Class AbstractStructureParser

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

• structure_file (str) - the input PD file to parse
• check_ss (bool) - if True, secondary structure errors in the file will cause SecStructureFormatError exceptions
• mapper (AbstractResidueMapper) - residue mapper, used to align ATOM records to SEQRES. If None, use the default (CombinedResidueMapper)

Raises:

• IOError - when the input file cannot be found

Overrides: object.__init__

(inherited documentation)

A StructureParser factory, which instantiates and returns the proper parser object based on the contents of the PDB file.

If the file contains a SEQRES section, RegularStructureParser is returned, otherwise LegacyStructureParser is instantiated. In the latter case LegacyStructureParser will read the sequence data directly from the ATOMs.

Parameters:

• structure_file (str) - the PDB file to parse
• check_ss (bool) - if True, secondary structure errors in the file will cause SecStructureFormatError exceptions
• mapper (AbstractResidueMapper) - residue mapper, used to align ATOM records to SEQRES. If None, use the default (CombinedResidueMapper)

Returns: AbstractStructureParser

Try to guess what is the sequence type of a chunk of PDB residue_labels. The list of labels is probed starting from the middle first, because PDB chains often contain modified / unknown residues at the termini. If none of the probed residues can be used to determine chain's type, just give up and return SequenceTypes.Unknown.

Parameters:

• residue_labels (iterable) - an iterable of PDB residue labels

Returns: csb.core.EnumItem

a SequenceTypes enum member

Try to guess what is the sequence type of a PDB residue_label.

Parameters:

• residue_label (str) - a PDB-conforming name of a residue

Returns: csb.core.EnumItem

a SequenceTypes enum member

Raises:

• UnknownPDBResidueError - when there is no such PDB residue name in the catalog tables

Find all available model identifiers in the structure.

Returns: list

a list of model IDs

Parse and return the Structure of the biological unit (quaternary structure) as annotated by the REMARK 350 BIOMOLECULE record.

Parameters:

• number (int) - biomolecule number
• single (bool) - if True, assign new single-letter chain identifiers. If False, assign multi-letter chain identifiers whith a number appended to the original identifier, like "A1", "A2", ...

Returns: Structure

structure of biological unit

Parse the specified models in the file and build an Ensemble.

Parameters:

• models (tuple) - an iterable object providing model identifiers. If not specified, all models will be parsed.

Returns: Ensemble

an ensemble with all parsed models

Try to parse a PDB residue_label and return its closest 'normal' string representation. If a sequence type (as_type) is defined, guess the alphabet based on that information, otherwise try first to parse it as a protein residue.

Parameters:

• residue_label (str) - a PDB-conforming name of a residue
• as_type - suggest a sequence type (SequenceTypes member) @type scb.core.EnumItem

Returns: str

a normalized residue name

Raises:

• UnknownPDBResidueError - when there is no such PDB residue name in the catalog table(s)

Same as parse_residue, but returns UNK/Any instead of raising UnknownPDBResidueError.

Parameters:

• residue_label (str) - a PDB-conforming name of a residue
• as_type - suggest a sequence type (SequenceTypes member) @type scb.core.EnumItem

Returns: str

a normalized residue name

Parse and return the Structure with the specified model identifier. If no explicit model is specified, parse the first model in the structure.

Parameters:

• model (str) - parse exactly the model with this ID

Returns: Structure

object representation of the selected model

Raises:

• ValueError - When an invalid model ID is specified
• PDBParseError - When the input PDB file suffers from unrecoverable corruption. More specialized exceptions will be raised depending on the context (see PDBParseError's subclasses).

filename

Current input PDB file name

Get Method:

unreachable.filename(self) - Current input PDB file name

Set Method:

unreachable.filename(self, name)

Type:

str

mapper

Current residue mapping strategy

Get Method:

unreachable.mapper(self) - Current residue mapping strategy

Set Method:

unreachable.mapper(self, value)

Type:

AbstractResidueMapper