Hi,
I'm trying to assign MMFF94 partial charges to a molecule
programatically with the Open Babel API in C++. I'm using version
2.3.1 of openbabel and running on Ubuntu.
My code snippet (based on the example from the OBChargeModel
documentation) is as follows:
OBChargeModel* mmffCharges
Hi everybody.
I'm trying to use Java implementation of open babel to solve a problem.
The problem is pretty simple. I have to convert some molecules in smiles
format in fingerprints in order to calculate after the tanimoto score.
I took a look at the documentation and I found that in pybel exists a
"First of all, you need to create a fastsearch index (see above). The
index is created with the following command:
babel mymols.sdf -ofs"
http://openbabel.org/docs/dev/Fingerprints/fingerprints.html
Could you please tell me the differences between the use of a 2D or a 3D
sdf file regarding the .
> My code snippet (based on the example from the OBChargeModel
> documentation) is as follows:
Have you created an OBConversion object? We changed the way plugins are loaded
in OB 2.3.x, and it currently requires that an OBConversion object is created
to find plugins. This will be fixed in 2.4,
FP2 is a Daylight-type fingerprint. It is based only on connectivity,
and does not incorporate any stereochemical information, so 2D or 3D
structures will give the same results.
- Noel
On 11 January 2012 14:23, David García Aristegui wrote:
> "First of all, you need to create a fastsearch index
>From Python, it goes something like this...
>>> import openbabel as ob
>>> conv = ob.OBConversion()
>>> mol = ob.OBMol()
>>> conv.SetInFormat("smi")
True
>>> conv.ReadString(mol, "CC(=O)Cl")
True
>>> fingerprinter = ob.OBFingerprint.FindFingerprint("FP2")
>>> print fingerprinter
>
>>> fp = ob.ve
On 11/01/2012 14:23, David García Aristegui wrote:
> "First of all, you need to create a fastsearch index (see above). The
> index is created with the following command:
>
> babel mymols.sdf -ofs"
>
> http://openbabel.org/docs/dev/Fingerprints/fingerprints.html
>
> Could you please tell me the diff
Thank you very much, Noel and Chris.
Best regards.
> On 11/01/2012 14:23, David García Aristegui wrote:
>> "First of all, you need to create a fastsearch index (see above). The
>> index is created with the following command:
>>
>> babel mymols.sdf -ofs"
>>
>> http://openbabel.org/docs/dev/Fingerpr
Noel O'Boyle wrote
>
>>From Python, it goes something like this...
>
import openbabel as ob
conv = ob.OBConversion()
mol = ob.OBMol()
conv.SetInFormat("smi")
> True
conv.ReadString(mol, "CC(=O)Cl")
> True
fingerprinter = ob.OBFingerprint.FindFingerprint("FP2")
