Cassidy clustering - Revision history

Frodo at 07:22, 13 March 2014

2014-03-13T07:22:03Z

← Older revision		Revision as of 07:22, 13 March 2014
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	I'll verify the binary-base64 mappings are correct but I'd recommend checking yourself as well.		I'll verify the binary-base64 mappings are correct but I'd recommend checking yourself as well.

	[[Category:~~Internal~~]]		[[Category:Curator]]
	[[Category:Cheminformatics]]		[[Category:Cheminformatics]]
	[[Category:Tutorials]]		[[Category:Tutorials]]

Frodo at 16:11, 14 February 2014

2014-02-14T16:11:59Z

← Older revision		Revision as of 16:11, 14 February 2014
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	[[Category:Internal]]		[[Category:Internal]]
	[[Category:Cheminformatics]]		[[Category:Cheminformatics]]
	[[Category:~~Tutorial~~]]		[[Category:Tutorials]]

Frodo at 02:59, 14 February 2014

2014-02-14T02:59:48Z

← Older revision		Revision as of 02:59, 14 February 2014
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	These are notes to myself from Teague/Cassidy for the new cluster.		These are notes to myself from Teague/Cassidy for the new cluster.

	~~[[Category::Internal]]~~

	I've written some code to generate Daylight-like fingerprints (Base-64) from the output of Chemaxon's generatemd. This is a wonderfully named program called "binstr2base64.py" although it can do the opposite as well. It's currently in /raid1/teague/Code/cluster/binstr2base64.py. It seems to work fine however there's a small bug when reading from the standard input after a SIGKILL interrupt. This is not really a big deal as it's pretty hard to recreate under normal circumstances.		I've written some code to generate Daylight-like fingerprints (Base-64) from the output of Chemaxon's generatemd. This is a wonderfully named program called "binstr2base64.py" although it can do the opposite as well. It's currently in /raid1/teague/Code/cluster/binstr2base64.py. It seems to work fine however there's a small bug when reading from the standard input after a SIGKILL interrupt. This is not really a big deal as it's pretty hard to recreate under normal circumstances.
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	How To (using eMolecules as a demo with 1024-bit ECFP4-like fingerprints):		How To (using eMolecules as a demo with 1024-bit ECFP4-like fingerprints):
	cd /raid1/people/teague/Code/cluster/test		cd /raid1/people/teague/Code/cluster/test
	gzip -dc gzip -dc /raid9/db/zinc-may08/byvendor/emol/emol_p0.smi.gz > emol_p0.smi		gzip -dc gzip -dc /raid9/db/zinc-may08/byvendor/emol/emol_p0.smi.gz > emol_p0.smi
	/raid3/software/jchem/current/bin/generatemd c emol_p0.smi -k CF -f 1024 -2 \| /raid1/people/teague/Code/cluster/binstr2base64.py \| paste -d' ' emol_p0.smi - > emol_p0.smi.fp		/raid3/software/jchem/current/bin/generatemd c emol_p0.smi -k CF -f 1024 -2 \| /raid1/people/teague/Code/cluster/binstr2base64.py \| paste -d' ' emol_p0.smi - > emol_p0.smi.fp
	rm emol_p0.smi		rm emol_p0.smi

	This will be a BIG file (and I've already generated it) so if you want a smaller test simply to verify IO & decoding you can use test.smi, which is the first 10 or so compounds. You'll have to generate the fingerprints yourself however.		This will be a BIG file (and I've already generated it) so if you want a smaller test simply to verify IO & decoding you can use test.smi, which is the first 10 or so compounds. You'll have to generate the fingerprints yourself however.

	A note for Cassidy:		A note for Cassidy:
	If you experience python errors run: source /raid3/software/python/bin/python-env.csh (or python-env.sh if you're using BASH)		If you experience python errors run:
			source /raid3/software/python/bin/python-env.csh (or python-env.sh if you're using BASH)

	I'll verify the binary-base64 mappings are correct but I'd recommend checking yourself as well.		I'll verify the binary-base64 mappings are correct but I'd recommend checking yourself as well.

			[[Category:Internal]]
			[[Category:Cheminformatics]]
			[[Category:Tutorial]]

Frodo: Created page with "These are notes to myself from Teague/Cassidy for the new cluster. Category::Internal I've written some code to generate Daylight-like fingerprints (Base-64) from the ..."

2014-01-29T20:40:54Z

Created page with "These are notes to myself from Teague/Cassidy for the new cluster. [[Category::Internal]] I've written some code to generate Daylight-like fingerprints (Base-64) from the ..."

New page

These are notes to myself from Teague/Cassidy for the new cluster.

[[Category::Internal]]

I've written some code to generate Daylight-like fingerprints (Base-64) from the output of Chemaxon's generatemd. This is a wonderfully named program called "binstr2base64.py" although it can do the opposite as well. It's currently in /raid1/teague/Code/cluster/binstr2base64.py. It seems to work fine however there's a small bug when reading from the standard input after a SIGKILL interrupt. This is not really a big deal as it's pretty hard to recreate under normal circumstances.

I haven't verified that the BASE-64 encoding is compatible with the mappings in fast_tanimoto.c but the decode-encode methods are consistent. i.e. running generatemd's output though binstr2base64 twice will give the same fingerprint (sans delimiters)

How To (using eMolecules as a demo with 1024-bit ECFP4-like fingerprints):
cd /raid1/people/teague/Code/cluster/test
gzip -dc gzip -dc /raid9/db/zinc-may08/byvendor/emol/emol_p0.smi.gz > emol_p0.smi
/raid3/software/jchem/current/bin/generatemd c emol_p0.smi -k CF -f 1024 -2 | /raid1/people/teague/Code/cluster/binstr2base64.py | paste -d' ' emol_p0.smi - > emol_p0.smi.fp
rm emol_p0.smi

This will be a BIG file (and I've already generated it) so if you want a smaller test simply to verify IO & decoding you can use test.smi, which is the first 10 or so compounds. You'll have to generate the fingerprints yourself however.

A note for Cassidy:
If you experience python errors run: source /raid3/software/python/bin/python-env.csh (or python-env.sh if you're using BASH)

I'll verify the binary-base64 mappings are correct but I'd recommend checking yourself as well.