Re: [Rdkit-discuss] Problems with SMILES using MolFromSmiles
A carboxylate has to be represented as C(=O)[O-]. Use ...[OH] for an uncharged carboxyl. Similarly, a tetravalent aliphatic N has to be given a + charge. -P. On Tue, Sep 24, 2019 at 9:15 PM Scalfani, Vincent wrote: > Dear Navid, > > > > RDKit rejects tetravalent Nitrogen by default. This thread below may help. > It shows how to load the SMILES with sanitization off, then perform a > partial sanitization. > > > > https://sourceforge.net/p/rdkit/mailman/message/32589379/ > > > > Vin > > > > > > > > *From:* Navid Shervani-Tabar > *Sent:* Tuesday, September 24, 2019 6:55 PM > *To:* RDKit Discuss > *Subject:* [Rdkit-discuss] Problems with SMILES using MolFromSmiles > > > > Hello, > > > > I have noticed that RDKit have some problems with some SMILES when trying > to use MolFromSmiles. With further attention, I have noticed that all of > these SMILES include nitrogen atoms. Some examples include: > > > > [NH3]CCC(=O)[O] > NC(=[NH2])C(=O)[O] > NC(=[NH2])[CH2].C(=O)=O > CNC(=[NH2])C(=O)[O] > CNC(=[NH2])C(=O)[O] > C[C@@H](C[NH3])C(=O)[O] > > > > I was wondering if there is a way to fix this issue and study those > molecules. Thanks! > > > > Best, > > Navid > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- -P. Sent from a cell phone. Pls forgive brvty and m1$tea@ks. ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problems with SMILES using MolFromSmiles
Dear Navid, RDKit rejects tetravalent Nitrogen by default. This thread below may help. It shows how to load the SMILES with sanitization off, then perform a partial sanitization. https://sourceforge.net/p/rdkit/mailman/message/32589379/ Vin From: Navid Shervani-Tabar Sent: Tuesday, September 24, 2019 6:55 PM To: RDKit Discuss Subject: [Rdkit-discuss] Problems with SMILES using MolFromSmiles Hello, I have noticed that RDKit have some problems with some SMILES when trying to use MolFromSmiles. With further attention, I have noticed that all of these SMILES include nitrogen atoms. Some examples include: [NH3]CCC(=O)[O] NC(=[NH2])C(=O)[O] NC(=[NH2])[CH2].C(=O)=O CNC(=[NH2])C(=O)[O] CNC(=[NH2])C(=O)[O] C[C@@H](C[NH3])C(=O)[O] I was wondering if there is a way to fix this issue and study those molecules. Thanks! Best, Navid ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Problems with SMILES using MolFromSmiles
Hello, I have noticed that RDKit have some problems with some SMILES when trying to use MolFromSmiles. With further attention, I have noticed that all of these SMILES include nitrogen atoms. Some examples include: [NH3]CCC(=O)[O] NC(=[NH2])C(=O)[O] NC(=[NH2])[CH2].C(=O)=O CNC(=[NH2])C(=O)[O] CNC(=[NH2])C(=O)[O] C[C@@H](C[NH3])C(=O)[O] I was wondering if there is a way to fix this issue and study those molecules. Thanks! Best, Navid ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Issue with Chirality
Dear All,
One question why this is not working ?
