Whole Library TC to Knowns Calculations: Difference between revisions
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| |------ smi.sdi | | |------ smi.sdi | ||
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| |------ db_smi | | |------ db_smi-------combined.smi | ||
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|------ combine_tc_matrix.py | |------ combine_tc_matrix.py | ||
1) Make those directories above. | |||
mkdir TC_calculations | |||
cd TC_calculations | |||
mkdir working | |||
mkdir scripts | |||
2) Query SMILES from ZINC or prepare by yourself. | |||
2.1) Query SMILES from ZINC | |||
See http://wiki.docking.org/index.php/Large-scale_SMILES_Requesting_and_Fingerprints_Converting | |||
2.2) Prepare by yourself | |||
2.2.1) Combine all SMILES of the leadlike molecules at your local directory | |||
2.2.2) Run a script to match ZINC IDs with SMILES | |||
2.3) Copy the combined SMILES file to db_smi directory | |||
3) Copy scripts from my path. | |||
cd scripts | |||
cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/check_outputs.csh . | |||
cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/combine_tc_matrix.py . | |||
cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/make_chunks_for_file_new.py . | |||
cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/submit.csh . | |||
cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/setup_tc_calculations.py . | |||
cd ../ | |||
4) Chunk combined SMILES file. | |||
cd working | |||
mkdir db_smi | |||
cd db_smi | |||
python ../../scripts/make_chunks_for_file_new.py combined.smi combined.smi 100 . | |||
5) Make sdi file. | |||
cd ../ | |||
ls `pwd`/db_smi/combined_*.smi > smi.sdi | |||
6) Set up your TC calculations | |||
python ../scripts/setup_tc_calculations.py . TC_cal_ smi.sdi 101 count | |||
7) Submit jobs | |||
csh ../scripts/submit.csh name.uint16.fp name.smi name.uint16.count | |||
name.uint16.fp, name.smi, name.uint16.count are a set of molecules from the bioactive molecules ( the like-molecules you want to look for in the sea of compounds). | |||
8) Check unfinished jobs | |||
cd db_smi | |||
csh ../../scripts/check_outputs.csh 101 combined | |||
9) Combine all the TC results | |||
python ../../scripts/combine_tc_matrix.py 101 combined |
Latest revision as of 20:25, 9 June 2018
Written by Jiankun Lyu, 20180524
The hierarchy of the directories:
TC_calculations---------- working | | | |------ smi.sdi | | | |------ db_smi-------combined.smi | | | ------- scripts ------ submit.csh | |------ check_outputs.csh | |------ setup_tc_calculations.py | |------ make_chunks_for_file_new.py | |------ combine_tc_matrix.py
1) Make those directories above.
mkdir TC_calculations cd TC_calculations mkdir working mkdir scripts
2) Query SMILES from ZINC or prepare by yourself.
2.1) Query SMILES from ZINC
See http://wiki.docking.org/index.php/Large-scale_SMILES_Requesting_and_Fingerprints_Converting
2.2) Prepare by yourself
2.2.1) Combine all SMILES of the leadlike molecules at your local directory
2.2.2) Run a script to match ZINC IDs with SMILES
2.3) Copy the combined SMILES file to db_smi directory
3) Copy scripts from my path.
cd scripts cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/check_outputs.csh . cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/combine_tc_matrix.py . cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/make_chunks_for_file_new.py . cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/submit.csh . cp /mnt/nfs/home/jklyu/zzz.script/TC_to_knowns/setup_tc_calculations.py . cd ../
4) Chunk combined SMILES file.
cd working mkdir db_smi cd db_smi python ../../scripts/make_chunks_for_file_new.py combined.smi combined.smi 100 .
5) Make sdi file.
cd ../ ls `pwd`/db_smi/combined_*.smi > smi.sdi
6) Set up your TC calculations
python ../scripts/setup_tc_calculations.py . TC_cal_ smi.sdi 101 count
7) Submit jobs
csh ../scripts/submit.csh name.uint16.fp name.smi name.uint16.count
name.uint16.fp, name.smi, name.uint16.count are a set of molecules from the bioactive molecules ( the like-molecules you want to look for in the sea of compounds).
8) Check unfinished jobs
cd db_smi csh ../../scripts/check_outputs.csh 101 combined
9) Combine all the TC results
python ../../scripts/combine_tc_matrix.py 101 combined