date:20161003

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Greg Landrum

Hmmm, I didn't see anything below that looks odd.
It's difficult for me to provide any more detailed help at the moment since
I'm on vacation and don't have access to either my linux machine or to a
good network connection (to get a proper docker environment set up).

David Hall's suggestion to just specify the python executable for cmake is
a good one.
Or you could try setting the alias:
alias python='/usr/bin/python3'
in your .bashrc file.
In either case, deleting the existing build directory and starting from
scratch (part of David's suggestion) is a good one.

Best,
-greg

On Mon, Oct 3, 2016 at 7:59 PM, Philip Adler  wrote:

> Greg (with apologies for the repeat for the benefit of the mailing list
> -gmail is great up until it isn't!),
>
> Please see below,
>
>
--
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Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread David Hall

What happens if you do this instead?

cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DPYTHON_EXECUTABLE=/usr/bin/python3.4
..

That seems to work for me on Ubuntu 14.04, also, delete your entire build
directory and make it again before running the command.

-David


On Mon, Oct 3, 2016 at 11:05 AM, Philip Adler  wrote:

> Dear All,
>
> I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as per
> the instructions at http://www.rdkit.org/docs/Install.html For reasons
> which I don't really want to get into we would prefer to avoid anaconda for
> the time being.
>
> That being said, when I try to test the build, I get a number of errors
> and failed tests (the build does not work when called from Python, which is
> unsurprising).
>
> For reference, the cmake command I issued was:
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D PYTHON_LIBRARY=/usr/lib/python
> 3.4/config-3.4m-x86_64-linux-gnu/libpython3.4.so -D
> PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
> PYTHON_EXECUTABLE=/usr/bin/python3.4 -DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/
> ..
>
> The tests which fail are as follows:
>
> The following tests FAILED:
>   5 - pyBV (SEGFAULT)
>   6 - pyDiscreteValueVect (SEGFAULT)
>   7 - pySparseIntVect (SEGFAULT)
>   8 - pyFPB (SEGFAULT)
>  11 - testPyGeometry (SEGFAULT)
>  14 - pyAlignment (Failed)
>  18 - pyForceFieldConstraints (SEGFAULT)
>  20 - pyDistGeom (Failed)
>  33 - pyDepictor (SEGFAULT)
>  45 - pyChemReactions (SEGFAULT)
>  50 - pyFilterCatalog (SEGFAULT)
>  52 - pyFragCatalog (SEGFAULT)
>  54 - pyMolDescriptors (SEGFAULT)
>  57 - pyPartialCharges (SEGFAULT)
>  59 - pyMolTransforms (SEGFAULT)
>  63 - pyForceFieldHelpers (SEGFAULT)
>  65 - pyDistGeom (SEGFAULT)
>  67 - pyMolAlign (SEGFAULT)
>  69 - pyChemicalFeatures (SEGFAULT)
>  71 - pyShapeHelpers (SEGFAULT)
>  73 - pyMolCatalog (SEGFAULT)
>  75 - pyMolDraw2D (SEGFAULT)
>  77 - pyFMCS (SEGFAULT)
>  80 - pyMolHash (SEGFAULT)
>  82 - pyMMPA (SEGFAULT)
>  84 - pyReducedGraphs (SEGFAULT)
>  86 - pySLNParse (SEGFAULT)
>  87 - pyGraphMolWrap (SEGFAULT)
>  88 - pyTestConformerWrap (SEGFAULT)
>  89 - pyTestThreads (SEGFAULT)
>  92 - pyMatCalc (SEGFAULT)
>  93 - pySimDivPickers (SEGFAULT)
>  94 - pyRanker (Failed)
>  96 - pyFeatures (SEGFAULT)
>  97 - pythonTestDbCLI (Failed)
>  98 - pythonTestDirML (Failed)
>  99 - pythonTestDirDataStructs (Failed)
> 101 - pythonTestDirSimDivFilters (Failed)
> 102 - pythonTestDirVLib (Failed)
> 103 - pythonTestDirChem (SEGFAULT)
>
> I must confess I'm a little out of my depth right now, so I don't even
> know where to begin debugging this. Any advice would be greatly appreciated,
>
> Best,
>
> Phil
>
> 
> --
> 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@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Brian Kelley

Phillip,  if you run

ctest --debug

This may help us diagnose the issue with paths and such.  Note that you will 
get a LOT of output.


Brian Kelley

> On Oct 3, 2016, at 4:05 PM, Philip Adler  wrote:
> 
> it does not seem that I am missing any dependencies.
> 
>> On Mon, Oct 3, 2016 at 3:55 PM, Paolo Tosco  wrote:
>> Hi Philip,
>> 
>> Just wondering if CMake is pulling in Python 2.7 because you are missing 
>> some Python dependencies on 3.4 (e.g., NumPy)?
>> 
>> p.
>> 
>>> On 3 Oct 2016, at 20:47, Philip Adler  wrote:
>>> 
>>> Those variables were set correctly in my CMakeCache.txt.
>>> 
 On Mon, Oct 3, 2016 at 2:47 PM, Peter Gedeck  
 wrote:
 You can also check the CMakeCache.txt file in the build directory. When I 
 last compiled for 3.5 on the Mac, I had to correct the PYTHON_INCLUDE_DIR. 
 
 Greg, PYTHON_INCLUDE_DIR was incorrectly set after "cmake ..". Executable 
 and library correctly found. 
 
 
 //Path to a program.
 PYTHON_EXECUTABLE:FILEPATH=/Users/peter/miniconda3/bin/python
 //Path to a file.
 PYTHON_INCLUDE_DIR:PATH=/System/Library/Frameworks/Python.framework/Headers
 //Path to a library.
 PYTHON_LIBRARY:FILEPATH=/Users/peter/miniconda3/lib/libpython3.5m.dylib
 
 
 Best,
 
 Peter
 
 
 
 
> On Mon, Oct 3, 2016 at 2:00 PM Philip Adler  wrote:
> Greg (with apologies for the repeat for the benefit of the mailing list 
> -gmail is great up until it isn't!),
> 
> Please see below,
> 
> import _frozen_importlib # frozen
> import imp # builtin
> import sys # builtin
> # installing zipimport hook
> # installed zipimport hook
> # /usr/lib/python3.4/encodings/__pycache__/__init__.cpython-34.pyc 
> matches /usr/lib/python3.4/encodings/__init__.py
> # code object from 
> '/usr/lib/python3.4/encodings/__pycache__/__init__.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc matches 
> /usr/lib/python3.4/codecs.py
> # code object from '/usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc'
> import 'codecs' # <_frozen_importlib.SourceFileLoader object at 
> 0x7f5aa7a14dd8>
> # /usr/lib/python3.4/encodings/__pycache__/aliases.cpython-34.pyc matches 
> /usr/lib/python3.4/encodings/aliases.py
> # code object from 
> '/usr/lib/python3.4/encodings/__pycache__/aliases.cpython-34.pyc'
> import 'encodings.aliases' # <_frozen_importlib.SourceFileLoader object 
> at 0x7f5aa7a2a908>
> import 'encodings' # <_frozen_importlib.SourceFileLoader object at 
> 0x7f5aa7a149b0>
> # /usr/lib/python3.4/encodings/__pycache__/utf_8.cpython-34.pyc matches 
> /usr/lib/python3.4/encodings/utf_8.py
> # code object from 
> '/usr/lib/python3.4/encodings/__pycache__/utf_8.cpython-34.pyc'
> import 'encodings.utf_8' # <_frozen_importlib.SourceFileLoader object at 
> 0x7f5aa79b75f8>
> # /usr/lib/python3.4/encodings/__pycache__/latin_1.cpython-34.pyc matches 
> /usr/lib/python3.4/encodings/latin_1.py
> # code object from 
> '/usr/lib/python3.4/encodings/__pycache__/latin_1.cpython-34.pyc'
> import 'encodings.latin_1' # <_frozen_importlib.SourceFileLoader object 
> at 0x7f5aa79b9160>
> # /usr/lib/python3.4/__pycache__/io.cpython-34.pyc matches 
> /usr/lib/python3.4/io.py
> # code object from '/usr/lib/python3.4/__pycache__/io.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/abc.cpython-34.pyc matches 
> /usr/lib/python3.4/abc.py
> # code object from '/usr/lib/python3.4/__pycache__/abc.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/_weakrefset.cpython-34.pyc matches 
> /usr/lib/python3.4/_weakrefset.py
> # code object from 
> '/usr/lib/python3.4/__pycache__/_weakrefset.cpython-34.pyc'
> import '_weakrefset' # <_frozen_importlib.SourceFileLoader object at 
> 0x7f5aa79b9e48>
> import 'abc' # <_frozen_importlib.SourceFileLoader object at 
> 0x7f5aa79b9630>
> import 'io' # <_frozen_importlib.SourceFileLoader object at 
> 0x7f5aa79b9390>
> # /usr/lib/python3.4/__pycache__/site.cpython-34.pyc matches 
> /usr/lib/python3.4/site.py
> # code object from '/usr/lib/python3.4/__pycache__/site.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/os.cpython-34.pyc matches 
> /usr/lib/python3.4/os.py
> # code object from '/usr/lib/python3.4/__pycache__/os.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/stat.cpython-34.pyc matches 
> /usr/lib/python3.4/stat.py
> # code object from '/usr/lib/python3.4/__pycache__/stat.cpython-34.pyc'
> import 'stat' # <_frozen_importlib.SourceFileLoader object at 
> 0x7f5aa79e4390>
> # /usr/lib/python3.4/__pycache__/posixpath.cpython-34.pyc matches 
> /usr/lib/python3.4/posixpath.py
> # code

