Class StructureSequenceMatcher

Method Details

• 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

• 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

• 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