date:20201016

Re: [Rdkit-discuss] conda install rdkit

2020-10-16 Thread Ling Chan

Bingo, it works! Thank you Christos.

So perhaps the problem lies with the rdkit channel, rather than on my end?

Ling


Christos Kannas  於 2020年10月16日週五 下午12:46寫道：

> Hi Ling,
>
> Maybe you should switch to conda-forge channel. Replace "-c rdkit" with
> "-c conda-forge".
> At least that's what I'm using personally and I have no problems so far.
> The latest version of rdkit there is 2020.03.6.
>
> Best,
>
> Christos
>
> Christos Kannas
>
> Scientific Software Developer (Cheminformatics)
>
> [image: View Christos Kannas's profile on LinkedIn]
> 
>
>
>
> 
>  Virus-free.
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>
> On Fri, 16 Oct 2020 at 21:00, Ling Chan  wrote:
>
>> Thank you Drew for your suggestion. I tried it, but it did not help.
>>
>> I also did a "conda clean -a" on top of that. Still, when I do
>> conda create -c rdkit -n rdkenv rdkit
>> it stubbornly points to
>> rdkit  rdkit/linux-64::rdkit-2018.03.2.0-py36h6bb024c_1
>>
>> and as I wrote before, I don't have a ".condarc" file in my home
>> directory. Moreover, there is no "pinned" file found in any of my
>> conda-meta directories. And even "conda update rdkit --no-pin" does not
>> update my rdkit.
>>
>> I have no idea where it picks up that 2018 rdkit version and sticks to it.
>>
>> Ling
>>
>> Drew Gibson  於 2020年10月12日週一 上午4:35寫道：
>>
>>> Hi,
>>>
>>> I had a similar issue in the past.  Try updating conda...
>>>
>>> conda update conda
>>>
>>> then try creating your RDKit environment again.
>>>
>>> Drew
>>>
>>> On Sat, 10 Oct 2020 at 23:47, Ling Chan  wrote:
>>>
 Dear colleagues,

 I am trying to install RDKit using conda. According to the manual at
 https://www.rdkit.org/docs/Install.html#how-to-install-rdkit-with-conda

 it is very simple. I just need to do

 conda create -c rdkit -n my-rdkit-env rdkit

 It used to work. Somehow when I try this again, things are not working. 
 When I investigated, it turns out that somehow the 2018.03.2.0 version of 
 rdkit was installed instead of the most current one. It seems to me that I 
 have screwed up my conda setup. Just wonder what have I screwed up? How 
 can I repair it?

 One hint could be found at the message when I did conda create. The line 
 for rdkit looks different from the other lines, as indicated below. 
 Unfortunately I still could not figure it out.

 Thank you for your insight.

 Ling


 =

 > conda create -c rdkit -n tempenv rdkit

 The following NEW packages will be INSTALLED:

   _libgcc_mutex  pkgs/main/linux-64::_libgcc_mutex-0.1-main
   blas   pkgs/main/linux-64::blas-1.0-mkl
   bzip2  pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
 
  python pkgs/main/linux-64::python-3.6.12-hcff3b4d_2
   python-dateutilpkgs/main/noarch::python-dateutil-2.8.1-py_0
   pytz   pkgs/main/noarch::pytz-2020.1-py_0
   rdkit  rdkit/linux-64::rdkit-2018.03.2.0-py36h6bb024c_1
   readline   pkgs/main/linux-64::readline-8.0-h7b6447c_0
   setuptools
 pkgs/main/linux-64::setuptools-50.3.0-py36hb0f4dca_1
   sixpkgs/main/noarch::six-1.15.0-py_0
  


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Re: [Rdkit-discuss] conda install rdkit

2020-10-16 Thread Christos Kannas

Hi Ling,

Maybe you should switch to conda-forge channel. Replace "-c rdkit" with "-c
conda-forge".
At least that's what I'm using personally and I have no problems so far.
The latest version of rdkit there is 2020.03.6.

