yuyuan871111/macfrag

MacFrag

MacFrag is an efficient molecule fragmentation method, which is capable of segmenting large-scale molecules in a rapid speed and generating diverse fragments that are more compliant with the “Rule of Three”.

Reference: Yanyan Diao, Feng Hu, Zihao Shen, Honglin Li*. MacFrag: segmenting large-scale molecules to obtain diverse fragments with high qualities. Bioinformatics, 2023. 39(1) : btad012

MacFrag is developed and maintained by Prof. HongLin Li's Group, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China. http://lilab-ecust.cn/

1. Usage in Linux exectable file:

1) untar the file:

tar zxvf MacFrag.tar.gz

2) usage example:

cd MacFrag.dist

./MacFrag -i /data/MacFrag/examp.smi -o /data/MacFrag/ -maxBlocks 6 -maxSR 8 -asMols False -minFragAtoms 1
#'/data/MacFrag/' is the absolute path

Optional arguments:
  -h, --help            show this help message and exit
  -input_file INPUT_FILE, -i INPUT_FILE
                        .smi or .sdf file of molecules to be fragmented
  -output_path OUTPUT_PATH, -o OUTPUT_PATH
                        path of the output fragments file
  -maxBlocks MAXBLOCKS  the maximum number of building blocks that the
                        fragments contain
  -maxSR MAXSR          only cyclic bonds in smallest SSSR ring of size larger
                        than this value will be cleaved
  -asMols ASMOLS        True of False; if True, MacFrag will return fragments
                        as molecules and the fragments.sdf file will be
                        output; if False, MacFrag will return fragments.smi
                        file with fragments representd as SMILES strings
  -minFragAtoms MINFRAGATOMS
                        the minimum number of atoms that the fragments contain

2. Source codes

MacFrag.py is the source codes. Users can define their own fragmentation rules or make other modifications. 

3. other files

1) chembl28_mw500.smi,  Mols collected from ChEMBL database with molecular weight lower than 500
2) chembl28_mw500-1000.smi,  Mols collected from ChEMBL database with molecular weight ranging from 500 to 1000
After merging the two .smi files, 1 921 745 molecules with molecular weights lower than 1000 will be obtained 
that were used to evaluate the qualities of fragments obtained by the three programs. 
3) time_compare.py,  A python script for calculating the run time of different fragmentation programs