SynthI - Revision history

Iamkaant: removed notes on analog generation

2022-03-15T03:34:25Z

removed notes on analog generation

← Older revision		Revision as of 03:34, 15 March 2022
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	Detailed guide is [https://github.com/Laboratoire-de-Chemoinformatique/SynthI here]		Detailed guide is [https://github.com/Laboratoire-de-Chemoinformatique/SynthI here]

	~~==== Preparing analogs with SynthI ====~~

	~~Working with https://cartblanche22.docking.org/searchZinc/ZINCoT000006Aq87, bash needed. Prepare .smi file with the list of SMILES (and names) of compds to prepare analogs for.~~


	~~First, we need to fragment our compounds:~~

	~~python /nfs/soft2/SynthI//SynthI_BulkFragmentationEnumerationAndAnaloguesDesign.py -i ligand.smi --nCores 5 --MaxNumberOfStages 1~~

	~~In the file ligand.smi_out you will get a list of synthons and reactions that are applied to the molecule:~~

	C[C@@H](NCc1cccc(-n2cccn2)c1)c1csc2ccccc12 ZINCoT000006Aq87 c1cn[nH:20]c1.c1cc(C[NH2:20])c[cH:21]c1.C[CH2:10]c1csc2ccccc12 R3.1_0\|R5.2_0 3 0 AvailableSynthons: NotAvailableSynthons:C[CH2:10]c1csc2ccccc12\|c1cc(C[NH2:20])c[cH:21]c1\|c1cn[nH:20]c1

	As the synthons generated contain molecular fragments, you will have to manually cap the BBs according to the reactions provided. Then search for similar BBs in SmallWorld. For each of the found lists of BBs do:

	~~awk '{print $1 " " $2}' thioph-Cl.tsv \| grep -v alignment > thioph-Cl.smi~~

	~~Then cat into one file and prepare synthons from the BBs found.~~

	~~python /nfs/soft2/SynthI/SynthI_BBsBulkClassificationAndSynthonization.py -i bb_analogs.smi~~

	~~Leave only SMILES and names~~

	~~awk '{print $1 " " $NF}' bb_analogs.smi_Synthmode.smi > bb_analogs_synth.smi~~


	~~===== A. Enumeration based on all found BBs =====~~
	~~Directory under "-oD" will contain eitherFinalOut_allEnumeratedCompounds_DuplicatesCanBePresent.smi or AnalogsForMol1.smi file with list of SMILES for generated compds~~

	~~Using all available reactions:~~

	~~mkdr ENUMERATED~~
	python /nfs/soft2/SynthI/SynthI_BulkFragmentationEnumerationAndAnaloguesDesign.py -i bb_analogs_synth.smi --nCores 10 -oD ENUMERATED --MaxNumberOfStages 5 --enumerationMode --MWupperTh 460 --MWlowerTh 200
	~~Morgan2 Tc of obtained compds to the parent.~~
	~~[[Image:Tanimoto.png\|300px]]~~

	~~Using the same reactions that were used for initial fragmentation:~~

	~~mkdir ENUMERATED-R3-R5~~
	python /nfs/soft2/SynthI/SynthI_BulkFragmentationEnumerationAndAnaloguesDesign.py -i bb_analogs_synth.smi --nCores 10 -oD ENUMERATED-R3-R5/ --MaxNumberOfStages 5 --enumerationMode --MWupperTh 460 --MWlowerTh 200 --fragmentationMode include_only --reactionsToWorkWith "R3, R5"
	~~Morgan2 Tc of obtained compds to the parent.~~
	~~[[Image:Tanimoto-synthi-enum-r3-r5.png\|300px]]~~


	~~===== B. Analogs from a synthon library =====~~

	python /nfs/soft2/SynthI/SynthI_BulkFragmentationEnumerationAndAnaloguesDesign.py -i ligand.smi --SynthLibrary bb_analogs_synth.smi --simTh 0.5 --analoguesLibGen --nCores 10 -oD ANALOGS --MaxNumberOfStages 5 --desiredNumberOfNewMols 1000 --enumerationMode --MWupperTh 460 --MWlowerTh 200
	~~Morgan2 Tc of obtained compds to the parent.~~
	~~[[Image:Tanimoto-synthi-analogs.png\|300px]]~~

	~~Analog generation doesn't seem to use similarity threshold value. Usage of large synthon library may be useful for analog generation, but speed needs to be tested.~~

	[[Category: Software]]		[[Category: Software]]

Iamkaant: Added the section on analog generation

2022-03-13T08:47:11Z

Added the section on analog generation

← Older revision		Revision as of 08:47, 13 March 2022
Line 49:		Line 49:

	Detailed guide is [https://github.com/Laboratoire-de-Chemoinformatique/SynthI here]		Detailed guide is [https://github.com/Laboratoire-de-Chemoinformatique/SynthI here]

			==== Preparing analogs with SynthI ====

			Working with https://cartblanche22.docking.org/searchZinc/ZINCoT000006Aq87, bash needed. Prepare .smi file with the list of SMILES (and names) of compds to prepare analogs for.


