Large-scale TC Calculations - Revision history

Jklyu at 05:44, 19 September 2017

2017-09-19T05:44:49Z

← Older revision		Revision as of 05:44, 19 September 2017
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	nohup /mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/cal_Tc_matrix_uint16/cal_Tc_matrix_uint16 /path/to/the/cluster_head_uint16.fp /path/to/the/cluster_head.smi /path/to/the/cluster_head_uint16.count /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic_uint16.fp /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic.smi /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic_uint16.count > log &		nohup /mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/cal_Tc_matrix_uint16/cal_Tc_matrix_uint16 /path/to/the/cluster_head_uint16.fp /path/to/the/cluster_head.smi /path/to/the/cluster_head_uint16.count /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic_uint16.fp /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic.smi /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic_uint16.count > log &

	2) Submit to the queue(~~old script should work~~)		2) Submit to the queue(calculate Tc to Agent)

	2.1) split the smiles and fingerprints files		2.1) split the smiles and fingerprints files

	2.2) ~~create the sdi file~~		python ~jklyu/work/cluster/script/make_chunks_for_file_new.py cluster_head.smi cluster_head.smi 500 .
			python ~jklyu/work/cluster/script/make_chunks_for_file_new.py cluster_head.fp cluster_head.fp 500 .

			2.2) copy precalculated fingerprints to each machine

			mkdir cp_fp_to_nodes
			cd cp_fp_to_nodes/
			csh ~jklyu/work/cluster/script/cp_files_2_scratch.csh
			cd ../

	2.3) submit jobs to the queue		2.3) submit jobs to the queue

			csh ~jklyu/work/cluster/script/run.Tc.matrix.new.csh ~jklyu/work/cluster/script

	2.4) collect data		2.4) collect data

			python ~jklyu/work/cluster/script/combine_and_find_closest_neighbor.py 502 cluster_head_

Jklyu at 23:27, 18 September 2017

2017-09-18T23:27:45Z

@@ Line 2: / Line 2: @@
 Please run [[Large-scale SMILES Requesting and Fingerprints Converting]] first to get the SMILES and fingerprints files, then run the TC calculations below.
   /mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/cal_Tc_matrix_uint16/cal_Tc_matrix_uint16 (1)first_fingerprint_file (2)first_smiles_file (3)first_count_file (4)second_fingerprint_file (5)second_smiles_file (6)second_count_file
@@ Line 8: / Line 10: @@
   nohup /mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/cal_Tc_matrix_uint16/cal_Tc_matrix_uint16 /path/to/the/cluster_head_uint16.fp /path/to/the/cluster_head.smi /path/to/the/cluster_head_uint16.count /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic_uint16.fp /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic.smi /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic_uint16.count > log &

Jklyu at 23:20, 18 September 2017

2017-09-18T23:20:25Z

← Older revision		Revision as of 23:20, 18 September 2017
Line 2:		Line 2:

	Please run [[Large-scale SMILES Requesting and Fingerprints Converting]] first to get the SMILES and fingerprints files, then run the TC calculations below.		Please run [[Large-scale SMILES Requesting and Fingerprints Converting]] first to get the SMILES and fingerprints files, then run the TC calculations below.

			/mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/cal_Tc_matrix_uint16/cal_Tc_matrix_uint16 (1)first_fingerprint_file (2)first_smiles_file (3)first_count_file (4)second_fingerprint_file (5)second_smiles_file (6)second_count_file

			Here is one example for calculating the best TC value to all aminergic knowns for each top docking cluster head:

			nohup /mnt/nfs/home/jklyu/zzz.github/ChemInfTools/utils/cal_Tc_matrix_uint16/cal_Tc_matrix_uint16 /path/to/the/cluster_head_uint16.fp /path/to/the/cluster_head.smi /path/to/the/cluster_head_uint16.count /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic_uint16.fp /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic.smi /mnt/nfs/reshwork/jklyu/fp_db/all_aminergic/all_aminergic_uint16.count > log &

Jklyu: Created page with "Written by Jiankun Lyu, 20170918 Please run Large-scale SMILES Requesting and Fingerprints Converting first to get the SMILES and fingerprints files, then run the TC calc..."

2017-09-18T23:09:44Z

Created page with "Written by Jiankun Lyu, 20170918 Please run Large-scale SMILES Requesting and Fingerprints Converting first to get the SMILES and fingerprints files, then run the TC calc..."

New page

Written by Jiankun Lyu, 20170918

Please run [[Large-scale SMILES Requesting and Fingerprints Converting]] first to get the SMILES and fingerprints files, then run the TC calculations below.