Introduction
- QMzyme version:
0.1.2
QMzyme is a Python toolkit to facilitate (quantum mechanical) QM-based enzyme
calculations. The GenerateModel class guides the process of generating
QM-calculation ready truncated or partitioned structures. The code
framework can accept all input files that MDAnalysis accepts to create an
MDAnalysis Universe object. The QMzyme framework works with MDAnalysis modules
to create more dynamic QMzyme data structures: QMzymeAtom,
QMzymeResidue, QMzymeRegion, and
QMzymeModel. QMzymeModel is an abstraction of a molecular system, such as a real enzyme, that
comprises at least one QMzymeRegion. Its utility comes from the ability to perform calculations on it.
Calculation methods (think Hamiltonians) are assigned at the QMzymeRegion level. QMzyme, as its namesake suggests,
takes a QM-centric perspective. Therefore, the CalculateModel and Writers modules are designed for compatibility with QM-focused
software, rather than MD-focused software, even though many MD software support QM program interfacing. The calculation
results will (ideally) be validatable through comparison to experiment, and (hopefully) provide new chemical or methodological insights.
If you have ideas or suggestions on how to improve QMzyme please do not hesitate to engage on the QMzyme Ideas GitHub Project space, or contribute directly by forking the repository and submitting a pull request. Questions can be directed via email to heidiklem@lsu.edu.
Examples/Tutorials
Code Documentation
Contributing to QMzyme!