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Philip Adler

it does not seem that I am missing any dependencies.

On Mon, Oct 3, 2016 at 3:55 PM, Paolo Tosco  wrote:

> Hi Philip,
>
> Just wondering if CMake is pulling in Python 2.7 because you are missing
> some Python dependencies on 3.4 (e.g., NumPy)?
>
> p.
>
> On 3 Oct 2016, at 20:47, Philip Adler  wrote:
>
> Those variables were set correctly in my CMakeCache.txt.
>
> On Mon, Oct 3, 2016 at 2:47 PM, Peter Gedeck 
> wrote:
>
>> You can also check the CMakeCache.txt file in the build directory. When I
>> last compiled for 3.5 on the Mac, I had to correct the PYTHON_INCLUDE_DIR.
>>
>> Greg, PYTHON_INCLUDE_DIR was incorrectly set after "cmake ..". Executable
>> and library correctly found.
>>
>> 
>> //Path to a program.
>> PYTHON_EXECUTABLE:FILEPATH=/Users/peter/miniconda3/bin/python
>> //Path to a file.
>> PYTHON_INCLUDE_DIR:PATH=/System/Library/Frameworks/Python.
>> framework/Headers
>> //Path to a library.
>> PYTHON_LIBRARY:FILEPATH=/Users/peter/miniconda3/lib/libpython3.5m.dylib
>> 
>>
>> Best,
>>
>> Peter
>>
>>
>>
>>
>> On Mon, Oct 3, 2016 at 2:00 PM Philip Adler 
>> wrote:
>>
>>> Greg (with apologies for the repeat for the benefit of the mailing list
>>> -gmail is great up until it isn't!),
>>>
>>> Please see below,
>>>
>>> import _frozen_importlib # frozen
>>> import imp # builtin
>>> import sys # builtin
>>> # installing zipimport hook
>>> # installed zipimport hook
>>> # /usr/lib/python3.4/encodings/__pycache__/__init__.cpython-34.pyc
>>> matches /usr/lib/python3.4/encodings/__init__.py
>>> # code object from '/usr/lib/python3.4/encodings/
>>> __pycache__/__init__.cpython-34.pyc'
>>> # /usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc matches
>>> /usr/lib/python3.4/codecs.py
>>> # code object from '/usr/lib/python3.4/__pycache_
>>> _/codecs.cpython-34.pyc'
>>> import 'codecs' # <_frozen_importlib.SourceFileLoader object at
>>> 0x7f5aa7a14dd8>
>>> # /usr/lib/python3.4/encodings/__pycache__/aliases.cpython-34.pyc
>>> matches /usr/lib/python3.4/encodings/aliases.py
>>> # code object from '/usr/lib/python3.4/encodings/
>>> __pycache__/aliases.cpython-34.pyc'
>>> import 'encodings.aliases' # <_frozen_importlib.SourceFileLoader object
>>> at 0x7f5aa7a2a908>
>>> import 'encodings' # <_frozen_importlib.SourceFileLoader object at
>>> 0x7f5aa7a149b0>
>>> # /usr/lib/python3.4/encodings/__pycache__/utf_8.cpython-34.pyc matches
>>> /usr/lib/python3.4/encodings/utf_8.py
>>> # code object from '/usr/lib/python3.4/encodings/
>>> __pycache__/utf_8.cpython-34.pyc'
>>> import 'encodings.utf_8' # <_frozen_importlib.SourceFileLoader object
>>> at 0x7f5aa79b75f8>
>>> # /usr/lib/python3.4/encodings/__pycache__/latin_1.cpython-34.pyc
>>> matches /usr/lib/python3.4/encodings/latin_1.py
>>> # code object from '/usr/lib/python3.4/encodings/
>>> __pycache__/latin_1.cpython-34.pyc'
>>> import 'encodings.latin_1' # <_frozen_importlib.SourceFileLoader object
>>> at 0x7f5aa79b9160>
>>> # /usr/lib/python3.4/__pycache__/io.cpython-34.pyc matches
>>> /usr/lib/python3.4/io.py
>>> # code object from '/usr/lib/python3.4/__pycache__/io.cpython-34.pyc'
>>> # /usr/lib/python3.4/__pycache__/abc.cpython-34.pyc matches
>>> /usr/lib/python3.4/abc.py
>>> # code object from '/usr/lib/python3.4/__pycache__/abc.cpython-34.pyc'
>>> # /usr/lib/python3.4/__pycache__/_weakrefset.cpython-34.pyc matches
>>> /usr/lib/python3.4/_weakrefset.py
>>> # code object from '/usr/lib/python3.4/__pycache_
>>> _/_weakrefset.cpython-34.pyc'
>>> import '_weakrefset' # <_frozen_importlib.SourceFileLoader object at
>>> 0x7f5aa79b9e48>
>>> import 'abc' # <_frozen_importlib.SourceFileLoader object at
>>> 0x7f5aa79b9630>
>>> import 'io' # <_frozen_importlib.SourceFileLoader object at
>>> 0x7f5aa79b9390>
>>> # /usr/lib/python3.4/__pycache__/site.cpython-34.pyc matches
>>> /usr/lib/python3.4/site.py
>>> # code object from '/usr/lib/python3.4/__pycache__/site.cpython-34.pyc'
>>> # /usr/lib/python3.4/__pycache__/os.cpython-34.pyc matches
>>> /usr/lib/python3.4/os.py
>>> # code object from '/usr/lib/python3.4/__pycache__/os.cpython-34.pyc'
>>> # /usr/lib/python3.4/__pycache__/stat.cpython-34.pyc matches
>>> /usr/lib/python3.4/stat.py
>>> # code object from '/usr/lib/python3.4/__pycache__/stat.cpython-34.pyc'
>>> import 'stat' # <_frozen_importlib.SourceFileLoader object at
>>> 0x7f5aa79e4390>
>>> # /usr/lib/python3.4/__pycache__/posixpath.cpython-34.pyc matches
>>> /usr/lib/python3.4/posixpath.py
>>> # code object from '/usr/lib/python3.4/__pycache_
>>> _/posixpath.cpython-34.pyc'
>>> # /usr/lib/python3.4/__pycache__/genericpath.cpython-34.pyc matches
>>> /usr/lib/python3.4/genericpath.py
>>> # code object from '/usr/lib/python3.4/__pycache_
>>> _/genericpath.cpython-34.pyc'
>>> import 'genericpath' # <_frozen_importlib.SourceFileLoader object at
>>> 0x7f5aa79e5c50>
>>> import 'posixpath' # <_frozen_importlib.SourceFileLoader object at
>>> 0x7f5aa79e45f8>
>>> #

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Philip Adler

Those variables were set correctly in my CMakeCache.txt.

