View source for PatternQuery:Use Cases

====Identify all binding sites of PA-IIL lectin in different organisms====
*Binding sites of this type of lectin comprise of two calcium atoms close to each other and a binded sugar residue.  
<syntaxhighlight lang="python">
Near(4, Atoms("Ca"), Atoms("Ca"))
  .ConnectedResidues(1)
  .Filter(lambda l:
    l.Count(Or(Rings(5 * ["C"] + ["O"]), Rings(4 * ["C"] + ["O"]))) > 0)
  .Filter(lambda l: l.Count(Atoms("P")) == 0)</syntaxhighlight>

At first we select all the pairs of calcium atoms, if they are in a vicinity of 4Å and less by <syntaxhighlight lang="python">Near(4, Atoms("Ca"), Atoms("Ca"))</syntaxhighlight> Subsequently all the bonded residues are checked if they contain either pyranose or furanose ring. only the patterns containing either pentose <syntaxhighlight lang="python">(Rings(5 * ["C"] + ["O"]))</syntaxhighlight> or furanose <syntaxhighlight lang="python">(Rings(4 * ["C"] + ["O"]))</syntaxhighlight> are returned. Since a sugar moiety is an integral part of nucleotides, there is a final simple check, assuring, that no patterns containing phosphorus, i.e. nucleotide are retained.