Bemis-Murcko Scaffold Analysis

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 .