Re: [Rdkit-discuss] Having trouble getting RDKIT to recognize LiAsF6

[Greg Landrum]

On Fri, Nov 24, 2017 at 10:32 PM, Yoolhee Kim 
wrote:

>
> Thank you for your reply!
>
> I'm not super familiar with RDKIT... could you please elaborate on how to
> fix this problem?
>
>
Ah, sorry, it's something that needs to be fixed in the C++ code. The bug
report is filed:
https://github.com/rdkit/rdkit/issues/1668
and a fix is on the way.

-greg
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[Rdkit-discuss] RPM maintenance status

[Gianluca Sforna]

Hi all,
I just realized I was unsubscribed from this list since some time so I
got back on the train.

For those wondering about the current status of the rdkit RPM package
in Fedora (and CentOS/RHEL via EPEL), I didn't abandoned maintenance
but, unfortunately, the latest few releases were impossibile to build
due to test failures in various architectures (we have half dozen of
them, little endian, big endian, you name it...).
If you want to have an idea about the situation, just have a look at:
https://koji.fedoraproject.org/koji/taskinfo?taskID=23207024
where I attempted a build of the latest release for Fedora rawhide
(a.k.a Fedora 28)

For now, I started filing bugs related to these failures, see for instance:
https://github.com/rdkit/rdkit/issues/1661
https://github.com/rdkit/rdkit/issues/1662
https://github.com/rdkit/rdkit/issues/1671
https://github.com/rdkit/rdkit/issues/1672
https://github.com/rdkit/rdkit/issues/1674

As soon we will have tests passing I will surely submit updates for
Fedora and CentOS/RHEL via EPEL. Of course, any help with the above
issues would be greatly appreciated.

In the meanwhile, I updated the packages in:
https://copr.fedorainfracloud.org/coprs/giallu/rdkit/

x86_64 only for Fedora 26, Fedora 27 and RHEL/CentOS 7

Hope that helps

Gianluca

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http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
Tinker Garage - http://tinkergarage.it

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Re: [Rdkit-discuss] Stop bond highlights

[Greg Landrum]

Hi Nick,

When you import IPythonConsole it monkey patches the substructure function
so that it saves info about the results when you do a substructure search
on a molecule.
The data member is called __sssAtoms, and if you delete that you should no
longer get the coloring:
Heres a bit of demo:

In [1]: from rdkit import Chem

In [2]: from rdkit.Chem.Draw import IPythonConsole

In [3]: m = Chem.MolFromSmiles('CCOC')

In [4]: m.GetSubstructMatch(Chem.MolFromSmiles('CO'))
Out[4]: (1, 2)

In [5]: m.__sssAtoms
Out[5]: [1, 2]

In [7]: del m.__sssAtoms


You, of course, need to check that the data member is there.

If you're unlikely to want to see highlighting at all, it's easier to just
turn if off:

In [12]: IPythonConsole.highlightSubstructs=False

In [13]: m.GetSubstructMatch(Chem.MolFromSmiles('CO'))
Out[13]: (1, 2)

In [14]: m.__sssAtoms
Out[14]: []



I hope this helps,
-greg



On Thu, Nov 23, 2017 at 2:05 PM, Nicholas Firth 
wrote:

> Howdy RDKitters,
>
> Been a while since I used this list, so forgive me if my question is
> silly.
>
> I'm seeing some weird behaviour from drawing molecules. I've got some
> wrapper classes that I'm using to write some de novo design code, which
> involves fragmenting molecules, and I've obviously been fairly lax with my
> namespacing. Essentially when I fragment my molecule the first bond that is
> cut is highlighted when I draw the original molecule but the rest of the
> cuts aren't (because I reassign variables). There's an example of what I
> mean here  (https://i.imgur.com/
> kvb3YyG.png)
>
> I tried to ClearComputedProps on the molecule but it still highlights the
> bond, does anyone know of a way to clear this from the molecule so that it
> doesn't get drawn? I'm going to clear up my programming issues to stop this
> particular artefact, but it would definitely be helpful to understand this
> for the rest of my code.
>
> Cheers,
> Nick
>
> 
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Re: [Rdkit-discuss] RPM distros

[Tim Dudgeon]

I got round to testing the debs and rpms but without success.

