Re: [Rdkit-devel] drawing amino acids
Greg,
I figured out what the problem is:
getStringSize() calculates the pixel height/width of a given atom label.
For labels such as NH3+ the argument this function is getting is
NH3+
which makes for a very long sting, which throws off the scale calculation.
I am not sure why it works correctly with the drawers other than SVG but
for wxWidgets I need to clean from the label , , , and
before computing the string width.
Hope this helps to someone who might have the same problem.
Best regards,
Igor
On Fri, Sep 8, 2017 at 8:29 AM, Igor Filippov <igor.v.filip...@gmail.com>
wrote:
> Great - thanks, I'll try it!
>
> Igor
>
> On Fri, Sep 8, 2017 at 8:27 AM, Greg Landrum <greg.land...@gmail.com>
> wrote:
>
>>
>> On Fri, Sep 8, 2017 at 2:10 PM, Igor Filippov <igor.v.filip...@gmail.com>
>> wrote:
>>
>>>
>>>>
>>>> Could it be that you didn't generate coordinates for the molecule?
>>>>
>>>> The result is the same for me whether I load the molecule from an SD
>>> file with coordinates, or generate 2D or 3D coordinates on the fly.
>>> Does it display correctly for you?
>>>
>>
>> Yeah, This snippet:
>>
>> In [21]: m = Chem.MolFromSmiles('NC(=O)C(N)[NH3+]')
>>
>> In [22]: nm = Draw.PrepareMolForDrawing(m)
>>
>> In [23]: d = Draw.MolDraw2DCairo(200,200)
>>
>> In [24]: d.DrawMolecule(nm)
>>
>> In [25]: d.FinishDrawing()
>>
>> In [26]: open('blah.png','wb+').write(d.GetDrawingText())
>> Out[26]: 2730
>>
>>
>> Produces the png file that's attached.
>>
>>
>>> BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know
>>>> about.
>>>>
>>> I am doing it from c++, is there an equivalent there?
>>>
>>
>> Sure, here's some testing code that uses it:
>> https://github.com/rdkit/rdkit/blob/9af90524a41825b67ffb19cd
>> bff9b363d5a7ca7e/Code/GraphMol/MolDraw2D/test1.cpp#L987
>>
>> There are a bunch of other examples in that file too.
>>
>> -greg
>>
>>
>
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Re: [Rdkit-devel] drawing amino acids
Great - thanks, I'll try it!
Igor
On Fri, Sep 8, 2017 at 8:27 AM, Greg Landrum <greg.land...@gmail.com> wrote:
>
> On Fri, Sep 8, 2017 at 2:10 PM, Igor Filippov <igor.v.filip...@gmail.com>
> wrote:
>
>>
>>>
>>> Could it be that you didn't generate coordinates for the molecule?
>>>
>>> The result is the same for me whether I load the molecule from an SD
>> file with coordinates, or generate 2D or 3D coordinates on the fly.
>> Does it display correctly for you?
>>
>
> Yeah, This snippet:
>
> In [21]: m = Chem.MolFromSmiles('NC(=O)C(N)[NH3+]')
>
> In [22]: nm = Draw.PrepareMolForDrawing(m)
>
> In [23]: d = Draw.MolDraw2DCairo(200,200)
>
> In [24]: d.DrawMolecule(nm)
>
> In [25]: d.FinishDrawing()
>
> In [26]: open('blah.png','wb+').write(d.GetDrawingText())
> Out[26]: 2730
>
>
> Produces the png file that's attached.
>
>
>> BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know
>>> about.
>>>
>> I am doing it from c++, is there an equivalent there?
>>
>
> Sure, here's some testing code that uses it:
> https://github.com/rdkit/rdkit/blob/9af90524a41825b67ffb19cdbff9b3
> 63d5a7ca7e/Code/GraphMol/MolDraw2D/test1.cpp#L987
>
> There are a bunch of other examples in that file too.
>
> -greg
>
>
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[Rdkit-devel] MolDraw2Dwx
Greg, I just noticed that stock MolDraw2Dwx.h will not build because of the line: setColour(drawOptions.backgroundColour); should be drawOptions() as it is a function call. Also, I would recommend adding the following lines into setFontSize(): if (font_size_in_points < 1.0) font_size_in_points = 1; I noticed that if font height is less than 1 it gets rounded to zero and wxWidgets has a problem with that. Warmest 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
Re: [Rdkit-devel] InChI 1.05
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 <greg.land...@gmail.com> 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 <igor.v.filip...@gmail.com> > 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 >> >> > -- 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
Re: [Rdkit-devel] InChI 1.05
I did run the tests and they went through just fine. Igor On Thu, Feb 23, 2017 at 8:47 AM, Gianluca Sforna <gia...@gmail.com> wrote: > On Thu, Feb 23, 2017 at 4:55 AM, Igor Filippov > <igor.v.filip...@gmail.com> 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 > -- 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
[Rdkit-devel] InChI 1.05
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
