org.biojava.nbio.structure.io

Class CompoundFinder

java.lang.Object

org.biojava.nbio.structure.io.CompoundFinder

public class CompoundFinder
extends Object

Heuristical finding of Compounds (called Entities in mmCIF dictionary) in a given Structure. Compounds 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 files where possibly no SEQRES is given.

Author:

duarte_j

Field Summary

Fields

Modifier and Type	Field and Description
static 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 double	IDENTITY_THRESHOLD Identity value for 2 chains to be considered part of same entity
static 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 and Description
CompoundFinder(Structure s)

Method Summary

Modifier and Type	Method and Description
List<Compound>	findCompounds() Utility method that employs some heuristics to find the Compounds for this Structure in case the information is missing in PDB/mmCIF file

Methods inherited from class java.lang.Object

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

Field Detail

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 Detail

CompoundFinder

public CompoundFinder(Structure s)

Method Detail

findCompounds

public List<Compound> findCompounds()

Utility method that employs some heuristics to find the Compounds for this Structure in case the information is missing in PDB/mmCIF file

Returns: