On 15/11/2010 21:58, Noel O'Boyle wrote:
> Hi Chris,
>
> I think that right now it's not possible. The ability to access a
> molecule's number would also be useful for filtering too.
>
> On 15 November 2010 20:57, christophersw...@btconnect.com
> <christophersw...@btconnect.com>  wrote:
>> I have sdf that contains only structures, I'd like each to have a unique 
>> title is this possible? Adding mol1, mol2, mol3 would be sufficient.
>>
Since 2.3.0 it is possible.

obabel mols.sdf -osdf --title newtitle --addoutindex

gives the molecules titles "newtitle 1" etc. --title will replace any 
existing title.

There is also AddInIndex which is added before filtering, but you 
won't see it in the output if you add a new title.

An example to demonstrate a number of features.
Read the first 50 molecules in a compressed dataset and print out the 
SMILES of those containing a pyridine ring, together with the index in 
the file, the ID (in an sdf property) and the output index.

obabel chembl_02.sdf.gz  -osmi  -l 50  -s c1ccccn1 --append chebi_id 
--addinindex --addoutindex

N1(CCN(CC1)c1c(cc2c3c1OCC(n3cc(c2=O)C(=O)O)C)F)C        3 100146 1
c1(c(=O)c2c(n(c1)OC)c(c(N1CC(CC1)CNCC)c(c2)F)F)C(=O)O   6 100195 2
S(=O)(=O)(Nc1ncc(cc1)C)c1c2c(c(N(C)C)ccc2)ccc1          22 100589 3
c1([nH]c2c(c1)cccc2)C(=O)N1CCN(c2c(N(CC)CC)cccn2)CC1    46 101536 4

If you also add --0xout out.svg you will get a 2D depiction (viewable 
in Firefox etc.) of these 4 molecules.

Chris

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