Andrii's notes on SynthI - Revision history

Iamkaant: added Synthons generated from CSSB00020671770

2022-03-28T19:40:26Z

added Synthons generated from CSSB00020671770

← Older revision		Revision as of 19:40, 28 March 2022
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	# Checking multistage reactions		# Checking multistage reactions
	# Merging of temp files once in a while -- DONE		# Merging of temp files once in a while -- DONE

			=Synthons generated from CSSB00020671770=
			[[Image:CSSB00020671770.png\|600px]]

Iamkaant at 19:33, 28 March 2022

2022-03-28T19:33:32Z

← Older revision		Revision as of 19:33, 28 March 2022
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	# Test sets for each reaction		# Test sets for each reaction
	# Checking multistage reactions		# Checking multistage reactions
	# Merging of temp files once in a while		# Merging of temp files once in a while -- DONE

Iamkaant at 05:00, 24 March 2022

2022-03-24T05:00:53Z

← Older revision		Revision as of 05:00, 24 March 2022
Line 80:		Line 80:
	# Test sets for each reaction		# Test sets for each reaction
	# Checking multistage reactions		# Checking multistage reactions
			# Merging of temp files once in a while

Iamkaant at 02:50, 22 March 2022

2022-03-22T02:50:16Z

← Older revision		Revision as of 02:50, 22 March 2022
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	# Output identifiers of enumerated compds: RXN_synt1_synt2 -- DONE		# Output identifiers of enumerated compds: RXN_synt1_synt2 -- DONE
	# Processing the end of synthon file		# Processing the end of synthon file
			# Test sets for each reaction
			# Checking multistage reactions

Iamkaant: Manual for enumeration using new code.

2022-03-22T02:48:46Z

Manual for enumeration using new code.

@@ Line 54: / Line 54: @@
 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.
 =TODO=
-# Work with 2 synthon files, instead of one.
+# Work with 2 synthon files, instead of one. -- DONE
-# Output identifiers of enumerated compds: RXN_synt1_synt2
+# Output identifiers of enumerated compds: RXN_synt1_synt2 -- DONE
 # Processing the end of synthon file

Iamkaant at 23:53, 16 March 2022

2022-03-16T23:53:32Z

← Older revision		Revision as of 23:53, 16 March 2022
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	Parent page: [[SynthI]]		Parent page: [[SynthI]]

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

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

			=TODO=

			# Work with 2 synthon files, instead of one.
			# Output identifiers of enumerated compds: RXN_synt1_synt2
			# Processing the end of synthon file

Iamkaant at 21:56, 15 March 2022

2022-03-15T21:56:28Z

← Older revision		Revision as of 21:56, 15 March 2022
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	=== A. Enumeration based on all found BBs ===		=== 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		Directory under "-oD" will contain eitherFinalOut_allEnumeratedCompounds_DuplicatesCanBePresent.smi or AnalogsForMol1.smi file with list of SMILES for generated compds.
	Different from analog generation, the output of enumeration does not contain the reactions and synthons used for compod. generation.
			Different from analog generation, the output of enumeration '''does not''' contain the reactions and synthons used for compod. generation.

	Using all available reactions:		Using all available reactions:

Iamkaant at 21:53, 15 March 2022

2022-03-15T21:53:18Z

← Older revision		Revision as of 21:53, 15 March 2022
Line 29:		Line 29:
	=== A. Enumeration based on all found BBs ===		=== 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		Directory under "-oD" will contain eitherFinalOut_allEnumeratedCompounds_DuplicatesCanBePresent.smi or AnalogsForMol1.smi file with list of SMILES for generated compds
			Different from analog generation, the output of enumeration does not contain the reactions and synthons used for compod. generation.

	Using all available reactions:		Using all available reactions:

Iamkaant at 03:37, 15 March 2022

2022-03-15T03:37:20Z

← Older revision		Revision as of 03:37, 15 March 2022
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			Parent page: [[SynthI]]

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

Iamkaant: Created page with "== Preparing analogs with SynthI == Working with https://cartblanche22.docking.org/searchZinc/ZINCoT000006Aq87, bash needed. Prepare .smi file with the list of SMILES (and n..."

2022-03-15T03:36:04Z

Created page with "== Preparing analogs with SynthI == Working with https://cartblanche22.docking.org/searchZinc/ZINCoT000006Aq87, bash needed. Prepare .smi file with the list of SMILES (and n..."

New page

== 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.