Package org.biojava.nbio.structure.io
Class StructureSequenceMatcher
- java.lang.Object
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- org.biojava.nbio.structure.io.StructureSequenceMatcher
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public class StructureSequenceMatcher extends Object
A utility class with methods for matching ProteinSequences with Structures.- Author:
- Spencer Bliven
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Constructor Summary
Constructors Constructor Description StructureSequenceMatcher()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static ProteinSequence
getProteinSequenceForStructure(Structure struct, Map<Integer,Group> groupIndexPosition)
Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups.static Structure
getSubstructureMatchingProteinSequence(ProteinSequence sequence, Structure wholeStructure)
static ResidueNumber[]
matchSequenceToStructure(ProteinSequence seq, Structure struct)
Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.static ProteinSequence
removeGaps(ProteinSequence gapped)
Removes all gaps ('-') from a protein sequencestatic <T> T[][]
removeGaps(T[][] gapped)
Creates a new list consisting of all columns of gapped where no row contained a null value.
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Constructor Detail
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StructureSequenceMatcher
public StructureSequenceMatcher()
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Method Detail
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getSubstructureMatchingProteinSequence
public static Structure getSubstructureMatchingProteinSequence(ProteinSequence sequence, Structure wholeStructure)
Get a substructure ofwholeStructure
containing only theGroups
that are included insequence
. The resulting structure will contain onlyATOM
residues; the SEQ-RES will be empty. TheChains
of the Structure will be new instances (cloned), but theGroups
will not.- Parameters:
sequence
- The input protein sequencewholeStructure
- The structure from which to take a substructure- Returns:
- The resulting structure
- Throws:
StructureException
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getProteinSequenceForStructure
public static ProteinSequence getProteinSequenceForStructure(Structure struct, Map<Integer,Group> groupIndexPosition)
Generates a ProteinSequence corresponding to the sequence of struct, and maintains a mapping from the sequence back to the original groups. Chains are appended to one another. 'X' is used for heteroatoms.- Parameters:
struct
- Input structuregroupIndexPosition
- An empty map, which will be populated with (residue index in returned ProteinSequence) -> (Group within struct)- Returns:
- A ProteinSequence with the full sequence of struct. Chains are concatenated in the same order as the input structures
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matchSequenceToStructure
public static ResidueNumber[] matchSequenceToStructure(ProteinSequence seq, Structure struct)
Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.Smith-Waterman alignment is used to match the sequences. Residues in the sequence but not the structure or mismatched between sequence and structure will have a null atom, while residues in the structure but not the sequence are ignored with a warning.
- Parameters:
seq
- The protein sequence. Should match the sequence of struct very closely.struct
- The corresponding protein structure- Returns:
- A list of ResidueNumbers of the same length as seq, containing either the corresponding residue or null.
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removeGaps
public static ProteinSequence removeGaps(ProteinSequence gapped)
Removes all gaps ('-') from a protein sequence- Parameters:
gapped
-- Returns:
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removeGaps
public static <T> T[][] removeGaps(T[][] gapped)
Creates a new list consisting of all columns of gapped where no row contained a null value. Here, "row" refers to the first index and "column" to the second, eg gapped.get(row).get(column)- Parameters:
gapped
- A rectangular matrix containing null to mark gaps- Returns:
- A new List without columns containing nulls
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