Re: [Rdkit-discuss] cmake error building master

2018-04-19 Thread Greg Landrum 
I've been building with 1.65.1 and 1.63, but I don't think I've tried 1.64
at all.

I will take a look at the other problems tomorrow morning

On Thu, Apr 19, 2018 at 8:12 PM, Jason Biggs  wrote:

> Greg,
> I have boost version 1.64.  I found reference to this error on the web,
> always in reference to boost version 1.64.  But what I don't see is whether
> this is fixed in later or previous versions.
>
> I forgot to include the first error I get, actually during the cmake
> stage, when it tries to download the maeparser tarball.  Somehow the curl
> command isn't downloading the file with the right name.  I get this error
>
> - Found Threads: TRUE
> -- Boost version: 1.64.0
> -- Found the following Boost libraries:
> --   serialization
> == Using strict rotor definition
> Downloading https://codeload.github.com/schrodinger/maeparser/tar.gz/
> 83368293dcc0eb07562dadfb7728b8d18d23a6cb...
>   % Total% Received % Xferd  Average Speed   TimeTime Time
> Current
>  Dload  Upload   Total   SpentLeft
> Speed
> 100 24984  100 249840 0  73460  0 --:--:-- --:--:-- --:--:--
> 274k
> CMake Error at Code/cmake/Modules/RDKitUtils.cmake:198 (MESSAGE):
>   The md5 checksum for
>   base/rdkit/External/CoordGen/master.tar.gz
>   is incorrect; expected: 32c0c3b315bba49fbf4c41a07aa58528, found:
>   d41d8cd98f00b204e9800998ecf8427e
> Call Stack (most recent call first):
>   External/CoordGen/CMakeLists.txt:9 (downloadAndCheckMD5)
>
>
>
> If I go to the Coordgen directory after getting this error, I see the
> following
>
> drwxr-xr-x 3 jasonb users 4.0K Apr 19 13:06 .
> drwxr-xr-x 7 jasonb users 4.0K Apr 19 13:05 ..
> -rw-r--r-- 1 jasonb users  25K Apr 19 13:06 83368293dcc0eb07562dadfb7728b8
> d18d23a6cb
> -rw-r--r-- 1 jasonb users 2.8K Apr 19 13:05 CMakeLists.txt
> -rw-r--r-- 1 jasonb users 5.6K Apr 19 13:05 CoordGen.h
> -rw-r--r-- 1 jasonb users0 Apr 19 13:06 master.tar.gz
> -rw-r--r-- 1 jasonb users  12K Apr 19 13:05 test.cpp
> drwxr-xr-x 2 jasonb users 4.0K Apr 19 13:05 Wrap
>
>
> So the curl command downloaded the tarball as "
> 83368293dcc0eb07562dadfb7728b8d18d23a6cb", and created an empty file
> "master.tar.gz" which of course doesn't match the md5 sum.  I definitely
> don't know enough about cmake, or curl for that matter, to see why this is
> happening.  But if I manually download the maeparser, the coordgenlibs, and
> the rapidjson files and put them in External/ then it works fine.
>
> Thanks,
> Jason
>
>
>
> Jason Biggs
>
>
> On Thu, Apr 19, 2018 at 12:42 PM, Greg Landrum 
> wrote:
>
>> Which version of boost is that?
>>
>> On Thu, 19 Apr 2018 at 19:34, Jason Biggs  wrote:
>>
>>> Trying to build on Scientific Linux release 6.9, and I'm getting boost
>>> serialization errors, both on the recent release branch and on master
>>>
>>>
>>> In file included from base/Boost/include/boost/numer
 ic/ublas/vector.hpp:21:0,
  from base/Boost/include/boost/numer
 ic/ublas/matrix.hpp:18,
  from base/rdkit/Code/GraphMol/Subst
 ruct/ullmann.hpp:41,
  from base/rdkit/Code/GraphMol/Subst
 ruct/SubstructMatch.cpp:29:
 base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
 ‘void boost::numeric::ublas::unbounded_array::serialize(Archive&, unsigned int)’:
 base/Boost/include/boost/numeric/ublas/storage.hpp:299:18: error:
 ‘make_array’ is not a member of ‘boost::serialization’
  ar & serialization::make_array(data_, s);
   ^
 base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
 ‘void boost::numeric::ublas::bounded_array::serialize(Archive&, unsigned int)’:
 base/Boost/include/boost/numeric/ublas/storage.hpp:494:18: error:
 ‘make_array’ is not a member of ‘boost::serialization’
  ar & serialization::make_array(data_, s);
>>>
>>>
>>>
>>> If I add
>>>
>>> #include 
>>>
>>>
>>> to the SubstructMatch.cpp file, as instructed here
>>> https://stackoverflow.com/q/44534516/4712538, then compilation
>>> continues fine.
>>>
>>>
>>> Jason
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot__
>>> _
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
>
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Re: [Rdkit-discuss] cmake error building master

