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README.txt
cansmirk.py
create_mmp_db.py
indexing.py
mol_transform.py
rfrag.py
search_mmp_db.py
test_list.py
test_rfrag.py

README.txt

This directory contains the scripts used to generate matched molecular pairs (MMPs) from an input list of SMILES. 
The fragment indexing algorithm used in the scripts is described in the following publications:

Hussain, J., & Rea, C. (2010). "Computationally efficient algorithm to identify matched molecular pairs (MMPs) 
in large data sets." Journal of chemical information and modeling, 50(3), 339-348.
https://doi.org/10.1021/ci900450m
	
Wagener, M., & Lommerse, J. P. (2006). "The quest for bioisosteric replacements." 
Journal of chemical information and modeling, 46(2), 677-685.

The scripts requires RDKit (www.rdkit.org) be installed and properly configured.

Help is available for all the scripts using the -h option

To find all the MMPs in your set 
--------------------------------

The program to generate the MMPs from a set is divided into two parts; fragmentation and indexing. 

Before running the programs, make sure your input set of SMILES:
    - does not contain mixtures (salts etc.) 
    - does not contain "*" atoms
    - has been canonicalised using RDKit.

If your smiles set doesn't satisfy the conditions above the programs are likely to fail or in the case of 
canonicalisation result in not identifying MMPs involving H atom substitution.

1) Fragmentation command:

python rfrag.py <SMILES_FILE >FRAGMENT_OUTPUT

Example command: 
python rfrag.py <data/sample.smi >data/sample_fragmented.txt

Format of SMILES_FILE is: SMILES ID <space or comma separated>
See data/sample.smi for an example input file

Format of output: WHOLE_MOL_SMILES,ID,SMILES_OF_CORE,SMILES_OF_CONTEXT
See data/sample_fragmented.txt for an example output file 

2) Index command:

python indexing.py <FRAGMENT_OUTPUT >MMP_OUTPUT.CSV

Format of output:
SMILES_OF_LEFT_MMP,SMILES_OF_RIGHT_MMP,ID_OF_LEFT_MMP,ID_OF_RIGHT_MMP,SMIRKS_OF_TRANSFORMATION,SMILES_OF_CONTEXT 

This program has several options (see help from program below):

Usage: indexing.py [options]

Program to generate MMPs

Options:
  -h, --help            show this help message and exit
  -s, --symmetric       Output symmetrically equivalent MMPs, i.e output both
                        cmpd1,cmpd2, SMIRKS:A>>B and cmpd2,cmpd1, SMIRKS:B>>A
  -m MAXSIZE, --maxsize=MAXSIZE
                        Maximum size of change (in heavy atoms) allowed in
                        matched molecular pairs identified. DEFAULT=10.
                        Note: This option overrides the ratio option if both
                        are specified.
  -r RATIO, --ratio=RATIO
                        Maximum ratio of change allowed in matched molecular
                        pairs identified. The ratio is: size of change /
                        size of cmpd (in terms of heavy atoms). DEFAULT=0.3.
                        Note: If this option is used with the maxsize option,
                        the maxsize option will be used.

Example commands (with sample outputs):

Default settings:
python indexing.py <data/sample_fragmented.txt >data/sample_mmps_default.csv

Output symmetrically equivalent MMPs (ie forward and reverse transforms):
python indexing.py -s <data/sample_fragmented.txt >data/sample_mmps_sym.csv

Output MMPs where maximum size of change is 3 heavy atoms:
python indexing.py -m 3 <data/sample_fragmented.txt >data/sample_mmps_maxheavy.csv

Output MMPs where no more that 10% of the compound has changed:
python indexing.py -r 0.1 <data/sample_fragmented.txt >data/sample_mmps_maxratio.csv

Output symmetrically equivalent MMPs where maximum size of change is 3 heavy atoms:
python indexing.py -s -m 3 <data/sample_fragmented.txt >data/sample_mmps_sym_maxheavy.csv
 
SMIRKS canonicalisation
-----------------------

The MMP identification script uses a SMIRKS canonicalisation routine so the same change always has the same output SMIRKS.

To canonicalise a SMIRKS (generated elsewhere) so it is in the same format as MMP identification scripts use command:

python cansmirks.py <SMIRKS_FILE >SMIRKS_OUTPUT_FILE

Example command:
python cansmirk.py <data/sample_smirks.txt >data/sample_cansmirks.txt

Format of SMIRKS_FILE: SMIRKS ID <space or comma separated>
See data/sample_smirks.txt for an example input file
  
Format of output: CANONICALISED_SMIRKS ID
See data/sample_cansmirks.txt for an example output file

Note: The script will NOT deal with SMARTS characters, so the SMIRKS must contain valid SMILES for left and right hand sides.

