rdkit-discuss

[Rdkit-discuss] rdkit installation problem

[kapil d. <kap...@gm...>]

Hi all,

I am new to rdkit and python.
trying to install rdkit in win7(64).
used following command from rdkit docs

*C:\Users\manoj\Desktop\SOFTWARE>conda create -c
https://conda.anaconda.org/rdkit <https://conda.anaconda.org/rdkit>*
* -n my-rdkit-env rdkit*
Fetching package metadata: ......
Solving package specifications: ..........

Package plan for installation in environment C:\Miniconda2\envs\my-rdkit-env:

The following NEW packages will be INSTALLED:

    boost:        1.60.0-py27_vc9_0    [vc9]
    mkl:          11.3.1-0
    msvc_runtime: 1.0.1-vc9_0          [vc9]
    numpy:        1.9.3-py27_1
    pip:          8.1.0-py27_0
    python:       2.7.11-2
    rdkit:        2014.09.2-np19py27_0
    setuptools:   20.2.2-py27_0
    wheel:        0.29.0-py27_0
    zlib:         1.2.8-vc9_2          [vc9]

Proceed ([y]/n)?

Extracting packages ...
[      COMPLETE      ]|##################################################| 100%
Linking packages ...
[      COMPLETE      ]|##################################################| 100%
#
# To activate this environment, use:
# > activate my-rdkit-env
#

*C:\Users\manoj\Desktop\SOFTWARE>activate my-rdkit-env*
Deactivating environment "C:\Miniconda2"...
Activating environment "C:\Miniconda2\envs\my-rdkit-env"...

*[my-rdkit-env] C:\Users\manoj\Desktop\SOFTWARE>python*
Python 2.7.11 |Continuum Analytics, Inc.| (default, Jan 29 2016, 14:26:21) [MSC
v.1500 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> *from rdkit import Chem*
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Miniconda2\envs\my-rdkit-env\lib\site-packages\rdkit\Chem\__init__.py
", line 18, in <module>
    from rdkit import rdBase
ImportError: DLL load failed: The specified module could not be found.

How can I get rid of this error ?
Why it is installing older version ?


-- 

With Kind Regards

Kapil Dhingra

Research Scholar, M.S.(Pharm.),

Department of Pharmacoinformatics,

NIPER, S.A.S. Nagar (*Mohali*), Punjab (India)- 160 062,

Mob. No.: +91 - 7508076738
E-mail id: kap...@gm...

[Rdkit-discuss] rdkit installation problem

[Moorthy S. <che...@gm...>]

Dear rdkit Team,

I was trying to install rdkit using conda, but I still see the error
message "ModuleNotFoundError: No module named 'rdkit'".

The following are my installation process and subsequent errors.
-----------------------------------------------------------------------
 *conda install -c rdkit rdkit=2020*

When I tried to install it using above command, it showed the following
error
Solving Environmen: Failed with initial frozen solve. Retrying with
flexible solve.

I solved the above problem using the following commands

*conda create --name myenv*
*conda activate myenv*

After the above command, it successfully processed to downloading and
extracting packages.  but I still see the error message while importing the
module.

It could be great if you please help solve this issue.

Best Regards
Suresh

[Rdkit-discuss] non-element elements

[Brian P. <Bri...@mo...>]

Hello RDKit people,

Is it possible to modify the properties of elements in the periodic 
table or to create new ones?  Use case: Suppose one had some molecules 
defined in terms of functional groups or united atoms or some other 
entities that are not pure elemental atoms. Could one map these things 
on to unused elements (e.g. my_functional_group --> U) and fix up the 
properties of U so that it had the appropriate valence etc. and could be 
present both in a molecule and in SMARTS patterns so that one could do 
substructure matches within RDKit?

Thanks,
Brian

Re: [Rdkit-discuss] non-element elements

[Francois B. <ml...@li...>]

On 04/02/2021 00:35, Brian Peterson wrote:
> Hello RDKit people,
> 
> Is it possible to modify the properties of elements in the periodic
> table or to create new ones?  Use case: Suppose one had some molecules
> defined in terms of functional groups or united atoms or some other
> entities that are not pure elemental atoms. Could one map these things
> on to unused elements (e.g. my_functional_group --> U) and fix up the
> properties of U so that it had the appropriate valence etc. and could
> be present both in a molecule and in SMARTS patterns so that one could
> do substructure matches within RDKit?

Maybe you can use the isotope number to encode some special meaning
for an atom.

Cf. http://www.rdkit.org/docs/GettingStartedInPython.html

"Other fragmentation approaches"
[...] attachment points are labelled (using isotopes) [...]

Those are preserved in the output SMILES.

> Thanks,
> Brian
> _______________________________________________
> Rdkit-discuss mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] rdkit installation problem

[kapil d. <kap...@gm...>]

Just a reminder for my query...

found some previous solutions ...
installed Microsoft Visual C++ 2010 Redistributable Package (x86)
copied msvcp100 msvcr100 dll in miniconda folder

no luck

should I switch to normal python instead of miniconda ?