On Mon, Oct 3, 2016 at 2:47 PM, Peter Gedeck  wrote:

> You can also check the CMakeCache.txt file in the build directory. When I
> last compiled for 3.5 on the Mac, I had to correct the PYTHON_INCLUDE_DIR.
>
> Greg, PYTHON_INCLUDE_DIR was incorrectly set after "cmake ..". Executable
> and library correctly found.
>
> 
> //Path to a program.
> PYTHON_EXECUTABLE:FILEPATH=/Users/peter/miniconda3/bin/python
> //Path to a file.
> PYTHON_INCLUDE_DIR:PATH=/System/Library/Frameworks/
> Python.framework/Headers
> //Path to a library.
> PYTHON_LIBRARY:FILEPATH=/Users/peter/miniconda3/lib/libpython3.5m.dylib
> 
>
> Best,
>
> Peter
>
>
>
>
> On Mon, Oct 3, 2016 at 2:00 PM Philip Adler  wrote:
>
>> Greg (with apologies for the repeat for the benefit of the mailing list
>> -gmail is great up until it isn't!),
>>
>> Please see below,
>>
>> import _frozen_importlib # frozen
>> import imp # builtin
>> import sys # builtin
>> # installing zipimport hook
>> # installed zipimport hook
>> # /usr/lib/python3.4/encodings/__pycache__/__init__.cpython-34.pyc
>> matches /usr/lib/python3.4/encodings/__init__.py
>> # code object from '/usr/lib/python3.4/encodings/
>> __pycache__/__init__.cpython-34.pyc'
>> # /usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc matches
>> /usr/lib/python3.4/codecs.py
>> # code object from '/usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc'
>> import 'codecs' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa7a14dd8>
>> # /usr/lib/python3.4/encodings/__pycache__/aliases.cpython-34.pyc
>> matches /usr/lib/python3.4/encodings/aliases.py
>> # code object from '/usr/lib/python3.4/encodings/
>> __pycache__/aliases.cpython-34.pyc'
>> import 'encodings.aliases' # <_frozen_importlib.SourceFileLoader object
>> at 0x7f5aa7a2a908>
>> import 'encodings' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa7a149b0>
>> # /usr/lib/python3.4/encodings/__pycache__/utf_8.cpython-34.pyc matches
>> /usr/lib/python3.4/encodings/utf_8.py
>> # code object from '/usr/lib/python3.4/encodings/
>> __pycache__/utf_8.cpython-34.pyc'
>> import 'encodings.utf_8' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa79b75f8>
>> # /usr/lib/python3.4/encodings/__pycache__/latin_1.cpython-34.pyc
>> matches /usr/lib/python3.4/encodings/latin_1.py
>> # code object from '/usr/lib/python3.4/encodings/
>> __pycache__/latin_1.cpython-34.pyc'
>> import 'encodings.latin_1' # <_frozen_importlib.SourceFileLoader object
>> at 0x7f5aa79b9160>
>> # /usr/lib/python3.4/__pycache__/io.cpython-34.pyc matches
>> /usr/lib/python3.4/io.py
>> # code object from '/usr/lib/python3.4/__pycache__/io.cpython-34.pyc'
>> # /usr/lib/python3.4/__pycache__/abc.cpython-34.pyc matches
>> /usr/lib/python3.4/abc.py
>> # code object from '/usr/lib/python3.4/__pycache__/abc.cpython-34.pyc'
>> # /usr/lib/python3.4/__pycache__/_weakrefset.cpython-34.pyc matches
>> /usr/lib/python3.4/_weakrefset.py
>> # code object from '/usr/lib/python3.4/__pycache_
>> _/_weakrefset.cpython-34.pyc'
>> import '_weakrefset' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa79b9e48>
>> import 'abc' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa79b9630>
>> import 'io' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa79b9390>
>> # /usr/lib/python3.4/__pycache__/site.cpython-34.pyc matches
>> /usr/lib/python3.4/site.py
>> # code object from '/usr/lib/python3.4/__pycache__/site.cpython-34.pyc'
>> # /usr/lib/python3.4/__pycache__/os.cpython-34.pyc matches
>> /usr/lib/python3.4/os.py
>> # code object from '/usr/lib/python3.4/__pycache__/os.cpython-34.pyc'
>> # /usr/lib/python3.4/__pycache__/stat.cpython-34.pyc matches
>> /usr/lib/python3.4/stat.py
>> # code object from '/usr/lib/python3.4/__pycache__/stat.cpython-34.pyc'
>> import 'stat' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa79e4390>
>> # /usr/lib/python3.4/__pycache__/posixpath.cpython-34.pyc matches
>> /usr/lib/python3.4/posixpath.py
>> # code object from '/usr/lib/python3.4/__pycache_
>> _/posixpath.cpython-34.pyc'
>> # /usr/lib/python3.4/__pycache__/genericpath.cpython-34.pyc matches
>> /usr/lib/python3.4/genericpath.py
>> # code object from '/usr/lib/python3.4/__pycache_
>> _/genericpath.cpython-34.pyc'
>> import 'genericpath' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa79e5c50>
>> import 'posixpath' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa79e45f8>
>> # /usr/lib/python3.4/__pycache__/_collections_abc.cpython-34.pyc matches
>> /usr/lib/python3.4/_collections_abc.py
>> # code object from '/usr/lib/python3.4/__pycache_
>> _/_collections_abc.cpython-34.pyc'
>> import '_collections_abc' # <_frozen_importlib.SourceFileLoader object
>> at 0x7f5aa79e5b70>
>> import 'os' # <_frozen_importlib.SourceFileLoader object at
>> 0x7f5aa79d0be0>
>> # /usr/lib/python3.4/__pycache__/_sitebuiltins.cpython-34.pyc matches
>>

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Peter Gedeck

You can also check the CMakeCache.txt file in the build directory. When I
last compiled for 3.5 on the Mac, I had to correct the PYTHON_INCLUDE_DIR.

Greg, PYTHON_INCLUDE_DIR was incorrectly set after "cmake ..". Executable
and library correctly found.


//Path to a program.
PYTHON_EXECUTABLE:FILEPATH=/Users/peter/miniconda3/bin/python
//Path to a file.
PYTHON_INCLUDE_DIR:PATH=/System/Library/Frameworks/Python.framework/Headers
//Path to a library.
PYTHON_LIBRARY:FILEPATH=/Users/peter/miniconda3/lib/libpython3.5m.dylib


Best,

Peter




On Mon, Oct 3, 2016 at 2:00 PM Philip Adler  wrote:

> Greg (with apologies for the repeat for the benefit of the mailing list
> -gmail is great up until it isn't!),
>
> Please see below,
>
> import _frozen_importlib # frozen
> import imp # builtin
> import sys # builtin
> # installing zipimport hook
> # installed zipimport hook
> # /usr/lib/python3.4/encodings/__pycache__/__init__.cpython-34.pyc matches
> /usr/lib/python3.4/encodings/__init__.py
> # code object from
> '/usr/lib/python3.4/encodings/__pycache__/__init__.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc matches
> /usr/lib/python3.4/codecs.py
> # code object from '/usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc'
> import 'codecs' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa7a14dd8>
> # /usr/lib/python3.4/encodings/__pycache__/aliases.cpython-34.pyc matches
> /usr/lib/python3.4/encodings/aliases.py
> # code object from
> '/usr/lib/python3.4/encodings/__pycache__/aliases.cpython-34.pyc'
> import 'encodings.aliases' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa7a2a908>
> import 'encodings' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa7a149b0>
> # /usr/lib/python3.4/encodings/__pycache__/utf_8.cpython-34.pyc matches
> /usr/lib/python3.4/encodings/utf_8.py
> # code object from
> '/usr/lib/python3.4/encodings/__pycache__/utf_8.cpython-34.pyc'
> import 'encodings.utf_8' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa79b75f8>
> # /usr/lib/python3.4/encodings/__pycache__/latin_1.cpython-34.pyc matches
> /usr/lib/python3.4/encodings/latin_1.py
> # code object from
> '/usr/lib/python3.4/encodings/__pycache__/latin_1.cpython-34.pyc'
> import 'encodings.latin_1' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa79b9160>
> # /usr/lib/python3.4/__pycache__/io.cpython-34.pyc matches
> /usr/lib/python3.4/io.py
> # code object from '/usr/lib/python3.4/__pycache__/io.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/abc.cpython-34.pyc matches
> /usr/lib/python3.4/abc.py
> # code object from '/usr/lib/python3.4/__pycache__/abc.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/_weakrefset.cpython-34.pyc matches
> /usr/lib/python3.4/_weakrefset.py
> # code object from
> '/usr/lib/python3.4/__pycache__/_weakrefset.cpython-34.pyc'
> import '_weakrefset' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa79b9e48>
> import 'abc' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa79b9630>
> import 'io' # <_frozen_importlib.SourceFileLoader object at 0x7f5aa79b9390>
> # /usr/lib/python3.4/__pycache__/site.cpython-34.pyc matches
> /usr/lib/python3.4/site.py
> # code object from '/usr/lib/python3.4/__pycache__/site.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/os.cpython-34.pyc matches
> /usr/lib/python3.4/os.py
> # code object from '/usr/lib/python3.4/__pycache__/os.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/stat.cpython-34.pyc matches
> /usr/lib/python3.4/stat.py
> # code object from '/usr/lib/python3.4/__pycache__/stat.cpython-34.pyc'
> import 'stat' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa79e4390>
> # /usr/lib/python3.4/__pycache__/posixpath.cpython-34.pyc matches
> /usr/lib/python3.4/posixpath.py
> # code object from
> '/usr/lib/python3.4/__pycache__/posixpath.cpython-34.pyc'
> # /usr/lib/python3.4/__pycache__/genericpath.cpython-34.pyc matches
> /usr/lib/python3.4/genericpath.py
> # code object from
> '/usr/lib/python3.4/__pycache__/genericpath.cpython-34.pyc'
> import 'genericpath' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa79e5c50>
> import 'posixpath' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa79e45f8>
> # /usr/lib/python3.4/__pycache__/_collections_abc.cpython-34.pyc matches
> /usr/lib/python3.4/_collections_abc.py
> # code object from
> '/usr/lib/python3.4/__pycache__/_collections_abc.cpython-34.pyc'
> import '_collections_abc' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa79e5b70>
> import 'os' # <_frozen_importlib.SourceFileLoader object at 0x7f5aa79d0be0>
> # /usr/lib/python3.4/__pycache__/_sitebuiltins.cpython-34.pyc matches
> /usr/lib/python3.4/_sitebuiltins.py
> # code object from
> '/usr/lib/python3.4/__pycache__/_sitebuiltins.cpython-34.pyc'
> import '_sitebuiltins' # <_frozen_importlib.SourceFileLoader object at
> 0x7f5aa79d0ba8>
> # /usr/lib/python3.4/__pycache__/sysconfig.cpython-34.pyc matches
>

