DISI - User contributions [en]

CB Iridium

2023-08-02T17:44:59Z

Cbedart:

== Creation of bespoke libraries ==

WIP

== Table of CB bespoke libraries ==
The prefix is "ca" as the reactions used are part of the project "Informatics platform for a pan-Canadian drug discovery chemical library".

Here are only listed molecules among groups 1 and 2 using CBscore of purchasability. As a reminder :
* Group1 = BB-50/BB-50
* Group2 = BB-50/BB-40 & BB-40/BB-40

<center>
{| class="wikitable" style="text-align: center;"
|+ Table of CB bespoke libraries
|-
! Library ID !! Local name !! Reaction name !! Count (Gps 1/2) !! University !! Main chemist
|-
| ca1 || Reaction1 || Imides || 4,524,815 ||Toronto || BATEY Robert
|-
| ca2 || Reaction2 || Aminothiatriazoles || / ||Toronto || BATEY Robert
|-
| ca3 || Reaction3 || Phosphine oxides || / ||Toronto || BATEY Robert
|-
| ca4 || Reaction4 || 5-aminotetrazoles from thioureas || / ||Toronto || BATEY Robert
|}
</center>

== Library enumeration in Iridium-compatible formats ==
Use of classical enumeration scripts adapted to output iridium-compatible formats

Useful commands :
<nowiki>ls * | find . -name "*.txt" | xargs wc -l</nowiki>

== Preprocessing on gimel5 ==
1. Transfert iridium-compatible files
<nowiki>scp -P 2222 -oHostKeyAlgorithms=+ssh-rsa -r /local/path/to/files/ cbedart@localhost:/ucsf/path/to/files/
</nowiki>

2. Reminder to work on gimel5
<nowiki>ssh gimel5</nowiki>

3. Create preprocessing files
<nowiki>cd /nfs/exb/zinc22/2dpre_results/bespoke_libraries/
mkdir ca1_imides_230102
mkdir ca1_imides_230102_DIFF
cd /nfs/home/khtang/code/TIN_Scripts/Iridium/preprocessing
sh
export EXPORT_DEST=/nfs/exb/zinc22/2dpre_results/bespoke_libraries/ca1_imides_230102
export BINPATH=/nfs/home/xyz/btingle/bin/2dload.testing/utils-2d
bash pre_process_partition.bash 1 /nfs/home/cbedart/exk/CB_bespoke_libraries/ca1_imides_230102 ca1</nowiki>
4.5m molecules - Time ~15 min

== Load2D on n-9-38 ==
1. Reminder to work on n-9-38
<nowiki>ssh n-9-38</nowiki>

2. Loading
<nowiki>sh
source /dev/shm/build_3d_common/lig_build_py3-3.7.1/bin/activate
</nowiki>

2023/01/02 = Currently not working

CB Iridium

2023-01-02T20:40:26Z

Cbedart:

== Table of CB bespoke libraries ==
The prefix is "ca" as the reactions used are part of the project "Informatics platform for a pan-Canadian drug discovery chemical library".

Here are only listed molecules among groups 1 and 2 using CBscore of purchasability. As a reminder :
* Group1 = BB-50/BB-50
* Group2 = BB-50/BB-40 & BB-40/BB-40

<center>
{| class="wikitable" style="text-align: center;"
|+ Table of CB bespoke libraries
|-
! Library ID !! Local name !! Reaction name !! Count (Gps 1/2) !! University !! Main chemist
|-
| ca1 || Reaction1 || Imides || 4,524,815 ||Toronto || BATEY Robert
|-
| ca2 || Reaction2 || Aminothiatriazoles || / ||Toronto || BATEY Robert
|-
| ca3 || Reaction3 || Phosphine oxides || / ||Toronto || BATEY Robert
|-
| ca4 || Reaction4 || 5-aminotetrazoles from thioureas || / ||Toronto || BATEY Robert
|}
</center>

== Library enumeration in Iridium-compatible formats ==
Use of classical enumeration scripts adapted to output iridium-compatible formats

