Bemis-Murcko Scaffold Analysis
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Written by Jiankun Lyu, 20170918
Please run Large-scale SMILES Requesting and Fingerprints Converting first to get the SMILES files, then run the scaffold analysis below.
The hierarchy of the directories:
scaffold_analysis/----- working/ | | | |------ combined.smi(soft link) | | | |------ chunked_smiles_files/ | | | ------- scripts/ ------ submit.csh | |------ setup_BM_scaffold_analysis.py | |------ combine_scaffold_smi.py | |------ scaffold_analysis.py
1) make directories and copy scripts
mkdir scaffold_analysis cd scaffold_analysis mkdir working mkdir scripts cd working mkdir chunked_smiles_files ln -s /path/to/combined.smi cd ../scripts cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/BM_scaffold_analysis/submit.csh . cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/BM_scaffold_analysis/setup_BM_scaffold_analysis.py . cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/BM_scaffold_analysis/combine_scaffold_smi.py . cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/BM_scaffold_analysis/scaffold_analysis.py .
cd ../
2) Split the SMILES file
cd working/chunked_smiles_files split -d -a 2 -l 300000 ../combined.smi combined.smi_ cd ../
3) Create a zincid.sdi file
ls /full/path/to/chunked_smiles_files/combined.smi_* > all_smiles.sdi
4) Set up files and directories
python ../scripts/setup_BM_scaffold_analysis.py . scaffold_analysis_ all_smiles.sdi 60 count
5) Submit jobs of scaffold analysis
csh ../scripts/submit.csh
6) Collect data from directories
python ../scripts/combine_scaffold_smi.py
7) Analyze data
python ../scripts/scaffold_analysis.py combined.scaffold.energy.smi output_prefix