Yingfeng,
This is a somewhat advanced topic. You need to do a partial sanitization.
There's some info here:
http://nbviewer.ipython.org/gist/greglandrum/4316433
-greg
On Thu, Feb 20, 2014 at 2:44 PM, Yingfeng Wang <ywang...@gmail.com> wrote:
> Adrian,
>
> Thanks. Actually, 'c1cc[nH]c1' is a fragment. I have a aromatic molecule,
> and break one ring bond. RDKit returns the Smiles format of the fragment.
> And I want to draw this fragment. In this case, it is 'c1cc[nH]c1'. So I
> am wondering whether there is a way to draw this kind of fragments.
>
> Again, thank you very much for your help.
>
> Yingfeng
>
>
> On Thu, Feb 20, 2014 at 7:09 AM, Adrian Jasiński <
> jasinski.adr...@gmail.com> wrote:
>
>> 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
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
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>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
>
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