Best,

Christos

Christos Kannas

Scientific Software Developer (Cheminformatics)

[image: View Christos Kannas's profile on LinkedIn]




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On Fri, 16 Oct 2020 at 21:00, Ling Chan  wrote:

> Thank you Drew for your suggestion. I tried it, but it did not help.
>
> I also did a "conda clean -a" on top of that. Still, when I do
> conda create -c rdkit -n rdkenv rdkit
> it stubbornly points to
> rdkit  rdkit/linux-64::rdkit-2018.03.2.0-py36h6bb024c_1
>
> and as I wrote before, I don't have a ".condarc" file in my home
> directory. Moreover, there is no "pinned" file found in any of my
> conda-meta directories. And even "conda update rdkit --no-pin" does not
> update my rdkit.
>
> I have no idea where it picks up that 2018 rdkit version and sticks to it.
>
> Ling
>
> Drew Gibson  於 2020年10月12日週一 上午4:35寫道：
>
>> Hi,
>>
>> I had a similar issue in the past.  Try updating conda...
>>
>> conda update conda
>>
>> then try creating your RDKit environment again.
>>
>> Drew
>>
>> On Sat, 10 Oct 2020 at 23:47, Ling Chan  wrote:
>>
>>> Dear colleagues,
>>>
>>> I am trying to install RDKit using conda. According to the manual at
>>> https://www.rdkit.org/docs/Install.html#how-to-install-rdkit-with-conda
>>>
>>> it is very simple. I just need to do
>>>
>>> conda create -c rdkit -n my-rdkit-env rdkit
>>>
>>> It used to work. Somehow when I try this again, things are not working. 
>>> When I investigated, it turns out that somehow the 2018.03.2.0 version of 
>>> rdkit was installed instead of the most current one. It seems to me that I 
>>> have screwed up my conda setup. Just wonder what have I screwed up? How can 
>>> I repair it?
>>>
>>> One hint could be found at the message when I did conda create. The line 
>>> for rdkit looks different from the other lines, as indicated below. 
>>> Unfortunately I still could not figure it out.
>>>
>>> Thank you for your insight.
>>>
>>> Ling
>>>
>>>
>>> =
>>>
>>> > conda create -c rdkit -n tempenv rdkit
>>>
>>> The following NEW packages will be INSTALLED:
>>>
>>>   _libgcc_mutex  pkgs/main/linux-64::_libgcc_mutex-0.1-main
>>>   blas   pkgs/main/linux-64::blas-1.0-mkl
>>>   bzip2  pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
>>> 
>>>  python pkgs/main/linux-64::python-3.6.12-hcff3b4d_2
>>>   python-dateutilpkgs/main/noarch::python-dateutil-2.8.1-py_0
>>>   pytz   pkgs/main/noarch::pytz-2020.1-py_0
>>>   rdkit  rdkit/linux-64::rdkit-2018.03.2.0-py36h6bb024c_1
>>>   readline   pkgs/main/linux-64::readline-8.0-h7b6447c_0
>>>   setuptools pkgs/main/linux-64::setuptools-50.3.0-py36hb0f4dca_1
>>>   sixpkgs/main/noarch::six-1.15.0-py_0
>>>  
>>>
>>>
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Re: [Rdkit-discuss] conda install rdkit

2020-10-16 Thread Ling Chan

Thank you Drew for your suggestion. I tried it, but it did not help.

I also did a "conda clean -a" on top of that. Still, when I do
conda create -c rdkit -n rdkenv rdkit
it stubbornly points to
rdkit  rdkit/linux-64::rdkit-2018.03.2.0-py36h6bb024c_1

and as I wrote before, I don't have a ".condarc" file in my home directory.
Moreover, there is no "pinned" file found in any of my conda-meta
directories. And even "conda update rdkit --no-pin" does not update my
rdkit.

I have no idea where it picks up that 2018 rdkit version and sticks to it.