			First, we need to fragment our compounds:

			python /nfs/soft2/SynthI//SynthI_BulkFragmentationEnumerationAndAnaloguesDesign.py -i ligand.smi --nCores 5 --MaxNumberOfStages 1

			In the file ligand.smi_out you will get a list of synthons and reactions that are applied to the molecule:

			C[C@@H](NCc1cccc(-n2cccn2)c1)c1csc2ccccc12 ZINCoT000006Aq87 c1cn[nH:20]c1.c1cc(C[NH2:20])c[cH:21]c1.C[CH2:10]c1csc2ccccc12 R3.1_0\|R5.2_0 3 0 AvailableSynthons: NotAvailableSynthons:C[CH2:10]c1csc2ccccc12\|c1cc(C[NH2:20])c[cH:21]c1\|c1cn[nH:20]c1

			As the synthons generated contain molecular fragments, you will have to manually cap the BBs according to the reactions provided. Then search for similar BBs in SmallWorld. For each of the found lists of BBs do:

			awk '{print $1 " " $2}' thioph-Cl.tsv \| grep -v alignment > thioph-Cl.smi

			Then cat into one file and prepare synthons from the BBs found.

			python /nfs/soft2/SynthI/SynthI_BBsBulkClassificationAndSynthonization.py -i bb_analogs.smi

			Leave only SMILES and names

			awk '{print $1 " " $NF}' bb_analogs.smi_Synthmode.smi > bb_analogs_synth.smi


			===== A. Enumeration based on all found BBs =====
			Directory under "-oD" will contain eitherFinalOut_allEnumeratedCompounds_DuplicatesCanBePresent.smi or AnalogsForMol1.smi file with list of SMILES for generated compds

			Using all available reactions:

			mkdr ENUMERATED
			python /nfs/soft2/SynthI/SynthI_BulkFragmentationEnumerationAndAnaloguesDesign.py -i bb_analogs_synth.smi --nCores 10 -oD ENUMERATED --MaxNumberOfStages 5 --enumerationMode --MWupperTh 460 --MWlowerTh 200
			Morgan2 Tc of obtained compds to the parent.
			[[Image:Tanimoto.png\|300px]]

			Using the same reactions that were used for initial fragmentation:

			mkdir ENUMERATED-R3-R5
			python /nfs/soft2/SynthI/SynthI_BulkFragmentationEnumerationAndAnaloguesDesign.py -i bb_analogs_synth.smi --nCores 10 -oD ENUMERATED-R3-R5/ --MaxNumberOfStages 5 --enumerationMode --MWupperTh 460 --MWlowerTh 200 --fragmentationMode include_only --reactionsToWorkWith "R3, R5"
			Morgan2 Tc of obtained compds to the parent.
			[[Image:Tanimoto-synthi-enum-r3-r5.png\|300px]]


			===== B. Analogs from a synthon library =====

			python /nfs/soft2/SynthI/SynthI_BulkFragmentationEnumerationAndAnaloguesDesign.py -i ligand.smi --SynthLibrary bb_analogs_synth.smi --simTh 0.5 --analoguesLibGen --nCores 10 -oD ANALOGS --MaxNumberOfStages 5 --desiredNumberOfNewMols 1000 --enumerationMode --MWupperTh 460 --MWlowerTh 200
			Morgan2 Tc of obtained compds to the parent.
			[[Image:Tanimoto-synthi-analogs.png\|300px]]

			Analog generation doesn't seem to use similarity threshold value. Usage of large synthon library may be useful for analog generation, but speed needs to be tested.

	[[Category: Software]]		[[Category: Software]]

Khtang at 01:33, 11 March 2022

2022-03-11T01:33:44Z

← Older revision		Revision as of 01:33, 11 March 2022
Line 2:		Line 2:

	== Setup ==		== Setup ==
	Anaconda3 is already install on /nfs/soft2/. To activate:		Anaconda3 and a copy of SynthI are already install on /nfs/soft2/. To activate:
	$ source /nfs/soft2/anaconda3/bin/activate		$ source /nfs/soft2/anaconda3/bin/activate SynthI-env
	=== Install Anaconda3 on your computer ===		=== Install Anaconda3 on your computer ===
	$ wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh		$ wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh

Khtang at 01:32, 11 March 2022

2022-03-11T01:32:45Z

← Older revision		Revision as of 01:32, 11 March 2022
Line 44:		Line 44:

	== Usage ==		== Usage ==
	The scripts are to be use as a Python library inside of customized script as in you can package it up using setuptools and install the package into your virtual environment or copy into your script as a module		The scripts are to be use as a Python library inside of customized script as in you can package it up using setuptools and install the package into your virtual environment or copy into the directory where your script is and import it as a module.

