add notice for the atom map id in the rxn.

[autodataming]

The map ids in the rxn should be consecutive!

Issue #, if available: #33

Description of changes:

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[mufeili]

Can we give some examples about how to relabel atom mapping numbers using consecutive integers?

[autodataming]

For example, the raw rxn smiles is "[H]C([H])([H])Oc1ccc(CCNC=O)cc1OC([H])([H])[H]>>[H]C([H])([H])Oc1cc2c(cc1OC([H])([H])[H])CCN=C2", if you directly add map for the rxn by RDT software.
the mapped rxn smiles is

[CH2:1]([CH2:2][NH:10][CH:11]=[O:21])[c:8]1[cH:7][cH:6][c:5]([O:4][CH3:3])[c:12]([cH:9]1)[O:13][CH3:14]>>[CH:11]1=[N:10][CH2:2][CH2:1][c:8]2[cH:9][c:12]([O:13][CH3:14])[c:5]([cH:6][c:7]12)[O:4][CH3:3]

the oxygen atom will be labelled as 21.

First, convert the raw rxn smiles to rxn smiles without hydrogen atoms.

#!python


from rdkit import Chem
def canonicalizatonsmi(smi):
    newsmi = Chem.MolToSmiles(Chem.MolFromSmiles(smi))
    return newsmi


def canon_reaction(rxnstring):
    #print("rxnstring:",rxnstring)
    r,p =rxnstring.split('>>')
    rs = r.split('.')
    #print("rs",rs)
    ps = p.split('.')
    #print("ps",p)
    rscans=[]
    pscans=[]
    for reactant in rs:
        temp=canonicalizatonsmi(reactant)
        #print(reactant,temp)
        rscans.append(temp)
    for product in ps:
        pscans.append(canonicalizatonsmi(product))


    rscan='.'.join(sorted(rscans))
    pscan='.'.join(pscans)
    newrxnsring='%s>>%s'%(rscan,pscan)
    return newrxnsring
from rdkit import Chem
rxnstring= '[H]C([H])([H])Oc1ccc(CCNC=O)cc1OC([H])([H])[H]>>[H]C([H])([H])Oc1cc2c(cc1OC([H])([H])[H])CCN=C2'
canon_reaction(rxnstring)

Then, add map for the reaction smiles.

[O:15]=[CH:1][NH:2][CH2:3][CH2:4][c:5]1[cH:6][cH:7][c:8]([O:9][CH3:10])[c:11]([O:12][CH3:13])[cH:14]1>>[CH:1]1=[N:2][CH2:3][CH2:4][c:5]2[cH:14][c:11]([O:12][CH3:13])[c:8]([O:9][CH3:10])[cH:7][c:6]12

the oxygen atom will be labelled as 15.

[mufeili]

Thanks for the example. Is it possible for us to have a python script that automatically performs:

1. Canonicalize the rxn SMILES
2. Add new atom mapping numbers

[autodataming]

Indigo support the python api, but the accuracy is worse.
RDT is better than Indigo, but it is a Java tools.
Other tools such as ChemAxon、rxnmapper need to further be evaluated.
I am not sure which tool is the best tool to add atom mapping numbers.
So I don't put "Add new atom mapping numbers" in the python script.