MacFrag

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# 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
```

MacFrag

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