de.bioforscher.singa.structure.parser.pdb.structures.tokens

Interface PDBToken

All Known Implementing Classes:

AtomToken, ChainTerminatorToken, HeaderToken, ModelToken, TitleToken

public interface PDBToken

Tokens are used to extract information from PDB lines. Each token is identified by a static record pattern. Afterwards the information from the line can be extracted.

Author:

cl

Method Summary

Modifier and Type	Method and Description
static String	endLine(String content)
default String	extract(String line) Extracts a value from pdb line.
static String	extractValueFromPDBLine(String line, PDBToken token) Extracts a value from a pdb line, given a token and line to extract from.
de.bioforscher.singa.core.utility.Range<Integer>	getColumns() Gets the columns (the staring and ending index) where a value can be extracted.
Pattern	getRecordNamePattern() Returns the record name for this token.

Method Detail

extractValueFromPDBLine

static String extractValueFromPDBLine(String line,
                                      PDBToken token)

Extracts a value from a pdb line, given a token and line to extract from.

Parameters:

line - The line to extract from.

token - The value for the token to extract.

Returns:

The trimmed value.

endLine

static String endLine(String content)

getRecordNamePattern

Pattern getRecordNamePattern()

Returns the record name for this token.

Returns:

The record name for this token.

getColumns

de.bioforscher.singa.core.utility.Range<Integer> getColumns()

Gets the columns (the staring and ending index) where a value can be extracted.

Returns:

The columns where a value can be extracted.

extract

default String extract(String line)

Extracts a value from pdb line.

Parameters:

line - The line to extract from.

Returns:

The trimmed value.