Enabling the use of restraints in alchemical simulations
A framework for generating restraints for MD simulations (from MD simulations).
The code currently implements a means of deriving Boresch-style restraints, with exporters for GROMACS. There is also experimental code for COM based restraints (i.e. harmonic distance or hard wall), which export to the gromacs pull code. These experimental implementations have yet to be completely tested.
In future implementations we aim to expand to other MD engines (notably OpenMM support will be coming in the near future as part of efforts to support the work done by OpenFE).
We also aim to eventually implement the following restraint types:
- Attach Pull Restraint style restraints
- Arbitrary multidimensional restraints (will require API overhaul)
Note: This is non-mature code, a lot is left to do and major changes will happen at any time.
Installation can either be done via PyPi or from source.
To install the latest release via PyPi do:
pip install MDRestraintsGenerator
Installing the latest development code from source can be done using the following:
git clone https://github.com/bigginlab/MDRestraintsGenerator.git cd MDRestraintsGenerator pip install .
How to use
The code currently focuses on implementing a means of deriving Boresch restraints for GROMACS simulations. To achieve this, the following underlying methods are provided:
- A function to pick stable points in ligands for restraint attachment
- A class for picking host restraint addition points (
- A class for analysing a list of possible Boresch restraints over a given MD simulation and
finding the most stable choice of restraint atoms (
Boresch restraints are implemented under the BoreschRestraint class. When using
restraints.FindBoreschRestraint, once run (using the
run() method), the preffered restraint
will be stored as such an object under the
restraint attribute. The BoreschRestraint class
offers three useful methods:
plot()function which outputs images of the distributions for the each component of the Boresch restraint (one bond, two angles, three dihedrals). In addition to the histograms, indicating both the mean and the picked frame positions, Q Q plots are also given to show how close to normality the distribution is. The latter can be useful when trying to work out if the chosen variable may occupy different binding orientations.
write()function, which writes out the
BoreschRestraint.topfiles. These are based on the "picked frame", either user supplied or, in most cases, automatically obtained via the
FindBoreschRestraintroutine as the "frame closest to the mean across all bond/angle/dihedral distributions". This
.grofile outputs the system at that frame, and the
.topfile contains the "intermoecular_interactions" section of a GROMACS
.topfile. This can then be pasted into an existing
.topfile to apply the restraint.
standard_statefunction, which currently resturns the analytical standard state correction for the restraint addition.
An example use script is provided under
scripts.BoreschRestraintGMX.py. Documentation docstrings
are provided for all functions and classes. These can be accessed by calling
A set of unit tests are provided under
MDRestraintsGenerator.tests. To run these you will need
pytest installed. The tests can be run in the following manner:
pytest -v MDRestraintsGenerator.tests
Copyright (c) 2020, Irfan Alibay
To cite this code, please refer the following:
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