2018-04-19 Thread Jason Biggs 
Greg,
I have boost version 1.64.  I found reference to this error on the web,
always in reference to boost version 1.64.  But what I don't see is whether
this is fixed in later or previous versions.

I forgot to include the first error I get, actually during the cmake stage,
when it tries to download the maeparser tarball.  Somehow the curl command
isn't downloading the file with the right name.  I get this error

- Found Threads: TRUE
-- Boost version: 1.64.0
-- Found the following Boost libraries:
--   serialization
== Using strict rotor definition
Downloading
https://codeload.github.com/schrodinger/maeparser/tar.gz/83368293dcc0eb07562dadfb7728b8d18d23a6cb.
..
  % Total% Received % Xferd  Average Speed   TimeTime Time
Current
 Dload  Upload   Total   SpentLeft
Speed
100 24984  100 249840 0  73460  0 --:--:-- --:--:-- --:--:--
274k
CMake Error at Code/cmake/Modules/RDKitUtils.cmake:198 (MESSAGE):
  The md5 checksum for
  base/rdkit/External/CoordGen/master.tar.gz
  is incorrect; expected: 32c0c3b315bba49fbf4c41a07aa58528, found:
  d41d8cd98f00b204e9800998ecf8427e
Call Stack (most recent call first):
  External/CoordGen/CMakeLists.txt:9 (downloadAndCheckMD5)



If I go to the Coordgen directory after getting this error, I see the
following

drwxr-xr-x 3 jasonb users 4.0K Apr 19 13:06 .
drwxr-xr-x 7 jasonb users 4.0K Apr 19 13:05 ..
-rw-r--r-- 1 jasonb users  25K Apr 19 13:06
83368293dcc0eb07562dadfb7728b8d18d23a6cb
-rw-r--r-- 1 jasonb users 2.8K Apr 19 13:05 CMakeLists.txt
-rw-r--r-- 1 jasonb users 5.6K Apr 19 13:05 CoordGen.h
-rw-r--r-- 1 jasonb users0 Apr 19 13:06 master.tar.gz
-rw-r--r-- 1 jasonb users  12K Apr 19 13:05 test.cpp
drwxr-xr-x 2 jasonb users 4.0K Apr 19 13:05 Wrap


So the curl command downloaded the tarball as
"83368293dcc0eb07562dadfb7728b8d18d23a6cb",
and created an empty file "master.tar.gz" which of course doesn't match the
md5 sum.  I definitely don't know enough about cmake, or curl for that
matter, to see why this is happening.  But if I manually download the
maeparser, the coordgenlibs, and the rapidjson files and put them in
External/ then it works fine.

Thanks,
Jason



Jason Biggs


On Thu, Apr 19, 2018 at 12:42 PM, Greg Landrum 
wrote:

> Which version of boost is that?
>
> On Thu, 19 Apr 2018 at 19:34, Jason Biggs  wrote:
>
>> Trying to build on Scientific Linux release 6.9, and I'm getting boost
>> serialization errors, both on the recent release branch and on master
>>
>>
>> In file included from base/Boost/include/boost/
>>> numeric/ublas/vector.hpp:21:0,
>>>  from base/Boost/include/boost/
>>> numeric/ublas/matrix.hpp:18,
>>>  from base/rdkit/Code/GraphMol/Substruct/ullmann.hpp:41,
>>>  from base/rdkit/Code/GraphMol/
>>> Substruct/SubstructMatch.cpp:29:
>>> base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
>>> ‘void boost::numeric::ublas::unbounded_array>> ALLOC>::serialize(Archive&, unsigned int)’:
>>> base/Boost/include/boost/numeric/ublas/storage.hpp:299:18: error:
>>> ‘make_array’ is not a member of ‘boost::serialization’
>>>  ar & serialization::make_array(data_, s);
>>>   ^
>>> base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
>>> ‘void boost::numeric::ublas::bounded_array>> ALLOC>::serialize(Archive&, unsigned int)’:
>>> base/Boost/include/boost/numeric/ublas/storage.hpp:494:18: error:
>>> ‘make_array’ is not a member of ‘boost::serialization’
>>>  ar & serialization::make_array(data_, s);
>>
>>
>>
>> If I add
>>
>> #include 
>>
>>
>> to the SubstructMatch.cpp file, as instructed here
>> https://stackoverflow.com/q/44534516/4712538, then compilation continues
>> fine.
>>
>>
>> Jason
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot__
>> _
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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Re: [Rdkit-discuss] cmake error building master

