TypeError: No registered converter was able to produce a C++ rvalue of type std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > from this Python object of type NoneType about auto_martini HOT 16 CLOSED

Hi,

Can you try to convert your SDF file to a smiles string? Openbabel will do
that for you. Otherwise I'll have a look next week.

Best,
Tristan
On Fri, Nov 13, 2015 at 17:11 filips [email protected] wrote:

Hi,
auto_martini works fine for an example smiles. But I can't convert any sdf
files. I've tried to use sdf with guanazole (attached) but this results in
errors:

./auto_martini --sdf gua-3D.sdf --mol DUPA --verbose
; ring atoms: [[0, 1, 3, 4, 5]]
; Heavy atoms: N C N N N C N
; [0] -27.8905921889
; [1] -34.1904545745
; [3] -28.3426150603
; [4] -24.8125930713
; [5] -37.4331878925
; [0, 3] -63.2728078673
; [0, 4] -62.3127221936
; [1, 4] -65.7449246813
; [1, 5] -72.926702717
; [3, 5] -67.0298714638
; CG bead: 1
; CG bead: 5
; with energy: -72.926702717
; Max. number of attempts: 4
; Atom partitioning: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1}
Traceback (most recent call last):
File "./auto_martini", line 1203, in
ringAtomsFlat, True)
File "./auto_martini", line 825, in printAtoms
molFrag = genMoleculeSMI(smiFrag)
File "./auto_martini", line 89, in genMoleculeSMI
mol = Chem.MolFromSmiles(args.smi)
TypeError: No registered converter was able to produce a C++ rvalue of type std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > from this Python object of type NoneType

Sample sdf files attached.
sdf files are here in gist:
https://gist.github.com/filipsPL/e1a7be4b989e50a4b10f

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#3.

from auto_martini.

Thanks,
That would probably be ok. However I would like to preserve 3D structure of the ligand (if it is possible), so sdf structure is a must.

from auto_martini.

Hi,

I've tested your 2 SDF files on my computer, and there's no error. My guess is that your version of RDKit is too old. Can you check which version you have, and possibly try to update it?

In [1]: from rdkit import rdBase

In [2]: rdBase.rdkitVersion
Out[2]: '2013.09.1'

Best,
Tristan

from auto_martini.

(Un)fortunatelly I've upgraded the RDKit recently:

In [1]: from rdkit import rdBase

In [2]: rdBase.rdkitVersion
Out[2]: '2015.03.1'

Maybe the RDKit is too new ❓

Edit: sorry, I've closed the issue by accident.

from auto_martini.

I'll try to update on my end to a more recent version of RDKit, but in the
meantime, see if you can create a virtual environment (conda or virtualenv)
with an older RDKit.

Best,
Tristan

On Mon, Nov 16, 2015 at 3:18 PM, filips [email protected] wrote:

Reopened #3 #3.

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#3 (comment).

from auto_martini.

Ok, I will try it with a virtualenv.

from auto_martini.

I've set up virtualenv with the same rdkit version as your:

>>> from rdkit import rdBase
>>> rdBase.rdkitVersion
'2013.09.1'

and run (venv)fs@card:~/auto_martini$ ./auto_martini --sdf gua-3D.sdf --mol DUPA --verbose This time the error is different than it was before:

; ring atoms: [[0, 1, 3, 4, 5]]
; Heavy atoms: N C N N N C N 
; [0] -27.8905921889
; [1] -34.1904545745
; [3] -28.3426150603
; [4] -24.8125930713
; [5] -37.4331878925
; [0, 3] -63.2728078673
; [0, 4] -62.3127221936
; [1, 4] -65.7449246813
; [1, 5] -72.926702717
; [3, 5] -67.0298714638
; CG bead: 1
; CG bead: 5
;      with energy: -72.926702717
; Max. number of attempts: 4
; Atom partitioning: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1}
Traceback (most recent call last):
  File "./auto_martini", line 1206, in <module>
    ringAtomsFlat, True)
  File "./auto_martini", line 828, in printAtoms
    molFrag = genMoleculeSMI(smiFrag)
  File "./auto_martini", line 92, in genMoleculeSMI
    mol = Chem.MolFromSmiles(args.smi)
Boost.Python.ArgumentError: Python argument types in
    rdkit.Chem.rdmolfiles.MolFromSmiles(NoneType)
did not match C++ signature:
    MolFromSmiles(std::string SMILES, bool sanitize=True, boost::python::dict replacements={})

PS: here is how to setup virtualenv with rdkit

from auto_martini.