The algorithm used to canonicalise SMIRKS is as follows:
1) Canonicalise the LHS.
2) For the LHS the 1st asterisk (attachment point) in the SMILES will have label 1, 2nd asterisk will have label 2 and so on
3) For the RHS, if you have a choice (ie. two attachment points are symmetrically equivalent), always put the label 
with lower numerical value on the earlier attachment point in the canonicalised SMILES

Applying SMIRKS to input compounds
----------------------------------

If you want to apply a SMIRKS/transform generated by the programs above to a compound, use the mol_transform.py program
with the following command:

python mol_transform.py -f TRANSFORM_FILE <SMILES_FILE >OUTPUT_FILE

If you want to use a set SMIRKS generated elsewhere, please make sure they have been canonicalised 
using the cansmirks.py command.

Example command:
mol_transform.py -f data/sample_smirks_mol_trans.txt <data/sample_smiles_mol_trans.smi >data/sample_mol_trans_output.txt

Format of SMILES_FILE: SMILES ID <space or comma separated>
See data/sample_smiles_mol_trans.smi for an example input file

Format of transform file: transform <one per line>
See data/sample_smirks_mol_trans.txt for an example transform file

Format of output: SMILES,ID,Transform,Modified_SMILES
See data/sample_mol_trans_output.txt for an example output file

Generating and searching an MMP database
----------------------------------------

The pair index used in the MMP identification algorithm can be written to a relational database. For the indexing.py
program described above, the index is written to memory and the program will identify all the MMPs in the dataset.
However, if you just want to ask a (series of) specific questions on a dataset, a relational database containing the
pair index (MMP db) can be used to do that.

The program create_mmp_db.py will build a MMP db for a given dataset and the program search_mmp_db.py can be used to
search the MMP db. The types of searching that can be performed on the db are as follows:

1) Find all MMPs of an input/query compound to the compounds in the db
2) Find all MMPs in the db where the LHS of the transform matches an input substructure
3) Find all MMPs that match the input transform/SMIRKS
4) Find all MMPs in the db where the LHS of the transform matches an input SMARTS 
5) Find all MMPs that match the LHS and RHS SMARTS of the input transform

The SMARTS searching utilises the DbCLI tools (http://code.google.com/p/rdkit/wiki/UsingTheDbCLI) that are part 
of the RDKit distribution.

Generating the db
-----------------

To generate an MMP db use the following command:

python create_mmp_db.py <FRAGMENT_OUTPUT

The program takes a FRAGMENT_OUTPUT generated by the rfrag.py command (described above) as input.
This program has several options (see help from program below):

Usage: create_mmp_db.py [options]

Program to create an MMP db.

Options:
  -h, --help            show this help message and exit
  -p PREFIX, --prefix=PREFIX
                        Prefix to use for the db file (and directory for
                        SMARTS index). DEFAULT=mmp
  -m MAXSIZE, --maxsize=MAXSIZE
                        Maximum size of change (in heavy atoms) that is stored
                        in the database. DEFAULT=15.
                        Note: Any MMPs that involve a change greater than this
                        value will not be stored in the database and hence not
                        be identified in the searching.
  -s, --smarts          Build SMARTS db so can perform SMARTS searching
                        against db. Note: Will make the build process somewhat
                        slower.
 
Example commands:

Default Settings:
python create_mmp_db.py <data/sample_fragmented.txt

A sqllite3 db file will be created called mmp.db

Generate a db with the prefix "my_MMP_db" and SMARTS searching capability:
python create_mmp_db.py -p my_MMP_db -s <data/sample_fragmented.txt

A sqllite3 db file will be created called my_MMP_db.db and a DbCLi files will be created in a directory called my_MMP_db_smarts

Generate a db with SMARTS searching capability and where only changes up to (and including) 10 heavy atoms are stored:
python create_mmp_db.py -m 10 -s <data/sample_fragmented.txt

Searching the db
----------------

To search the MMP db use the following command:

python search_mmp_db.py [options] <INPUT_FILE

This program has several options (see help from program below):

