ggasoftware / indigo Goto Github PK

Indigo: a cheminformatics toolkit. Bingo: RDBMS data cartridge for Oracle, MS SQL Server, and PostgreSQL

Home Page: https://lifescience.opensource.epam.com/indigo

C# 6.90% C 3.58% C++ 78.03% Java 5.41% Python 2.99% Shell 0.13% CMake 1.10% Batchfile 0.34% PLSQL 0.06% NSIS 0.18% TSQL 1.27%

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mojca dimitry42 smikes diniska rillke harcharansidhu ergo70 schimi69 pkpkpk metamolecular 5455945 connlan yfyh2013 akhilsoman

indigo's Issues

amide groups drawn incorrectly

When I use Indigo to draw compounds with amide (such as L-glutamine or L-asparagine) using InChI as the input, the double bond is between the C=N instead of C=O.

For example the InChI for L-glutamine is:
InChI=1S/C5H10N2O3/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H2,7,8)(H,9,10)/t3-/m0/s1
and the resulting image is:

HDC

When calling indigoRenderWriteHDC the image always renders the same size. The "render-image-size" setting does not seem to have any effect. Is this the intended design, or is it a bug?

Difficulty Building with Visual Studio 2010

I downloaded the project and converted the indigo-depict solution to a Visual Studio 2010 solution. When I attempted to build I go 10 link errors. Is there something I am missing during the build, or is there documentation on how to build somewhere? Thanks.

tinyxml.lib(tinyxml.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance

LIBCMT.lib(invarg.obj) : error LNK2005: ___pInvalidArgHandler already defined in LIBCMTD.lib(invarg.obj)

LIBCMT.lib(invarg.obj) : error LNK2005: __initp_misc_invarg already defined in LIBCMTD.lib(invarg.obj)

LIBCMT.lib(invarg.obj) : error LNK2005: __call_reportfault already defined in LIBCMTD.lib(invarg.obj)

LIBCMT.lib(invarg.obj) : error LNK2005: __set_invalid_parameter_handler already defined in LIBCMTD.lib(invarg.obj)

LIBCMT.lib(invarg.obj) : error LNK2005: __get_invalid_parameter_handler already defined in LIBCMTD.lib(invarg.obj)

LIBCMT.lib(invarg.obj) : error LNK2005: __invoke_watson already defined in LIBCMTD.lib(invarg.obj)

LIBCMT.lib(invarg.obj) : error LNK2005: "void __cdecl _invoke_watson(unsigned short const *,unsigned short const *,unsigned short const *,unsigned int,unsigned int)" (?_invoke_watson@@YAXPBG00II@Z) already defined in LIBCMTD.lib(invarg.obj)

LIBCMT.lib(invarg.obj) : error LNK2005: __invalid_parameter already defined in LIBCMTD.lib(invarg.obj)

LIBCMT.lib(invarg.obj) : error LNK2005: "void __cdecl _invalid_parameter(unsigned short const *,unsigned short const *,unsigned short const *,unsigned int,unsigned int)" (?_invalid_parameter@@YAXPBG00II@Z) already defined in LIBCMTD.lib(invarg.obj)

android

is it possible to use this library with android? if so, how would i go about doing it? thank you

Postgres cartridge - confusing similarity search results

foo=# SELECT bingo.getversion() ;
   getversion    
-----------------
 1.7.9.0 linux64
(1 row)


foo=# SELECT version();
                                           version                                            
----------------------------------------------------------------------------------------------
 PostgreSQL 9.1.9 on x86_64-unknown-linux-gnu, compiled by gcc (Debian 4.8.1-6) 4.8.1, 64-bit
(1 row)

Input data:

We get the same inchi string using smiles from both sources:

foo=# SELECT bingo.inchi('CN1C=NC2=C1C(=O)N(C)C(=O)N2C', '') = bingo.inchi('Cn1cnc2c1c(=O)n(C)c(=O)n2C', '');
 ?column? 
----------
 t
(1 row)

Exact search with 'MAS' option treats both representations as identical.

foo=# SELECT 'Cn1cnc2c1c(=O)n(C)c(=O)n2C' @  ('CN1C=NC2=C1C(=O)N(C)C(=O)N2C', 'MAS') :: bingo.exact;
 ?column? 
----------
 t
(1 row)

But when we try similarity search we get extremely low Tanimoto Coefficient.

foo=# SELECT bingo.getsimilarity('Cn1cnc2c1c(=O)n(C)c(=O)n2C', 'CN1C=NC2=C1C(=O)N(C)C(=O)N2C', 'tanimoto');
 getsimilarity 
---------------
       0.21875
(1 row)

