date:20180914

Re: [Rdkit-discuss] rdkit: conda install fails on macOS

2018-09-14 Thread Czodrowski, Dr. Paul

Josh & other RDKitters,

I got it to work with Python 3.5.6.

Josh, thanks for pointing out this interpreter version issue!

Cheers,

Paul

Von: Czodrowski, Dr. Paul 
Gesendet: Freitag, 14. September 2018 13:27:53
An: Joshua Meyers
Cc: RDKit Discuss
Betreff: Re: [Rdkit-discuss] rdkit: conda install fails on macOS

Dear Josh,

thanks a lot: I downgraded Python to 3.6.1, but the error seems to be 
persistent:

Python 3.6.1 |Continuum Analytics, Inc.| (default, May 11 2017, 13:04:09)

[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import rdkit

Traceback (most recent call last):

  File "", line 1, in 

  File "/anaconda3/lib/python3.6/site-packages/rdkit/__init__.py", line 2, in 

from .rdBase import rdkitVersion as __version__

ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so, 2): 
Library not loaded: @rpath/libboost_python3.dylib

  Referenced from: /anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so

  Reason: image not found

>>>

Cheers,

Paul

Von: Joshua Meyers 
Gesendet: Freitag, 14. September 2018 10:14:50
An: Czodrowski, Dr. Paul
Cc: RDKit Discuss
Betreff: Re: [Rdkit-discuss] rdkit: conda install fails on macOS

+1 I had this error yesterday,
Quick fix is to roll Python back to version 3.6.1 again (conda install 
python=3.6.1)

Josh

On 14 September 2018 at 08:34, Czodrowski, Dr. Paul 
mailto:pczod...@uni-mainz.de>> wrote:

>>> import rdkit

Traceback (most recent call last):

  File "", line 1, in 

  File "/anaconda3/lib/python3.6/site-packages/rdkit/__init__.py", line 2, in 

from .rdBase import rdkitVersion as __version__

ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so, 2): 
Library not loaded: @rpath/libboost_python3.dylib

  Referenced from: /anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so

  Reason: image not found

Dear RDKitters,

the conda install (conda install -c rdkit rdkit) worked fine, but I'm facing 
the above error. Does anyone have an idea what is going on?

Cheers,

Paul

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Re: [Rdkit-discuss] rdkit: conda install fails on macOS

2018-09-14 Thread Czodrowski, Dr. Paul

Dear Josh,


thanks a lot: I downgraded Python to 3.6.1, but the error seems to be 
persistent:


Python 3.6.1 |Continuum Analytics, Inc.| (default, May 11 2017, 13:04:09)

[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> import rdkit

Traceback (most recent call last):

  File "", line 1, in 

  File "/anaconda3/lib/python3.6/site-packages/rdkit/__init__.py", line 2, in 


from .rdBase import rdkitVersion as __version__

ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so, 2): 
Library not loaded: @rpath/libboost_python3.dylib

  Referenced from: /anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so

  Reason: image not found

>>>




Cheers,

Paul


Von: Joshua Meyers 
Gesendet: Freitag, 14. September 2018 10:14:50
An: Czodrowski, Dr. Paul
Cc: RDKit Discuss
Betreff: Re: [Rdkit-discuss] rdkit: conda install fails on macOS

+1 I had this error yesterday,
Quick fix is to roll Python back to version 3.6.1 again (conda install 
python=3.6.1)

Josh

On 14 September 2018 at 08:34, Czodrowski, Dr. Paul 
mailto:pczod...@uni-mainz.de>> wrote:



>>> import rdkit

Traceback (most recent call last):

  File "", line 1, in 

  File "/anaconda3/lib/python3.6/site-packages/rdkit/__init__.py", line 2, in 


from .rdBase import rdkitVersion as __version__

ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so, 2): 
Library not loaded: @rpath/libboost_python3.dylib

  Referenced from: /anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so

  Reason: image not found



Dear RDKitters,


the conda install (conda install -c rdkit rdkit) worked fine, but I'm facing 
the above error. Does anyone have an idea what is going on?


Cheers,

Paul


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Re: [Rdkit-discuss] organometallics?

