Version 1.4.2, reinitialized.

.gitignore

@@ -0,0 +1,16 @@
+__pycache__
+*.pyc
+package.json
+.vscode
+tags
+.idea
+
+timer.dat
+git-commands.txt
+icolos/config/unit_tests_config/config.json
+
+tests/junk
+*.log
+.directory
+*_cache
+*.ipynb_checkpoints

CHANGELOG.md

@@ -0,0 +1,68 @@
+# Update log
+
+### Version 1.4.0 | 2022-01-19
+#### Features
+- Added support for non-equilibrium relative binding free energy calculation with PMX.
+- Added Glide support for feeding in "in" files from Maestro directly.
+- Added AutoDock Vina as docking backend.
+
+#### Internal
+- Limited refactoring of support functions.
+
+### Version 1.3.0 | 2021-11-18
+#### Features
+- Added Iterator mechanism for parallel step execution.
+- Pose rescoring my RMSD workflow.
+- MMGBSA workflow with GROMACS.
+
+#### Internal
+- Improved error logging from subprocesses.
+- Improvements to MDpocket workflows.
+- Refactored example workflows + added new examples.
+
+### Version 1.2.0 | 2021-09-15
+#### Features
+- Added MDpocket workflow for pocket identification.
+- Expanded scope of GROMACS workflow for improved ligand/cofactor parametrisation.
+- Improved FEP+ workflow map construction and analysis.
+- Performance optimisation for Turbomole and Prime.
+- Added PDBFixer step.
+- Added ensemble docking.
+
+#### Internal
+- Improved temporary file handling.
+
+### Version 1.1.0 | 2021-06-30
+#### Features
+- Added `Ligprep` workflow step.
+- Added `Glide` workflow step.
+- Added run-time global variables.
+- Added JSON input type (`REINVENT`-compatible).
+- Additional `GROMACS` binaries, and automated ligand parametrisation.
+- Added support for Schrodinger's `FEP+` workflow.
+- Added support for `OptunaAZ` model building.
+
+#### Bug fixes
+- Fixed problems in tabular write-out (no compound names and sometimes lost column order).
+- Fixed bug in aggregation (`highest_is_best` parameter was not working properly).
+- Fixed instability with step write-out (occurred when no conformers were associated with a compound).
+- Fixed bug in the parallelization of `Ligprep`.
+
+#### Internal
+- Refactored structure for `Schrodinger` binaries.
+- Reworked the write-out functionality.
+- Reworked internal file handling.
+- Reworked generic data handling.
+
+### Version 1.0.0 | 2021-05-21
+#### Features
+- Basic functionality (data handling, backend wrapping).
+- Various steps implemented (`Turbomole`, `Cosmo`, `OMEGA`, `GROMACS`, ...).
+
+### Bug fixes
+- Fixed issues with `Turbomole` execution.
+- Enforced GROMACS execution in `tmp_dir`.
+
+### Internal
+- Adapted `pydantic` interface.
+

DOCKERFILE

@@ -0,0 +1,7 @@
+#syntax=docker/dockerfile:1
+
+FROM continuumio/miniconda3
+
+COPY environment.yml .
+
+RUN conda env create -f environment.yml

