Re: [Rdkit-devel] InChI 1.05

2017-02-24 Thread Igor Filippov 
Greg,

Thank you for the kind words!
I should note that I am using a slightly older version of rdkit (half a
year to a year old), but I don't think it makes a difference as far as
InChI is concerned.

Best regards,
Igor


On Fri, Feb 24, 2017 at 8:43 AM, Greg Landrum 
wrote:

> Thanks Igor! I was not looking forward to getting this working, so it's
> great that someone else managed to.
>
> I need to do a bit more tweaking in order to get the download to work
> using the cmake code instead of the download_inchi.sh script, but I should
> be done with that pretty quickly.
>
> I'll have a branch up for review soon (assuming that nothing goes wrong)
>
> -greg
>
>
> On Thu, Feb 23, 2017 at 4:55 AM, Igor Filippov 
> wrote:
>
>> As InChI 1.05 is officially out I've tinkered with RDKit build system a
>> bit
>> to include the new version. Two updated files - CMakeLists.txt   and
>> download-inchi.sh
>> from External/INCHI-API/ are attached in case it may be useful to others.
>>
>> Best regards,
>> Igor
>>
>>
>> 
>> --
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>>
>
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Re: [Rdkit-devel] InChI 1.05

2017-02-24 Thread Greg Landrum 
Thanks Igor! I was not looking forward to getting this working, so it's
great that someone else managed to.

I need to do a bit more tweaking in order to get the download to work using
the cmake code instead of the download_inchi.sh script, but I should be
done with that pretty quickly.

I'll have a branch up for review soon (assuming that nothing goes wrong)

-greg


On Thu, Feb 23, 2017 at 4:55 AM, Igor Filippov 
wrote:

> As InChI 1.05 is officially out I've tinkered with RDKit build system a bit
> to include the new version. Two updated files - CMakeLists.txt   and
> download-inchi.sh
> from External/INCHI-API/ are attached in case it may be useful to others.
>
> Best regards,
> Igor
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Rdkit-devel mailing list
> Rdkit-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>
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Re: [Rdkit-devel] InChI 1.05

2017-02-23 Thread Igor Filippov 
I did run the tests and they went through just fine.

Igor

On Thu, Feb 23, 2017 at 8:47 AM, Gianluca Sforna  wrote:

> On Thu, Feb 23, 2017 at 4:55 AM, Igor Filippov
>  wrote:
> > As InChI 1.05 is officially out I've tinkered with RDKit build system a
> bit
> > to include the new version. Two updated files - CMakeLists.txt   and
> > download-inchi.sh
> > from External/INCHI-API/ are attached in case it may be useful to others.
>
> Did you try and run the tests after compiling rdkit against 1.05? IIRC
> I had failing tests with prereleases
>
>
> --
> Gianluca Sforna
>
> http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
> Tinker Garage - http://tinkergarage.it
>
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Re: [Rdkit-devel] InChI 1.05

2017-02-23 Thread Gianluca Sforna 
On Thu, Feb 23, 2017 at 4:55 AM, Igor Filippov
 wrote:
> As InChI 1.05 is officially out I've tinkered with RDKit build system a bit
> to include the new version. Two updated files - CMakeLists.txt   and
> download-inchi.sh
> from External/INCHI-API/ are attached in case it may be useful to others.

Did you try and run the tests after compiling rdkit against 1.05? IIRC
I had failing tests with prereleases


-- 
Gianluca Sforna

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

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[Rdkit-devel] InChI 1.05

2017-02-22 Thread Igor Filippov 
As InChI 1.05 is officially out I've tinkered with RDKit build system a bit
to include the new version. Two updated files - CMakeLists.txt   and
download-inchi.sh
from External/INCHI-API/ are attached in case it may be useful to others.

Best regards,
Igor
add_custom_target(inchi_support ALL)

if(RDK_BUILD_INCHI_SUPPORT)
  # search system InChI
  find_package(Inchi)

