[Rdkit-discuss] I set up a rdkit-users-jp

2017-06-22 Thread 久保竜一 
Hi there!

I set up a group for RDKit users in Japan, rdkit-users-jp.
We will discuss about using RDKit, documents translation in Japanese, and
so on.

Please join us freely.

ML: https://groups.google.com/forum/#!forum/rdkit-users-jp
WEB: https://rdkit-users-jp.github.io/
Twitter: hash_tag #rdkitjp

best regards,
kubor

---
Ryuichi KUBO
Twitter: @kubor_
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Re: [Rdkit-discuss] RMSD value between two non-covalent molecular complexes

2017-06-22 Thread Francois BERENGER 

On 06/22/2017 11:20 PM, gosia olejniczak wrote:

Hi again,

i found where the problem was (it seems):

as i was reading in molecules from sdf file through "SDMolSupplier" by 
doing:


suppl = Chem.SDMolSupplier(filename)

the hydrogen atoms were removed (what was not obvious since e.g. 
GetNumAtoms with "heavy" flag was returning the total number of atoms - 
including hydrogens, but none of the functions like "GetAtomIdx" etc. 
was seeing hydrogens - i looked in the code, maybe it is because in the 
"Code/GraphMol/ROMol.cpp" in all such functions the "GetNumAtoms" and 
not "GetNumHeavyAtoms" is called?)


then i guess that it must have messed up something somewhere, so that 
instead of seeing "x+h2o" the code did as if there was only "x" on a file


but if i read in the molecules as:
suppl = Chem.SDMolSupplier(filename, removeHs=False)


I was also surprised recently by this quite unfortunate default 
parameter value, when reading some carefully prepared 3D conformers, 
with hydrogens and partial charges ...


then all seems to be ok (rmsd values seem to include h2o; also h2o are 
drawn with py3Dmol);


best regards,
gosia



2017-06-21 16:37 GMT+02:00 gosia olejniczak >:


Hi Paolo,

Thank you for the prompt answer!

i'll try it out, but:
- the whole complex "X+h2o" is read from one sdf file
- Chem.Mol.GetNumAtoms gives the correct number of atoms (= it
includes h2o) [*]

so i'm wondering what is the best way to specify two fragments "x"
and "h2o", so that i could use them as arguments to CombineMols()?
does it make sense to:
1. search for h2o pattern in "x+h2o" (GetSubstructMatch)
2. remove h2o from the "x+h2o" complex (DeleteSubstruct) and get
only "x" -> save it
3. remove x from the "x+h2o" complex (DeleteSubstruct) and get only
"h2o" -> save it
4. then finally use CombineMols() with separate fragments from 2.
and 3.?
that seems a bit silly, maybe there is a simpler way?

thank you!
all the best,
gosia

[*] still, the plot of its 3D structure drawn with py3Dmol only
shows "x" and not "x+h2o"...

2017-06-21 16:01 GMT+02:00 Paolo Tosco mailto:paolo.to...@unito.it>>:

Hi Gosia,

you may want to look at the CombineMols() function in the
rdmolops module. If you make a single molecule out of the two
fragments, then you should manage to get what you are looking for.

Cheers,
p.


On 06/21/17 14:47, gosia olejniczak wrote:

dear RDKit experts,

is it possible to calculate RMSD value between two
non-covalent molecular complexes?

For instance:
complex1: X(conformer1) + H2O
complex2: X(conformer2) + H2O

i tried GetBestRMS and GetO3A.Align but the program clearly
neglects H2O and calculates the RMSD only between
X(conformer1) and X(conformer2)

thank you!
best regards,
gosia



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Re: [Rdkit-discuss] Is there a Ubuntu ppa or some repository with the latest rdkit release as .deb ?

2017-06-22 Thread Dimitri Maziuk 

On 2017-06-22 01:36, Francois BERENGER wrote:


make deb # in rdkit source tree

Some people might ask for a make rpm target also.