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Philip Adler

Greg (with apologies for the repeat for the benefit of the mailing list
-gmail is great up until it isn't!),

Please see below,

import _frozen_importlib # frozen
import imp # builtin
import sys # builtin
# installing zipimport hook
# installed zipimport hook
# /usr/lib/python3.4/encodings/__pycache__/__init__.cpython-34.pyc matches
/usr/lib/python3.4/encodings/__init__.py
# code object from '/usr/lib/python3.4/encodings/
__pycache__/__init__.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc matches
/usr/lib/python3.4/codecs.py
# code object from '/usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc'
import 'codecs' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa7a14dd8>
# /usr/lib/python3.4/encodings/__pycache__/aliases.cpython-34.pyc matches
/usr/lib/python3.4/encodings/aliases.py
# code object from '/usr/lib/python3.4/encodings/
__pycache__/aliases.cpython-34.pyc'
import 'encodings.aliases' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa7a2a908>
import 'encodings' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa7a149b0>
# /usr/lib/python3.4/encodings/__pycache__/utf_8.cpython-34.pyc matches
/usr/lib/python3.4/encodings/utf_8.py
# code object from '/usr/lib/python3.4/encodings/
__pycache__/utf_8.cpython-34.pyc'
import 'encodings.utf_8' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79b75f8>
# /usr/lib/python3.4/encodings/__pycache__/latin_1.cpython-34.pyc matches
/usr/lib/python3.4/encodings/latin_1.py
# code object from '/usr/lib/python3.4/encodings/
__pycache__/latin_1.cpython-34.pyc'
import 'encodings.latin_1' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79b9160>
# /usr/lib/python3.4/__pycache__/io.cpython-34.pyc matches
/usr/lib/python3.4/io.py
# code object from '/usr/lib/python3.4/__pycache__/io.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/abc.cpython-34.pyc matches
/usr/lib/python3.4/abc.py
# code object from '/usr/lib/python3.4/__pycache__/abc.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/_weakrefset.cpython-34.pyc matches
/usr/lib/python3.4/_weakrefset.py
# code object from '/usr/lib/python3.4/__pycache_
_/_weakrefset.cpython-34.pyc'
import '_weakrefset' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79b9e48>
import 'abc' # <_frozen_importlib.SourceFileLoader object at 0x7f5aa79b9630>
import 'io' # <_frozen_importlib.SourceFileLoader object at 0x7f5aa79b9390>
# /usr/lib/python3.4/__pycache__/site.cpython-34.pyc matches
/usr/lib/python3.4/site.py
# code object from '/usr/lib/python3.4/__pycache__/site.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/os.cpython-34.pyc matches
/usr/lib/python3.4/os.py
# code object from '/usr/lib/python3.4/__pycache__/os.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/stat.cpython-34.pyc matches
/usr/lib/python3.4/stat.py
# code object from '/usr/lib/python3.4/__pycache__/stat.cpython-34.pyc'
import 'stat' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79e4390>
# /usr/lib/python3.4/__pycache__/posixpath.cpython-34.pyc matches
/usr/lib/python3.4/posixpath.py
# code object from '/usr/lib/python3.4/__pycache__/posixpath.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/genericpath.cpython-34.pyc matches
/usr/lib/python3.4/genericpath.py
# code object from '/usr/lib/python3.4/__pycache_
_/genericpath.cpython-34.pyc'
import 'genericpath' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79e5c50>
import 'posixpath' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79e45f8>
# /usr/lib/python3.4/__pycache__/_collections_abc.cpython-34.pyc matches
/usr/lib/python3.4/_collections_abc.py
# code object from '/usr/lib/python3.4/__pycache_
_/_collections_abc.cpython-34.pyc'
import '_collections_abc' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79e5b70>
import 'os' # <_frozen_importlib.SourceFileLoader object at 0x7f5aa79d0be0>
# /usr/lib/python3.4/__pycache__/_sitebuiltins.cpython-34.pyc matches
/usr/lib/python3.4/_sitebuiltins.py
# code object from '/usr/lib/python3.4/__pycache__/_sitebuiltins.cpython-34.
pyc'
import '_sitebuiltins' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79d0ba8>
# /usr/lib/python3.4/__pycache__/sysconfig.cpython-34.pyc matches
/usr/lib/python3.4/sysconfig.py
# code object from '/usr/lib/python3.4/__pycache__/sysconfig.cpython-34.pyc'
import 'sysconfig' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa799b710>
# /usr/lib/python3.4/__pycache__/_sysconfigdata.cpython-34.pyc matches
/usr/lib/python3.4/_sysconfigdata.py
# code object from '/usr/lib/python3.4/__pycache_
_/_sysconfigdata.cpython-34.pyc'
# 
/usr/lib/python3.4/plat-x86_64-linux-gnu/__pycache__/_sysconfigdata_m.cpython-34.pyc
matches /usr/lib/python3.4/plat-x86_64-linux-gnu/_sysconfigdata_m.py
# code object from '/usr/lib/python3.4/plat-x86_64-linux-gnu/__pycache__/_
sysconfigdata_m.cpython-34.pyc'
import '_sysconfigdata_m' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa799d2b0>
import '_sysconfigdata' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa799d080>
#

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Greg Landrum

Yeah, but that ldd output indicates that python2.7 is being pulled in. As
is, curiously, the python2.7 version of boost.
Can you please try:
python3.4 -v -c 'from rdkit import rdBase'
and send the command and output from that?