def mol3D(mol):
tot = AllChem.EmbedMolecule(mol)
try:
X = AllChem.Get3DDistanceMatrix(mol)
except:
print('err')
print(tot)
n = mol.GetNumAtoms()
X = np.zeros(n,n)
return X
mol = Chem.MolFromSmiles('CC[C@H](C)O')
X = mol3D(mol)
Result:
err
-1
---
ValueErrorTraceback (most recent call last)
in mol3D(mol)
3 try:
> 4 X = AllChem.Get3DDistanceMatrix(mol)
5 except:
ValueError: Bad Conformer Id
During handling of the above exception, another exception occurred:
Thanks in advance,
Guillaume
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Re: [Rdkit-discuss] Fwd: sending warnings to stderr/stdout to files
Hi Mike, The following code works for me: import sys from io import StringIO from rdkit import Chem saved_std_err = sys.stderr log = sys.stderr = StringIO() Chem.WrapLogs() # do whatever you want with rdkit whatever_used_to_be_printed_by_rdkit_in_console_as_str = log.getvalue() sys.stderr = saved_std_err This populated the stream in memory, if you replace StringIO with FileIO I think you can directly redirect it to file, but have not tested that. Let me know if this works for you. Lukas From: Date: Tuesday, 24 September 2019 at 16:52 To: RDKIT mailing list Subject: [Rdkit-discuss] Fwd: sending warnings to stderr/stdout to files Hi Rdkit forum, Easy question, perhaps difficult to answer… I’ve been reading a lot of support messages, many a very old about how to get warnings (only visible at the cmd line) to be send to files. I can get error messages sent, but not warnings. The type I’m trying to capture are – which I can see when I run code at the cmd line, but not in jupyter-notebook. “charges were rearranged” “Omitted undefined stereo” Ideally I’d like to run the code in jupyter-notebook and also at the cmd line with python script.py etc and get the warnings into a file. Can you provide me with a simple example as to how to do this? Thanks, mike Dr Mike Mazanetz, FRSC Director Honorary Lecturer School of Natural and Computing Sciences University of Aberdeen +44 (0) 141 533 0930 +44 (0) 7780 672509 mi...@novadatasolutions.co.uk www.novadatasolutions.co.uk skype michael.mazanetz NovaData Solutions Ltd. PO Box 639 Abingdon-on-Thames Oxfordshire OX14 9JD United Kingdom ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Fwd: errors with stereoisomers
Hi Mike,
The usual incantation when working with suppliers, and this is shown in a
lot of sample code, is to check to see if the molecule that is returned is
None (which indicates a problem processing it).
The simple way to do this, and to report the error molecules to stdout (you
can change this) is:
for i,mol in enumerate(supplier):
if mol is None:
print(supplier.GetItemText(i))
continue
do_whatever_you_want(mol)
If you're using the [] notation to retrieve a molecule from the supplier
(as in your example above), you just need to do a check like:
mol = suppl[0]
if mol is None:
there_is_a_problem()
else:
do_whatever_you_want()
-greg
On Tue, Sep 24, 2019 at 4:53 PM wrote:
> Hello RDKit gurus,
>
>
>
> I've found an interesting issue with V2000 SDF files which have a carbon
> marked as "Either or unmarked stereocentre", a 3 in the atom-block.
>
>
>
> The enclosed molecule throws these errors – note also that the word
> “begining" is spelt wrong in the stderr.
>
>
>
> Is there a way to “try-catch” when I run these commands, as the program
> crashes when it hits a molecule it can not pass.
>
> suppl = Chem.SDMolSupplier(‘sdf_file.sdf’)
>
> Chem.MolTo-whatever(suppl[x])
>
>
>
> So that if a molecule fails here it can be sent to sdterr?
>
>
>
> Thanks,
>
> mike
>
>
>
> Python command line:
>
>
>
>
>
> Pre-condition Violation
>
> bad dir
>
> Violation occurred on line 1755 in file
> /opt/conda/conda-bld/rdkit_1561471048963/work/Code/GraphMol/Chirality.cpp
>
> Failed Expression: dir == Bond::ENDUPRIGHT || dir == Bond::ENDDOWNRIGHT
>
>
>
>
>
> [14:34:59] Unexpected error hit on line 317044
>
> [14:34:59] ERROR: moving to the begining of the next molecule
>
> Traceback (most recent call last):
>
> File "AllChem_prop.py", line 178, in
>
> main()
>
> File "AllChem_prop.py", line 170, in main
>
> calc_values = calc_SDF(file_names)
>
> File "AllChem_prop.py", line 105, in calc_SDF
>
> orig = Chem.MolToSmiles(suppl[i])
>
> Boost.Python.ArgumentError: Python argument types in
>
> rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
>
> did not match C++ signature:
>
> MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool
> kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
> allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)
>
>
>
>
>
>
>
> Jupyter-notebook
>
>
>
> ArgumentError Traceback (most recent call last)
>
> in
>
> 1 suppl = Chem.SDMolSupplier('enamine_fail_3.sdf')
>
> > 2 Chem.MolToSmiles(suppl[0],kekuleSmiles=True)
>
> 3 Chem.rdDepictor.Compute2DCoords(suppl[0])
>
> 4 Draw.MolToImage(suppl[0], size=(300, 300))
>
>
>
> ArgumentError: Python argument types in
>
> rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
>
> did not match C++ signature:
>
> MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool
> kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
> allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)
>
>
>
>
>
>
>
>
>
>
>
> Dr Mike Mazanetz, FRSC
>
> Director
>
>
>
> Honorary Lecturer
>
> School of Natural and Computing Sciences
>
> University of Aberdeen
>
>
>
> +44 (0) 141 533 0930
>
> +44 (0) 7780 672509
>
> mi...@novadatasolutions.co.uk
>
> www.novadatasolutions.co.uk
>
> skype michael.mazanetz
>
>
>
> NovaData Solutions Ltd.