You'd have to track any changes that redhat, canonical, suse, and 
whoever else's out there might make to e.g. filesystem layout, linked 
libraries, python and so on.


There is snap packages and AppImage packages. I've no idea if either is 
suitable for shared libraries with python libraries etc.


I'd just grab the newer source .deb and try to build it on your system.

Dima


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Re: [Rdkit-discuss] RMSD value between two non-covalent molecular complexes

2017-06-22 Thread gosia olejniczak 
Hi again,

i found where the problem was (it seems):

as i was reading in molecules from sdf file through "SDMolSupplier" by
doing:

suppl = Chem.SDMolSupplier(filename)

the hydrogen atoms were removed (what was not obvious since e.g.
GetNumAtoms with "heavy" flag was returning the total number of atoms -
including hydrogens, but none of the functions like "GetAtomIdx" etc. was
seeing hydrogens - i looked in the code, maybe it is because in the
"Code/GraphMol/ROMol.cpp" in all such functions the "GetNumAtoms" and not
"GetNumHeavyAtoms" is called?)

then i guess that it must have messed up something somewhere, so that
instead of seeing "x+h2o" the code did as if there was only "x" on a file

but if i read in the molecules as:
suppl = Chem.SDMolSupplier(filename, removeHs=False)

then all seems to be ok (rmsd values seem to include h2o; also h2o are
drawn with py3Dmol);

best regards,
gosia



2017-06-21 16:37 GMT+02:00 gosia olejniczak :

> Hi Paolo,
>
> Thank you for the prompt answer!
>
> i'll try it out, but:
> - the whole complex "X+h2o" is read from one sdf file
> - Chem.Mol.GetNumAtoms gives the correct number of atoms (= it includes
> h2o) [*]
>
> so i'm wondering what is the best way to specify two fragments "x" and
> "h2o", so that i could use them as arguments to CombineMols()?
> does it make sense to:
> 1. search for h2o pattern in "x+h2o" (GetSubstructMatch)
> 2. remove h2o from the "x+h2o" complex (DeleteSubstruct) and get only "x"
> -> save it
> 3. remove x from the "x+h2o" complex (DeleteSubstruct) and get only "h2o"
> -> save it
> 4. then finally use CombineMols() with separate fragments from 2. and 3.?
> that seems a bit silly, maybe there is a simpler way?
>
> thank you!
> all the best,
> gosia
>
> [*] still, the plot of its 3D structure drawn with py3Dmol only shows "x"
> and not "x+h2o"...
>
> 2017-06-21 16:01 GMT+02:00 Paolo Tosco :
>
>> Hi Gosia,
>>
>> you may want to look at the CombineMols() function in the rdmolops
>> module. If you make a single molecule out of the two fragments, then you
>> should manage to get what you are looking for.
>>
>> Cheers,
>> p.
>>
>>
>> On 06/21/17 14:47, gosia olejniczak wrote:
>>
>> dear RDKit experts,
>>
>> is it possible to calculate RMSD value between two non-covalent molecular
>> complexes?
>>
>> For instance:
>> complex1: X(conformer1) + H2O
>> complex2: X(conformer2) + H2O
>>
>> i tried GetBestRMS and GetO3A.Align but the program clearly neglects H2O
>> and calculates the RMSD only between X(conformer1) and X(conformer2)
>>
>> thank you!
>> best regards,
>> gosia
>>
>>
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>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-22 Thread JP 
Just to give this closure on the list -- the problem was that I had static
libraries for boost (.a files).  Once I rebuilt boost as shared libraries
(.so) everything worked fine.

Thanks to Greg and Paolo for their help.