2018-09-14 Thread Michal Krompiec

Hi Greg,
I'm very glad, too :).
That would be great as it would be faithful to the notion of a single
coordination bond between the metal atom and the ligand (as opposed to
several coordination bonds to individual atoms of the ligand).
Best,
Michal

On Fri, 14 Sep 2018 at 11:03, Greg Landrum  wrote:

> I'm glad to hear that things work. :-)
>
> I noticed that there is information about the atoms associated with a
> linkage point in the bond records of those v3000 SDFs:
> M  V30 39 9 38 37 ENDPTS=(2 20 21) ATTACH=ALL
>
> I need to do a bit more looking, but it may be possible to add the ability
> to directly parse and interpret this information; that would make things
> easier and the drawings would be less crappy.
>
> -greg
>
>
>
> On Fri, Sep 14, 2018 at 10:55 AM Michal Krompiec <
> michal.kromp...@gmail.com> wrote:
>
>> Hi Greg,
>> Thanks, molfile you attached shows how the problem can be solved for
>> neutral pi-alkene ligands. I just tried and you can draw this in
>> MarvinSketch in KNIME, and pass (as MOL) to RDKit nodes without problems!
>> pi-allyl and cyclopentadienyl also worked when I drew them as Lewis
>> structures with an explicit negative charge and coordinate bonds to all
>> carbon atoms (see attached). Their 2D depiction perhaps isn't beautiful but
>> it is not a problem for me.
>> Best,
>> Michal
>>
>> On Fri, 14 Sep 2018 at 08:07, Greg Landrum 
>> wrote:
>>
>>> That's more or less what the current code does: dative bonds from an
>>> atom to a metal do not affect the perceived valence of the source atom:
>>>
>>> In [13]: m = Chem.MolFromSmiles('[Fe]<-N(C)(C)C')
>>>
>>> In [14]: m.Debug()
>>> Atoms:
>>> 0 26 Fe chg: 0  deg: 1 exp: 1 imp: 0 hyb: 4 arom?: 0 chi: 0
>>> 1 7 N chg: 0  deg: 4 exp: 3 imp: 0 hyb: 5 arom?: 0 chi: 0
>>> 2 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
>>> 3 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
>>> 4 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
>>> Bonds:
>>> 0 1->0 order: 17 conj?: 0 aromatic?: 0
>>> 1 1->2 order: 1 conj?: 0 aromatic?: 0
>>> 2 1->3 order: 1 conj?: 0 aromatic?: 0
>>> 3 1->4 order: 1 conj?: 0 aromatic?: 0
>>>
>>>
>>> For what it's worth, if you draw coordinate bonds from atoms to the
>>> metal in the MOL file, you get something sensible back from the RDKit.
>>> I've attached a tweaked version of one of Michal's example files showing
>>> how to do this.
>>>
>>> Dealing with the dummy atoms directly is tricky because we'd need to
>>> figure out which atoms they are associated with. I think that there's a way
>>> to do it, but that's not handled in the .mol file you sent
>>>
>>> Best,
>>> -greg
>>>
>>>
>>>
>>>
>>> On Thu, Sep 13, 2018 at 6:51 PM Maciek Wójcikowski <
>>> mac...@wojcikowski.pl> wrote:
>>>
 I would suggest that all coordination bonds to metal that exceed the
 accepted valence of an atom could be mark as zero-ordered. This is what
 happens in recent PDB reader changes and fixed a lot of problems with
 sanitization.
 
 Pozdrawiam,  |  Best regards,
 Maciek Wójcikowski
 mac...@wojcikowski.pl


 czw., 13 wrz 2018 o 18:16 Jan Halborg Jensen 
 napisał(a):

> Here’s a modest step in the right direction
> https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/
>
> Best regards, Jan
>
> On 13 Sep 2018, at 15:14, Greg Landrum  wrote:
>
> Hi Michal,
>
> Though the RDKit theoretically has many of the infrastructure pieces
> required to handle organometallics (though there's not a lot you can do
> with them once you've loaded them), the difficult part almost always ends
> up being finding input files that have reasonably machine-readable
> structures in them.
>
> If you have some examples you can share, I'd be happy to take a look
> to see if I can suggest ways to read them in.
>
> Best,
> -greg
>
>
> On Wed, Sep 12, 2018 at 10:30 PM Michal Krompiec <
> michal.kromp...@gmail.com> wrote:
>
>> Hello,
>> I've been asked to analyze a dataset of organometallic compounds
>> (provided in SDF), but it turns out that most of them are not compatible
>> with RDKit (due to having pi-alkene, pi-allyl, cyclopentadienyl et al.
>> ligands). The structures can be correctly represented in Marvin, though.
>> Can anybody point me to a toolkit (or RDKit hack) that can handle these?
>> Best,
>> Michal
>>
>> 
>> Dr. Michal Krompiec
>> Adjunct Professor
>> School of Chemistry, University of Southampton
>> Highfield, Southampton SO17 1BJ, UK
>>
>> and
>> Head of Computational Modelling | Performance Materials | Early
>> Research and Business Development
>> Merck
>> ___
>> Rdkit-discuss mailing list
>>

