From 9455dbdaa96944df1c8df4d560358917db79a9b5 Mon Sep 17 00:00:00 2001 From: DKokh <49686679+DKokh@users.noreply.github.com> Date: Thu, 24 Sep 2020 14:56:53 +0200 Subject: [PATCH 1/2] Update README.md --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index b97f7a6..6c4e63f 100644 --- a/README.md +++ b/README.md @@ -33,9 +33,10 @@ Schloss-Wolfsbrunnenweg 35 *This open source software code was developed in part in the __Human Brain Project__, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreements No. 785907 (Human Brain Project SGA2).* ## __Packages requirements:__ -__Python 3.x__ +__Python 3.x__: we strongly reccomend to create conda envirenment (see https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) -__Python Libraries:__ numpy; pandas; matplotlib; seaborn; RDkit; sklearn; scipy; ngview; __MDAnalysis Version: 0.20.1__ (Important: an old module for H-bond analysis is currently used, it will be removed in version 2.0 ) +__Python Libraries:__ numpy; pandas; matplotlib; seaborn; RDkit; sklearn; scipy; ngview; (installation of ngview can be tricky, the following way may work: after installation of the Python envirenment - conda install -c conda-forge nglview=2.7.1 and then jupyter-nbextension enable nglview --py --sys-prefix) +__MDAnalysis Version: 0.20.1__ (Important: an old module for H-bond analysis is currently used, it will be removed in version 2.0 ) __Chimera__ - only for the scripts used for preprocessing pdb files (structure protonation and generation of the ligand mol2 file); not required if protonation and mol2 file are already prepared by a user) From 3f0d3eb1d4b4879eba065d758735692c4494568f Mon Sep 17 00:00:00 2001 From: DKokh <49686679+DKokh@users.noreply.github.com> Date: Thu, 24 Sep 2020 14:58:25 +0200 Subject: [PATCH 2/2] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 6c4e63f..33f62d9 100644 --- a/README.md +++ b/README.md @@ -36,6 +36,7 @@ Schloss-Wolfsbrunnenweg 35 __Python 3.x__: we strongly reccomend to create conda envirenment (see https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) __Python Libraries:__ numpy; pandas; matplotlib; seaborn; RDkit; sklearn; scipy; ngview; (installation of ngview can be tricky, the following way may work: after installation of the Python envirenment - conda install -c conda-forge nglview=2.7.1 and then jupyter-nbextension enable nglview --py --sys-prefix) + __MDAnalysis Version: 0.20.1__ (Important: an old module for H-bond analysis is currently used, it will be removed in version 2.0 ) __Chimera__ - only for the scripts used for preprocessing pdb files (structure protonation and generation of the ligand mol2 file); not required if protonation and mol2 file are already prepared by a user)