I assume it is due the way of handling aromaticity:

from indigo import *
from indigo_renderer import *

indigo = Indigo()
renderer = IndigoRenderer(indigo)
indigo.setOption("render-output-format", "png")
indigo.setOption("render-image-size", 200, 250);
indigo.setOption("render-background-color", 1.0, 1.0, 1.0);

m1 = indigo.loadMolecule('CN1C=NC2=C1C(=O)N(C)C(=O)N2C')
renderer.renderToFile(m1, "caffeine_m1.png");

m2 = indigo.loadMolecule('Cn1cnc2c1c(=O)n(C)c(=O)n2C')
renderer.renderToFile(m2, "caffeine_m2.png");

SIGABRT on freelibrary mono->indigo calls

Hello everyone,

We are getting this error after upgrade to indigo 1.1.11, Platform is Linux 64 running indigo via mono .net wrapper:

Stacktrace:

at <0xffffffff>
at (wrapper managed-to-native) com.ggasoftware.indigo.LibraryLoader/LinuxLoader.dlclose (intptr) <0xffffffff>
at com.ggasoftware.indigo.LibraryLoader.FreeLibrary (intptr) <0x0007f>
at com.ggasoftware.indigo.IndigoDllLoader.Finalize () <0x000c7>
at (wrapper runtime-invoke) object.runtime_invoke_virtual_void__this__ (object,intptr,intptr,intptr) <0xffffffff>

Native stacktrace:

/opt/mono/bin/mono() [0x4942c6]
/lib64/libpthread.so.0(+0xf500) [0x7fceafec4500]
/lib64/libc.so.6(gsignal+0x35) [0x7fceafb548a5]
/lib64/libc.so.6(abort+0x175) [0x7fceafb56085]
/lib64/libc.so.6(+0x707b7) [0x7fceafb927b7]
/lib64/libc.so.6(+0x760e6) [0x7fceafb980e6]
/lib64/libc.so.6(+0x78c13) [0x7fceafb9ac13]
/tmp/GGA_indigo/indigo-dotnet/1.1.4933.3712/Linux/x64/libindigo.so(+0xb7dc1) [0x7fce9f213dc1]
/tmp/GGA_indigo/indigo-dotnet/1.1.4933.3712/Linux/x64/libindigo.so(+0xb8ed7) [0x7fce9f214ed7]
/tmp/GGA_indigo/indigo-dotnet/1.1.4933.3712/Linux/x64/libindigo.so(+0xb9321) [0x7fce9f215321]
/lib64/libc.so.6(__cxa_finalize+0x9d) [0x7fceafb5813d]
/tmp/GGA_indigo/indigo-dotnet/1.1.4933.3712/Linux/x64/libindigo.so(+0x88ce3) [0x7fce9f1e4ce3]

Debug info from gdb:

Got a SIGABRT while executing native code. This usually indicates
a fatal error in the mono runtime or one of the native libraries

used by your application.

Links broken/hijacted in description and info.md

The documentation can actually be found at http://lifescience.opensource.epam.com/indigo/ the existing links take me to http://www.epam.com/ (with no clear link to the actual information)

Linking Error in Visual Studio 2010 in Debug

I downloaded the project and converted the indigo-depict solution to a Visual Studio 2010 solution. When I attempted to build I go 10 link errors. The problem seems to be a conflict between debug and release libraries. The solution builds and links in Release mode.

tinyxml.lib(tinyxml.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance

error : bingo buffer: internal error: corrupted block 8999 data len is -8

Error occurs while I update the postgresql database, how to solve it ? Thank you !

build fails (Command 'make package' returned non-zero exit status 2)

running

python build_scripts/indigo-release-libs.py --preset=linux64

fails with the following:
(tried with master and indigo-1.1-rc.zip as well, same effect)

