breadth-first-fragmentation

Usage

Installation

Install latest from the GitHub repository:

$ pip install git+https://github.com/panukorn17/breadth-first-fragmentation.git

or from conda

$ conda install ptaleo17::breadth-first-fragmentation

or from pypi

$ pip install breadth_first_fragmentation

Documentation

Documentation can be found hosted on this GitHub repository’s pages. Additionally you can find package manager specific guidelines on conda and pypi respectively.

How to use

from breadth_first_fragmentation.fragmentation import break_into_fragments_defragmo

smi = 'CCCN(CCc1cccc(-c2ccccc2)c1)C(=O)C1OC(C(=O)O)=CC(N)C1NC(C)=O'
break_into_fragments_defragmo(smi, min_length=0, verbose=1)

Head fragment:  *CCC
Recurse tail:  N(*)(CCc1cccc(-c2ccccc2)c1)C(=O)C1OC(C(=O)O)=CC(N)C1NC(C)=O
Tail:  *CCc1cccc(-c2ccccc2)c1
Recurse Head:  N(*)(*)C(=O)C1OC(C(=O)O)=CC(N)C1NC(C)=O
Head fragment:  *N(*)*
Recurse tail:  C(*)(=O)C1OC(C(=O)O)=CC(N)C1NC(C)=O
Head fragment:  *C(*)=O
Recurse tail:  C1(*)OC(C(=O)O)=CC(N)C1NC(C)=O
Head fragment:  *NC1C(N)C=C(C(=O)O)OC1*
Recurse tail:  C(*)(C)=O
Final Fragment:  C(*)(C)=O

('CCCN(CCc1cccc(-c2ccccc2)c1)C(=O)C1OC(C(=O)O)=CC(N)C1NC(C)=O',
 '*CCC *CCc1cccc(-c2ccccc2)c1 *N(*)* *C(*)=O *NC1C(N)C=C(C(=O)O)OC1* C(*)(C)=O',
 6)

Visual representation of the breadth-first-fragmentation algorithm:

smi = 'CCCN(CCc1cccc(-c2ccccc2)c1)C(=O)C1OC(C(=O)O)=CC(N)C1NC(C)=O'
break_into_fragments_defragmo(smi, min_length=3, verbose=1)

Head fragment:  *CCC
Recurse tail:  N(*)(CCc1cccc(-c2ccccc2)c1)C(=O)C1OC(C(=O)O)=CC(N)C1NC(C)=O
Tail:  *CCc1cccc(-c2ccccc2)c1
Recurse Head:  N(*)(*)C(=O)C1OC(C(=O)O)=CC(N)C1NC(C)=O
Head fragment:  *C(=O)N(*)*
Recurse tail:  C1(*)OC(C(=O)O)=CC(N)C1NC(C)=O
Head fragment:  *NC1C(N)C=C(C(=O)O)OC1*
Recurse tail:  C(*)(C)=O
Final Fragment:  C(*)(C)=O

('CCCN(CCc1cccc(-c2ccccc2)c1)C(=O)C1OC(C(=O)O)=CC(N)C1NC(C)=O',
 '*CCC *CCc1cccc(-c2ccccc2)c1 *C(=O)N(*)* *NC1C(N)C=C(C(=O)O)OC1* C(*)(C)=O',
 5)