This repository is an open, growing collection of easy-to-run molecular modeling workflows. These can be thought of as "runnable methods sections" - modular computational workflows that let scientists easily:
You can run the official workflows apps right from your browser with the MST web application.
If you'd like to run them from the command line, or start working on your own, you'll need to install:
After that, you can install everything else you need by running:
pip install git+https://github.com/molecular-workflow-repository/molflow.gitmolflow's config file, located at ~/.molflow/config, is created the first time you run the command, and includes configuration options for where to search for local workflows. One of the standard places is in the ~/.molflow/workflows/ directory: any subdirectories under there that have the required workflow.py and metadata.yml files will appear in molflow's list.
To get the set of standard and sample workflows, run the following:
mkdir -p ~/.molflow/workflows/
cd ~/.molflow/workflows/
git clone https://github.com/molecular-workflow-repository/add_two_to_it.git
git clone https://github.com/molecular-workflow-repository/convert.git
git clone https://github.com/molecular-workflow-repository/count_atoms.git
git clone https://github.com/molecular-workflow-repository/parameterize_small_molecule.gitLook for more at the Molecular Workflow Repository!
Future versions of molflow will be able to query this remote and automatically grab workflows you want to use from it.
Installing this package will put the molflow executable in your path.
To get a list of available workflows, run molflow list:
$ molflow list
Workflow location: ~/.molflow/workflowsadd_two_to_it (v0.1.0): Add 2 to integer, float, or complex number.
convert (v0.1.0): Translate a molecule between a variety of file formats, chemical ids, and python objects.
count_atoms (v0.0.1): Returns the number of atoms in a molecule.
mm_minimize (v0.0.1): Minimize a biomolecule and automatically parameterize any bound small molecules.
parameterize_small_molecule (v0.0.1): Automatically parameterize a small molecule.
vertical_detachment_energy (v0.0.1): Calculate the energy necessary to photoionize a closed-shell molecule. [...]
To get detailed information about available workflows, including versions available, run molflow list -v:
$ molflow list -v
Workflow location: ~/.molflow/workflowsadd_two_to_it (v0.1.0): Add 2 to integer, float, or complex number. Versions: v0.1.0 Branches: master
convert (v0.1.0): Translate a molecule between a variety of file formats, chemical ids, and python objects. Versions: v0.1.0 Branches: master
count_atoms (v0.0.1): Returns the number of atoms in a molecule. Versions: v0.0.1 Branches: master [...]
To get more information about a workflow, run molflow info [workflow name]:
$ molflow info add_two_to_it
Name: add_two_to_it
Default Version: v0.1.0
Inputs:
- number: (number) Number to add two to
Outputs:
- result: (number) Original number plus two
Description: Add 2 to integer, float, or complex number.
[...]This page contains a more complete description of the metadata included with each workflow.
molflow run [workflow name] [input name] [input file], e.g.:
$ molflow run add_two_to_it 4.0
Output directory: ~/add_two_to_it.runStarting workflow 'add_two_to_it' add_one.1: engine: 'Docker engine on host: http+docker://localunixsocket' image: docker.io/python:3.6-slim job_id: e94dfa025d722c5d0dc668ef552b5c312bc0e83a8c3da43aa2a9cefd87df7063 [...] Finished workflow 'add_two_to_it'.
Output locations: result:
add_two_to_it.run/result.txt
NOTE: This requires that docker is running locally on your machine.
- To run a workflow using a specific version or branch, run `molflow run -v [version or branchname] [workflow name] [input name] [input file]`.WIP
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