Useful commands :
<nowiki>ls * | find . -name "*.txt" | xargs wc -l</nowiki>

== Preprocessing on gimel5 ==
1. Transfert iridium-compatible files
<nowiki>scp -P 2222 -oHostKeyAlgorithms=+ssh-rsa -r /local/path/to/files/ cbedart@localhost:/ucsf/path/to/files/
</nowiki>

2. Reminder to work on gimel5
<nowiki>ssh gimel5</nowiki>

3. Create preprocessing files
<nowiki>cd /nfs/exb/zinc22/2dpre_results/bespoke_libraries/
mkdir ca1_imides_230102
mkdir ca1_imides_230102_DIFF
cd /nfs/home/khtang/code/TIN_Scripts/Iridium/preprocessing
sh
export EXPORT_DEST=/nfs/exb/zinc22/2dpre_results/bespoke_libraries/ca1_imides_230102
export BINPATH=/nfs/home/xyz/btingle/bin/2dload.testing/utils-2d
bash pre_process_partition.bash 1 /nfs/home/cbedart/exk/CB_bespoke_libraries/ca1_imides_230102 ca1</nowiki>
4.5m molecules - Time ~15 min

== Load2D on n-9-38 ==
1. Reminder to work on n-9-38
<nowiki>ssh n-9-38</nowiki>

2. Loading
<nowiki>sh
source /dev/shm/build_3d_common/lig_build_py3-3.7.1/bin/activate
</nowiki>

2023/01/02 = Currently not working

CB Iridium

2023-01-02T20:40:02Z

Cbedart: Created page with "== 0. Table of CB bespoke libraries == The prefix is "ca" as the reactions used are part of the project "Informatics platform for a pan-Canadian drug discovery chemical libra..."

== 0. Table of CB bespoke libraries ==
The prefix is "ca" as the reactions used are part of the project "Informatics platform for a pan-Canadian drug discovery chemical library".

Here are only listed molecules among groups 1 and 2 using CBscore of purchasability. As a reminder :
* Group1 = BB-50/BB-50
* Group2 = BB-50/BB-40 & BB-40/BB-40

<center>
{| class="wikitable" style="text-align: center;"
|+ Table of CB bespoke libraries
|-
! Library ID !! Local name !! Reaction name !! Count (Gps 1/2) !! University !! Main chemist
|-
| ca1 || Reaction1 || Imides || 4,524,815 ||Toronto || BATEY Robert
|-
| ca2 || Reaction2 || Aminothiatriazoles || / ||Toronto || BATEY Robert
|-
| ca3 || Reaction3 || Phosphine oxides || / ||Toronto || BATEY Robert
|-
| ca4 || Reaction4 || 5-aminotetrazoles from thioureas || / ||Toronto || BATEY Robert
|}
</center>

== 1. Library enumeration in Iridium-compatible formats ==
Use of classical enumeration scripts adapted to output iridium-compatible formats

Useful commands :
<nowiki>ls * | find . -name "*.txt" | xargs wc -l</nowiki>

== 2. Preprocessing on gimel5 ==
1. Transfert iridium-compatible files
<nowiki>scp -P 2222 -oHostKeyAlgorithms=+ssh-rsa -r /local/path/to/files/ cbedart@localhost:/ucsf/path/to/files/
</nowiki>

2. Reminder to work on gimel5
<nowiki>ssh gimel5</nowiki>

3. Create preprocessing files
<nowiki>cd /nfs/exb/zinc22/2dpre_results/bespoke_libraries/
mkdir ca1_imides_230102
mkdir ca1_imides_230102_DIFF
cd /nfs/home/khtang/code/TIN_Scripts/Iridium/preprocessing
sh
export EXPORT_DEST=/nfs/exb/zinc22/2dpre_results/bespoke_libraries/ca1_imides_230102
export BINPATH=/nfs/home/xyz/btingle/bin/2dload.testing/utils-2d
bash pre_process_partition.bash 1 /nfs/home/cbedart/exk/CB_bespoke_libraries/ca1_imides_230102 ca1</nowiki>
4.5m molecules - Time ~15 min

