Class VentoFoggia

java.lang.Object
org.openscience.cdk.isomorphism.Pattern
org.openscience.cdk.isomorphism.VentoFoggia
public final class VentoFoggia extends Pattern
A structure pattern which utilises the Vento-Foggia (VF) algorithm [Cordella Luigi P et. al.. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE. 2004. 26]. Find and count the number molecules which contain the query substructure. 
IAtomContainer query   = ...;
Pattern        pattern = VentoFoggia.findSubstructure(query);

int hits = 0;
for (IAtomContainer m : ms)
    if (pattern.matches(m))
        hits++;
Finding the matching to molecules which contain the query substructure. It is more efficient to obtain the match(IAtomContainer) and check it's size rather than test if it Pattern.matches(IAtomContainer). These methods automatically verify stereochemistry. 
IAtomContainer query   = ...;
Pattern        pattern = VentoFoggia.findSubstructure(query);

int hits = 0;
for (IAtomContainer m : ms) {
    int[] match = pattern.match(m);
    if (match.length > 0)
        hits++;
}
Author:
John May

  • Method Details

    • match

      public int[] match(IAtomContainer target)
      Find a matching of this pattern in the target. If no such order exist an empty mapping is returned. Depending on the implementation stereochemistry may be checked (recommended). 
      Pattern        pattern = ...; // create pattern
for (IAtomContainer m : ms) {
    int[] mapping = pattern.match(m);
    if (mapping.length > 0) {
        // found mapping!
    }
}
      Specified by:
      match in class Pattern
      Parameters:
      target - the container to search for the pattern in
      Returns:
      the mapping from the pattern to the target or an empty array

    • matchAll

      public Mappings matchAll(IAtomContainer target)
      Find all mappings of this pattern in the target. Stereochemistry should not be checked to allow filtering with Mappings.stereochemistry(). 
      Pattern pattern = Pattern.findSubstructure(query);
for (IAtomContainer m : ms) {
    for (int[] mapping : pattern.matchAll(m)) {
        // found mapping
    }
}
      Using the fluent interface (see Mappings) we can search and manipulate the mappings. Here's an example of finding the first 5 mappings and creating an array. If the mapper is lazy other states are simply not explored. 
      // find only the first 5 mappings and store them in an array
Pattern pattern  = Pattern.findSubstructure(query);
int[][] mappings = pattern.matchAll(target)
                          .limit(5)
                          .toArray();
      Specified by:
      matchAll in class Pattern
      Parameters:
      target - the container to search for the pattern in
      Returns:
      the mapping from the pattern to the target
      See Also:

    • findSubstructure

      public static Pattern findSubstructure(IAtomContainer query)
      Create a pattern which can be used to find molecules which contain the query structure.
      Parameters:
      query - the substructure to find
      Returns:
      a pattern for finding the query

    • findIdentical

      public static Pattern findIdentical(IAtomContainer query)
      Create a pattern which can be used to find molecules which are the same as the query structure.
      Parameters:
      query - the substructure to find
      Returns:
      a pattern for finding the query

    • findSubstructure

      public static Pattern findSubstructure(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)
      Create a pattern which can be used to find molecules which contain the query structure.
      Parameters:
      query - the substructure to find
      atomMatcher - how atoms are matched
      bondMatcher - how bonds are matched
      Returns:
      a pattern for finding the query

    • findIdentical

      public static Pattern findIdentical(IAtomContainer query, AtomMatcher atomMatcher, BondMatcher bondMatcher)
      Create a pattern which can be used to find molecules which are the same as the query structure.
      Parameters:
      query - the substructure to find
      atomMatcher - how atoms are matched
      bondMatcher - how bonds are matched
      Returns:
      a pattern for finding the query