From 9a2ec7c3d10621b63b72fbb3359c193ace6bbd5d Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 21 Jan 2025 15:50:45 -0800 Subject: [PATCH 1/7] move env yaml to top dir --- devtools/conda-envs/CI_env.yaml => environment.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename devtools/conda-envs/CI_env.yaml => environment.yaml (89%) diff --git a/devtools/conda-envs/CI_env.yaml b/environment.yaml similarity index 89% rename from devtools/conda-envs/CI_env.yaml rename to environment.yaml index 16e9c23..4cd1dd2 100644 --- a/devtools/conda-envs/CI_env.yaml +++ b/environment.yaml @@ -1,4 +1,4 @@ -name: test +name: lomap-env channels: - conda-forge dependencies: From 40d981b45d38e6952d1ed728728906a4acf3adbc Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 21 Jan 2025 16:01:02 -0800 Subject: [PATCH 2/7] updating install instructions --- README.md | 16 +++++++++++++--- docs/installation.rst | 8 ++++++++ 2 files changed, 21 insertions(+), 3 deletions(-) create mode 100644 docs/installation.rst diff --git a/README.md b/README.md index c629369..58b2d63 100644 --- a/README.md +++ b/README.md @@ -29,12 +29,22 @@ See [AUTHORS.md](https://github.com/OpenFreeEnergy/Lomap/blob/main/AUTHORS.md) ## Installation +### Latest Release `conda install -c conda-forge lomap2` -Alternatively, you can install the prerequisites and then install from source -with: +### Development Version +Alternatively, you can install the development version of `lomap` directly from the `main` branch of this repository. -`python setup.py install` +First install the package dependencies using conda (or mamba) in a virtual environemnt with: + +```bash +conda env create -f environment.yaml +conda activate lomap-env +``` + +Then install `lomap` with: + +`pip install -e .` Usage ----- diff --git a/docs/installation.rst b/docs/installation.rst new file mode 100644 index 0000000..500f1d5 --- /dev/null +++ b/docs/installation.rst @@ -0,0 +1,8 @@ +Installation +============ + +## Installation + +To install `lomap`, run + +`conda install -c conda-forge lomap2` From 535cbd08406241e187d5e4e2826976d8478e7644 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 21 Jan 2025 16:03:28 -0800 Subject: [PATCH 3/7] updating env.yaml path --- .github/workflows/CI.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 9545b82..507b997 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -51,7 +51,7 @@ jobs: - uses: mamba-org/setup-micromamba@v1 if: ${{ matrix.rdkit-version != 'latest' }} with: - environment-file: devtools/conda-envs/CI_env.yaml + environment-file: environment.yaml cache-environment: true cache-downloads: true cache-environment-key: environment-${{ steps.date.outputs.date }} @@ -64,7 +64,7 @@ jobs: - uses: mamba-org/setup-micromamba@v1 if: ${{ matrix.rdkit-version == 'latest' }} with: - environment-file: devtools/conda-envs/CI_env.yaml + environment-file: environment.yaml cache-environment: true cache-downloads: true cache-environment-key: environment-${{ steps.date.outputs.date }} From efd69e0ff2d5d4265d6731f77d9c10fe28290f6a Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Mon, 27 Jan 2025 14:33:09 -0800 Subject: [PATCH 4/7] cleaning up indexx --- docs/index.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 4a09147..5999831 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -6,12 +6,13 @@ Welcome to Lomap's documentation! ================================= -Lomap (Lead Optimisation Mapper) is a tool for planning perturbation networks for free energy calculations. +Lomap (Lead Optimization Mapper) is a tool for planning perturbation networks for free energy calculations. .. toctree:: - :maxdepth: 2 + :maxdepth: 1 :caption: Contents: + installation.rst api.rst legacy.rst citing.rst @@ -23,4 +24,3 @@ Indices and tables * :ref:`genindex` * :ref:`modindex` -* :ref:`search` From b64d8f4f30129522087f66bf8d066a41cfcc65a4 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Mon, 27 Jan 2025 14:33:50 -0800 Subject: [PATCH 5/7] format README --- README.md | 44 +++++++++++++++++++++++--------------------- 1 file changed, 23 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 58b2d63..655004e 100644 --- a/README.md +++ b/README.md @@ -2,23 +2,23 @@ [![Documentation Status](https://readthedocs.org/projects/lomap/badge/?version=latest)](https://lomap.readthedocs.io/en/latest/?badge=latest) # Lomap -Alchemical free energy calculations hold increasing promise -as an aid to drug discovery efforts. However, applications of -these techniques in discovery projects have been relatively -rare, partly because of the difficulty of planning and setting up -calculations. The lead optimization mapper (LOMAP) was -introduced as an automated algorithm to plan efficient relative -free energy calculations between potential ligands within +Alchemical free energy calculations hold increasing promise +as an aid to drug discovery efforts. However, applications of +these techniques in discovery projects have been relatively +rare, partly because of the difficulty of planning and setting up +calculations. The lead optimization mapper (LOMAP) was +introduced as an automated algorithm to plan efficient relative +free energy calculations between potential ligands within a substantial of compounds. The original LOMAP code was mainly -based on commercial APIs such as OpenEye and Schrodinger. The aim +based on commercial APIs such as OpenEye and Schrodinger. The aim of this project is to develop a new version of LOMAP based on free -avalaible APIs such as RDKit offering the scientific community a +avalaible APIs such as RDKit offering the scientific community a free tool to plan in advance binding free energy calculations. ## Prerequisites * RDKit Release > 2021 * NetworkX -* Matplotlib +* Matplotlib * python > 3.8 Authors @@ -30,25 +30,27 @@ See [AUTHORS.md](https://github.com/OpenFreeEnergy/Lomap/blob/main/AUTHORS.md) ## Installation ### Latest Release + +You can install using conda (or mamba). Note the package name is `lomap2`: `conda install -c conda-forge lomap2` ### Development Version Alternatively, you can install the development version of `lomap` directly from the `main` branch of this repository. -First install the package dependencies using conda (or mamba) in a virtual environemnt with: +First install the package dependencies using conda (or mamba) in a virtual environment with: ```bash conda env create -f environment.yaml conda activate lomap-env ``` -Then install `lomap` with: +Then install `lomap` locally with: `pip install -e .` Usage ----- -As a commandline tool LOMAP can be simply used as: +As a command line tool, LOMAP can be simply used as: ` lomap test/basic/ ` @@ -80,31 +82,31 @@ db_mol = lomap.DBMolecules("python string pointing to a directory with mol2 file db_mol = lomap.DBMolecules("python string pointing to a directory with mol2 files", output=True, radial=True, hub=filename.mol2, fast=True) # Calculate the similarity matrix betweeen the database molecules. Two molecules are generated -# related to the scrict rule and loose rule +# related to the scrict rule and loose rule strict, loose = db_mol.build_matrices() # Generate the NetworkX graph and output the results -nx_graph = db_mol.build_graph() +nx_graph = db_mol.build_graph() -# Calculate the Maximum Common Subgraph (MCS) between -# the first two molecules in the molecule database +# Calculate the Maximum Common Subgraph (MCS) between +# the first two molecules in the molecule database # ignoring hydrogens and depicting the mapping in a file - + MC = lomap.MCS.getMapping(db_mol[0].getMolecule(), db_mol[1].getMolecule(), hydrogens=False, fname='mcs.png') # Alchemical transformation are usually performed between molecules with # the same charges. However, it is possible to allow this transformation -# manually setting the electrostatic score for the whole set of molecules -# producing a connected graph. The electrostatic scrore must be in the +# manually setting the electrostatic score for the whole set of molecules +# producing a connected graph. The electrostatic scrore must be in the # range [0,1] db_mol = lomap.DBMolecules("python string pointing to a directory with mol2 files", output=True, ecrscore=0.1) strict, loose = db_mol.build_matrices() -nx_graph = db_mol.build_graph() +nx_graph = db_mol.build_graph() ``` ## History From 641d09e1e246d50b64f165f79d45b7665f830842 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Mon, 27 Jan 2025 14:34:49 -0800 Subject: [PATCH 6/7] updating installation docs --- docs/installation.rst | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index 500f1d5..1975c1a 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -1,8 +1,25 @@ Installation ============ -## Installation +Latest Release +-------------- -To install `lomap`, run +You can install lomap using conda (or mamba). Note the package name is ``lomap2``: +.. parsed-literal:: + conda install -c conda-forge lomap2 -`conda install -c conda-forge lomap2` +Development Version +------------------- +Alternatively, you can install the development version of ``lomap``` directly from the ``main`` branch of this repository. + +First install the package dependencies using conda (or mamba) in a virtual environment with: + +.. parsed-literal:: + conda env create -f environment.yaml + conda activate lomap-env + + +Then install ``lomap`` locally with: + +.. parsed-literal:: + pip install -e . From 626a4ede3e74e46d62620afdf7dfdb19545cc70a Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Tue, 28 Jan 2025 20:15:42 +0000 Subject: [PATCH 7/7] Update docs/installation.rst --- docs/installation.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/installation.rst b/docs/installation.rst index 1975c1a..dd572e8 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -5,6 +5,7 @@ Latest Release -------------- You can install lomap using conda (or mamba). Note the package name is ``lomap2``: + .. parsed-literal:: conda install -c conda-forge lomap2