-greg



On Mon, Oct 3, 2016 at 5:45 PM, Philip Adler  wrote:

> Python2.7 is the default install for Ubuntu 14.04, but I ran the first
> command using python3.4
>
> On Mon, Oct 3, 2016 at 11:43 AM, Greg Landrum 
> wrote:
>
>> You built against python3.4, but it looks like you are running python2.7
>>
>> -greg
>>
>>
>> On Mon, Oct 3, 2016 at 5:39 PM, Philip Adler 
>> wrote:
>>
>>> Greg,
>>>
>>> The output of the commands is as follows:
>>>
>>> Segmentation fault (core dumped)
>>>
>>> and
>>>
>>> linux-vdso.so.1 =>  (0x7fff3d6be000)
>>> libRDGeneral.so.1 => /usr/lib/libRDGeneral.so.1 (0x7f03d51df000)
>>> libRDBoost.so.1 => /usr/lib/libRDBoost.so.1 (0x7f03d4fdc000)
>>> libpython3.4m.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython3.4m.so.1.0
>>> (0x7f03d49a7000)
>>> libboost_python-py34.so.1.54.0 => 
>>> /usr/lib/x86_64-linux-gnu/libboost_python-py34.so.1.54.0
>>> (0x7f03d475b000)
>>> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
>>> (0x7f03d4457000)
>>> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
>>> (0x7f03d4241000)
>>> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7f03d3e7c000)
>>> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7f03d3b76000)
>>> libpython2.7.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0
>>> (0x7f03d3612000)
>>> libboost_python-py27.so.1.54.0 => 
>>> /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.54.0
>>> (0x7f03d33c5000)
>>> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>>> (0x7f03d31a7000)
>>> libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1
>>> (0x7f03d2f7d000)
>>> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x7f03d2d64000)
>>> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7f03d2b6)
>>> libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1
>>> (0x7f03d295d000)
>>> /lib64/ld-linux-x86-64.so.2 (0x7f03d56fc000)
>>>
>>> Thanks,
>>>
>>> Phil
>>>
>>>
>>> On Mon, Oct 3, 2016 at 11:34 AM, Greg Landrum 
>>> wrote:
>>>
 Hi Phil,

 I can't think of any particular reason that Ubuntu 14.04 should be a
 problem, so this should be solvable.

 This kind of thing (every python test failing) is typically a problem
 with either the python version or the boost libraries.

 The first check is to see what error message you get when you do:
 python -c 'from rdkit import rdBase'

 That will hopefully point to a particular library that is the problem.
 Another useful diagnosis command is:
 ldd $RDBASE/rdkit/rdBase.so

 That will show which dynamic libraries are being pulled in.

 -greg


 On Mon, Oct 3, 2016 at 5:05 PM, Philip Adler 
 wrote:

> Dear All,
>
> I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as
> per the instructions at http://www.rdkit.org/docs/Install.html For
> reasons which I don't really want to get into we would prefer to avoid
> anaconda for the time being.
>
> That being said, when I try to test the build, I get a number of
> errors and failed tests (the build does not work when called from Python,
> which is unsurprising).
>
> For reference, the cmake command I issued was:
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D PYTHON_LIBRARY=/usr/lib/python
> 3.4/config-3.4m-x86_64-linux-gnu/libpython3.4.so -D
> PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
> PYTHON_EXECUTABLE=/usr/bin/python3.4 
> -DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/
> ..
>
> The tests which fail are as follows:
>
> The following tests FAILED:
>   5 - pyBV (SEGFAULT)
>   6 - pyDiscreteValueVect (SEGFAULT)
>   7 - pySparseIntVect (SEGFAULT)
>   8 - pyFPB (SEGFAULT)
>  11 - testPyGeometry (SEGFAULT)
>  14 - pyAlignment (Failed)
>  18 - pyForceFieldConstraints (SEGFAULT)
>  20 - pyDistGeom (Failed)
>  33 - pyDepictor (SEGFAULT)
>  45 - pyChemReactions (SEGFAULT)
>  50 - pyFilterCatalog (SEGFAULT)
>  52 - pyFragCatalog (SEGFAULT)
>  54 - pyMolDescriptors (SEGFAULT)
>  57 - pyPartialCharges (SEGFAULT)
>  59 - pyMolTransforms (SEGFAULT)
>  63 - pyForceFieldHelpers (SEGFAULT)
>  65 - pyDistGeom (SEGFAULT)
>  67 - pyMolAlign (SEGFAULT)
>  69 - pyChemicalFeatures (SEGFAULT)
>  71 - pyShapeHelpers (SEGFAULT)
>  73 - pyMolCatalog (SEGFAULT)
>  75 - pyMolDraw2D (SEGFAULT)
>  77 - pyFMCS (SEGFAULT)
>  80 - pyMolHash

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Greg Landrum

You built against python3.4, but it looks like you are running python2.7

-greg


On Mon, Oct 3, 2016 at 5:39 PM, Philip Adler  wrote:

> Greg,
>
> The output of the commands is as follows:
>
> Segmentation fault (core dumped)
>
> and
>
> linux-vdso.so.1 =>  (0x7fff3d6be000)
> libRDGeneral.so.1 => /usr/lib/libRDGeneral.so.1 (0x7f03d51df000)
> libRDBoost.so.1 => /usr/lib/libRDBoost.so.1 (0x7f03d4fdc000)
> libpython3.4m.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython3.4m.so.1.0
> (0x7f03d49a7000)
> libboost_python-py34.so.1.54.0 => 
> /usr/lib/x86_64-linux-gnu/libboost_python-py34.so.1.54.0
> (0x7f03d475b000)
> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
> (0x7f03d4457000)
> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
> (0x7f03d4241000)
> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7f03d3e7c000)
> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7f03d3b76000)
> libpython2.7.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0
> (0x7f03d3612000)
> libboost_python-py27.so.1.54.0 => 
> /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.54.0
> (0x7f03d33c5000)
> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x7f03d31a7000)
> libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1
> (0x7f03d2f7d000)
> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x7f03d2d64000)
> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7f03d2b6)
> libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1
> (0x7f03d295d000)
> /lib64/ld-linux-x86-64.so.2 (0x7f03d56fc000)
>
> Thanks,
>
> Phil
>
>
> On Mon, Oct 3, 2016 at 11:34 AM, Greg Landrum 
> wrote:
>
>> Hi Phil,
>>
>> I can't think of any particular reason that Ubuntu 14.04 should be a
>> problem, so this should be solvable.
>>
>> This kind of thing (every python test failing) is typically a problem
>> with either the python version or the boost libraries.
>>
>> The first check is to see what error message you get when you do:
>> python -c 'from rdkit import rdBase'
>>
>> That will hopefully point to a particular library that is the problem.
>> Another useful diagnosis command is:
>> ldd $RDBASE/rdkit/rdBase.so
>>
>> That will show which dynamic libraries are being pulled in.
>>
>> -greg
>>
>>
>> On Mon, Oct 3, 2016 at 5:05 PM, Philip Adler 
>> wrote:
>>
>>> Dear All,
>>>
>>> I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as
>>> per the instructions at http://www.rdkit.org/docs/Install.html For
>>> reasons which I don't really want to get into we would prefer to avoid
>>> anaconda for the time being.
>>>
>>> That being said, when I try to test the build, I get a number of errors
>>> and failed tests (the build does not work when called from Python, which is
>>> unsurprising).
>>>
>>> For reference, the cmake command I issued was:
>>>
>>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D PYTHON_LIBRARY=/usr/lib/python
>>> 3.4/config-3.4m-x86_64-linux-gnu/libpython3.4.so -D
>>> PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
>>> PYTHON_EXECUTABLE=/usr/bin/python3.4 -DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/
>>> ..
>>>
>>> The tests which fail are as follows:
>>>
>>> The following tests FAILED:
>>>   5 - pyBV (SEGFAULT)
>>>   6 - pyDiscreteValueVect (SEGFAULT)
>>>   7 - pySparseIntVect (SEGFAULT)
>>>   8 - pyFPB (SEGFAULT)
>>>  11 - testPyGeometry (SEGFAULT)
>>>  14 - pyAlignment (Failed)
>>>  18 - pyForceFieldConstraints (SEGFAULT)
>>>  20 - pyDistGeom (Failed)
>>>  33 - pyDepictor (SEGFAULT)
>>>  45 - pyChemReactions (SEGFAULT)
>>>  50 - pyFilterCatalog (SEGFAULT)
>>>  52 - pyFragCatalog (SEGFAULT)
>>>  54 - pyMolDescriptors (SEGFAULT)
>>>  57 - pyPartialCharges (SEGFAULT)
>>>  59 - pyMolTransforms (SEGFAULT)
>>>  63 - pyForceFieldHelpers (SEGFAULT)
>>>  65 - pyDistGeom (SEGFAULT)
>>>  67 - pyMolAlign (SEGFAULT)
>>>  69 - pyChemicalFeatures (SEGFAULT)
>>>  71 - pyShapeHelpers (SEGFAULT)
>>>  73 - pyMolCatalog (SEGFAULT)
>>>  75 - pyMolDraw2D (SEGFAULT)
>>>  77 - pyFMCS (SEGFAULT)
>>>  80 - pyMolHash (SEGFAULT)
>>>  82 - pyMMPA (SEGFAULT)
>>>  84 - pyReducedGraphs (SEGFAULT)
>>>  86 - pySLNParse (SEGFAULT)
>>>  87 - pyGraphMolWrap (SEGFAULT)
>>>  88 - pyTestConformerWrap (SEGFAULT)
>>>  89 - pyTestThreads (SEGFAULT)
>>>  92 - pyMatCalc (SEGFAULT)
>>>  93 - pySimDivPickers (SEGFAULT)
>>>  94 - pyRanker (Failed)
>>>  96 - pyFeatures (SEGFAULT)
>>>  97 - pythonTestDbCLI (Failed)
>>>  98 - pythonTestDirML (Failed)
>>>  99 - pythonTestDirDataStructs (Failed)
>>> 101 - pythonTestDirSimDivFilters (Failed)
>>> 102 - pythonTestDirVLib (Failed)
>>> 103 - pythonTestDirChem (SEGFAULT)
>>>
>>> I must confess I'm a little out of my depth right now, so I don't even
>>> know where to begin debugging

