CB Iridium - Revision history

Cbedart at 17:44, 2 August 2023

2023-08-02T17:44:59Z

← Older revision		Revision as of 17:44, 2 August 2023
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			== Creation of bespoke libraries ==

			WIP

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

Cbedart at 20:40, 2 January 2023

2023-01-02T20:40:26Z

← Older revision		Revision as of 20:40, 2 January 2023
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	== 0. Table of CB bespoke libraries ==		== 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".		The prefix is "ca" as the reactions used are part of the project "Informatics platform for a pan-Canadian drug discovery chemical library".

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	</center>		</center>

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

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

	== 2. Preprocessing on gimel5 ==		== Preprocessing on gimel5 ==
	1. Transfert iridium-compatible files		1. Transfert iridium-compatible files
	<nowiki>scp -P 2222 -oHostKeyAlgorithms=+ssh-rsa -r /local/path/to/files/ cbedart@localhost:/ucsf/path/to/files/		<nowiki>scp -P 2222 -oHostKeyAlgorithms=+ssh-rsa -r /local/path/to/files/ cbedart@localhost:/ucsf/path/to/files/
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	4.5m molecules - Time ~15 min		4.5m molecules - Time ~15 min

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

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..."

2023-01-02T20:40:02Z

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..."

New page

== 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