Official home of the InChI

Version 1.07.1 (09/08/2024)

• 64-bit makefile now supports native/default MacOS^® Clang compiler
• AuxInfos in CLI version of InChI are now identical to v1.06
• Intel^® oneAPI DPC++/C++ compiler can now be used with Microsoft^® Visual Studio solutions/projects on Microsoft^® Windows
• "Replace memchr() check with a new function to check the element group" pull request merged
• "Faster Element Symbol Handling" pull request merged
• "replace all instances of old license text. Fixes #33" pull request merged
• "Issues with InChI I/O with /FixedH / Issue #27 and "Seqmentation fault in inchi-1.exe with /InChI2InChI validation / Issue #28 have been fixed
• Addressing Google® oss-fuzz issues
• Minor bugs fixes

Using precompiled binaries

64-bit and 32-bit precompiled binaries (executable, .dll/.so and ELF files) are located in the following folders:

Microsoft® Windows
Files (given in compressed .zip format)	Location(s)	Compiler
inchi-1.exe	64-bit: INCHI-1-BIN/windows/64bit	Microsoft® Visual Studio C++ (MSVC)
	32-bit: INCHI-1-BIN/windows/32bit	MinGW-w64/GCC
libinchi.dll + corresponding inchi_main.exe	64-bit: INCHI-1-BIN/windows/64bit/dll	Microsoft® Visual Studio C++ (MSVC)
	32-bit: INCHI-1-BIN/windows/32bit/dll	MinGW-w64/GCC

UNIX-based OSs (except MacOS®)
Files (given in compressed .gz format)	Location(s)	Compiler
inchi-1 (ELF file)	64-bit: INCHI-1-BIN/linux/64bit/ 32-bit: INCHI-1-BIN/linux/32bit/	GCC
libinchi.so.1.07 + corresponding inchi_main (ELF file)	64-bit: INCHI-1-BIN/linux/64bit/so/ 32-bit: INCHI-1-BIN/linux/32bit/so/	GCC

Precompiled binaries for MacOS^® (i.e. .app executables and .dylib libraries) will be provided very soon. Until then, please note that InChI can now be compiled from source on MacOS^® using native/default Clang or GCC (if installed).

Compiling InChI v.1.07 from source

Microsoft^® Windows: Solution/project files for Microsoft^® Visual C++ (MSVC)/Clang/LLVM and Intel^® oneAPI DPC++/C++ Compiler are provided for both command line and API versions of InChI v.1.07. The solution/project files are located in the following folders:

• INCHI-1-SRC/INCHI_EXE/inchi-1/vc14 (command line version)
• INCHI-1-SRC/INCHI_API/demos/inchi_main/vc14 (API version consisting of libinchi.dll and its corresponding executable inchi_main.exe)
• INCHI-1-SRC/INCHI_API/libinchi/vc14 (API version consisting only of libinchi.dll).

UNIX-based OSs/MacOS^®/Microsoft^® Windows: For GCC and Clang/LLVM compilers, InChI v.1.07 can be compiled from the source using Make software. makefile/makefile32 files are provided in the following folders:

• INCHI-1-SRC/INCHI_EXE/inchi-1/gcc (command line version)
• INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc (API version consisting of libinchi.dll/libinchi.so.1.07/libinchi.dylib.1.07 and its corresponding executable/ELF inchi_main.exe/inchi_main)
• INCHI-1-SRC/INCHI_API/libinchi/gcc (API version consisting only of libinchi.dll/libinchi.so.1.07/libinchi.dylib.1.07).

makefile/makefile32 files are configured to detect OSs automatically, so it is no longer needed to specify OS explicitly or run batch/bash script(s) before compiling. GCC and Clang/LLVM compilers are also automatically detected by makefile/makefile32 files, with GCC set as default compiler. If both GCC and Clang/LLVM compilers are installed, setting Clang/LLVM as default compiler can be done simply by changing CCN parameter from value 1 to 2 in makefile/makefile32.

Support for native/default MacOS^® Clang compiler is now provided with 64-bit versions of makefile files (we would like to thank John Mayfield for his assistance with this matter).

If makefile/makefile32 is used for compiling libinchi on Microsoft^® Windows, libinchi.dll is now generated instead of libinchi.so.1.07.