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Philip Adler

Greg,

The output of the commands is as follows:

Segmentation fault (core dumped)

and

linux-vdso.so.1 =>  (0x7fff3d6be000)
libRDGeneral.so.1 => /usr/lib/libRDGeneral.so.1 (0x7f03d51df000)
libRDBoost.so.1 => /usr/lib/libRDBoost.so.1 (0x7f03d4fdc000)
libpython3.4m.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython3.4m.so.1.0
(0x7f03d49a7000)
libboost_python-py34.so.1.54.0 =>
/usr/lib/x86_64-linux-gnu/libboost_python-py34.so.1.54.0
(0x7f03d475b000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x7f03d4457000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x7f03d4241000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7f03d3e7c000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x7f03d3b76000)
libpython2.7.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0
(0x7f03d3612000)
libboost_python-py27.so.1.54.0 =>
/usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.54.0
(0x7f03d33c5000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x7f03d31a7000)
libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1
(0x7f03d2f7d000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x7f03d2d64000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7f03d2b6)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x7f03d295d000)
/lib64/ld-linux-x86-64.so.2 (0x7f03d56fc000)

Thanks,

Phil


On Mon, Oct 3, 2016 at 11:34 AM, Greg Landrum 
wrote:

> Hi Phil,
>
> I can't think of any particular reason that Ubuntu 14.04 should be a
> problem, so this should be solvable.
>
> This kind of thing (every python test failing) is typically a problem with
> either the python version or the boost libraries.
>
> The first check is to see what error message you get when you do:
> python -c 'from rdkit import rdBase'
>
> That will hopefully point to a particular library that is the problem.
> Another useful diagnosis command is:
> ldd $RDBASE/rdkit/rdBase.so
>
> That will show which dynamic libraries are being pulled in.
>
> -greg
>
>
> On Mon, Oct 3, 2016 at 5:05 PM, Philip Adler 
> wrote:
>
>> Dear All,
>>
>> I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as
>> per the instructions at http://www.rdkit.org/docs/Install.html For
>> reasons which I don't really want to get into we would prefer to avoid
>> anaconda for the time being.
>>
>> That being said, when I try to test the build, I get a number of errors
>> and failed tests (the build does not work when called from Python, which is
>> unsurprising).
>>
>> For reference, the cmake command I issued was:
>>
>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D PYTHON_LIBRARY=/usr/lib/python
>> 3.4/config-3.4m-x86_64-linux-gnu/libpython3.4.so -D
>> PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
>> PYTHON_EXECUTABLE=/usr/bin/python3.4 -DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/
>> ..
>>
>> The tests which fail are as follows:
>>
>> The following tests FAILED:
>>   5 - pyBV (SEGFAULT)
>>   6 - pyDiscreteValueVect (SEGFAULT)
>>   7 - pySparseIntVect (SEGFAULT)
>>   8 - pyFPB (SEGFAULT)
>>  11 - testPyGeometry (SEGFAULT)
>>  14 - pyAlignment (Failed)
>>  18 - pyForceFieldConstraints (SEGFAULT)
>>  20 - pyDistGeom (Failed)
>>  33 - pyDepictor (SEGFAULT)
>>  45 - pyChemReactions (SEGFAULT)
>>  50 - pyFilterCatalog (SEGFAULT)
>>  52 - pyFragCatalog (SEGFAULT)
>>  54 - pyMolDescriptors (SEGFAULT)
>>  57 - pyPartialCharges (SEGFAULT)
>>  59 - pyMolTransforms (SEGFAULT)
>>  63 - pyForceFieldHelpers (SEGFAULT)
>>  65 - pyDistGeom (SEGFAULT)
>>  67 - pyMolAlign (SEGFAULT)
>>  69 - pyChemicalFeatures (SEGFAULT)
>>  71 - pyShapeHelpers (SEGFAULT)
>>  73 - pyMolCatalog (SEGFAULT)
>>  75 - pyMolDraw2D (SEGFAULT)
>>  77 - pyFMCS (SEGFAULT)
>>  80 - pyMolHash (SEGFAULT)
>>  82 - pyMMPA (SEGFAULT)
>>  84 - pyReducedGraphs (SEGFAULT)
>>  86 - pySLNParse (SEGFAULT)
>>  87 - pyGraphMolWrap (SEGFAULT)
>>  88 - pyTestConformerWrap (SEGFAULT)
>>  89 - pyTestThreads (SEGFAULT)
>>  92 - pyMatCalc (SEGFAULT)
>>  93 - pySimDivPickers (SEGFAULT)
>>  94 - pyRanker (Failed)
>>  96 - pyFeatures (SEGFAULT)
>>  97 - pythonTestDbCLI (Failed)
>>  98 - pythonTestDirML (Failed)
>>  99 - pythonTestDirDataStructs (Failed)
>> 101 - pythonTestDirSimDivFilters (Failed)
>> 102 - pythonTestDirVLib (Failed)
>> 103 - pythonTestDirChem (SEGFAULT)
>>
>> I must confess I'm a little out of my depth right now, so I don't even
>> know where to begin debugging this. Any advice would be greatly appreciated,
>>
>> Best,
>>
>> Phil
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Greg Landrum

Hi Phil,

I can't think of any particular reason that Ubuntu 14.04 should be a
problem, so this should be solvable.

This kind of thing (every python test failing) is typically a problem with
either the python version or the boost libraries.

The first check is to see what error message you get when you do:
python -c 'from rdkit import rdBase'

That will hopefully point to a particular library that is the problem.
Another useful diagnosis command is:
ldd $RDBASE/rdkit/rdBase.so

That will show which dynamic libraries are being pulled in.

-greg


On Mon, Oct 3, 2016 at 5:05 PM, Philip Adler  wrote:

> Dear All,
>
> I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as per
> the instructions at http://www.rdkit.org/docs/Install.html For reasons
> which I don't really want to get into we would prefer to avoid anaconda for
> the time being.
>
> That being said, when I try to test the build, I get a number of errors
> and failed tests (the build does not work when called from Python, which is
> unsurprising).
>
> For reference, the cmake command I issued was:
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D PYTHON_LIBRARY=/usr/lib/python
> 3.4/config-3.4m-x86_64-linux-gnu/libpython3.4.so -D
> PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
> PYTHON_EXECUTABLE=/usr/bin/python3.4 -DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/
> ..
>
> The tests which fail are as follows:
>
> The following tests FAILED:
>   5 - pyBV (SEGFAULT)
>   6 - pyDiscreteValueVect (SEGFAULT)
>   7 - pySparseIntVect (SEGFAULT)
>   8 - pyFPB (SEGFAULT)
>  11 - testPyGeometry (SEGFAULT)
>  14 - pyAlignment (Failed)
>  18 - pyForceFieldConstraints (SEGFAULT)
>  20 - pyDistGeom (Failed)
>  33 - pyDepictor (SEGFAULT)
>  45 - pyChemReactions (SEGFAULT)
>  50 - pyFilterCatalog (SEGFAULT)
>  52 - pyFragCatalog (SEGFAULT)
>  54 - pyMolDescriptors (SEGFAULT)
>  57 - pyPartialCharges (SEGFAULT)
>  59 - pyMolTransforms (SEGFAULT)
>  63 - pyForceFieldHelpers (SEGFAULT)
>  65 - pyDistGeom (SEGFAULT)
>  67 - pyMolAlign (SEGFAULT)
>  69 - pyChemicalFeatures (SEGFAULT)
>  71 - pyShapeHelpers (SEGFAULT)
>  73 - pyMolCatalog (SEGFAULT)
>  75 - pyMolDraw2D (SEGFAULT)
>  77 - pyFMCS (SEGFAULT)
>  80 - pyMolHash (SEGFAULT)
>  82 - pyMMPA (SEGFAULT)
>  84 - pyReducedGraphs (SEGFAULT)
>  86 - pySLNParse (SEGFAULT)
>  87 - pyGraphMolWrap (SEGFAULT)
>  88 - pyTestConformerWrap (SEGFAULT)
>  89 - pyTestThreads (SEGFAULT)
>  92 - pyMatCalc (SEGFAULT)
>  93 - pySimDivPickers (SEGFAULT)
>  94 - pyRanker (Failed)
>  96 - pyFeatures (SEGFAULT)
>  97 - pythonTestDbCLI (Failed)
>  98 - pythonTestDirML (Failed)
>  99 - pythonTestDirDataStructs (Failed)
> 101 - pythonTestDirSimDivFilters (Failed)
> 102 - pythonTestDirVLib (Failed)
> 103 - pythonTestDirChem (SEGFAULT)
>
> I must confess I'm a little out of my depth right now, so I don't even
> know where to begin debugging this. Any advice would be greatly appreciated,
>
> Best,
>
> Phil
>
> 
> --
> 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@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Peter Gedeck