[...]
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o:dlopen-test.c:(.text.startup+0x266): more undefined references to `dlsym' follow
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o: In function `main':
dlopen-test.c:(.text.startup+0x2c1): undefined reference to `dlclose'
dlopen-test.c:(.text.startup+0x2d0): undefined reference to `dlclose'
collect2: ld returned 1 exit status
make[2]: *** [dist/Linux/x64/shared/dlopen-test] Error 1
make[1]: *** [indigo/api/CMakeFiles/dlopen-test.dir/all] Error 2
make: *** [all] Error 2
[  4%] Built target z
[ 12%] Built target common
[ 13%] Built target tinyxml
[ 20%] Built target graph
[ 32%] Built target molecule
[ 38%] Built target reaction
[ 42%] Built target layout
Linking C executable ../../dist/Linux/x64/shared/dlopen-test
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o: In function `dlOpenWithCheck':
dlopen-test.c:(.text+0x7): undefined reference to `dlopen'
dlopen-test.c:(.text+0x19): undefined reference to `dlerror'
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o: In function `main':
dlopen-test.c:(.text.startup+0x10e): undefined reference to `dlclose'
dlopen-test.c:(.text.startup+0x15f): undefined reference to `dlsym'
dlopen-test.c:(.text.startup+0x1cb): undefined reference to `dlsym'
dlopen-test.c:(.text.startup+0x1dd): undefined reference to `dlsym'
dlopen-test.c:(.text.startup+0x244): undefined reference to `dlsym'
dlopen-test.c:(.text.startup+0x256): undefined reference to `dlsym'
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o:dlopen-test.c:(.text.startup+0x266): more undefined references to `dlsym' follow
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o: In function `main':
dlopen-test.c:(.text.startup+0x2c1): undefined reference to `dlclose'
dlopen-test.c:(.text.startup+0x2d0): undefined reference to `dlclose'
collect2: ld returned 1 exit status
make[2]: *** [dist/Linux/x64/shared/dlopen-test] Error 1
make[1]: *** [indigo/api/CMakeFiles/dlopen-test.dir/all] Error 2
make: *** [all] Error 2
[  4%] Built target z
[ 12%] Built target common
[ 13%] Built target tinyxml
[ 20%] Built target graph
[ 32%] Built target molecule
[ 38%] Built target reaction
[ 42%] Built target layout
Linking C executable ../../dist/Linux/x64/shared/dlopen-test
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o: In function `dlOpenWithCheck':
dlopen-test.c:(.text+0x7): undefined reference to `dlopen'
dlopen-test.c:(.text+0x19): undefined reference to `dlerror'
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o: In function `main':
dlopen-test.c:(.text.startup+0x10e): undefined reference to `dlclose'
dlopen-test.c:(.text.startup+0x15f): undefined reference to `dlsym'
dlopen-test.c:(.text.startup+0x1cb): undefined reference to `dlsym'
dlopen-test.c:(.text.startup+0x1dd): undefined reference to `dlsym'
dlopen-test.c:(.text.startup+0x244): undefined reference to `dlsym'
dlopen-test.c:(.text.startup+0x256): undefined reference to `dlsym'
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o:dlopen-test.c:(.text.startup+0x266): more undefined references to `dlsym' follow
CMakeFiles/dlopen-test.dir/tests/c/dlopen-test.c.o: In function `main':
dlopen-test.c:(.text.startup+0x2c1): undefined reference to `dlclose'
dlopen-test.c:(.text.startup+0x2d0): undefined reference to `dlclose'
collect2: ld returned 1 exit status
make[2]: *** [dist/Linux/x64/shared/dlopen-test] Error 1
make[1]: *** [indigo/api/CMakeFiles/dlopen-test.dir/all] Error 2
make: *** [all] Error 2
Traceback (most recent call last):
  File "build_scripts/indigo-release-libs.py", line 72, in <module>
    subprocess.check_call("make package", shell=True)
  File "/usr/lib/python2.7/subprocess.py", line 511, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'make package' returned non-zero exit status 2

any idea why?

Saving reaction as CML outputs malformed data

The following code can be used to reproduce the problem. Only the "reactantlist" part is written as CML to out buffer or file. The written CML data is not well formed.

