Large-scale SMILES Requesting and Fingerprints Converting - Revision history

Jklyu at 01:34, 19 September 2017

2017-09-19T01:34:21Z

← Older revision		Revision as of 01:34, 19 September 2017
Line 62:		Line 62:

	7) Collect data from the compressed files		7) Collect data from the compressed files
	~~cd db_zincid~~		python ../../scripts/combine_smi_and_fp.py 500 (prefix)
	python ../../scripts/combine_smi_and_fp.py

Jklyu at 00:13, 19 September 2017

2017-09-19T00:13:24Z

← Older revision		Revision as of 00:13, 19 September 2017
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	csh ../scripts/submit.csh		csh ../scripts/submit.csh

	6) Check if every job ~~finishes~~		6) Check if every job finishe
	csh ../scripts/check_outputs.csh (number_of_jobs) (prefix)		cd db_zincid
			csh ../../scripts/check_outputs.csh (number_of_jobs) (prefix)
	if you find any missing files, please edit dirlist in the working directory and resubmit them.		if you find any missing files, please edit dirlist in the working directory and resubmit them.

Jklyu at 00:08, 19 September 2017

2017-09-19T00:08:01Z

← Older revision		Revision as of 00:08, 19 September 2017
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	3) Create a zincid.sdi file		3) Create a zincid.sdi file
	ls /full/path/to/db_zincid/top(number).zincid_* > zincid.sdi		ls /full/path/to/db_zincid/top(number)_*.zincid > zincid.sdi

	4) Set up requesting files and directories		4) Set up requesting files and directories

Jklyu at 23:46, 18 September 2017

2017-09-18T23:46:22Z

← Older revision		Revision as of 23:46, 18 September 2017
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	cd ../		cd ../

	2) Get ZINC ID and energy columns from the extract_all.sort.uniq.txt file		2) Get ZINC ID and energy columns from the extract_all.sort.uniq.txt file and split the zincid file
	cd working/db_zincid		cd working/db_zincid
	head -(number) ../extract_all.sort.uniq.txt \| awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets		head -(number) ../extract_all.sort.uniq.txt \| awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets
Line 60:		Line 60:
	if you find any missing files, please edit dirlist in the working directory and resubmit them.		if you find any missing files, please edit dirlist in the working directory and resubmit them.

	6) Collect data from the compressed files		7) Collect data from the compressed files
	cd db_zincid		cd db_zincid
	python ../../scripts/combine_smi_and_fp.py		python ../../scripts/combine_smi_and_fp.py

Jklyu: Created page with "Written by Jiankun Lyu, 20170918 The hierarchy of the directories: smiles_requesting/----- working/ | | | |----..."

2017-09-18T23:05:18Z

Created page with "Written by Jiankun Lyu, 20170918 The hierarchy of the directories: smiles_requesting/----- working/ | | | |----..."

New page

Written by Jiankun Lyu, 20170918

The hierarchy of the directories:

smiles_requesting/----- working/
| |
| |------ extract_all.sort.uniq.txt file(soft link)
| |
| |------ db_zincid/
|
|
|
------- scripts/ ------ submit.csh
|
|------ make_chunks_for_file_new.py
|
|------ setup_converting_fps_files.py
|
|------ combine_smi_and_fp.py
|
|------ check_outputs.csh

This tutorial is for requesting a large number of SMILES for docking results from ZINC server. Usually, the number is larger than 5M ZINC IDs.

1) make directories and copy scripts

mkdir smiles_requesting
cd smiles_requesting
mkdir working
mkdir scripts
cd working
mkdir db_zincid
ln -s /path/to/extract_all.sort.uniq.txt
cd ../scripts
cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/submit.csh .
cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/setup_converting_fps_files.py .
cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/combine_smi_and_fp.py .
cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/check_outputs.csh .
cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/make_chunks_for_file_new.py .
cd ../

2) Get ZINC ID and energy columns from the extract_all.sort.uniq.txt file
cd working/db_zincid
head -(number) ../extract_all.sort.uniq.txt | awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets
python ../../scripts/make_chunks_for_file_new.py extract_all.top(number).sort.uniq.zincid.energy top(number).zincid 500 .
cd ../

3) Create a zincid.sdi file
ls /full/path/to/db_zincid/top(number).zincid_* > zincid.sdi

4) Set up requesting files and directories
python ../scripts/setup_converting_fps_files.py . converting_fps_ zincid.sdi 500 count

5) Submit requesting and converting jobs
csh ../scripts/submit.csh

6) Check if every job finishes
csh ../scripts/check_outputs.csh (number_of_jobs) (prefix)
if you find any missing files, please edit dirlist in the working directory and resubmit them.

6) Collect data from the compressed files
cd db_zincid
python ../../scripts/combine_smi_and_fp.py