  # check whether we have custom InChI source
  if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src/INCHI_BASE/src/ichican2.c)
message(STATUS  "Found InChI software locally")
if(INCHI_FOUND)
  message(WARNING "** Local InChI software takes precedence when both 
system InChI and local InChI are found")
endif(INCHI_FOUND)
# cp --parents -auf INCHI_API/libinchi/src/ 
~/polymer/rdkit-master/External/INCHI-API/src/
# cp --parents -auf INCHI_BASE/src 
~/polymer/rdkit-master/External/INCHI-API/src/
rdkit_library(Inchi
src/INCHI_BASE/src/ichican2.c
src/INCHI_BASE/src/ichicano.c
src/INCHI_BASE/src/ichi_io.c
src/INCHI_BASE/src/ichierr.c
src/INCHI_BASE/src/ichicans.c
src/INCHI_BASE/src/ichiisot.c
src/INCHI_API/libinchi/src/ichilnct.c
src/INCHI_BASE/src/ichimak2.c
src/INCHI_BASE/src/ichimake.c
src/INCHI_BASE/src/ichimap1.c
src/INCHI_BASE/src/ichimap2.c
src/INCHI_BASE/src/ichimap4.c
src/INCHI_BASE/src/ichinorm.c
src/INCHI_BASE/src/ichiparm.c
src/INCHI_BASE/src/ichiprt1.c
src/INCHI_BASE/src/ichiprt2.c
src/INCHI_BASE/src/ichiprt3.c
src/INCHI_BASE/src/ichiqueu.c
src/INCHI_BASE/src/ichiring.c
src/INCHI_BASE/src/ichisort.c
src/INCHI_BASE/src/ichister.c
src/INCHI_BASE/src/ichitaut.c
src/INCHI_BASE/src/ichi_bns.c
src/INCHI_API/libinchi/src/inchi_dll.c
src/INCHI_BASE/src/ichiread.c
src/INCHI_BASE/src/ichirvr1.c
src/INCHI_BASE/src/ichirvr2.c
src/INCHI_BASE/src/ichirvr3.c
src/INCHI_BASE/src/ichirvr4.c
src/INCHI_BASE/src/ichirvr5.c
src/INCHI_BASE/src/ichirvr6.c
src/INCHI_BASE/src/ichirvr7.c
src/INCHI_BASE/src/ikey_dll.c
src/INCHI_BASE/src/ikey_base26.c
src/INCHI_API/libinchi/src/inchi_dll_main.c
src/INCHI_API/libinchi/src/inchi_dll_a.c
src/INCHI_API/libinchi/src/inchi_dll_a2.c
src/INCHI_API/libinchi/src/inchi_dll_b.c
src/INCHI_API/libinchi/src/ixa/ixa_inchikey_builder.c
src/INCHI_API/libinchi/src/ixa/ixa_read_mol.c
src/INCHI_API/libinchi/src/ixa/ixa_status.c
src/INCHI_API/libinchi/src/ixa/ixa_builder.c
src/INCHI_API/libinchi/src/ixa/ixa_mol.c
src/INCHI_API/libinchi/src/ixa/ixa_read_inchi.c
src/INCHI_BASE/src/mol_fmt1.c
src/INCHI_BASE/src/mol_fmt2.c
src/INCHI_BASE/src/mol_fmt3.c
src/INCHI_BASE/src/mol2atom.c
src/INCHI_BASE/src/mol_fmt4.c
src/INCHI_BASE/src/readinch.c
src/INCHI_BASE/src/runichi.c
src/INCHI_BASE/src/runichi2.c
src/INCHI_BASE/src/runichi3.c
src/INCHI_BASE/src/runichi4.c
src/INCHI_BASE/src/sha2.c
src/INCHI_BASE/src/strutil.c
src/INCHI_BASE/src/util.c  SHARED)
install(TARGETS Inchi DESTINATION ${RDKit_LibDir})
set(INCHI_LIBRARIES Inchi)
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/INCHI_BASE/src/)
ADD_DEFINITIONS("-DTARGET_API_LIB")
  else(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src/INCHI_BASE/src/ichican2.c)
if (INCHI_FOUND)
  include_directories(${INCHI_INCLUDE_DIR})
  ADD_DEFINITIONS("-DTARGET_API_LIB")
else (INCHI_FOUND)
  # system InChI is missing
  message(WARNING  "** NO INCHI SOFTWARE FOUND\n"
  "InChI support will be turned off. If you want to add InChI 
support, please follow the instructions inside 
$RDBASE/External/INCHI-API/README to download a copy of InChI software and then 
rerun cmake.")
  set(RDK_BUILD_INCHI_SUPPORT OFF)
endif(INCHI_FOUND)
  endif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src/INCHI_BASE/src/ichican2.c)

endif(RDK_BUILD_INCHI_SUPPORT)

# check whether InChI support is ON after the search
if(RDK_BUILD_INCHI_SUPPORT)
  rdkit_library(RDInchiLib inchi.cpp SHARED LINK_LIBRARIES ${INCHI_LIBRARIES} 
GraphMol RDGeneral Depictor SubstructMatch SmilesParse 
${Boost_THREAD_LIBRARY} ${CMAKE_THREAD_LIBS_INIT})   
  rdkit_headers(inchi.h DEST GraphMol)
  if(RDK_BUILD_PYTHON_WRAPPERS)
add_subdirectory(Wrap)
  endif(RDK_BUILD_PYTHON_WRAPPERS)

  add_definitions(-DBUILD_INCHI_SUPPORT)

rdkit_test(testInchi test.cpp 
LINK_LIBRARIES 
${INCHI_LIBRARIES} 
   RDInchiLib ${INCHI_LIBRARIES} 
   FileParsers SmilesParse Descriptors Depictor SubstructMatch GraphMol 
   RDGeneral DataStructs RDGeneral RDGeometryLib 
   ${Boost_THREAD_LIBRARY} ${CMAKE_THREAD_LIBS_INIT})
endif(RDK_BUILD_INCHI_SUPPORT)

if(RDK_BUILD_PYTHON_WRAPPERS)
  # we need an inchi.py... copy in the appropriate one
  if(RDK_BUILD_INCHI_SUPPORT)
   add_custom_command(TARGET inchi_support
  COMMAND ${CMAKE_COMMAND} -E copy 
${CMAKE_CURRENT_SOURCE_DIR}/python/inchi.py
 ${CMAKE_SOURCE_DIR}/rdkit/Chem/inchi.py)
  else(RDK_BUILD_INCHI_SUPPORT)
add_custom_command(TARGET inchi_support
  COMMAND ${CMAKE_COMMAND} -E copy 
${CMAKE_CURRENT_SOURCE_DIR}/python/noinchi.py