Editing PatternQuery:Use Cases

In this section you can find several biologically relevant examples of different queries.

==== Find all post-translational modified aminoacids ====
*i.e. Those incorporated in the protein backbone and not hetero atoms
 <syntaxhighlight lang="python">
NotAminoAcids().
    Filter(lambda m: m.Count(HetResidues()) == 0) </syntaxhighlight>
This query queries all the non-standard amino acids for their presence among Hetatom entries. Equivalently:<syntaxhighlight lang="python">
NotAminoAcids().
    Filter(lambda m: m.Contains(HetResidues()).Not())</syntaxhighlight>

====Find all heteroatoms, which are not covalently bonded to the protein structure====
* Takes all the heteroatoms and queries them for being connected to any amino acid of a given protein
<syntaxhighlight lang="python">
HetResidues().
    Filter(lambda m: m.IsNotConnectedTo(AminoAcids()))</syntaxhighlight>

====Identify Zinc fingers====
*There is a variety of different zinc fingers based on the surrounding residues, in our example we will focus on those comprising two zinc and two his residues (Cys2His2).

<syntaxhighlight lang="python">
Atoms("Zn").
    ConnectedResidues(1).
    Filter(lambda m: 
      (m.Count(Residues("His")) == 2) & (m.Count(Residues("Cys")) == 2)) </syntaxhighlight>

At first the zinc atoms are selected together with their bonded residues. Additionally, these patterns are filtered according to the content of their amino acids.

====Identify all the residues, which contain a sugar ring====
* This task can be decomposed to two individual subtasks, since sugars contain either pentose or furanose ring. Pentose ring contains 4 carbon and an oxygen atom. Similarly, furanose ring is composed of 5 carbon atoms and an oxygen atom.

<syntaxhighlight lang="python">
Or(Rings(4 * ["C"] + ["O"]).ConnectedResidues(0), 
   Rings(5 * ["C"] + ["O"]).ConnectedResidues(0)) </syntaxhighlight>

By specifying the <code>Ring()</code> queries, we select only the ring part of the molecule. By extending the <code>Ring()</code> query with <syntaxhighlight lang="python">ConnectedResidues(0)</syntaxhighlight> only the residue which includes this ring is selected. Last but not least we can join both queries with <syntaxhighlight lang="python">Or()</syntaxhighlight> in order to merge results.

====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.