Hmm. What's your boost version?

http://askubuntu.com/questions/147474/how-can-i-find-boost-version

On Tue, Nov 17, 2015 at 1:29 PM, filips [email protected] wrote:

I've set up virtualenv with the same rdkit version as your:

from rdkit import rdBase
rdBase.rdkitVersion
'2013.09.1'

and run (venv)fs@card:~/auto_martini$ ./auto_martini --sdf gua-3D.sdf
--mol DUPA --verbose This time the error is different than it was before:

; ring atoms: [[0, 1, 3, 4, 5]]
; Heavy atoms: N C N N N C N
; [0] -27.8905921889
; [1] -34.1904545745
; [3] -28.3426150603
; [4] -24.8125930713
; [5] -37.4331878925
; [0, 3] -63.2728078673
; [0, 4] -62.3127221936
; [1, 4] -65.7449246813
; [1, 5] -72.926702717
; [3, 5] -67.0298714638
; CG bead: 1
; CG bead: 5
; with energy: -72.926702717
; Max. number of attempts: 4
; Atom partitioning: {0: 0, 1: 0, 2: 0, 3: 0, 4: 1, 5: 1, 6: 1}
Traceback (most recent call last):
File "./auto_martini", line 1206, in
ringAtomsFlat, True)
File "./auto_martini", line 828, in printAtoms
molFrag = genMoleculeSMI(smiFrag)
File "./auto_martini", line 92, in genMoleculeSMI
mol = Chem.MolFromSmiles(args.smi)
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolFromSmiles(NoneType)
did not match C++ signature:
MolFromSmiles(std::string SMILES, bool sanitize=True, boost::python::dict replacements={})

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#3 (comment).

from auto_martini.

dpkg -s libboost-dev | grep 'Version'
Version: 1.48.0.2

from auto_martini.

I use 1.54. Can you try to upgrade your version of Boost? It looks like the
error is taking place when RDKit tries to use the Boost library. You should
be able to do this in a virtual environment relatively painlessly. I know
conda can install boost easily.

On Tue, Nov 17, 2015 at 1:42 PM, filips [email protected] wrote:

dpkg -s libboost-dev | grep 'Version'
Version: 1.48.0.2

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#3 (comment).

from auto_martini.

Thanks, now I have boost: 1.55 Version: 1.55.0-1ppa1~precise1 and still the same error:

Traceback (most recent call last):
  File "./auto_martini", line 1206, in <module>
    ringAtomsFlat, True)
  File "./auto_martini", line 828, in printAtoms
    molFrag = genMoleculeSMI(smiFrag)
  File "./auto_martini", line 92, in genMoleculeSMI
    mol = Chem.MolFromSmiles(args.smi)
Boost.Python.ArgumentError: Python argument types in
    rdkit.Chem.rdmolfiles.MolFromSmiles(NoneType)
did not match C++ signature:
    MolFromSmiles(std::string SMILES, bool sanitize=True, boost::python::dict replacements={})

Any further ideas? Meanwhile I will try to install auto_martini on another "fresh" computer and see if it is possible.

from auto_martini.

Oh ok, then try to change of branch:

git checkout refactor
python auto_martini.py --sdf gua-3D.sdf --mol DUPA --verbose

it's not a release branch yet, but it fixes some problems we have with
reading in some SMILES string within the code.

Cheers,
Tristan

On Tue, Nov 17, 2015 at 4:48 PM, filips [email protected] wrote:

Thanks, now I have boost: 1.55 Version: 1.55.0-1ppa1~precise1 and still
the same error:

Traceback (most recent call last):
File "./auto_martini", line 1206, in
ringAtomsFlat, True)
File "./auto_martini", line 828, in printAtoms
molFrag = genMoleculeSMI(smiFrag)
File "./auto_martini", line 92, in genMoleculeSMI
mol = Chem.MolFromSmiles(args.smi)
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolFromSmiles(NoneType)
did not match C++ signature:
MolFromSmiles(std::string SMILES, bool sanitize=True, boost::python::dict replacements={})

Any further ideas? Meanwhile I will try to install auto_martini on another
"fresh" computer and see if it is possible.

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#3 (comment).

from auto_martini.

Ok, this works fine. Thanks!

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TypeError: No registered converter was able to produce a C++ rvalue of type std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > from this Python object of type float

from auto_martini.

can u plz tell me why this error is coming

from auto_martini.

@Alka00 I've never seen this error, but it seems to be linked to RDKit. Maybe have a look at your RDKit installation. If needed, please get in touch with their support.

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