mariap3636 / createrms

Creates Reaction Molecular Signatures (RMS) from MetaCyc reactions data and MOLfiles

CREATION OF REACTION MOLECULAR SIGNATURES FROM METACYC REACTIONS

=================================================================== Last modification : 20/07/2015

Requirements:

• MetaCyc flat files (to download)
  • reactions.dat
  • MOL files in the "MetaCyc-MOLfiles" directory
• ChemAxon's molconvert
• molsig (http://molsig.sourceforge.net/)
• a MySQL database

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Step 1: Protonation and aromatization of MOL files

Input: all MOL files of the MetaCyc-MOLfiles directory Outputs: converted MOL files are in MolFiles_FULL directory (for protonation) and in MolFiles_FULL_aroma directory (for protonation and aromatization )

$ python add_hydrogens_aromatization.py molconvert_PATH

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Step 2: Compute Molecular Signatures on all molecules

Inputs:

• arg1: directory where are located the MOLfiles for the computation of molecular signatures
• arg2: scan / sscan / fsscan molsig parameter
• arg3: o/n = with/without aromatization

Outputs: mol-sig-results/sscan[0-6] for signature heights between 0 and 3

$ python molsigLauncher.py MolFiles_FULL_aroma sscan n

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Step 3: Compute the Reaction Molecular Signatures

Inputs:

• arg1: scan / sscan / fsscan molsig parameter
• arg2: o/n = with/without aromatization

Outputs: File with computed ReactionMolecular Signatures for all reactions for heights between 0 and 3.

$ python rms_compute.py sscan n > rms_sscan.txt

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Step 4: Insertion of RMS in database

DB tables creation

    
 -- Reaction - RMS correpondency table
DROP TABLE IF EXISTS Reaction_RMS_CPD;
CREATE TABLE Reaction_RMS_CPD(
height INT(3),
MR_id VARCHAR(255),
RMS TEXT(80000)
);
ALTER TABLE Reaction_RMS_CPD ADD INDEX(MR_id);


    
-- RMS - MD5 encoded RMS (RMSh)
DROP TABLE IF EXISTS RMS_RMSh_CPD;
CREATE TABLE RMS_RMSh_CPD(
RMS TEXT(80000),
RMSh VARCHAR(255)
);
ALTER TABLE RMS_RMSh_CPD ADD INDEX (RMSh);
    

-- Reaction - RMSh correspondency table
DROP TABLE IF EXISTS Reaction_RMSh_CPD;
CREATE TABLE Reaction_RMSh_CPD(
MR_id VARCHAR(255),
RMSh VARCHAR(255),
height INT(3),
reaction_type enum('balanced','unbalanced','no-pwy') DEFAULT 'unbalanced'
);
ALTER IGNORE TABLE Reaction_RMSh_CPD ADD UNIQUE INDEX(MR_id, RMSh, height);
    

Insert file in database

• insert rms_sscan.txt in Reaction_RMS_CPD table:

LOAD DATA LOCAL INFILE 'rms_sscan.txt' INTO TABLE Reaction_RMS_CPD FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n' ;

Transform text RMS in MD5 encoded RMSh

INSERT IGNORE INTO RMS_RMSh_CPD
SELECT RMS, MD5(RMS)
FROM Reaction_RMS_CPD
GROUP BY RMS;
     
INSERT IGNORE INTO Reaction_RMSf_CPD(MR_id, RMSh,height)
SELECT MR_id, RMSh, height
FROM Reaction_RMS_CPD 
    INNER JOIN RMS_RMSh_CPD USING(RMS);
        

    
-- AS at height 0 balanced reactions have their RMS = '0.0', it's a way to detect unbalanced reactions
UPDATE Reaction_RMSh_CPD AS RRF, Reaction_RMS_CPD AS RR
SET RRF.reaction_type = 'balanced'
WHERE RRF.MR_id = RR.MR_id AND RR.height=0 AND RR.RMS = '0.0'; 
    
     
    
DELETE FROM Reaction_RMSf_CPD WHERE RMSh IS NULL;

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###Step 5: Creation of intelligible RMS identifiers: RMSid

Extract from the database the MR_RMSf_chain.txt file using this SQL request:

mysql -ABN DATBASENAME -e " SELECT MR_id, GROUP_CONCAT(RMSf ORDER BY diameter SEPARATOR '$')
FROM Reaction_RMSf_CPD WHERE reaction_type = 'balanced'
GROUP BY MR_id ORDER BY MR_id DESC ;" > MR_RMSf_chain.txt 

Launch of the RMSid creator $ python rms_id_creator.py MR_RMSf_chain.txt > rmsf_d_rmsid_cpd.txt

Integration of RMSids in the database

DROP TABLE IF EXISTS RMSh_RMSid_CPD;
CREATE TABLE RMSh_RMSid_CPD(
 RMSh VARCHAR(255),
 height INT(11),
 RMSid VARCHAR(255)
);
ALTER TABLE RMSh_RMSid_CPD ADD UNIQUE INDEX (RMSh,RMSid);

• insert rmsf_d_rmsid_cpd.txt in RMSf_RMSid_CPD table:

LOAD DATA LOCAL INFILE 'rmsf_d_rmsid_cpd.txt' INTO TABLE RMSf_RMSid_CPD FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n' ;

DROP TABLE IF EXISTS Reaction_RMSid_CPD;
CREATE TABLE Reaction_RMSid_CPD(
 MR_id VARCHAR(255),
 RMSid VARCHAR(255),
 height INT(3)
);
INSERT INTO Reaction_RMSid_CPD
SELECT t1.MR_id, t2.RMSid,t2.height
FROM Reaction_RMSh_CPD AS t1
  INNER JOIN RMSh_RMSid_CPD AS t2 USING (RMSh,height);

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