Ling

Drew Gibson  於 2020年10月12日週一 上午4:35寫道：

> Hi,
>
> I had a similar issue in the past.  Try updating conda...
>
> conda update conda
>
> then try creating your RDKit environment again.
>
> Drew
>
> On Sat, 10 Oct 2020 at 23:47, Ling Chan  wrote:
>
>> Dear colleagues,
>>
>> I am trying to install RDKit using conda. According to the manual at
>> https://www.rdkit.org/docs/Install.html#how-to-install-rdkit-with-conda
>>
>> it is very simple. I just need to do
>>
>> conda create -c rdkit -n my-rdkit-env rdkit
>>
>> It used to work. Somehow when I try this again, things are not working. When 
>> I investigated, it turns out that somehow the 2018.03.2.0 version of rdkit 
>> was installed instead of the most current one. It seems to me that I have 
>> screwed up my conda setup. Just wonder what have I screwed up? How can I 
>> repair it?
>>
>> One hint could be found at the message when I did conda create. The line for 
>> rdkit looks different from the other lines, as indicated below. 
>> Unfortunately I still could not figure it out.
>>
>> Thank you for your insight.
>>
>> Ling
>>
>>
>> =
>>
>> > conda create -c rdkit -n tempenv rdkit
>>
>> The following NEW packages will be INSTALLED:
>>
>>   _libgcc_mutex  pkgs/main/linux-64::_libgcc_mutex-0.1-main
>>   blas   pkgs/main/linux-64::blas-1.0-mkl
>>   bzip2  pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0
>> 
>>  python pkgs/main/linux-64::python-3.6.12-hcff3b4d_2
>>   python-dateutilpkgs/main/noarch::python-dateutil-2.8.1-py_0
>>   pytz   pkgs/main/noarch::pytz-2020.1-py_0
>>   rdkit  rdkit/linux-64::rdkit-2018.03.2.0-py36h6bb024c_1
>>   readline   pkgs/main/linux-64::readline-8.0-h7b6447c_0
>>   setuptools pkgs/main/linux-64::setuptools-50.3.0-py36hb0f4dca_1
>>   sixpkgs/main/noarch::six-1.15.0-py_0
>>  
>>
>>
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>>
>
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Re: [Rdkit-discuss] MMFFMolProperties objects

2020-10-16 Thread Paolo Tosco

Hi Ling,

MMFFOptimizeMolecule  is a shorthand that does not allow passing a
MMFFMolProperties object.
Instead, you may follow the approach described in this gist:

https://gistpreview.github.io/?24c2338ce18943da3e878de5585eb83a

Cheers,
p.

On Fri, Oct 16, 2020 at 7:04 AM Ling Chan  wrote:

> Dear colleagues,
>
> I am trying to energy minimize a molecule without the electric term.
>
> I figure that I can use the SetMMFFEleTerm function, as described in
>
> http://rdkit.org/docs/source/rdkit.ForceField.rdForceField.html#rdkit.ForceField.rdForceField.MMFFMolProperties.SetMMFFEleTerm
>
> which operates on a MMFFMolProperties object, which can be obtained using
> MMFFGetMoleculeProperties, as described in
>
> https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html#rdkit.Chem.rdForceFieldHelpers.MMFFGetMoleculeProperties
>
> But there is no MMFFSetMoleculeProperties function. So how can I make use
> of this updated MMFFMolProperties object?
>
> I also tried to see if the SetMMFFEleTerm function can act in place, by
> having
>
> Chem.rdForceFieldHelpers.MMFFGetMoleculeProperties(mol).SetMMFFEleTerm(False)
> prior to
> AllChem.MMFFOptimizeMolecule(mol)
> But this does not work.
>
> Thanks for your help.
>
> Ling Chan
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Re: [Rdkit-discuss] conda install rdkit

Re: [Rdkit-discuss] conda install rdkit

Re: [Rdkit-discuss] conda install rdkit

Re: [Rdkit-discuss] MMFFMolProperties objects

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