m = Chem.MolFromSmiles('ccc[nH]c', sanitize=False)
I think that in this example there is a problem with your SMILES.
Why you use lower case?
In SMILES format it's a aromatic molecule but you don't have the beginning
and ending of aromatic bond noted by number.
If you have aromatic molecule you should write it like that:
>>>> m = Chem.MolFromSmiles('c1cc[nH]c1')
if it is not aromatic than use upper case:
>>>> m = Chem.MolFromSmiles('CCC[NH]C')
and than try:
>>>> AllChem.Compute2DCoords(m)
for second example:
>>>> m = Chem.MolFromSmiles('CCCCCCCCCCCCCCCCC(=O)OCCO')
>>>> AllChem.Compute2DCoords(m)
2014-02-19 21:46 GMT+01:00 Yingfeng Wang <ywang...@gmail.com>:
> Here are more details.
>
> If I use
>
> m = Chem.MolFromSmiles('ccc[nH]c', sanitize=False)
> AllChem.Compute2DCoords(m)
>
> It works.
>
> But I get trouble with
> >>> m = Chem.MolFromSmiles('CCCCCCCCCCCCCCCCC(=O)OCCO', sanitize=False)
> >>> AllChem.Compute2DCoords(m)
>
> I got
>
> ****
> Pre-condition Violation
> getNumImplicitHs() called without preceding call to calcImplicitValence()
> Violation occurred on line 170 in file
> /home/yf1/software/RDKit/install_version/latest/Code/GraphMol/Atom.cpp
> Failed Expression: d_implicitValence>-1
> ****
>
>
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> RuntimeError: Pre-condition Violation
>
>
>
> On Wed, Feb 19, 2014 at 3:27 PM, Yingfeng Wang <ywang...@gmail.com> wrote:
>
>> Adrian,
>>
>> I meet a weird case.
>>
>> >>> import matplotlib.offsetbox
>> >>> from rdkit import Chem
>> >>> from rdkit.Chem import AllChem
>> >>> from rdkit.Chem import Draw
>> >>> m = Chem.MolFromSmiles('ccc[nH]c')
>>
>> I got
>> non-ring atom 0 marked aromatic
>> >>> AllChem.Compute2DCoords(m)
>> Traceback (most recent call last):
>> File "<stdin>", line 1, in <module>
>> Boost.Python.ArgumentError: Python argument types in
>> rdkit.Chem.rdDepictor.Compute2DCoords(NoneType)
>> did not match C++ signature:
>> Compute2DCoords(RDKit::ROMol {lvalue} mol, bool canonOrient=True,
>> bool clearConfs=True, boost::python::dict {lvalue} coordMap={}, unsigned
>> int nFlipsPerSample=0, unsigned int nSample=0, int sampleSeed=0, bool
>> permuteDeg4Nodes=False, double bondLength=-1.0)
>>
>>
>> Actually, "ccc[nH]c" is a fragment. Could you please help me to know
>> whether there is a work around to this case?
>>
>> Thanks.
>>
>> Yingfeng
>>
>>
>>
>>
>> On Mon, Feb 17, 2014 at 2:58 PM, Yingfeng Wang <ywang...@gmail.com>wrote:
>>
>>> Adrian,
>>>
>>> Thanks, it works.
>>>
>>> Yingfeng
>>>
>>>
>>> On Mon, Feb 17, 2014 at 12:50 PM, Adrian Jasiński <
>>> jasinski.adr...@gmail.com> wrote:
>>>
>>>> If you read all from tutorial you will find a example:
>>>>
>>>> >>> suppl = Chem.SDMolSupplier('data/cdk2.sdf')>>> ms = [x for x in suppl
>>>> >>> if x is not None]>>> for m in ms: tmp=AllChem.Compute2DCoords(m)>>>
>>>> >>> from rdkit.Chem import Draw>>>
>>>> >>> Draw.MolToFile(ms[0],'images/cdk2_mol1.png')>>>
>>>> >>> Draw.MolToFile(ms[1],'images/cdk2_mol2.png')
>>>>
>>>>
>>>> for this example with you pasted you can just write mol to file:
>>>>
>>>>
>>>> >>> from rdkit.Chem import AllChem
>>>>
>>>>
>>>>
>>>>
>>>> >>> from rdkit import Chem
>>>> >>> m = Chem.MolFromSmiles('c1nccc2n1ccc2')
>>>>
>>>> >>> AllChem.Compute2DCoords(m)
>>>>
>>>> Draw.MolToFile(m,'example.png')
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> pozdrawiam
>>>> Adrian Jasiński
>>>>
>>>>
>>>> 2014-02-17 18:34 GMT+01:00 Yingfeng Wang <ywang...@gmail.com>:
>>>>
>>>>> I want to draw a 2D figure of a compound. And I follow the example
>>>>> given at the following link,
>>>>>
>>>>> http://www.rdkit.org/docs/GettingStartedInPython.html
>>>>>
>>>>> My code is given as follows,
>>>>>
>>>>> >>> from rdkit.Chem import AllChem
>>>>> >>> from rdkit import Chem
>>>>> >>> m = Chem.MolFromSmiles('c1nccc2n1ccc2')
>>>>> >>> AllChem.Compute2DCoords(m)
>>>>> 0
>>>>> >>> template = Chem.MolFromSmiles('c1nccc2n1ccc2')
>>>>> >>> AllChem.Compute2DCoords(template)
>>>>> 0
>>>>> >>> AllChem.GenerateDepictionMatching2DStructure(m,template)
>>>>> >>>
>>>>>
>>>>>
>>>>> However, I got nothing. I am wondering what the correct way is to
>>>>> generate the 2D figure of "c1nccc2n1ccc2". Thanks.
>>>>>
>>>>> Yingfeng
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Managing the Performance of Cloud-Based Applications
>>>>> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
>>>>> Read the Whitepaper.
>>>>>
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
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>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>
>>>>>
>>>>
>>>
>>
>
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