Package org.biojava.nbio.structure.io
Class EntityFinder
- java.lang.Object
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- org.biojava.nbio.structure.io.EntityFinder
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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 toSeqRes2AtomAligner
but it is intended for raw PDB/mmCIF files where possibly no SEQRES is given.- Author:
- Jose Duarte
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Field Summary
Fields Modifier and Type Field 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 entitystatic double
IDENTITY_THRESHOLD
Identity value for 2 chains to be considered part of same entitystatic 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
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Constructor Summary
Constructors Constructor Description EntityFinder()
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Method Summary
All Methods Static Methods Concrete Methods 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 theEntityInfo
s for the polymeric chains given in constructor.
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Field Detail
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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
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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
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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
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Constructor Detail
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EntityFinder
public EntityFinder()
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Method Detail
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findPolyEntities
public static List<EntityInfo> findPolyEntities(List<List<Chain>> polyModels)
Utility method that employs some heuristics to find theEntityInfo
s for the polymeric chains given in constructor. To be used in case the information is missing in PDB/mmCIF file- Returns:
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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
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