On 21 June 2017 at 11:02, Greg Landrum  wrote:

> Let's move this off the list for a bit until we get it resolved.
>
> Can you please do: "VERBOSE=1 make testReaction" and send the output just
> to me?
>
> Thanks,
> -greg
>
>
> On Wed, Jun 21, 2017 at 10:24 AM, JP  wrote:
>
>> Looks like it is finding the correct version of boost (and it is finding
>> boost serialize).
>>
>> /opt/rdkit/rdkit-Release_2017_03_2/build$ cmake -D
>> RDK_BUILD_INCHI_SUPPORT=ON -D BOOST_ROOT=/opt/boost_1_61_0/ -D
>> Boost_NO_SYSTEM_PATHS=ON ..
>> -- Could NOT find InChI in system locations (missing:  INCHI_LIBRARY
>> INCHI_INCLUDE_DIR)
>> CUSTOM_INCHI_PATH = /opt/rdkit/rdkit-Release_2017_03_2/External/INCHI-API
>> -- Found InChI software locally
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> --   python
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> --   thread
>> --   system
>> --   chrono
>> --   date_time
>> --   atomic
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> --   serialization
>> == Using strict rotor definition
>> == Updating Filters.cpp from pains file
>> == Done updating pains files
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> --   regex
>> -- Configuring done
>> -- Generating done
>> -- Build files have been written to: /opt/rdkit/rdkit-Release_2017_
>> 03_2/build
>>
>> But the error prevails.
>>
>> If I set up rdkit to use just the system wide boost (1.58), not my
>> specific install (1.61), rdkit builds successfully.  I do this by clearing
>> BOOST_ROOT, LD_LIBRARY_PATH, and removing the boost-related cmake flags.
>> So this is certainly an issue with wrong libraries being picked up.
>>
>>
>>
>>
>> On 21 June 2017 at 07:29, Greg Landrum  wrote:
>>
>>> did you build boost serialize?
>>>
>>> On Mon, Jun 19, 2017 at 12:03 PM, JP 
>>> wrote:
>>>
 Hi Greg !

 Unfortunately that didn't help (I delete everything in my build
 directory, then):

 cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
 -DBoost_NO_SYSTEM_PATHS=ON ..

 and make as usual.

 [ 62%] Linking CXX executable testReaction
 ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
 to `boost::archive::text_iarchive_impl>>> chive>::load_override(boost::archive::class_name_type&)'
 ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
 to 
 `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
 const&)'
 collect2: error: ld returned 1 exit status
 Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
 recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
 make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
 CMakeFiles/Makefile2:4157: recipe for target
 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
 make[1]: *** [Code/GraphMol/ChemReactions/C
 MakeFiles/testReaction.dir/all] Error 2
 Makefile:160: recipe for target 'all' failed
 make: *** [all] Error 2

 Perhaps this isn't related to the system vs user-install, boost after
 all?


 On 19 June 2017 at 10:38, Greg Landrum  wrote:

> If you have a system boost install that you do not want to use, you
> should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake 
> arguments.
> This will (well, should) disable any usage of the system boost.
>
> -greg
>
>
> On Mon, Jun 19, 2017 at 9:39 AM, JP 
> wrote:
>
>> HI Paul,
>>
>> Funny you should mention that.  I have boost 1.61 (installed manually
>> in /opt) and system boost I installed via sudo apt-get install
>>
>> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev |
>> grep 'Version'
>> Version: 1.58.0.1ubuntu1
>>
>> However I pass the BOOST path to cmake via:
>>
>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
>>  ..
>>
>> (I also have the $BOOST_ROOT env variable set, so I think that is
>> redundant.  Whatever).  cmake output clearly shows it is finding/using
>> boost 1.61
>>
>> Using make VERBOSE=1 I get:
>>
>> [ 62%] Linking CXX executable testReaction
>> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions
>> && /usr/bin/cmake -E cmake_link_script 
>> CMakeFiles/testReaction.dir/link.txt
>> --verbose=1
>> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function
>> -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG
>> CMakeFiles/testReaction.dir/testReaction.cpp.o  -o testReaction
>> -rdynamic ../../../lib/libRDKitChemReactions.so.1.201