Re: [Open Babel] netcharge of a molecule
On Jan 26, 2018, at 07:27, Sundar wrote:
> How to calculate the net charge of a molecule in openbabel?
The OBMolecule object has a method called "GetTotalCharge()":
http://openbabel.org/api/2.3.0/classOpenBabel_1_1OBMol.shtml#ab78d46b60f04702fa6f450ef6f8dae62
Or, if you are using the pybel interface, use the '.charge' attribute:
>>> import pybel
>>> mol = pybel.readstring("smi", "[NH4+]")
>>> mol.charge
1
Or, if you want it from the command-line, you can use the 'report' output
format and look for the line starting "TOTAL CHARGE"
% echo "[NH4+]" | obabel -ismi - -oreport - | grep "^TOTAL CHARGE"
1 molecule converted
TOTAL CHARGE: 1
Andrew
da...@dalkescientific.com
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[Open Babel] Using OBPairData in python
Dear developers,
I was wondering what is the proper way to use OBPairData in python. For
example, I want to store an OBPairData with attribute 'nLonePair' in an
OBAtom. I managed to do this with the following code but don't know if it
is the best way.
d = ob.OBPairData()
d.SetAttribute('nLonePair')
nLonePair = 2
d.SetValue(str(nLonePair))
atom.CloneData(d)
I wanted to use atom.SetData() as I found in the document
but
an error shows up saying OBAtom does not have attribute SetData. So I used
CloneData instead, which seems to do the job.
Now I want to retrieve the value of the OBPairData. In C++ I would do
things like
pairData = (OBPairData*)atom.GetData('nLonePair')
nLonePair = pairData.GetValue()
However, when in python I do
pairData = openbabel.OBPairData(atom.GetData('nLonePair')),
an error shows up saying __init__() takes exactly 1 argument (2 given). I
checked the swig file openbabel.py and OBPairData.__init__() does take
'self' as the only argument. The problem is that atom.GetData() returns a
OBGenericData type which, without converting to an OBPairData type, doesn't
allow a GetValue() method afaik.
To sum up,
1. Is my way of storing an OBPairData in an atom correct?
2. How do I retrieve the value of an OBPairData in python?
3. Just by the way, is there anything in openbabel/pybel that keeps track
of the number of lone pairs in an atom?
Thank you in advance,
Xianghai
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Re: [Open Babel] Using OBPairData in python
Hi there,
Regarding 1, yes, but have you instead considered using a Python dictionary
or list to store the information? If I were you, I would avoid crossing
over to C++ to store this information.
Regarding 2, see
https://openbabel.org/docs/dev/UseTheLibrary/PythonDoc.html#accessing-obpairdata-obunitcell-and-other-obgenericdata.
Essentially, toPairData() does the cast.
Regarding 3, the number of lone pairs can be deduced from the atomic number
and the valence so we don't need to track the number of lone pairs.
Regards,
- Noel
On 25 January 2018 at 01:43, Xianghai Sheng wrote:
> Dear developers,
>
> I was wondering what is the proper way to use OBPairData in python. For
> example, I want to store an OBPairData with attribute 'nLonePair' in an
> OBAtom. I managed to do this with the following code but don't know if it
> is the best way.
>
> d = ob.OBPairData()
> d.SetAttribute('nLonePair')
> nLonePair = 2
> d.SetValue(str(nLonePair))
> atom.CloneData(d)
>
> I wanted to use atom.SetData() as I found in the document
> but
> an error shows up saying OBAtom does not have attribute SetData. So I used
> CloneData instead, which seems to do the job.
>
> Now I want to retrieve the value of the OBPairData. In C++ I would do
> things like
> pairData = (OBPairData*)atom.GetData('nLonePair')
> nLonePair = pairData.GetValue()
> However, when in python I do
> pairData = openbabel.OBPairData(atom.GetData('nLonePair')),
> an error shows up saying __init__() takes exactly 1 argument (2 given). I
> checked the swig file openbabel.py and OBPairData.__init__() does take
> 'self' as the only argument. The problem is that atom.GetData() returns a
> OBGenericData type which, without converting to an OBPairData type, doesn't
> allow a GetValue() method afaik.
>
> To sum up,
> 1. Is my way of storing an OBPairData in an atom correct?
> 2. How do I retrieve the value of an OBPairData in python?
> 3. Just by the way, is there anything in openbabel/pybel that keeps track
> of the number of lone pairs in an atom?
>
> Thank you in advance,
> Xianghai
>
>
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[Open Babel] Error in file conversion
Dear all, I see that when I convert a file from sdf to pdb or pdbqt. Obabel guesses a few atoms as ALA (could be an amino acid Alanine). Does anyone know any possible cause? Attached are the files. Thanks, Jubilant 443884.sdf Description: Binary data 443884.pdb Description: Protein Databank data 443884.pdbqt Description: Binary data -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
