Package org.biojava.nbio.structure.io

Class EntityFinder

java.lang.Object

org.biojava.nbio.structure.io.EntityFinder

public class EntityFinder
extends Object

Heuristical finding of Entities (called Compounds in legacy PDB format) in a given Structure. Entities are the groups of sequence identical NCS-related polymer chains in the Structure. This is related to SeqRes2AtomAligner but it is intended for raw PDB/mmCIF files where possibly no SEQRES is given.

Author:

Jose Duarte

Field Summary

Fields

Modifier and Type	Field	Description
static final double	GAP_COVERAGE_THRESHOLD	Gap coverage value (num gaps over length of sequence) for each chain of the match: 2 chains with more gap coverage than this value will not be considered part of the same entity
static final double	IDENTITY_THRESHOLD	Identity value for 2 chains to be considered part of same entity
static final double	RATIO_GAPS_FOR_MISMATCH	Above this ratio of mismatching residue types for same residue numbers we consider the 2 chains to have mismatching residue numbers and warn about it

Constructor Summary

Constructors

Constructor	Description
EntityFinder()

Method Summary

Modifier and Type	Method	Description
static void	createPurelyNonPolyEntities(List<List<Chain>> nonPolyModels, List<List<Chain>> waterModels, List<EntityInfo> entities)	Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them.
static List<EntityInfo>	findPolyEntities(List<List<Chain>> polyModels)	Utility method that employs some heuristics to find the EntityInfos for the polymeric chains given in constructor.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

RATIO_GAPS_FOR_MISMATCH

public static final double RATIO_GAPS_FOR_MISMATCH

Above this ratio of mismatching residue types for same residue numbers we consider the 2 chains to have mismatching residue numbers and warn about it

See Also:

• Constant Field Values

IDENTITY_THRESHOLD

public static final double IDENTITY_THRESHOLD

Identity value for 2 chains to be considered part of same entity

See Also:

• Constant Field Values

GAP_COVERAGE_THRESHOLD

public static final double GAP_COVERAGE_THRESHOLD

Gap coverage value (num gaps over length of sequence) for each chain of the match: 2 chains with more gap coverage than this value will not be considered part of the same entity

See Also:

• Constant Field Values

Constructor Details

EntityFinder

public EntityFinder()

Method Details

findPolyEntities

public static List<EntityInfo> findPolyEntities(List<List<Chain>> polyModels)

Utility method that employs some heuristics to find the EntityInfos for the polymeric chains given in constructor. To be used in case the information is missing in PDB/mmCIF file

Returns:

createPurelyNonPolyEntities

public static void createPurelyNonPolyEntities(List<List<Chain>> nonPolyModels,
 List<List<Chain>> waterModels,
 List<EntityInfo> entities)

Given all chains of all models find entities for the nonpolymers and water chains within them, assigning entity ids, types and descriptions to them. The result is written back to the passed entities List.

Parameters:

nonPolyModels -

waterModels -

entities -