Package org.biojava.nbio.structure.io
Class CompoundFinder
- java.lang.Object
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- org.biojava.nbio.structure.io.CompoundFinder
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public class CompoundFinder extends java.lang.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 toSeqRes2AtomAligner
but it is intended for raw PDB files where possibly no SEQRES is given.- Author:
- duarte_j
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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 CompoundFinder(Structure s)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.util.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
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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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CompoundFinder
public CompoundFinder(Structure s)
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Method Detail
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findCompounds
public java.util.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:
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