Hi,
Thank you for your answer. Since I have posted this question, I have
realized that it can not be done with obabel directly, so I have
looked into the API. I am using C++ and not python and I have found
recently the following way of doing it:
OpenBabel::OBConversion obconversion;
OpenBabel::OBMol mol;
obconversion.SetInFormat("smi");
OpenBabel::OBSmartsPattern smarts;
smarts.Init("XXX"); // The wanted pattern
vector<vector<int> > maplist;
int total = 0;
bool notatend = obconversion.ReadFile(&mol,"Library.smi");
while (notatend) {
smarts.Match(mol);
maplist = smarts.GetUMapList();
total += maplist.size();
mol.Clear();
notatend = obconversion.Read(&mol);
}
cout << "Number of iterations " << total << endl;
It gives me the same value as other chemoinformatic tools I am using.
Nicolas
2014-04-17 4:17 GMT-04:00 Pascal Muller <pascal.jm.mul...@gmail.com>:
> Hi,
>
>
>>
>> I am trying to count how many times a given moiety can be found in a
>> database.
>
> (...)
>>
>> If not, how can it be done with the API?
>>
>
>
> You could try something like this, with pybel:
>
>
> #!/usr/bin/env python
> import sys
> import pybel
>
> # ref :
> # O=C(NCCCC1CCCC1)c1cccc(c1)C(=O)N moldId
>
> substruct = "NC=O"
> substructSmart = pybel.Smarts(substruct)
>
> for mol in pybel.readfile("smi", sys.argv[1]):
> subtructCount = len(substructSmart.findall(mol)) # That's the data
> you're wanting
> print substruct, ":", subtructCount, "in", mol.OBMol.GetTitle()
>
>
>
> Output:
> NC=O : 2 in molId
>
> Is it ok for you?
>
> Regards,
> Pascal
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