LICENCE

@@ -0,0 +1,169 @@
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README.md

@@ -0,0 +1,75 @@
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black) 
+
+
+# `Icolos`: Workflow manager
+
+The `Icolos` tool is a workflow manager, that aims at separating execution logic from actual implementation as much as
+possible. Workflows are specified in `JSON` files (see folder `examples`), linking steps together. Currently wrapped are
+a diverse set of tools and internal steps, including QM and MD software.
+
+
+## Introduction
+`Icolos` provides a single, unified interface to a host of software for common computational chemistry calculations, with built in parallelization,
+and straight-forward extensibiltiy to add additional functionality. It was principally developed to handle structural calculations for `REINVENT` jobs, however, various workflows have also been used as stand-alone pipelines.
+
+Workflows are constructed from elementary 'steps', individual blocks which specify a sequential list of operations (normally corresponding to a single program being executed),
+with control of the command-line options provided through step settings, and options to control other aspects of the step's behaviour included in the `additional` block.
+
+For many use cases, one of the template workflows might suit your needs, or need a few tweaks to do what you want. The JSONs in the example folder are less regularly updated
+with new features and are mostly used for integration testing.
+
+## Initial configuration
+You are welcome to clone the repository and use a local version, and in particular if you would like to experiment with the code base and/or contribute features, please get 
+in contact with us.
+
+## Installation
+After cloning, first install the `icolosprod` `conda` environment:
+```
+conda create -f environment_min.yml
+```
+
+## Execution
+Once a `JSON` is specified, the workflow can be executed like so:
+
+```
+conda activate icolosprod
+python executor.py -conf workflow.json
+```
+
+## `SLURM` Execution
+Once specified, a workflow can be called like this in a `bash` script:
+
+```
+#!/bin/bash -l
+#SBATCH -N 1
+#SBATCH -t 0-02:59:00
+#SBATCH -p core
+#SBATCH --ntasks-per-node=5
+#SBATCH --mem-per-cpu=2G
+
+source /<conda_path>/miniconda3/bin/activate /<conda_path>/minconda3/envs/icolosprod
+python /<icolos_path>/Icolos/executor.py -conf workflow.json
+```
+For GROMACS workflows requiring the GPU partition, you will need to adapt the header accordingly, e.g. like so:
+
+```
+#!/bin/bash
+#SBATCH -J gmx_cco1_fold_microsecond
+#SBATCH -o MygpuJob_out_%j.txt
+#SBATCH -e MygpuJob_err_%j.txt
+#SBATCH --nodes=1
+#SBATCH --ntasks=4
+#SBATCH --cpus-per-task=4
+#SBATCH --gres=gpu:4
+#SBATCH --gres-flags=enforce-binding
+#SBATCH --mem-per-cpu=4g
+#SBATCH -p gpu
+#SBATCH --time=370:00:00
+
+```
+
+## Developers
+- Christian Margreitter <christian.margreitter@astrazeneca.com>
+- J. Harry Moore <harry.moore@astrazeneca.com>
+- Matthias R. Bauer <mattias.r.b@gmail.com>

environment_min.yml

@@ -0,0 +1,24 @@
+name: icolosprod
+channels:
+  - psi4
+  - conda-forge
+  - defaults
+  - rdkit
+dependencies:
+  - biopython>=1.79
+  - ipython
+  - pip
+  - python>=3.9
+  - scikit-learn>=1.0.1
+  - modal>=0.4
+  - psi4>=1.4
+  - pdbfixer
+  - pydantic>=1.8
+  - pyvis
+  - requests
+  - openbabel>=3
+  - rdkit>=2021.09.2
+  - pip:
+    - black
+    - regex
+    - peptidebuilder>=1.1

examples/hpc_script/NIBR_reinvent.sh

@@ -0,0 +1,11 @@
+#!/bin/bash -l
+#SBATCH -N 1
+#SBATCH -t 0-02:59:00
+#SBATCH -p core
+#SBATCH --ntasks-per-node=5
+#SBATCH --mem-per-cpu=2G
+
+source /projects/cc/mai/miniconda3/bin/activate /projects/cc/mai/miniconda3/envs/Icolos
+python /projects/cc/mai/IcolosDev/executor.py -conf /projects/cc/mai/material/Icolos/templates/NIBR/12-06-21nibr.json -debug \
+       --global_variables "entrypoint_dir:<path>/icolos, input_path_json:{entrypoint_dir}/tests/data/reinvent/small_input.json, output_path_json:{entrypoint_dir}/tests/junk/nibr_reinvent.json"
+

examples/hpc_script/SLURM_script.sh

@@ -0,0 +1,11 @@
+#!/bin/bash -l
+#SBATCH -N 1
+#SBATCH -t 0-02:59:00
+#SBATCH -p core
+#SBATCH --ntasks-per-node=5
+#SBATCH --mem-per-cpu=2G
+
+source /projects/cc/mai/miniconda3/bin/activate /projects/cc/mai/miniconda3/envs/Icolos
+python /projects/cc/mai/Icolos/executor.py -conf /projects/cc/mai/examples/Icolos/MPI_test/workflow_ReSCoSS.json \
+       --global_variables "output_dir:<path>/icolos/tests/junk" -debug
+