Hello

Python failures are usually an indication of problems with the boost
library. You might pickup libraries for the wrong Python version.

Best

Peter
On Mon, Oct 3, 2016 at 11:06 AM Philip Adler  wrote:

> Dear All,
>
> I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as per
> the instructions at http://www.rdkit.org/docs/Install.html For reasons
> which I don't really want to get into we would prefer to avoid anaconda for
> the time being.
>
> That being said, when I try to test the build, I get a number of errors
> and failed tests (the build does not work when called from Python, which is
> unsurprising).
>
> For reference, the cmake command I issued was:
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D
> PYTHON_LIBRARY=/usr/lib/python3.4/config-3.4m-x86_64-linux-gnu/
> libpython3.4.so -D PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
> PYTHON_EXECUTABLE=/usr/bin/python3.4
> -DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/ ..
>
> The tests which fail are as follows:
>
> The following tests FAILED:
>   5 - pyBV (SEGFAULT)
>   6 - pyDiscreteValueVect (SEGFAULT)
>   7 - pySparseIntVect (SEGFAULT)
>   8 - pyFPB (SEGFAULT)
>  11 - testPyGeometry (SEGFAULT)
>  14 - pyAlignment (Failed)
>  18 - pyForceFieldConstraints (SEGFAULT)
>  20 - pyDistGeom (Failed)
>  33 - pyDepictor (SEGFAULT)
>  45 - pyChemReactions (SEGFAULT)
>  50 - pyFilterCatalog (SEGFAULT)
>  52 - pyFragCatalog (SEGFAULT)
>  54 - pyMolDescriptors (SEGFAULT)
>  57 - pyPartialCharges (SEGFAULT)
>  59 - pyMolTransforms (SEGFAULT)
>  63 - pyForceFieldHelpers (SEGFAULT)
>  65 - pyDistGeom (SEGFAULT)
>  67 - pyMolAlign (SEGFAULT)
>  69 - pyChemicalFeatures (SEGFAULT)
>  71 - pyShapeHelpers (SEGFAULT)
>  73 - pyMolCatalog (SEGFAULT)
>  75 - pyMolDraw2D (SEGFAULT)
>  77 - pyFMCS (SEGFAULT)
>  80 - pyMolHash (SEGFAULT)
>  82 - pyMMPA (SEGFAULT)
>  84 - pyReducedGraphs (SEGFAULT)
>  86 - pySLNParse (SEGFAULT)
>  87 - pyGraphMolWrap (SEGFAULT)
>  88 - pyTestConformerWrap (SEGFAULT)
>  89 - pyTestThreads (SEGFAULT)
>  92 - pyMatCalc (SEGFAULT)
>  93 - pySimDivPickers (SEGFAULT)
>  94 - pyRanker (Failed)
>  96 - pyFeatures (SEGFAULT)
>  97 - pythonTestDbCLI (Failed)
>  98 - pythonTestDirML (Failed)
>  99 - pythonTestDirDataStructs (Failed)
> 101 - pythonTestDirSimDivFilters (Failed)
> 102 - pythonTestDirVLib (Failed)
> 103 - pythonTestDirChem (SEGFAULT)
>
> I must confess I'm a little out of my depth right now, so I don't even
> know where to begin debugging this. Any advice would be greatly appreciated,
>
> Best,
>
> Phil
>
> --
> 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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> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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[Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

2016-10-03 Thread Philip Adler

Dear All,

I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04 as per
the instructions at http://www.rdkit.org/docs/Install.html For reasons
which I don't really want to get into we would prefer to avoid anaconda for
the time being.

That being said, when I try to test the build, I get a number of errors and
failed tests (the build does not work when called from Python, which is
unsurprising).

For reference, the cmake command I issued was:

cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D PYTHON_LIBRARY=/usr/lib/
python3.4/config-3.4m-x86_64-linux-gnu/libpython3.4.so -D
PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
PYTHON_EXECUTABLE=/usr/bin/python3.4
-DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/ ..

The tests which fail are as follows:

The following tests FAILED:
  5 - pyBV (SEGFAULT)
  6 - pyDiscreteValueVect (SEGFAULT)
  7 - pySparseIntVect (SEGFAULT)
  8 - pyFPB (SEGFAULT)
 11 - testPyGeometry (SEGFAULT)
 14 - pyAlignment (Failed)
 18 - pyForceFieldConstraints (SEGFAULT)
 20 - pyDistGeom (Failed)
 33 - pyDepictor (SEGFAULT)
 45 - pyChemReactions (SEGFAULT)
 50 - pyFilterCatalog (SEGFAULT)
 52 - pyFragCatalog (SEGFAULT)
 54 - pyMolDescriptors (SEGFAULT)
 57 - pyPartialCharges (SEGFAULT)
 59 - pyMolTransforms (SEGFAULT)
 63 - pyForceFieldHelpers (SEGFAULT)
 65 - pyDistGeom (SEGFAULT)
 67 - pyMolAlign (SEGFAULT)
 69 - pyChemicalFeatures (SEGFAULT)
 71 - pyShapeHelpers (SEGFAULT)
 73 - pyMolCatalog (SEGFAULT)
 75 - pyMolDraw2D (SEGFAULT)
 77 - pyFMCS (SEGFAULT)
 80 - pyMolHash (SEGFAULT)
 82 - pyMMPA (SEGFAULT)
 84 - pyReducedGraphs (SEGFAULT)
 86 - pySLNParse (SEGFAULT)
 87 - pyGraphMolWrap (SEGFAULT)
 88 - pyTestConformerWrap (SEGFAULT)
 89 - pyTestThreads (SEGFAULT)
 92 - pyMatCalc (SEGFAULT)
 93 - pySimDivPickers (SEGFAULT)
 94 - pyRanker (Failed)
 96 - pyFeatures (SEGFAULT)
 97 - pythonTestDbCLI (Failed)
 98 - pythonTestDirML (Failed)
 99 - pythonTestDirDataStructs (Failed)
101 - pythonTestDirSimDivFilters (Failed)
102 - pythonTestDirVLib (Failed)
103 - pythonTestDirChem (SEGFAULT)

I must confess I'm a little out of my depth right now, so I don't even know
where to begin debugging this. Any advice would be greatly appreciated,

Best,

Phil
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Re: [Rdkit-discuss] Conformer getPositions to return numpy array

2016-10-03 Thread Jan Domanski

Thanks this is great, just found it when needed again after those few years
;-)

On 29 August 2014 at 19:35, Greg Landrum  wrote:

