure: Bio.PDB.Structure.Structure, chain_id: str | None, residues: list[int] | None, all_atom: bool = False, model_index=0) -> tuple[list[dict[str, numpy.ndarray]], list[Bio.PDB.Residue.Residue]] :canonical: ovo.core.utils.pdb.get_atom_coordinates ```{autodoc2-docstring} ovo.core.utils.pdb.get_atom_coordinates ``` ```` ````{py:function} _align_sequences_and_get_indices(seqs: list[str]) :canonical: ovo.core.utils.pdb._align_sequences_and_get_indices ```{autodoc2-docstring} ovo.core.utils.pdb._align_sequences_and_get_indices ``` ```` ````{py:function} align_multiple_proteins_pdb(pdb_strs: list[str], chain_residue_mappings: list[list[tuple[str, list[int] | None]] | None], force_sequence_alignment: bool = False, all_atom: bool = False, verbose: bool = False) -> tuple[list[str], float] :canonical: ovo.core.utils.pdb.align_multiple_proteins_pdb ```{autodoc2-docstring} ovo.core.utils.pdb.align_multiple_proteins_pdb ``` ```` ````{py:function} get_aligned_structure_as_string(structure) -> str :canonical: ovo.core.utils.pdb.get_aligned_structure_as_string ```{autodoc2-docstring} ovo.core.utils.pdb.get_aligned_structure_as_string ``` ```` ````{py:function} pad_line(line) :canonical: ovo.core.utils.pdb.pad_line ```{autodoc2-docstring} ovo.core.utils.pdb.pad_line ``` ```` ````{py:function} pdb_to_mmcif_iter(pdb_data: str, structure_id: str, bfactor_to_plddt=False, fractional_plddt=False) :canonical: ovo.core.utils.pdb.pdb_to_mmcif_iter ```{autodoc2-docstring} ovo.core.utils.pdb.pdb_to_mmcif_iter ``` ```` ````{py:function} pdb_to_mmcif(pdb_data: str, structure_id: str, bfactor_to_plddt=False, fractional_plddt=False) :canonical: ovo.core.utils.pdb.pdb_to_mmcif ```{autodoc2-docstring} ovo.core.utils.pdb.pdb_to_mmcif ``` ```` ```{py:exception} ChainNotFoundError() :canonical: ovo.core.utils.pdb.ChainNotFoundError Bases: {py:obj}`Exception` ``` ````{py:function} get_sequences_from_pdb_str(pdb_str: str, chains: list[str] = None, by_residue_number: bool = False) -> dict[str, str] | dict[str, dict[str, str]] :canonical: ovo.core.utils.pdb.get_sequences_from_pdb_str ```{autodoc2-docstring} ovo.core.utils.pdb.get_sequences_from_pdb_str ``` ```` ````{py:function} get_remark_header(pdb_path: str) -> tuple[str, list[str]] :canonical: ovo.core.utils.pdb.get_remark_header ```{autodoc2-docstring} ovo.core.utils.pdb.get_remark_header ``` ```` ````{py:data} REMARK_KEYS :canonical: ovo.core.utils.pdb.REMARK_KEYS :value: > ['Input contig', 'Standardized contig', 'Chains', 'Input hotspots', 'Standardized hotspots'] ```{autodoc2-docstring} ovo.core.utils.pdb.REMARK_KEYS ``` ```` ````{py:function} get_standardized_remarks_from_pdb_str(pdb_str: str) -> dict[str, str] :canonical: ovo.core.utils.pdb.get_standardized_remarks_from_pdb_str ```{autodoc2-docstring} ovo.core.utils.pdb.get_standardized_remarks_from_pdb_str ``` ```` ````{py:function} trim_pdb_str(pdb_input_string: str, target_chain: str, start_res: int, end_res: int) -> str :canonical: ovo.core.utils.pdb.trim_pdb_str ```{autodoc2-docstring} ovo.core.utils.pdb.trim_pdb_str ``` ```` ````{py:function} filter_pdb_str(pdb_input_string: str, segments: list[str], add_ter=False) -> str :canonical: ovo.core.utils.pdb.filter_pdb_str ```{autodoc2-docstring} ovo.core.utils.pdb.filter_pdb_str ``` ````