ZINC processing pipeline - Revision history

Frodo at 05:28, 14 February 2014

2014-02-14T05:28:10Z

← Older revision		Revision as of 05:28, 14 February 2014
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			OBSOLETE.

	Each molecule in ZINC is processed via our ZINC processing pipeline. This process is embodied in a set of scripts that we continue to refine as we discover problems.		Each molecule in ZINC is processed via our ZINC processing pipeline. This process is embodied in a set of scripts that we continue to refine as we discover problems.

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	-- John Irwin. March 2009.		-- John Irwin. March 2009.

			[[Category:jji]]

Therese: 4 revisions

2012-10-08T20:33:21Z

4 revisions

← Older revision

Revision as of 20:33, 8 October 2012

Mysinger: Adjust current ring puckering settings

2012-03-15T20:52:04Z

Adjust current ring puckering settings

← Older revision		Revision as of 20:52, 15 March 2012
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	* 11. For each subset (ref, mid, hi, lo) use Corina to generate 3D model of the relevant protonated state.		* 11. For each subset (ref, mid, hi, lo) use Corina to generate 3D model of the relevant protonated state.
	corina -d rc,flapn,de=5,mc=2 -i t=mol2 -o t=mol2		corina -d rc,flapn,de=6,mc=4 -i t=mol2 -o t=mol2

	That's really it. There is more to do with loading ZINC, but to generate the models, that is what we think you need to know. Good luck!		That's really it. There is more to do with loading ZINC, but to generate the models, that is what we think you need to know. Good luck!

	-- John Irwin. March 2009.		-- John Irwin. March 2009.

Frodo at 17:28, 10 March 2009

2009-03-10T17:28:56Z

← Older revision		Revision as of 17:28, 10 March 2009
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	* 6. get rid of bogus stereochemistry at nitrogen:		* 6. get rid of bogus stereochemistry at nitrogen:
	sed -e 's/\[N@\]/N/g' -e 's/\[N@@\]/N/g' -e 's/\[N@H+\]/\[NH+\]/g' -e 's/\[N@@H+		sed -e 's/\[N@\]/N/g' -e 's/\[N@@\]/N/g' -e 's/\[N@H+\]/\[NH+\]/g' -e 's/\[N@@H+\]/\[NH+\]/g' -e 's/\[N@@+\]/\[N+\]/g' -e 's/\[N@+\]/\[N+\]/g' $1 > d.ism
	\]/\[NH+\]/g' -e 's/\[N@@+\]/\[N+\]/g' -e 's/\[N@+\]/\[N+\]/g' $1 > d.ism

	* 7. If the molecule is already in ZINC, eliminate it from the list.		* 7. If the molecule is already in ZINC, eliminate it from the list.
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	epik $EPIK -imae A.mae -omae B.mae -WAIT		epik $EPIK -imae A.mae -omae B.mae -WAIT

	* 11. For each subset (ref, mid, hi, lo) use Corina to generate 3D model of the relevant protonated state. corina -d rc,flapn,de=5,mc=2 -i t=mol2 -o t=mol2		* 11. For each subset (ref, mid, hi, lo) use Corina to generate 3D model of the relevant protonated state.
			corina -d rc,flapn,de=5,mc=2 -i t=mol2 -o t=mol2

	That's really it. There is more to do with loading ZINC, but to generate the models, that is what we think you need to know. Good luck!		That's really it. There is more to do with loading ZINC, but to generate the models, that is what we think you need to know. Good luck!

	-- John Irwin. March 2009.		-- John Irwin. March 2009.

Frodo at 17:27, 10 March 2009

2009-03-10T17:27:47Z

← Older revision		Revision as of 17:27, 10 March 2009
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	Frankly, we hope people will simply use ZINC rather than trying to reproduce it. Still, in the interests of clarity, transparency, truth, justice and the Canadian Way (TM), here is our current protocol.		Frankly, we hope people will simply use ZINC rather than trying to reproduce it. Still, in the interests of clarity, transparency, truth, justice and the Canadian Way (TM), here is our current protocol.

	1. If you have 2D SDF, convert it to isomeric SMILES.		* 1. If you have 2D SDF, convert it to isomeric SMILES.
	2. sed -e 's/N=S=N/nsn/g' 2.ism > 2-out.ism
	3. Use molinspiration mitools/mib to eliminate broken SMILES: /java -jar /raid1/soft/mitools/mib.jar -singlepart -onlyOrganic -normalizeCharges -f $1 -out smi		* 2. sed -e 's/N=S=N/nsn/g' 2.ism > 2-out.ism
	4. Use OEChem to remove molecules with problematic functional groups: filter.py rules.txt 4.ism 4-out.ism > filterlog.txt
			* 3. Use molinspiration mitools/mib to eliminate broken SMILES:
			java -jar /raid1/soft/mitools/mib.jar -singlepart -onlyOrganic -normalizeCharges -f $1 -out smi

			* 4. Use OEChem to remove molecules with problematic functional groups:
			filter.py rules.txt 4.ism 4-out.ism > filterlog.txt
	see http://blaster.docking.org/filtering/rules_default.txt for current rules.		see http://blaster.docking.org/filtering/rules_default.txt for current rules.
	5. select only 4 of stereochemical expansions from previous step. We just take the first 4, but you can imagine better ways of making the selection.
	6. get rid of bogus stereochemistry at nitrogen: sed -e 's/\[N@\]/N/g' -e 's/\[N@@\]/N/g' -e 's/\[N@H+\]/\[NH+\]/g' -e 's/\[N@@H+		* 5. select only 4 of stereochemical expansions from previous step. We just take the first 4, but you can imagine better ways of making the selection.

