public class StructureSequenceMatcher
extends java.lang.Object
Constructor | Description |
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StructureSequenceMatcher() |
Modifier and Type | Method | Description |
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static ProteinSequence |
getProteinSequenceForStructure(Structure struct,
java.util.Map<java.lang.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 sequence
|
static <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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public static Structure getSubstructureMatchingProteinSequence(ProteinSequence sequence, Structure wholeStructure)
wholeStructure
containing only the Groups
that are included in
sequence
. The resulting structure will contain only ATOM
residues; the SEQ-RES will be empty.
The Chains
of the Structure will be new instances (cloned), but the Groups
will not.sequence
- The input protein sequencewholeStructure
- The structure from which to take a substructureStructureException
public static ProteinSequence getProteinSequenceForStructure(Structure struct, java.util.Map<java.lang.Integer,Group> groupIndexPosition)
struct
- Input structuregroupIndexPosition
- An empty map, which will be populated with
(residue index in returned ProteinSequence) -> (Group within struct)public static ResidueNumber[] matchSequenceToStructure(ProteinSequence seq, Structure struct)
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.
seq
- The protein sequence. Should match the sequence of struct very
closely.struct
- The corresponding protein structurepublic static ProteinSequence removeGaps(ProteinSequence gapped)
gapped
- public static <T> T[][] removeGaps(T[][] gapped)
gapped
- A rectangular matrix containing null to mark gaps