[Rdkit-discuss] rdkit: conda install fails on macOS

2018-09-14 Thread Czodrowski, Dr. Paul



>>> import rdkit

Traceback (most recent call last):

  File "", line 1, in 

  File "/anaconda3/lib/python3.6/site-packages/rdkit/__init__.py", line 2, in 


from .rdBase import rdkitVersion as __version__

ImportError: dlopen(/anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so, 2): 
Library not loaded: @rpath/libboost_python3.dylib

  Referenced from: /anaconda3/lib/python3.6/site-packages/rdkit/rdBase.so

  Reason: image not found



Dear RDKitters,


the conda install (conda install -c rdkit rdkit) worked fine, but I'm facing 
the above error. Does anyone have an idea what is going on?


Cheers,

Paul
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Re: [Rdkit-discuss] organometallics?

2018-09-14 Thread Greg Landrum

That's more or less what the current code does: dative bonds from an atom
to a metal do not affect the perceived valence of the source atom:

In [13]: m = Chem.MolFromSmiles('[Fe]<-N(C)(C)C')

In [14]: m.Debug()
Atoms:
0 26 Fe chg: 0  deg: 1 exp: 1 imp: 0 hyb: 4 arom?: 0 chi: 0
1 7 N chg: 0  deg: 4 exp: 3 imp: 0 hyb: 5 arom?: 0 chi: 0
2 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
3 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
4 6 C chg: 0  deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0
Bonds:
0 1->0 order: 17 conj?: 0 aromatic?: 0
1 1->2 order: 1 conj?: 0 aromatic?: 0
2 1->3 order: 1 conj?: 0 aromatic?: 0
3 1->4 order: 1 conj?: 0 aromatic?: 0


For what it's worth, if you draw coordinate bonds from atoms to the metal
in the MOL file, you get something sensible back from the RDKit.
I've attached a tweaked version of one of Michal's example files showing
how to do this.

Dealing with the dummy atoms directly is tricky because we'd need to figure
out which atoms they are associated with. I think that there's a way to do
it, but that's not handled in the .mol file you sent

Best,
-greg




On Thu, Sep 13, 2018 at 6:51 PM Maciek Wójcikowski 
wrote:

> I would suggest that all coordination bonds to metal that exceed the
> accepted valence of an atom could be mark as zero-ordered. This is what
> happens in recent PDB reader changes and fixed a lot of problems with
> sanitization.
> 
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
>
> czw., 13 wrz 2018 o 18:16 Jan Halborg Jensen 
> napisał(a):
>
>> Here’s a modest step in the right direction
>> https://www.wildcardconsulting.dk/useful-information/how-to-solve-problems-with-coordinate-bonds-in-rdkit/
>>
>> Best regards, Jan
>>
>> On 13 Sep 2018, at 15:14, Greg Landrum  wrote:
>>
>> Hi Michal,
>>
>> Though the RDKit theoretically has many of the infrastructure pieces
>> required to handle organometallics (though there's not a lot you can do
>> with them once you've loaded them), the difficult part almost always ends
>> up being finding input files that have reasonably machine-readable
>> structures in them.
>>
>> If you have some examples you can share, I'd be happy to take a look to
>> see if I can suggest ways to read them in.
>>
>> Best,
>> -greg
>>
>>
>> On Wed, Sep 12, 2018 at 10:30 PM Michal Krompiec <
>> michal.kromp...@gmail.com> wrote:
>>
>>> Hello,
>>> I've been asked to analyze a dataset of organometallic compounds
>>> (provided in SDF), but it turns out that most of them are not compatible
>>> with RDKit (due to having pi-alkene, pi-allyl, cyclopentadienyl et al.
>>> ligands). The structures can be correctly represented in Marvin, though.
>>> Can anybody point me to a toolkit (or RDKit hack) that can handle these?
>>> Best,
>>> Michal
>>>
>>> 
>>> Dr. Michal Krompiec
>>> Adjunct Professor
>>> School of Chemistry, University of Southampton
>>> Highfield, Southampton SO17 1BJ, UK
>>>
>>> and
>>> Head of Computational Modelling | Performance Materials | Early Research
>>> and Business Development
>>> Merck
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>> ___
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>>
>>
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>>
>


pd_dba2.dative.mol
Description: Binary data
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Re: [Rdkit-discuss] rdkit: conda install fails on macOS

Re: [Rdkit-discuss] rdkit: conda install fails on macOS

Re: [Rdkit-discuss] organometallics?

[Rdkit-discuss] rdkit: conda install fails on macOS

Re: [Rdkit-discuss] organometallics?

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