			Please note: Prior to BBs synthonization the SMILES should be preprocessed and conterions and solvents should be removed. SynthI-BBs consider every molecule while processing mixture SMILES and for each of them synthons will be generated if possible, therefore take care of them before synthonization.

	Detailed guide is [https://github.com/Laboratoire-de-Chemoinformatique/SynthI here]		Detailed guide is [https://github.com/Laboratoire-de-Chemoinformatique/SynthI here]

	[[Category: Software]]		[[Category: Software]]

Khtang at 01:11, 11 March 2022

2022-03-11T01:11:45Z

← Older revision		Revision as of 01:11, 11 March 2022
Line 43:		Line 43:
	(synthI_env) $		(synthI_env) $

	=== Usage ===		== Usage ==
	The scripts are to be use as a Python library inside of customized script as in you can package it up using setuptools and install the package into your virtual environment or copy into your script as a module		The scripts are to be use as a Python library inside of customized script as in you can package it up using setuptools and install the package into your virtual environment or copy into your script as a module

Khtang at 01:10, 11 March 2022

2022-03-11T01:10:54Z

← Older revision		Revision as of 01:10, 11 March 2022
Line 1:		Line 1:
	SynthI is a open-source tool for synthons-based library design written by [http://infochim.u-strasbg.fr/ Laboratoire-de-Chemoinformatique] at University of Strasbourg		SynthI is a open-source tool for synthons-based library design written by [http://infochim.u-strasbg.fr/ Laboratoire-de-Chemoinformatique] from University of Strasbourg

	== Setup ==		== Setup ==
Line 42:		Line 42:
	(base) $ conda activate /home/user/anaconda3/envs/synthI_env		(base) $ conda activate /home/user/anaconda3/envs/synthI_env
	(synthI_env) $		(synthI_env) $

			=== Usage ===
			The scripts are to be use as a Python library inside of customized script as in you can package it up using setuptools and install the package into your virtual environment or copy into your script as a module

			Detailed guide is [https://github.com/Laboratoire-de-Chemoinformatique/SynthI here]

			[[Category: Software]]

Khtang: Created page with "SynthI is a open-source tool for synthons-based library design written by [http://infochim.u-strasbg.fr/ Laboratoire-de-Chemoinformatique] at University of Strasbourg == Setu..."

2022-03-11T01:01:46Z

Created page with "SynthI is a open-source tool for synthons-based library design written by [http://infochim.u-strasbg.fr/ Laboratoire-de-Chemoinformatique] at University of Strasbourg == Setu..."

New page

SynthI is a open-source tool for synthons-based library design written by [http://infochim.u-strasbg.fr/ Laboratoire-de-Chemoinformatique] at University of Strasbourg

== Setup ==
Anaconda3 is already install on /nfs/soft2/. To activate:
$ source /nfs/soft2/anaconda3/bin/activate
=== Install Anaconda3 on your computer ===
$ wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh

$ sh Anaconda3-2021.11-Linux-x86_64.sh
Welcome to Anaconda3 5.3.1
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
.
.
.
Anaconda3 will now be installed into this location:
/home/khtang/anaconda3
[/home/khtang/anaconda3] >>> /nfs/home/khtang/anaconda3
PREFIX=/mnt/nfs/home/khtang/anaconda3
.
.
.
Do you wish the installer to initialize Anaconda3
in your /nfs/home/khtang/.bashrc ? [yes|no]
[no] >>> no
Do you wish to proceed with the installation of Microsoft VSCode? [yes|no]
>>> no

$ source /<path to anaconda3>/bin/activate

=== Download and setup SynthI ===
==== Install dependencies ====
If you are on the cluster, SynthI is installed on /nfs/soft2/SynthI
$ source /nfs/soft2/anaconda3/bin/activate SynthI-env
$ conda deactivate //to exit environment
Install stand-alone
$ git clone https://github.com/Laboratoire-de-Chemoinformatique/SynthI.git
$ cd SynthI
$ source /<path to anaconda3>/bin/activate
(base) $ conda env create -f SynthI_environment.yml -p /home/user/anaconda3/envs/synthI_env
(base) $ conda activate /home/user/anaconda3/envs/synthI_env
(synthI_env) $