== 2. Load2D on n-9-38 ==
1. Reminder to work on n-9-38
<nowiki>ssh n-9-38</nowiki>

2. Loading
<nowiki>sh
source /dev/shm/build_3d_common/lig_build_py3-3.7.1/bin/activate
</nowiki>

2023/01/02 = Currently not working

CB DOCK 3.8 tutorial

2022-12-15T18:37:40Z

Cbedart: /* Pydock3 dockopt */

== Things to remember ==
* Be in gimel5 : ''ssh gimel5''

== DOCK 3.8 installation ==

1) Download pydock3 :
<nowiki>
git clone https://github.com/docking-org/pydock3</nowiki>

2) Download DOCK engine :
<nowiki>
cd ./pydock3/
git clone https://github.com/docking-org/DOCK.git</nowiki>

3) Add in your ~/.profile file :
* python 3.8.5 environment (gimel5)
* DOCKEXEC & DOCKBASE environment variables
<nowiki>
source /nfs/soft/ian/python3.8.5.sh
export DOCKEXEC=''>PATH<''/pydock3/DOCK/ucsfdock/docking/DOCK/dock64
export DOCKBASE=''>PATH<''/pydock3/DOCK/ucsfdock</nowiki>
* Do not forget to source ~/.profile in case you plan to use DOCK & pydock3 immediately

== Pydock3 blastermaster ==
* Protein preparation
* WIP

== Pydock3 dockopt ==
* https://wiki.docking.org/index.php/Dockopt_(pydock3_script)

0) Don't forget to be on gimel5

1) Create actives.tgz and decoys.tgz files :
* Create "actives" and "decoys" folders, and put every db2 files you have inside
* Compression using :
<nowiki>tar -cvzf actives.tgz $PWD/actives/*
tar -cvzf decoys.tgz $PWD/decoys/*</nowiki>

2) Copy rec.pdb and xtal-lig.pdb in the main folder

3) Initialization of dockopt :
<nowiki>pydock3 dockopt - init JobName</nowiki>

4) Define environment variables and run dockopt :
<nowiki>cd JobName/
export SBATCH_EXEC=/usr/bin/sbatch
export SQUEUE_EXEC=/usr/bin/squeue
export TMPDIR=/scratch
pydock3 dockopt - run slurm</nowiki>

== DOCK 3.8 docking ==

1) Create your run directory and copy dockfiles from blastermaster :

2) Import ligands, and create ligand index file :
* Important notice : The index file '''must''' be filled with absolute paths
<nowiki>
find $PWD -type f -name '*.db2*' > sdi.in</nowiki>

3) Create an init.sh file to initialize the main environment variables that will be used during docking :
<nowiki>export INPUT_SOURCE=$PWD/sdi.in
export EXPORT_DEST=$PWD/output
export DOCKFILES=$PWD/dockfiles</nowiki>

4) Load your init.sh file :
<nowiki>source ./init.sh</nowiki>

5) Run docking :
* In case of db2.gz files from TLDR, use --use-db2=true --use-db2-tgz=false options
* In gimel5, --use-slurm=true is mandatory
<nowiki>
bash $DOCKBASE/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true</nowiki>

== DOCK 3.8 analysis ==

=== top_poses.py ===

1) Load a specific python environment :
* (why is it different from the version used to run pydock3 ?)
<nowiki>source /nfs/soft/python/versions/python-3.8-install/bin/env.sh</nowiki>

2) Main commands :
* https://wiki.docking.org/index.php/Docking_Analysis_in_DOCK3.8#Note_on_Parallel_Processing
* 2022/12/13 : instructions doesn't seem to work, only the script and the main path
<nowiki>python3 $DOCKBASE/analysis/top_poses.py output/</nowiki>

CB DOCK 3.8 tutorial

2022-12-15T16:42:46Z

Cbedart:

== Things to remember ==
* Be in gimel5 : ''ssh gimel5''

== DOCK 3.8 installation ==

1) Download pydock3 :
<nowiki>
git clone https://github.com/docking-org/pydock3</nowiki>

2) Download DOCK engine :
<nowiki>
cd ./pydock3/
git clone https://github.com/docking-org/DOCK.git</nowiki>

