MolQL

MolQL (Molecular Query Language) is a declarative language for describing selections/substructures of molecular data. The language provides a wide range of queries and can be used as a compilation target for various selection expressions such as the ones provided by PyMol, JMOL, or VMD.

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Example: Select helices

Jmol

helix

PyMol

ss h

VMD

structure H

MolQL (Script)

(sel.atom.res
  (atom.sec-struct.is helix))

... all compile to MolQL:

(structure.generator.atom-groups
  :atom-test (core.flags.has-any
    (structure.atom-property.macromolecular
      .secondary-structure-flags)
    (structure.type
      .secondary-structure-flags helix)))