2018-04-19 Thread Greg Landrum 
Which version of boost is that?

On Thu, 19 Apr 2018 at 19:34, Jason Biggs  wrote:

> Trying to build on Scientific Linux release 6.9, and I'm getting boost
> serialization errors, both on the recent release branch and on master
>
>
> In file included from
>> base/Boost/include/boost/numeric/ublas/vector.hpp:21:0,
>>  from
>> base/Boost/include/boost/numeric/ublas/matrix.hpp:18,
>>  from base/rdkit/Code/GraphMol/Substruct/ullmann.hpp:41,
>>  from
>> base/rdkit/Code/GraphMol/Substruct/SubstructMatch.cpp:29:
>> base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
>> ‘void boost::numeric::ublas::unbounded_array::serialize(Archive&,
>> unsigned int)’:
>> base/Boost/include/boost/numeric/ublas/storage.hpp:299:18: error:
>> ‘make_array’ is not a member of ‘boost::serialization’
>>  ar & serialization::make_array(data_, s);
>>   ^
>> base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
>> ‘void boost::numeric::ublas::bounded_array> ALLOC>::serialize(Archive&, unsigned int)’:
>> base/Boost/include/boost/numeric/ublas/storage.hpp:494:18: error:
>> ‘make_array’ is not a member of ‘boost::serialization’
>>  ar & serialization::make_array(data_, s);
>
>
>
> If I add
>
> #include 
>
>
> to the SubstructMatch.cpp file, as instructed here
> https://stackoverflow.com/q/44534516/4712538, then compilation continues
> fine.
>
>
> Jason
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
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[Rdkit-discuss] cmake error building master

2018-04-19 Thread Jason Biggs 
Trying to build on Scientific Linux release 6.9, and I'm getting boost
serialization errors, both on the recent release branch and on master


In file included from
> base/Boost/include/boost/numeric/ublas/vector.hpp:21:0,
>  from base/Boost/include/boost/numeric/ublas/matrix.hpp:18,
>  from base/rdkit/Code/GraphMol/Substruct/ullmann.hpp:41,
>  from
> base/rdkit/Code/GraphMol/Substruct/SubstructMatch.cpp:29:
> base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
> ‘void boost::numeric::ublas::unbounded_array::serialize(Archive&,
> unsigned int)’:
> base/Boost/include/boost/numeric/ublas/storage.hpp:299:18: error:
> ‘make_array’ is not a member of ‘boost::serialization’
>  ar & serialization::make_array(data_, s);
>   ^
> base/Boost/include/boost/numeric/ublas/storage.hpp: In member function
> ‘void boost::numeric::ublas::bounded_array ALLOC>::serialize(Archive&, unsigned int)’:
> base/Boost/include/boost/numeric/ublas/storage.hpp:494:18: error:
> ‘make_array’ is not a member of ‘boost::serialization’
>  ar & serialization::make_array(data_, s);



If I add

#include 


to the SubstructMatch.cpp file, as instructed here
https://stackoverflow.com/q/44534516/4712538, then compilation continues
fine.


Jason
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[Rdkit-discuss] optimised geometry

2018-04-19 Thread Mariana Assmann 

Hi,

I am creating conformers and want to optimise them (MMFF94). Is it 
possible to extract the xyz coordinates or a z-matrix for the molecules 
afterwards? (I did find the Get3DDistanceMatrix method). Is the input 
for the MMFF94 the distance matrix?


Thanks,
Mariana

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