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:https://lilab-ecust.cn/
tar zxvf MacFrag.tar.gz
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
MacFrag.py is the source codes. Users can define their own fragmentation rules or make other modifications.
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