From daacdba706a111847b86da4f0b74db53808c6e2c Mon Sep 17 00:00:00 2001 From: DaniDelHoyo Date: Tue, 5 Nov 2024 13:36:10 -0800 Subject: [PATCH 1/4] Updated linux vina tutorial --- installation-linux/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/installation-linux/README.md b/installation-linux/README.md index 9b2aba4..7beb5b3 100644 --- a/installation-linux/README.md +++ b/installation-linux/README.md @@ -53,14 +53,14 @@ Running the following commands will install meeko and ringtail in the currently active micromamba environment. ``` -pip install meeko==0.6.0a3 pip install ringtail +pip install meeko==0.6.0a3 ``` Running the following commands should display help messages: ``` mk_prepare_ligand.py -rt_process_vs.py +rt_process_vs ``` A new release of Meeko will be available soon. @@ -126,10 +126,10 @@ Copy the files in [toy-example-data](../toy-example-data) to the working dir and ``` scrub.py "Oc1ccccc1" -o phenol.sdf mk_prepare_ligand.py -i phenol.sdf -o phenol.pdbqt -mk_prepare_receptor.py --pdb pocket.pdb --ligand pocket.pdb --padding 5 -o receptor +mk_prepare_receptor.py --read_pdb pocket.pdb --box_enveloping pocket.pdb --padding 5 -o receptor -p -j -v mkdir results ./vina_1.2.5_linux_x86_64 --receptor receptor.pdbqt --config receptor.box.txt --ligand phenol.pdbqt --out results/phenol.pdbqt -rt_process_vs.py write -o results.db -fp results -m vina -ai -rf receptor.pdbqt +rt_process_vs write -o results.db -fp results -m vina -ai -rf receptor.pdbqt -sr mkdir passing_sdf rt_process_vs.py read -i results.db -e -2 -sdf passing_sdf ``` From d69d54b26b1a2122526755833fb865ee1aaaa7c7 Mon Sep 17 00:00:00 2001 From: DaniDelHoyo Date: Tue, 5 Nov 2024 13:45:14 -0800 Subject: [PATCH 2/4] Imports needed --- installation-linux/README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/installation-linux/README.md b/installation-linux/README.md index 7beb5b3..87097e5 100644 --- a/installation-linux/README.md +++ b/installation-linux/README.md @@ -35,6 +35,7 @@ micromamba install python=3.11 -y micromamba install pymol-open-source -y micromamba install rdkit numpy scipy -y micromamba install chemicalite matplotlib=3.7 pandas -y +micromamba install importlib_resources gemmi -y ``` Several packages are being installed in a single line. @@ -60,7 +61,7 @@ pip install meeko==0.6.0a3 Running the following commands should display help messages: ``` mk_prepare_ligand.py -rt_process_vs +rt_process_vs -h ``` A new release of Meeko will be available soon. @@ -131,7 +132,7 @@ mkdir results ./vina_1.2.5_linux_x86_64 --receptor receptor.pdbqt --config receptor.box.txt --ligand phenol.pdbqt --out results/phenol.pdbqt rt_process_vs write -o results.db -fp results -m vina -ai -rf receptor.pdbqt -sr mkdir passing_sdf -rt_process_vs.py read -i results.db -e -2 -sdf passing_sdf +rt_process_vs read -i results.db -e -2 -sdf passing_sdf ``` A file "phenol.sdf" should have been added to "passing\_sdf". From b28f98084d3b6ad8b271da6a67d87626f9efebc7 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 5 Nov 2024 21:49:09 -0800 Subject: [PATCH 3/4] remove importlib_resources --- installation-linux/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/installation-linux/README.md b/installation-linux/README.md index 87097e5..a536830 100644 --- a/installation-linux/README.md +++ b/installation-linux/README.md @@ -35,7 +35,7 @@ micromamba install python=3.11 -y micromamba install pymol-open-source -y micromamba install rdkit numpy scipy -y micromamba install chemicalite matplotlib=3.7 pandas -y -micromamba install importlib_resources gemmi -y +micromamba install gemmi -y ``` Several packages are being installed in a single line. From 52a826f507a6fa7d4fda253300f8b27509827274 Mon Sep 17 00:00:00 2001 From: Daniel Del Hoyo Gomez Date: Wed, 6 Nov 2024 17:01:06 -0800 Subject: [PATCH 4/4] ligand box fix --- installation-linux/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/installation-linux/README.md b/installation-linux/README.md index a536830..1074c26 100644 --- a/installation-linux/README.md +++ b/installation-linux/README.md @@ -127,7 +127,7 @@ Copy the files in [toy-example-data](../toy-example-data) to the working dir and ``` scrub.py "Oc1ccccc1" -o phenol.sdf mk_prepare_ligand.py -i phenol.sdf -o phenol.pdbqt -mk_prepare_receptor.py --read_pdb pocket.pdb --box_enveloping pocket.pdb --padding 5 -o receptor -p -j -v +mk_prepare_receptor.py --read_pdb pocket.pdb --box_enveloping ligand.pdb --padding 5 -o receptor -p -j -v mkdir results ./vina_1.2.5_linux_x86_64 --receptor receptor.pdbqt --config receptor.box.txt --ligand phenol.pdbqt --out results/phenol.pdbqt rt_process_vs write -o results.db -fp results -m vina -ai -rf receptor.pdbqt -sr