Options:
  -h, --help            show this help message and exit
  -t TYPE, --type=TYPE  Type of search required. Options are: mmp, subs,
                        trans, subs_smarts, trans_smarts
  -m MAXSIZE, --maxsize=MAXSIZE
                        Maximum size of change (in heavy atoms) allowed in
                        matched molecular pairs identified. DEFAULT=10.
                        Note: This option overrides the ratio option if both
                        are specified.
  -r RATIO, --ratio=RATIO
                        Only applicable with the mmp search type. Maximum
                        ratio of change allowed in matched molecular pairs
                        identified. The ratio is: size of change /
                        size of cmpd (in terms of heavy atoms) for the QUERY
                        MOLECULE. DEFAULT=0.3. Note: If this option is used
                        with the maxsize option, the maxsize option will be
                        used.
  -p PREFIX, --prefix=PREFIX
                        Prefix for the db file. DEFAULT=mmp


A description of the different search options are shown below:

a) mmp: Find all MMPs of a input/query compound to the compounds in the db

b) subs: Find all MMPs in the db where the LHS of the transform matches an input
substructure. Make sure the attached points are donated by an asterisk and the
input substructure has been canonicalised (eg. [*]c1ccccc1). Note: Up to 3 attachment
points are allowed.

c) trans: Find all MMPs that match the input transform/SMIRKS. Make sure the input
SMIRKS has been canonicalised using the cansmirk.py program.

d) subs_smarts: Find all MMPs in the db where the LHS of the transform matches an
input SMARTS. The attachment points in the SMARTS can be donated by [#0] (eg.
[#0]c1ccccc1).

e) trans_smarts: Find all MMPs that match the LHS and RHS SMARTS of the input transform.
The transform SMARTS are input as LHS_SMARTS>>RHS_SMARTS (eg.
[#0]c1ccccc1>>[#0]c1ccncc1). Note: This search can take a long time to run if a
very general SMARTS expression is used.

Example commands to search a db:
The db was created using command: python create_mmp_db.py -m 10 -s <data/sample_fragmented.txt

a) To carry out a mmp search:
python search_mmp_db.py -t mmp <data/sample_db_input_smi.txt >data/sample_db_search_smi_output.txt

Format of input file: SMILES ID <space or comma separated. The ID field is optional>
See data/sample_db_input_smi.txt for an example input file 

Format of output: SMILES_QUERY,SMILES_OF_MMP,QUERY_ID,RETRIEVED_ID,CHANGED_SMILES,CONTEXT_SMILES
See data/sample_db_search_smi_output.txt for an example output file

b) To carry out a LHS transform substructure search:
python search_mmp_db.py -t subs <data/sample_db_input_subs.txt >data/sample_db_search_subs_output.txt

Format of input file: Substructure_SMILES ID <space or comma separated. The ID field is optional>
See data/sample_db_input_subs.txt for an example input file 

Format of output: Input_substructure[,input_id],SMILES_MMP1,SMILES_MMP2,MMP1_ID,MMP2_ID,Transform,Context
See data/sample_db_search_subs_output.txt for an example output file

c) To carry out a transform search:
python search_mmp_db.py -t trans <data/sample_db_input_trans.txt >data/sample_db_search_trans_output.txt

Format of input file: SMIRKS ID <space or comma separated. The ID field is optional>
See data/sample_db_input_trans.txt for an example input file 

Format of output: [input_id,]SMILES_MMP1,SMILES_MMP2,MMP1_ID,MMP2_ID,Transform,Context
See data/sample_db_search_trans_output.txt for an example output file

d) To carry out a LHS transform substructure SMARTS search:
search_mmp_db.py -t subs_smarts <data/sample_db_input_subs_smarts.txt >data/sample_db_search_subs_smart_output.txt

Format of input file: SMARTS ID <space or comma separated. The ID field is optional>
See data/sample_db_input_subs_smarts.txt for an example input file 

Format of output: [input_id,]SMILES_MMP1,SMILES_MMP2,MMP1_ID,MMP2_ID,Transform,Context
See data/sample_db_search_subs_smart_output.txt for an example output file

e) To carry out a transform SMARTS search (with max size change of 6 heavy atoms):
search_mmp_db.py -t trans_smarts -m 6 <data/sample_db_input_trans_smarts.txt >data/sample_db_search_trans_smarts_output.txt

Format of input file: SMARTS ID <space or comma separated. The ID field is optional>
See data/sample_db_input_trans_smarts.txt for an example input file 

Format of output: input_transform_SMARTS,[input_id,]SMILES_MMP1,SMILES_MMP2,MMP1_ID,MMP2_ID,Transform,Context
See data/sample_db_search_trans_smarts_output.txt for an example output file
  
In the event you use the scripts for publication please reference the original publication:

Hussain, J., & Rea, C. (2010). "Computationally efficient algorithm to identify matched molecular pairs (MMPs) 
in large data sets." Journal of chemical information and modeling, 50(3), 339-348.
https://doi.org/10.1021/ci900450m
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