> Hi Jan,
>
> On Friday, August 29, 2014, Jan Domanski  wrote:
>
>> Hi there,
>>
>> I'm trying to wrap the very handy method getPositions from
>> rdkit/Code/GraphMol/Wrap/Conformer.cpp to return coordinates of a
>> conformer as a numpy array.
>>
>> So far I was able to return a tuple of tuples, as below
>>
>>   PyObject *convertPoint(RDGeom::Point3D ){
>> PyObject *res = PyTuple_New(3);
>> PyTuple_SetItem(res,0,PyFloat_FromDouble(point.x));
>> PyTuple_SetItem(res,1,PyFloat_FromDouble(point.y));
>> PyTuple_SetItem(res,2,PyFloat_FromDouble(point.z));
>> return res;
>>   }
>>
>>   PyObject* GetPos(const Conformer *conf) {
>> RDGeom::POINT3D_VECT pos=conf->getPositions();
>> PyObject *res = PyTuple_New(pos.size());
>> for(int idx=0;idx>   PyTuple_SetItem(res,idx,convertPoint(pos[idx]));
>> }
>> return res;
>>   }
>>
>> Getting the PyArray_SimpleNew was a little tricky in my hands, but I
>> assume that's what I need to use somehow. Does anybody have any pointers?
>>
>
> There are some examples in the RDKit source that may be helpful. Here's
> one of them:
> https://github.com/rdkit/rdkit/blob/master/Code/Numerics/Alignment/Wrap/
> rdAlignment.cpp#L134
>
> -greg
>
>
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Re: [Rdkit-discuss] MolFromMolBlock does not read properties

2016-10-03 Thread Maciek Wójcikowski

I could only imagine the errors when using threading/multiprocessing +
reusing SDMolSupplier object... So if I understand correctly the official
line of RDKit is: "a multimol file => supplier => file(-like) objects".


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-10-03 14:53 GMT+02:00 Brian Kelley :

> I'll admit that using StringIO here feels more pythonic, although SetData
> can be reused without a reconstructing the class.
>
> I suppose I would prefer having something like
>
> MolToSDDataBlock
>
> Which can be used in conjunction with MolToMolBlock.  I have often found
> that many times data changes without molecule change so perhaps both could
> be useful.
>
> 
> Brian Kelley
>
> > On Oct 3, 2016, at 7:08 AM, Andrew Dalke 
> wrote:
> >
> >> On Oct 2, 2016, at 10:48 PM, Maciek Wójcikowski wrote:
> >> Yes I get it, but obviously there is no MolFromSDBlock, so one would
> suspect MolFromMolBlock to support both formats. As I understand correctly
> the only way of reading SD from variable is as presented in my example? Or
> is there some marvelous undocumented API? ;)
> >
> > Six years ago, Greg Landrum at http://www.mail-archive.com/
> rdkit-discuss@lists.sourceforge.net/msg01436.html suggested:
> >
> >   nsuppl = Chem.SDMolSupplier()
> >   nsuppl.SetData(mb)
> >   mol = nsuppl.next()
> >
> > This is simpler than passing in a StringIO().
> >
> > I knew about this posting because my own code has MolFromSDBlock()
> wrapper layer, and a comment pointing to that URL as explanation.
> >
> >
> >> On Oct 2, 2016, at 11:06 PM, Brian Kelley wrote:
> >> The general idea, I believe, is that if the format can result in
> multiple molecules a supplier should be used.
> >
> > I wrote the function to make it easier to deal with web service input or
> database records where the text contains one and only one record in SD
> format. This is a proper subset of the SD format, which contains 0 or more
> records.
> >
> > If there are no records then my function returns a None, so I don't need
> to deal with a StopIteration. I don't care if there is more than one
> record, so I ignore anything past the first record.
> >
> > The use case occurs pretty frequently in my work, so I figured a
> MolFromSDBlock() for my own use was worthwhile.
> >
> > Cheers,
> >
> >Andrew
> >da...@dalkescientific.com
> >
> >
> > 
> --
> > 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@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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Re: [Rdkit-discuss] MolFromMolBlock does not read properties

2016-10-03 Thread Brian Kelley

I was assuming the issue is the string overload for filename versus string data 
which causes the need for the SetData function.

What I meant by not re-constructing the class is:

nsuppl = Chem.SDMolSupplier()
nsuppl.SetData(mb)
mol = nsuppl.next()

nsuppl.SetData(mb2)
mol = nsuppl.next()

A minor optimization which isn't as easily possible with the StringIO 
implementation.


Brian Kelley

> On Oct 3, 2016, at 9:04 AM, Greg Landrum  wrote:
> 
> 
> 
>> On Mon, Oct 3, 2016 at 2:53 PM, Brian Kelley  wrote:
>> I'll admit that using StringIO here feels more pythonic, although SetData 
>> can be reused without a reconstructing the class.
> 
> I guess pythonic is in the eyes of the beholder, but I don't understand that 
> at all... 
> 
>> I suppose I would prefer having something like
>> 
>> MolToSDDataBlock
>> 
>> Which can be used in conjunction with MolToMolBlock.  I have often found 
>> that many times data changes without molecule change so perhaps both could 
>> be useful.
> 
> But then that's a different problem entirely. :-)
> 
> -greg
> 
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Re: [Rdkit-discuss] MolFromMolBlock does not read properties

2016-10-03 Thread Maciek Wójcikowski

Thank you Andrew! Indeed it's working and it's a tiny bit faster too.

Best,
M


Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-10-03 13:08 GMT+02:00 Andrew Dalke :

> On Oct 2, 2016, at 10:48 PM, Maciek Wójcikowski wrote:
> > Yes I get it, but obviously there is no MolFromSDBlock, so one would
> suspect MolFromMolBlock to support both formats. As I understand correctly
> the only way of reading SD from variable is as presented in my example? Or
> is there some marvelous undocumented API? ;)
>
> Six years ago, Greg Landrum at http://www.mail-archive.com/
> rdkit-discuss@lists.sourceforge.net/msg01436.html suggested:
>
>nsuppl = Chem.SDMolSupplier()
>nsuppl.SetData(mb)
>mol = nsuppl.next()
>
> This is simpler than passing in a StringIO().
>
> I knew about this posting because my own code has MolFromSDBlock() wrapper
> layer, and a comment pointing to that URL as explanation.
>
>
> On Oct 2, 2016, at 11:06 PM, Brian Kelley wrote:
> > The general idea, I believe, is that if the format can result in
> multiple molecules a supplier should be used.
>
> I wrote the function to make it easier to deal with web service input or
> database records where the text contains one and only one record in SD
> format. This is a proper subset of the SD format, which contains 0 or more
> records.
>
> If there are no records then my function returns a None, so I don't need
> to deal with a StopIteration. I don't care if there is more than one
> record, so I ignore anything past the first record.
>
> The use case occurs pretty frequently in my work, so I figured a
> MolFromSDBlock() for my own use was worthwhile.
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
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Re: [Rdkit-discuss] MolFromMolBlock does not read properties

2016-10-03 Thread Andrew Dalke

On Oct 2, 2016, at 10:48 PM, Maciek Wójcikowski wrote:
> Yes I get it, but obviously there is no MolFromSDBlock, so one would suspect 
> MolFromMolBlock to support both formats. As I understand correctly the only 
> way of reading SD from variable is as presented in my example? Or is there 
> some marvelous undocumented API? ;)

Six years ago, Greg Landrum at 
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01436.html 
suggested:

   nsuppl = Chem.SDMolSupplier()
   nsuppl.SetData(mb)
   mol = nsuppl.next()

This is simpler than passing in a StringIO().

I knew about this posting because my own code has MolFromSDBlock() wrapper 
layer, and a comment pointing to that URL as explanation.

On Oct 2, 2016, at 11:06 PM, Brian Kelley wrote:
> The general idea, I believe, is that if the format can result in multiple 
> molecules a supplier should be used.

I wrote the function to make it easier to deal with web service input or 
database records where the text contains one and only one record in SD format. 
This is a proper subset of the SD format, which contains 0 or more records.

If there are no records then my function returns a None, so I don't need to 
deal with a StopIteration. I don't care if there is more than one record, so I 
ignore anything past the first record.

The use case occurs pretty frequently in my work, so I figured a 
MolFromSDBlock() for my own use was worthwhile.

Cheers,

Andrew
da...@dalkescientific.com

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Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

[Rdkit-discuss] Trouble compiling and installing on Ubuntu 14.04

Re: [Rdkit-discuss] Conformer getPositions to return numpy array

Re: [Rdkit-discuss] MolFromMolBlock does not read properties

Re: [Rdkit-discuss] MolFromMolBlock does not read properties

Re: [Rdkit-discuss] MolFromMolBlock does not read properties

Re: [Rdkit-discuss] MolFromMolBlock does not read properties

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