3) Add in your ~/.profile file :
* python 3.8.5 environment (gimel5)
* DOCKEXEC & DOCKBASE environment variables
<nowiki>
source /nfs/soft/ian/python3.8.5.sh
export DOCKEXEC=''>PATH<''/pydock3/DOCK/ucsfdock/docking/DOCK/dock64
export DOCKBASE=''>PATH<''/pydock3/DOCK/ucsfdock</nowiki>
* Do not forget to source ~/.profile in case you plan to use DOCK & pydock3 immediately

== Pydock3 blastermaster ==
* Protein preparation
* WIP

== Pydock3 dockopt ==
* https://wiki.docking.org/index.php/Dockopt_(pydock3_script)

0) Don't forget to be on gimel5

1) Create actives.tgz and decoys.tgz files :
* Create "actives" and "decoys" folders, and put every db2 files you have inside
* Compression using :
<nowiki>tar -cvzf actives.tgz $PWD/actives/*
tar -cvzf decoys.tgz $PWD/decoys/*</nowiki>

2) Copy rec.pdb and xtal-lig.pdb in the main folder

3) Initialization of dockopt :
<nowiki>pydock3 dockopt - init --job_dir_name=JobName</nowiki>

4) Run dockopt :

== DOCK 3.8 docking ==

1) Create your run directory and copy dockfiles from blastermaster :

2) Import ligands, and create ligand index file :
* Important notice : The index file '''must''' be filled with absolute paths
<nowiki>
find $PWD -type f -name '*.db2*' > sdi.in</nowiki>

3) Create an init.sh file to initialize the main environment variables that will be used during docking :
<nowiki>export INPUT_SOURCE=$PWD/sdi.in
export EXPORT_DEST=$PWD/output
export DOCKFILES=$PWD/dockfiles</nowiki>

4) Load your init.sh file :
<nowiki>source ./init.sh</nowiki>

5) Run docking :
* In case of db2.gz files from TLDR, use --use-db2=true --use-db2-tgz=false options
* In gimel5, --use-slurm=true is mandatory
<nowiki>
bash $DOCKBASE/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true</nowiki>

== DOCK 3.8 analysis ==

=== top_poses.py ===

1) Load a specific python environment :
* (why is it different from the version used to run pydock3 ?)
<nowiki>source /nfs/soft/python/versions/python-3.8-install/bin/env.sh</nowiki>

2) Main commands :
* https://wiki.docking.org/index.php/Docking_Analysis_in_DOCK3.8#Note_on_Parallel_Processing
* 2022/12/13 : instructions doesn't seem to work, only the script and the main path
<nowiki>python3 $DOCKBASE/analysis/top_poses.py output/</nowiki>

CB DOCK 3.8 tutorial

2022-12-15T16:19:15Z

Cbedart: /* top_poses.py */

== Things to remember ==
* Be in gimel5 : ''ssh gimel5''

== DOCK 3.8 installation ==

1) Download pydock3 :
<nowiki>
git clone https://github.com/docking-org/pydock3</nowiki>

2) Download DOCK engine :
<nowiki>
cd ./pydock3/
git clone https://github.com/docking-org/DOCK.git</nowiki>

3) Add in your ~/.profile file :
* python 3.8.5 environment (gimel5)
* DOCKEXEC & DOCKBASE environment variables
<nowiki>
source /nfs/soft/ian/python3.8.5.sh
export DOCKEXEC=''>PATH<''/pydock3/DOCK/ucsfdock/docking/DOCK/dock64
export DOCKBASE=''>PATH<''/pydock3/DOCK/ucsfdock</nowiki>
* Do not forget to source ~/.profile in case you plan to use DOCK & pydock3 immediately

== Pydock3 blastermaster ==
* Protein preparation
* WIP

== DOCK 3.8 docking ==

1) Create your run directory and copy dockfiles from blastermaster :

2) Import ligands, and create ligand index file :
* Important notice : The index file '''must''' be filled with absolute paths
<nowiki>
find $PWD -type f -name '*.db2*' > sdi.in</nowiki>