Additional notes:

• Intel® oneAPI DPC++/C++ compiler support for UNIX-based OSs/MacOS^® will be available in v.1.07.2. Please note that the support will not be provided for Intel® C++ Compiler Classic (icc) as it has been discontinued since oneAPI 2024.0 release.
• Compiling from source using CMake will be available soon. In the meanwhile, you can check Gianluca Sforna's fork.

Known issues

If API version (i.e. libinchi.so.1.07 and inchi_main ELF file) is compiled using Clang/LLVM on Linux OS, and libinchi.so.1.07 cannot be found by inchi_main, LD_LIBRARY_PATH should be set either temporarily or permanently before inchi_main ELF file is used. It might be worth trying to change the value of LINKER_CWD_PATH to -Wl,-R,"",-rpath,$(LIB_DIR) (i.e. replacing = with ,) in corresponding makefile/makefile32; however, please note that during our tests, this option failed to generate libinchi.so.1.07 with Clang/LLVM on Linux. More reliably, LD_LIBRARY_PATH can be set in several ways:

• Temporarily:

  • by running a shell script ldlp_fix.sh (located in /INCHI_API/bin/Linux) with either of these two commands:

    • . ldlp_fix.sh

    • source ldlp_fix.sh;

      path to libinchi.so.1.07 can be edited in ldlp_fix.sh

  • using command line interface:

    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/libinchi.so.1.07
    

• Permanently:

  • by adding the following line in ~/.bashrc:

     ```
     LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/path/to/libinchi.so.1.07"
     ```
    

  • by adding the libinchi.so.1.07 path to ld.so.conf, which means adding a file /etc/ld.so.conf.d/local.conf containing just one line:

     ```
     path/to/libinchi.so.1.07
     ```
    
     and then running `sudo ldconfig`.
    

  • Open-source utility patchelf can also be of use.

If a similar issue occurs on MacOS^®, one of the above solutions should be applied for setting DYLD_LIBRARY_PATH and/or DYLD_FALLBACK_LIBRARY_PATH (which behave like LD_LIBRARY_PATH).

Optional features

• In order to further improve code security, bounds checking functions (see Annex K of C11 standard) can be optionally used in InChI v.1.07. Since a number of C compilers (e.g. GNU GCC) do not support bounds checking functions, they can be installed using some of the third-party open-source libraries such as:

  • safec libc extension with all C11 Annex K functions -- actively maintained
  • Safe C lib
  • Implementation of C11 Annex K "Bounds-checking interfaces" ISO/IEC 9899:2011

  The use of bounds checking functions in InChI v.1.07 can be enabled/disabled in bcf_s.h.

• If you wish to use Intel^® oneAPI Threading Building Blocks (oneTBB), please follow the instructions given in header files mode.h and tbbmalloc_proxy.h. Please note that the pre-compiled binaries do not use oneTBB.

Experimental features under development

Some of the experimental/engineering/hidden options featured in InChI 1.07 which are known to be not fully functional are:

• In command line version:

  • 32-bit Microsoft® Visual Studio C++ (MSVC) Win32 compiler-specific issue with the following options:

    • AMI Allow multiple input files (wildcards supported)
    • AMIOutStd Write output to stdout (in AMI mode)
    • AMILogStd Write log to stderr (in AMI mode)
    • AMIPrbNone Suppress creation of problem files (in AMI mode)

• In API/.dll/.so version:
  • PT_22_00 Account for PT_22_00 tautomerism (experimental)
  • PT_16_00 Account for PT_16_00 tautomerism (experimental)
  • PT_06_00 Account for PT_06_00 tautomerism (experimental)
  • PT_39_00 Account for PT_39_00 tautomerism (experimental)
  • PT_13_00 Account for PT_13_00 tautomerism (experimental)
  • PT_18_00 Account for PT_18_00 tautomerism (experimental)
  • Polymers105 Allow processing of polymers (experimental, legacy mode of v. 1.05)
  • NoEdits Disable polymer CRU frame shift and folding
  • NPZz Allow non-polymer-related Zz atoms (pseudo element placeholders)
  • SAtZz Allow stereo at atoms connected to Zz(default: disabled)
  • InChI2Struct Test mode: Mol/SDfile -> InChI -> Structure -> (InChI+AuxInfo) -- produces Fatal Error (2)3 just like in InChI v.1.06
  • InChI2InChI Convert Convert InChI string(s) into InChI string(s) -- produces Fatal Error(2)3 just like in InChI v.1.06

Please refrain from using the above mentioned options as they might not function properly, or will not be recognised. Regular updates with regard to their functionality will be posted on this page.