>
> PO Box 639
>
> Abingdon-on-Thames
>
> Oxfordshire
>
> OX14 9JD
>
> United Kingdom
>
>
>
> ___
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> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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[Rdkit-discuss] Fwd: errors with stereoisomers
Hello RDKit gurus,
I've found an interesting issue with V2000 SDF files which have a carbon marked
as "Either or unmarked stereocentre", a 3 in the atom-block.
The enclosed molecule throws these errors – note also that the word “begining"
is spelt wrong in the stderr.
Is there a way to “try-catch” when I run these commands, as the program crashes
when it hits a molecule it can not pass.
suppl = Chem.SDMolSupplier(‘sdf_file.sdf’)
Chem.MolTo-whatever(suppl[x])
So that if a molecule fails here it can be sent to sdterr?
Thanks,
mike
Python command line:
Pre-condition Violation
bad dir
Violation occurred on line 1755 in file
/opt/conda/conda-bld/rdkit_1561471048963/work/Code/GraphMol/Chirality.cpp
Failed Expression: dir == Bond::ENDUPRIGHT || dir == Bond::ENDDOWNRIGHT
[14:34:59] Unexpected error hit on line 317044
[14:34:59] ERROR: moving to the begining of the next molecule
Traceback (most recent call last):
File "AllChem_prop.py", line 178, in
main()
File "AllChem_prop.py", line 170, in main
calc_values = calc_SDF(file_names)
File "AllChem_prop.py", line 105, in calc_SDF
orig = Chem.MolToSmiles(suppl[i])
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool
kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)
Jupyter-notebook
ArgumentError Traceback (most recent call last)
in
1 suppl = Chem.SDMolSupplier('enamine_fail_3.sdf')
> 2 Chem.MolToSmiles(suppl[0],kekuleSmiles=True)
3 Chem.rdDepictor.Compute2DCoords(suppl[0])
4 Draw.MolToImage(suppl[0], size=(300, 300))
ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=True, bool
kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
allBondsExplicit=False, bool allHsExplicit=False, bool doRandom=False)
Dr Mike Mazanetz, FRSC
Director
Honorary Lecturer
School of Natural and Computing Sciences
University of Aberdeen
+44 (0) 141 533 0930
+44 (0) 7780 672509
mi...@novadatasolutions.co.uk
www.novadatasolutions.co.uk
skype michael.mazanetz
NovaData Solutions Ltd.
PO Box 639
Abingdon-on-Thames
Oxfordshire
OX14 9JD
United Kingdom
enamine_fail_3.sdf
Description: chemical/mdl-sdfile
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[Rdkit-discuss] Fwd: sending warnings to stderr/stdout to files
Hi Rdkit forum, Easy question, perhaps difficult to answer… I’ve been reading a lot of support messages, many a very old about how to get warnings (only visible at the cmd line) to be send to files. I can get error messages sent, but not warnings. The type I’m trying to capture are – which I can see when I run code at the cmd line, but not in jupyter-notebook. “charges were rearranged” “Omitted undefined stereo” Ideally I’d like to run the code in jupyter-notebook and also at the cmd line with python script.py etc and get the warnings into a file. Can you provide me with a simple example as to how to do this? Thanks, mike Dr Mike Mazanetz, FRSC Director Honorary Lecturer School of Natural and Computing Sciences University of Aberdeen +44 (0) 141 533 0930 +44 (0) 7780 672509 mi...@novadatasolutions.co.uk www.novadatasolutions.co.uk skype michael.mazanetz NovaData Solutions Ltd. PO Box 639 Abingdon-on-Thames Oxfordshire OX14 9JD United Kingdom ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