3) Create an init.sh file to initialize the main environment variables that will be used during docking :
<nowiki>export INPUT_SOURCE=$PWD/sdi.in
export EXPORT_DEST=$PWD/output
export DOCKFILES=$PWD/dockfiles</nowiki>

4) Load your init.sh file :
<nowiki>source ./init.sh</nowiki>

5) Run docking :
* In case of db2.gz files from TLDR, use --use-db2=true --use-db2-tgz=false options
* In gimel5, --use-slurm=true is mandatory
<nowiki>
bash $DOCKBASE/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true</nowiki>

== DOCK 3.8 analysis ==

=== top_poses.py ===

1) Load a specific python environment :
* (why is it different from the version used to run pydock3 ?)
<nowiki>source /nfs/soft/python/versions/python-3.8-install/bin/env.sh</nowiki>

2) Main commands :
* https://wiki.docking.org/index.php/Docking_Analysis_in_DOCK3.8#Note_on_Parallel_Processing
* 2022/12/13 : instructions doesn't seem to work, only the script and the main path
<nowiki>python3 $DOCKBASE/analysis/top_poses.py output/</nowiki>

CB DOCK 3.8 tutorial

2022-12-13T20:49:34Z

Cbedart: /* DOCK 3.8 analysis */

== Things to remember ==
* Be in gimel5 : ''ssh gimel5''

== DOCK 3.8 installation ==

1) Download pydock3 :
<nowiki>
git clone https://github.com/docking-org/pydock3</nowiki>

2) Download DOCK engine :
<nowiki>
cd ./pydock3/
git clone https://github.com/docking-org/DOCK.git</nowiki>

3) Add in your ~/.profile file :
* python 3.8.5 environment (gimel5)
* DOCKEXEC & DOCKBASE environment variables
<nowiki>
source /nfs/soft/ian/python3.8.5.sh
export DOCKEXEC=''>PATH<''/pydock3/DOCK/ucsfdock/docking/DOCK/dock64
export DOCKBASE=''>PATH<''/pydock3/DOCK/ucsfdock</nowiki>
* Do not forget to source ~/.profile in case you plan to use DOCK & pydock3 immediately

== Pydock3 blastermaster ==
* Protein preparation
* WIP

== DOCK 3.8 docking ==

1) Create your run directory and copy dockfiles from blastermaster :

2) Import ligands, and create ligand index file :
* Important notice : The index file '''must''' be filled with absolute paths
<nowiki>
find $PWD -type f -name '*.db2*' > sdi.in</nowiki>

3) Create an init.sh file to initialize the main environment variables that will be used during docking :
<nowiki>export INPUT_SOURCE=$PWD/sdi.in
export EXPORT_DEST=$PWD/output
export DOCKFILES=$PWD/dockfiles</nowiki>

4) Load your init.sh file :
<nowiki>source ./init.sh</nowiki>

5) Run docking :
* In case of db2.gz files from TLDR, use --use-db2=true --use-db2-tgz=false options
* In gimel5, --use-slurm=true is mandatory
<nowiki>
bash $DOCKBASE/docking/submit/subdock.bash --use-db2=true --use-db2-tgz=false --use-slurm=true</nowiki>

== DOCK 3.8 analysis ==

=== top_poses.py ===

1) Load a specific python environment :
* (why is it different from the version used to run pydock3 ?)
<nowiki>source /nfs/soft/python/versions/python-3.8-install/python-3.8-install/bin/env.sh</nowiki>

2) Main commands :
* https://wiki.docking.org/index.php/Docking_Analysis_in_DOCK3.8#Note_on_Parallel_Processing
* 2022/12/13 : instructions doesn't seem to work, only the script and the main path
<nowiki>python3 ../pydock3/DOCK/ucsfdock/analysis/top_poses.py output/</nowiki>

CB DOCK 3.8 tutorial

2022-12-13T20:10:07Z

Cbedart: /* DOCK 3.8 docking */

CB DOCK 3.8 tutorial

2022-12-13T16:20:06Z

Cbedart: Creation