			* 6. get rid of bogus stereochemistry at nitrogen:
			sed -e 's/\[N@\]/N/g' -e 's/\[N@@\]/N/g' -e 's/\[N@H+\]/\[NH+\]/g' -e 's/\[N@@H+
	\]/\[NH+\]/g' -e 's/\[N@@+\]/\[N+\]/g' -e 's/\[N@+\]/\[N+\]/g' $1 > d.ism		\]/\[NH+\]/g' -e 's/\[N@@+\]/\[N+\]/g' -e 's/\[N@+\]/\[N+\]/g' $1 > d.ism
	~~7. If the molecule is already in ZINC, eliminate it from the list.~~
	~~8. Generate trial 3D structure with corina. corina -d neu,wh,rc,mc=1,canon -i t=smiles -o t=sdf < 1a.ism > 2.sdf~~
	~~9. generate reference pH state using Schrodinger's Epik. epik -ph 7.05 -ms 1 -imae A.mae -omae B.mae -WAIT~~
	~~10. generate mid, hi and lo pH subsets~~
	~~mid: setenv EPIK "-ph 7.0 -pht 1 -tp 0.20"~~
	~~hi: setenv EPIK "-ph 8.5 -pht 0.75 -tp 0.20"~~
	~~lo: setenv EPIK "-ph 5.5 -pht 0.75 -tp 0.20"~~
	~~epik $EPIK -imae A.mae -omae B.mae -WAIT~~

	For each subset (ref, mid, hi, lo) ~~process as follows:~~		* 7. If the molecule is already in ZINC, eliminate it from the list.
	a. Corina to generate 3D model of the relevant protonated state. corina -d rc,flapn,de=5,mc=2 -i t=mol2 -o t=mol2
			* 8. Generate trial 3D structure with corina.
			corina -d neu,wh,rc,mc=1,canon -i t=smiles -o t=sdf < 1a.ism > 2.sdf

			* 9. generate reference pH state using Schrodinger's Epik.
			epik -ph 7.05 -ms 1 -imae A.mae -omae B.mae -WAIT

			* 10. generate mid, hi and lo pH subsets
			mid: setenv EPIK "-ph 7.0 -pht 1 -tp 0.20"
			hi: setenv EPIK "-ph 8.5 -pht 0.75 -tp 0.20"
			lo: setenv EPIK "-ph 5.5 -pht 0.75 -tp 0.20"
			epik $EPIK -imae A.mae -omae B.mae -WAIT

			* 11. For each subset (ref, mid, hi, lo) use Corina to generate 3D model of the relevant protonated state. corina -d rc,flapn,de=5,mc=2 -i t=mol2 -o t=mol2

	That's really it.		That's really it. There is more to do with loading ZINC, but to generate the models, that is what we think you need to know. Good luck!
	There is more to do with loading ZINC, but to generate the models, that is what we think you need to know. Good luck!

	-- John Irwin. March 2009.		-- John Irwin. March 2009.

Frodo at 17:26, 10 March 2009

2009-03-10T17:26:05Z

New page

Each molecule in ZINC is processed via our ZINC processing pipeline. This process is embodied in a set of scripts that we continue to refine as we discover problems.

Frankly, we hope people will simply use ZINC rather than trying to reproduce it. Still, in the interests of clarity, transparency, truth, justice and the Canadian Way (TM), here is our current protocol.

1. If you have 2D SDF, convert it to isomeric SMILES.
2. sed -e 's/N=S=N/nsn/g' 2.ism > 2-out.ism
3. Use molinspiration mitools/mib to eliminate broken SMILES: /java -jar /raid1/soft/mitools/mib.jar -singlepart -onlyOrganic -normalizeCharges -f $1 -out smi
4. Use OEChem to remove molecules with problematic functional groups: filter.py rules.txt 4.ism 4-out.ism > filterlog.txt
see http://blaster.docking.org/filtering/rules_default.txt for current rules.
5. select only 4 of stereochemical expansions from previous step. We just take the first 4, but you can imagine better ways of making the selection.
6. get rid of bogus stereochemistry at nitrogen: sed -e 's/\[N@\]/N/g' -e 's/\[N@@\]/N/g' -e 's/\[N@H+\]/\[NH+\]/g' -e 's/\[N@@H+
\]/\[NH+\]/g' -e 's/\[N@@+\]/\[N+\]/g' -e 's/\[N@+\]/\[N+\]/g' $1 > d.ism
7. If the molecule is already in ZINC, eliminate it from the list.
8. Generate trial 3D structure with corina. corina -d neu,wh,rc,mc=1,canon -i t=smiles -o t=sdf < 1a.ism > 2.sdf
9. generate reference pH state using Schrodinger's Epik. epik -ph 7.05 -ms 1 -imae A.mae -omae B.mae -WAIT
10. generate mid, hi and lo pH subsets
mid: setenv EPIK "-ph 7.0 -pht 1 -tp 0.20"
hi: setenv EPIK "-ph 8.5 -pht 0.75 -tp 0.20"
lo: setenv EPIK "-ph 5.5 -pht 0.75 -tp 0.20"
epik $EPIK -imae A.mae -omae B.mae -WAIT

For each subset (ref, mid, hi, lo) process as follows:
a. Corina to generate 3D model of the relevant protonated state. corina -d rc,flapn,de=5,mc=2 -i t=mol2 -o t=mol2

That's really it.
There is more to do with loading ZINC, but to generate the models, that is what we think you need to know. Good luck!

-- John Irwin. March 2009.