const char* rxnV2 = "$RXN\r\nDiels Alder V2000\r\n  \r\n\r\n  2  1\r\n$MOL\r\n\r\n\r\n\r\n  6  5  0  0  0  0  0  0  0  0999 V2000\r\n    0.6489    0.9959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n    0.0656    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n    0.0656   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n    0.6489   -0.9959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n   -0.6489    0.8250    0.0000 R1  0  0  0  0  0  0  0  0  0  0  0  0\r\n   -0.6489   -0.8250    0.0000 R2  0  0  0  0  0  0  0  0  0  0  0  0\r\n  1  2  2  0        0\r\n  2  3  1  0        0\r\n  3  4  2  0        0\r\n  2  5  1  0        0\r\n  3  6  1  0        0\r\nM  END\r\n$MOL\r\n\r\n\r\n\r\n  4  3  0  0  0  0  0  0  0  0999 V2000\r\n   -0.2917    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n   -0.2917   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n    0.2917    0.9959    0.0000 R3  0  0  0  0  0  0  0  0  0  0  0  0\r\n    0.2917   -0.9959    0.0000 R4  0  0  0  0  0  0  0  0  0  0  0  0\r\n  1  2  2  0        0\r\n  1  3  1  0        0\r\n  2  4  1  0        0\r\nM  END\r\n$MOL\r\n\r\n\r\n\r\n 10 10  0  0  0  0  0  0  0  0999 V2000\r\n   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n   -0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\r\n    1.4289    0.8250    0.0000 R3  0  0  0  0  0  0  0  0  0  0  0  0\r\n    1.4289   -0.8250    0.0000 R4  0  0  0  0  0  0  0  0  0  0  0  0\r\n   -1.4289    0.8250    0.0000 R1  0  0  0  0  0  0  0  0  0  0  0  0\r\n   -1.4289   -0.8250    0.0000 R2  0  0  0  0  0  0  0  0  0  0  0  0\r\n  1  2  2  0        0\r\n  2  3  1  0        0\r\n  3  4  1  0        0\r\n  4  5  1  0        0\r\n  5  6  1  0        0\r\n  6  1  1  0        0\r\n  5  7  1  0        0\r\n  4  8  1  0        0\r\n  1  9  1  0        0\r\n  2 10  1  0        0\r\nM  END\r\n";
    int rxn = indigoLoadReactionFromBuffer(rxnV2, strlen(rxnV2) + 1);
    int bufHandle = indigoWriteBuffer();
    int saver = indigoCreateSaver(bufHandle, "cml");
    indigoAppend(saver, rxn);
    indigoClose(saver);

    char* out;
    int outSize = 0;
    char* tempBuffer;
    if((indigoToBuffer(bufHandle, &tempBuffer, &outSize) > 0) && (outSize > 0))
    {
        out = new char[outSize];
        memcpy_s(out, outSize, tempBuffer, outSize);
    }

The output is:

<?xml version="1.0" ?>
<cml>
<reaction title="Diels Alder V2000">
<reactantList>
<molecule title="">
  <atomArray>
    <atom id="a0" elementType="C"
         x2="0.648900" y2="0.995900"/>
    <atom id="a1" elementType="C"
         x2="0.065600" y2="0.412500"/>
    <atom id="a2" elementType="C"
         x2="0.065600" y2="-0.412500"/>
    <atom id="a3" elementType="C"
         x2="0.648900" y2="-0.995900"/>
    <atom id="a4" elementType="R1"

Cannot find source file: tests/c/indigo-test.c

running build_scripts/indigo-release-libs.py fails due to a test-related file not being checked in to the repository. Commenting out any test-related lines from api/{,plugins/inchi/,renderer}CMakeLists.txt works around this problem, but obviously is not the most advantageous.

Memory exception while rendering a RXN file as CDXML

I think the code that renders a reaction file to CDXML is missing from: "indigo/render2d/src/render_cdxml.cpp".

The method RenderParamCdxmlInterface::render is responsible for rendering CDXML format for both molecules and reactions but the code only considers params.mols structure. There is no usage of params.rxns that contains reaction components.

To reproduce:

Read a reaction file
set indigoSetOption("render-output-format", "cdxml");
Write a CDXML file using indigoRender or indigoRenderToFile
Memory exception occurs. Fails at (_getBounds(params, mols[i]->asMolecule(), p.str_min, p.str_max, p.scale);

Unable to get INCHIKEY value for an inchi string

The following code returns a NULL pointer for inchikey:

    int mol = indigoLoadMoleculeFromString("C1CCCCC1");
    const char* inchi = indigoInchiGetInchi(mol);   // InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2
    const char* inchik = indigoInchiGetInchiKey(inchi); // NULL pointer

The problem lies in indigoInchiGetInchiKey method of indigo_inchi_api.cpp file. The passed in inchi_string is somehow assigned to self.tmp_string which is cleared for output in IndigoInchi::InChIKey method of indigo_inchi_core.cpp.

Depiction getting cropped with indigo-depict

Hello
When using indigo-depic the 2D depiction is getting cropped.

Here is a test case.
indigo-depict - "CN1CC[C@]2([C@@H]1C[C@@H](CC2)O)C3=CC(=C(C=C3)OC)OC" test.png

I tried playing with margins and pixels without success.

Thanks

how to create project with visual studio 2012

hello everyone,how can i use cmake create VS C++ project?TH'X ALL