Python¶
Notes on the Python level of the package.
Other Python Gromacs interfaces¶
- gmxscript : all-python CLI
- wrapper manages files, provides “checkpointed” re-runnable workflow with mdp rewriting and CLI replacement
- GromacsWrapper
- (Beckstein) : all-python CLI wrapper provides thorough scriptable interface with error handling
- pmx (D. Seeliger) : Manipulate
- Gromacs files and data structures
- grompy (Rene Pool) : patches old Gromacs
- code to provide ctypes interface to Gromacs libraries
- gmx_wrapper : very
- bare-bones CLI wrapper
- GromacsPipeline
- (Redmine 1625) adds SIP bindings to run Gromacs analysis modules in a single pass on a trajectory
Existing Python tools to leverage¶
Some of the tools available from the gmx command-line interface
are bundled largely for convenience,
and Python users may be better served by turning to other projects
rather than relying on exposing
redundant functionality from libgromacs.
In other cases, Gromacs developers may simply want to be aware of the
other tools and interoperability requirements.
- pypdb A Python API for the RCSB Protein Data Bank (PDB)
- chemlab Qt-powered molecular viewer
- chemview molecular viewer for IPython from the author of chemlab
- MDTraj Read, write and analyze MD trajectories
- MDAnalysis analyze trajectories from molecular dynamics
- Biopython tools for computational molecular biology
- several packages named “Biopy” do not seem relevant
- PyMOL molecular viewer
- mmLib Python Macromolecular Library analysis, manipulation, and viewing
- msmbuilder Statistical models for Biomolecular Dynamics
- PyEMMA estimation, validation and analysis Markov models from molecular dynamics (MD) data
- ExSTACY Collection of tools that couples large ensemble Molecular Dynamics calculations with analysis to provide improvements in sampling. Includes
- EnsembleMD framework for running ensemble workflows
- COCO
- LSDMap Locally Scaled Diffusion Maps
- pyPcazip principle component analysis
- Plumed free energy calculation using collective variables
- pdb tools
- OpenMM
- msmbuilder
- BioXL
Naming¶
The package should have a name that does not collide with other known projects, particularly any projects on pypi. “gmx” is available on pypi, but similar existing package names include
gmx-scriptpython-gmx
pygmx is the name used for a bindings package posted to the Gromacs
list that resides at https://biod.pnpi.spb.ru/~alexxy/pygmx
There are several packages named grompy
The Beckstein lab has GromacsWrapper which exists on
PythonHosted.org, GitHub, and PyPi.
Note that our CMake project is called gmxpy through (at least) release 0.0.7.
Python version¶
The Python 2 end-of-support has been extended to 2020. It is reasonable to assume that Python 2.7.15 is the final version of Python 2 and that it will be officially end-of-lifed in 2020. On the one hand, Python 2 will be a mature language with no further interface changes. On the other hand, the loss of the commitment to bug fixes means it has already started fading away.
Python 3.3 has a lot of improvements and changes, including better 2.7 compatibility
Python 3.4
- built-in pip
- enum types
- new pickle protocol
Python 3.5
- typing and coroutines
- RecursionError exception
- Generators have gi_yieldfrom
- memoryview tuple indexing
- hexadecimal methods
Linux distributions released after June 2013 and supported at least to June 2019.
gmxapi policy¶
GROMACS will officially switch from Python 2.7 to Python 3+
during the GROMACS 2020 development cycle for its infrastructure.
gmxapi 0.0.7 officially supports Python 2.7 and Python 3.4+.
gmxapi will continue to support Python 2.7 for as long as is feasible,
but should default to Python 3 style and syntax.
As much as possible, current code is in a version-agnostic style, avoiding
dependencies on 3to2 or six.
Future versions may use compatibility tools.
At some point, Python 2 compatibility will be achieved with conversion tools
during package installation instead of in the Python source code so that we can
remove from __future__ imports and other clunky work-arounds.