Dear Basil,
the API has slightly changed since that commit; SanitizeMMFFMol() has
become MMFFSanitizeMolecule().
However, currently you may sanitize molecules as usual, i.e. import your
molecule with
m = Chem.MolFromSmiles("O=C(C)c1cccnc1")
Then you do not need any additional sanitization steps.
Only in the (rather special and unlikely) case that you need to import a
molecule where you do not want the order of double bonds in
aromatic/conjugated systems to be altered with respect to the original
one by sequential aromatisation/kekulization operations, then you should
import without sanitizing, followed by MMFF-friendly sanitization
m = Chem.MolFromSmiles("O=C(C)c1cccnc1", False)
AllChem.MMFFSanitizeMolecule(m)
Best regards,
Paolo
On 10/10/2013 11:35 AM, Dr. Basil Hartzoulakis wrote:
Hi,
I have been testing some of the work flows that Paolo has exemplified
here
https://github.com/rdkit/rdkit/commit/b1acab59b02425d61151db7313ea024eebcfd9f5
but the Sanitize command produces an AttributeError.
-------------------------------------------------------
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> m = Chem.MolFromSmiles("O=C(C)c1cccnc1", False)
>>> AllChem.SanitizeMMFFMol(m)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
AttributeError: 'module' object has no attribute 'SanitizeMMFFMol'
-----------------------------------------------------------------------
My RDKit installation went fine on Centos 6.4 (with anaconda and boost
1.49)
with no errors after the ctest.
Has anybody any ideas what could be wrong or where to look further?
Thanks in advance
Basil
-----------------------------------------
Basil Hartzoulakis, PhD
Chemiverse Ltd
email: [email protected]
linkedin: http://uk.linkedin.com/in/drugdesigner
Skype: vasileios.hartzoulakis
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Department of Drug Science and Technology
Via Pietro Giuria, 9 - 10125 Torino (Italy)
Tel: +39 011 670 7680 | Mob: +39 348 5537206
Fax: +39 011 670 7687 | E-mail: [email protected]
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