For the debs the following were built:

RDKit-2018.03.1.dev1-Linux-Development.deb
RDKit-2018.03.1.dev1-Linux-Extras.deb
RDKit-2018.03.1.dev1-Linux-Python.deb
RDKit-2018.03.1.dev1-Linux-Runtime.deb

On a clean Ubuntu Xenial system, with just python added (apt-get -y 
install python) the packages installed fine:


# dpkg -i *.deb
Selecting previously unselected package rdkit-development.
(Reading database ... 5666 files and directories currently installed.)
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Development.deb ...
Unpacking rdkit-development (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-extras.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Extras.deb ...
Unpacking rdkit-extras (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-python.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Python.deb ...
Unpacking rdkit-python (2018.03.1.dev1) ...
Selecting previously unselected package rdkit-runtime.
Preparing to unpack RDKit-2018.03.1.dev1-Linux-Runtime.deb ...
Unpacking rdkit-runtime (2018.03.1.dev1) ...
Setting up rdkit-development (2018.03.1.dev1) ...
Setting up rdkit-extras (2018.03.1.dev1) ...
Setting up rdkit-python (2018.03.1.dev1) ...
Setting up rdkit-runtime (2018.03.1.dev1) ...

There seem to be header files in /usr/include/rdkit and the RDKit 
installation (.py and .so files) in /usr/lib/python2.7/dist-packages/rdkit


But RDKit doesn't work from Python:

# python
Python 2.7.12 (default, Nov 19 2016, 06:48:10)
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rdkit
Traceback (most recent call last):
  File "", line 1, in 
  File "/usr/lib/python2.7/dist-packages/rdkit/__init__.py", line 2, in 


    from .rdBase import rdkitVersion as __version__
ImportError: libpython2.7.so.1.0: cannot open shared object file: No 
such file or directory

>>>


For the rpms the story is similar. The same 4 files are built as rpms.
Installing them on a clean centos7 machine went fine and the files seem 
to get installed to the same places.

But RDKit again couldn't be used from Python, but with a different error:

# python
Python 2.7.5 (default, Aug  4 2017, 00:39:18)
[GCC 4.8.5 20150623 (Red Hat 4.8.5-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rdkit
Traceback (most recent call last):
  File "", line 1, in 
ImportError: No module named rdkit
>>>


On 15/11/2017 20:18, David Hall wrote:

apt install rpm

should get you rpmbuild

-David

On Nov 15, 2017, at 2:59 PM, Tim Dudgeon > wrote:


OK, makes sense, but I'm building on a Debian system. So neither 'yum 
install rpm-build' nor 'apt-get install rpm-build' doesn't work.


So (sorry for the stupid question) can DEBs only be built on a Debian 
based system and RPMs om a Red Hat based system?



On 15/11/2017 19:31, Paolo Tosco wrote:


Hi Tim,

It looks like you are missing the rpmbuild binary on the machine 
where you are trying to build the RPM.

Issuing a

yum install rpm-build

as root should get it installed.

Cheers,
p.

On 11/15/17 19:00, Tim Dudgeon wrote:


So this now seems to have been merged to master so I gave it a try:

root@f083c3e3b6a1:/rdkit/build# cmake -DRDK_BUILD_INCHI_SUPPORT=ON 
-DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/usr/ ..
-- Could NOT find InChI in system locations (missing:  
INCHI_LIBRARY INCHI_INCLUDE_DIR)

CUSTOM_INCHI_PATH = /rdkit/External/INCHI-API
-- Found InChI software locally
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   python
Python Install directory /usr/lib/python2.7/dist-packages
-- Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR 
EIGEN3_VERSION_OK) (Required is at least version "2.91.0")

Eigen3 not found, disabling the Descriptors3D build.
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   thread
--   system
--   chrono
--   date_time
--   atomic
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   serialization
== Using strict rotor definition
== Updating Filters.cpp from pains file
== Done updating pains files
-- Boost version: 1.62.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: /rdkit/build


root@f083c3e3b6a1:/rdkit/build# cpack -G DEB
CPack: Create package using DEB
CPack: Install projects
CPack: - Run preinstall target for: RDKit
CPack: - Install project: RDKit
CPack: -   Install component: runtime
CPack: -   Install component: base
CPack: -   Install component: data
CPack: -   Install component: docs
CPack: -   Install component: dev
CPack: -   Install component: python
CPack: -   Install component: extras
CPack: Create package
CPack: - package: 
/rdkit/build/RDKit-2018.03.1.dev1-Linux-Development.deb generated.
CPack: - package: 
/rdkit/build/RDKit-2018.03.1.dev1-Linux-Extras.deb generated.