org.biojava.nbio.structure.io

Class StructureSequenceMatcher

java.lang.Object

org.biojava.nbio.structure.io.StructureSequenceMatcher

public class StructureSequenceMatcher
extends Object

A utility class with methods for matching ProteinSequences with Structures.

Author:

Spencer Bliven

Constructor Summary

Constructors

Constructor and Description
StructureSequenceMatcher()

Method Summary

Modifier and Type	Method and 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) Get a substructure of wholeStructure containing only the Groups that are included in sequence.
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.

Methods inherited from class java.lang.Object

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

Constructor Detail

StructureSequenceMatcher

public StructureSequenceMatcher()

Method Detail

getSubstructureMatchingProteinSequence

public static Structure getSubstructureMatchingProteinSequence(ProteinSequence sequence,
                                                               Structure wholeStructure)

Get a substructure of 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.

Parameters:

sequence - The input protein sequence

wholeStructure - The structure from which to take a substructure

Returns:

The resulting structure

Throws:

StructureException

See Also:

#matchSequenceToStructure(ProteinSequence, Structure)}

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 structure

groupIndexPosition - 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

See Also:

SeqRes2AtomAligner#getFullAtomSequence(List, Map)}, which does the heavy lifting.

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.

removeGaps

public static ProteinSequence removeGaps(ProteinSequence gapped)

Removes all gaps ('-') from a protein sequence

Parameters:

gapped -

Returns:

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