Editing PatternQuery:Language Reference (section)

== Introduction ==

PatternQuery (PQ) is a user friendly chemical language primarily designed for defining atom patterns in molecules. PQ combines the clarity and brevity of programming languages with  the versatility of natural language, aiming for an efficient inclusion of chemical and biochemical knowledge into the definition of patterns. PQ allows definitions based on chemical connectivity and three-dimensional structure at the same time. Additionally, in the case of molecules based on residue chains (such as proteins, nucleic acids, saccharides, etc.), PQ allows the user to include any amount of information regarding the residue level structure directly into the definition of the patternss.

PatternQuery is a subset of the Python programming language. Therefore, if you have experience with it, it should not be a problem to use PQ as well.

* The language is case sensitive - "filter" is NOT the same as "FiLtEr".

Some of the functions return '''<code>PatternSeq</code>''' while other return '''<code>Pattern</code>'''. 
* '''<code>Pattern</code>''' is a set of atoms.
* '''<code>PatternSeq</code>''' is a sequence of '''<code>Pattern</code>''' (the sets of atoms).

When a molecule is queried, say using the expression <code>Rings(5 * ["C"] + ["O"])</code> a sequences of patterns each containing 6 atoms (5 C and 1 O) is returned. However, some functions such as <code>Filter</code> need to operate on a single pattern (the set of atoms) - not the whole sequences. The query <code>Residues().Filter(lambda r: r.Count(Atoms()) > 10)</code> first finds all residue patterns ('''<code>PatternSeq</code>''') and then passes every single '''<code>Pattern</code>''' (set of atoms) to a function that counts the atoms in the pattern and returns True if there is at least 11 of them. This is the reasoning behind these two types.