Official home of the InChI

• Release 1.07-Beta5 (24/04/2024):
  • Addressing Google® oss-fuzz issues
  • Licence updated
• Release 1.07-Beta4 (24/03/2024):
  • "/b-layer" issue / Issue #9 has been fixed
  • Incorrect output message regarding CPU architecture on ARM64 CPUs / Issue #10 has been fixed
  • Further Google® oss-fuzz issues have been addressed

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 and 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

Compiling InChI v.1.07 from source

Project files for Microsoft^® Visual C++ (MSVC)/Clang/LLVM users are provided for both command line and API versions of InChI v.1.07. The 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).

For other C compilers, 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 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).

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. If both GCC and Clang/LLVM compilers are detected, GCC is used by default; setting Clang/LLVM as default compiler can be done simply by changing CCN parameter from 1 to 2 in makefile/makefile32.

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

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 mentioned in the previous section do not use oneTBB.

Known issues

1. In case GCC is used to compile InChI v.1.07, GCC version 11.x is recommended, since compiling any InChI version (incl. v.1.07 and v.1.06) using GCC versions 12.x and 13.x can produce very rare segmentation errors whilst processing the following PubChem structures: 453841144, 453979403, 450031964, 449987684, 448775139, 448753468, 448623641. This issue is expected to be fixed in the forthcoming update of InChI v.1.07.

2. 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).

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.