Dear All, I encountered problems while reading compounds containing Nitro group (-NO2) or building molecules containing smarts like [N+][O-]. It seems that rdkit only allows the maximum valence of N to be 3 in these processes. One example is as followings (the sdf file is attached):
>>> spl=cm.SDMolSupplier('pyrazoloacridine.sdf')
>>> print spl[0]
None
>>> mm=cm.MolFromMolFile('pyrazoloacridine.sdf')
Traceback (most recent call last):
File "<pyshell#20>", line 1, in <module>
mm=cm.MolFromMolFile('pyrazoloacridine.sdf')
ValueError: Sanitization error: Explicit valence for atom # 13 N greater
than permitted
Could anyone provide some solution for this problem? I did't notice this
problem when I started building model. But now I cannot run through the
whole dataset probably because of this problem. Thanks in advance.
Cheers,
Tao-wei Huang
--
Tao-wei Huang
Department of Chemistry and Chemical Biology
Rensselaer Polytechnic Institute
Phone: 518-275-7997
Einstein: 'Everything should be made as simple as possible, but no simpler'
pyrazoloacridine.sdf
Description: Binary data