On Mon, Mar 14, 2016 at 10:20 AM, kapil dhingra <kap...@gm...>
wrote:

> Hi all,
>
> I am new to rdkit and python.
> trying to install rdkit in win7(64).
> used following command from rdkit docs
>
> *C:\Users\manoj\Desktop\SOFTWARE>conda create -c https://conda.anaconda.org/rdkit <https://conda.anaconda.org/rdkit>*
> * -n my-rdkit-env rdkit*
> Fetching package metadata: ......
> Solving package specifications: ..........
>
> Package plan for installation in environment C:\Miniconda2\envs\my-rdkit-env:
>
> The following NEW packages will be INSTALLED:
>
>     boost:        1.60.0-py27_vc9_0    [vc9]
>     mkl:          11.3.1-0
>     msvc_runtime: 1.0.1-vc9_0          [vc9]
>     numpy:        1.9.3-py27_1
>     pip:          8.1.0-py27_0
>     python:       2.7.11-2
>     rdkit:        2014.09.2-np19py27_0
>     setuptools:   20.2.2-py27_0
>     wheel:        0.29.0-py27_0
>     zlib:         1.2.8-vc9_2          [vc9]
>
> Proceed ([y]/n)?
>
> Extracting packages ...
> [      COMPLETE      ]|##################################################| 100%
> Linking packages ...
> [      COMPLETE      ]|##################################################| 100%
> #
> # To activate this environment, use:
> # > activate my-rdkit-env
> #
>
> *C:\Users\manoj\Desktop\SOFTWARE>activate my-rdkit-env*
> Deactivating environment "C:\Miniconda2"...
> Activating environment "C:\Miniconda2\envs\my-rdkit-env"...
>
> *[my-rdkit-env] C:\Users\manoj\Desktop\SOFTWARE>python*
> Python 2.7.11 |Continuum Analytics, Inc.| (default, Jan 29 2016, 14:26:21) [MSC
> v.1500 64 bit (AMD64)] on win32
> Type "help", "copyright", "credits" or "license" for more information.
> Anaconda is brought to you by Continuum Analytics.
> Please check out: http://continuum.io/thanks and https://anaconda.org
> >>> *from rdkit import Chem*
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "C:\Miniconda2\envs\my-rdkit-env\lib\site-packages\rdkit\Chem\__init__.py
> ", line 18, in <module>
>     from rdkit import rdBase
> ImportError: DLL load failed: The specified module could not be found.
>
> How can I get rid of this error ?
> Why it is installing older version ?
>
>
> --
>
> With Kind Regards
>
> Kapil Dhingra
>
> Research Scholar, M.S.(Pharm.),
>
> Department of Pharmacoinformatics,
>
> NIPER, S.A.S. Nagar (*Mohali*), Punjab (India)- 160 062,
>
> Mob. No.: +91 - 7508076738
> E-mail id: kap...@gm...
>



-- 

Best Regards

Kapil Dhingra

Research Scholar, M.S.(Pharm.),

Department of Pharmacoinformatics,

NIPER, S.A.S. Nagar (*Mohali*), Punjab (India)- 160 062,

Mob. No.: +91 - 7508076738
E-mail id: kap...@gm...

Re: [Rdkit-discuss] rdkit installation problem

[Riccardo V. <ric...@gm...>]

Hi Kapil,

I was able to reproduce the problem, I'm having the impression that this
might be a regression due to changes implemented in conda 4.0+. I couldn't
find a way to use 'conda update' to upgrade the initial configuration to
the latest rdkit package, so - as a shortest term solution - I would
suggest reinstalling the environment from scratch. You should be able to
remove the existing environment with something like

> deactivate my-rdkit-env
> conda remove -n my-rdkit-env --all

and then create it again, but this time specifying the desired rdkit
version:

>conda create -n my-rdkit-env -c rdkit rdkit=2015.*

this should select rdkit 2015.09.2, numpy 1.10 and boost 1.56

I hope that helps, ​please let me know if the problems persist,

Best,
Riccardo

Re: [Rdkit-discuss] rdkit installation problem

[kapil d. <kap...@gm...>]

Hi Riccardo,

Thanks for the solution.
Problem is solved now. This time I installed by explicitly mentioning the
versions of rdkit and boost (2015.09.2 and 1.56.0 resp.)
I think the problem with the previously mentioned command is that,  it was
installing rdkit (2014.09.2) and boost (1.60.0)
Thanks again..

On Tue, Mar 15, 2016 at 1:37 PM, Riccardo Vianello <
ric...@gm...> wrote:

> Hi Kapil,
>
> I was able to reproduce the problem, I'm having the impression that this
> might be a regression due to changes implemented in conda 4.0+. I couldn't
> find a way to use 'conda update' to upgrade the initial configuration to
> the latest rdkit package, so - as a shortest term solution - I would
> suggest reinstalling the environment from scratch. You should be able to
> remove the existing environment with something like
>
> > deactivate my-rdkit-env
> > conda remove -n my-rdkit-env --all
>
> and then create it again, but this time specifying the desired rdkit
> version:
>
> >conda create -n my-rdkit-env -c rdkit rdkit=2015.*
>
> this should select rdkit 2015.09.2, numpy 1.10 and boost 1.56
>
> I hope that helps, ​please let me know if the problems persist,
>
> Best,
> Riccardo
>
>


-- 

Best Regards

Kapil Dhingra

Research Scholar, M.S.(Pharm.),

Department of Pharmacoinformatics,

NIPER, S.A.S. Nagar (*Mohali*), Punjab (India)- 160 062,

Mob. No.: +91 - 7508076738
E-mail id: kap...@gm...