Dear Andrius, In the more general case of a .mol/.sdf file about models with multiple atoms and at least one explicit bond, the reference executable of InChI 1.07.1 is able to process data in the v3000 dialect. Their executable published by August 21st, 2024 on <https://github.com/IUPAC-InChI/InChI/releases> for instance is able to assign pyridine (written by OpenBabel) its InChI string. For documentation, I attach the log of a test run in Linux Debian 13/trixie with InChI's reference executable 1.07.1.
--- Issue 52 (on InChI's GitHub repository) addresses a particular case -- .mol or .sdf with exactly one explicit atom only. In this instance, some programs write a bound block (for instance the sketcher InChI's demo page currently uses, and OpenBabel) though there is no _explicit_ second atom to bound to. The file then reads ``` M V30 BEGIN BOND M V30 END BOND ``` The reference executable of InChI 1.07.1 considers this to be an error. Other programs (for instance Marvin) write a bound block only if there are at least two atoms with an explicit bound. The current implementation in OpenBabel 3.1.1 (as packaged for Debian by September 4, 2024) can process either one of the two forms thanks to the internal design of OpenBabel. Best regards, Norwid
@debian:~/Desktop/inchi_test$ md5sum INCHI-1-BIN.zip 7829bc3ce6235d10a8e8bb8f594618c0 INCHI-1-BIN.zip @debian:~/Desktop/inchi_test$ unzip INCHI-1-BIN.zip Archive: INCHI-1-BIN.zip creating: INCHI-1-BIN/ creating: INCHI-1-BIN/windows/ creating: INCHI-1-BIN/windows/32bit/ inflating: INCHI-1-BIN/windows/32bit/inchi-1.exe extracting: INCHI-1-BIN/windows/32bit/inchi-1.zip creating: INCHI-1-BIN/windows/32bit/dll/ inflating: INCHI-1-BIN/windows/32bit/dll/inchi_main.exe extracting: INCHI-1-BIN/windows/32bit/dll/libinchi.zip extracting: INCHI-1-BIN/windows/32bit/dll/inchi_main.zip inflating: INCHI-1-BIN/windows/32bit/dll/libinchi.dll inflating: INCHI-1-BIN/windows/winchi-1.exe creating: INCHI-1-BIN/windows/64bit/ inflating: INCHI-1-BIN/windows/64bit/inchi-1.exe extracting: INCHI-1-BIN/windows/64bit/inchi-1.zip creating: INCHI-1-BIN/windows/64bit/dll/ inflating: INCHI-1-BIN/windows/64bit/dll/inchi_main.exe extracting: INCHI-1-BIN/windows/64bit/dll/libinchi.zip extracting: INCHI-1-BIN/windows/64bit/dll/inchi_main.zip inflating: INCHI-1-BIN/windows/64bit/dll/libinchi.dll inflating: INCHI-1-BIN/readme.md creating: INCHI-1-BIN/linux/ creating: INCHI-1-BIN/linux/32bit/ inflating: INCHI-1-BIN/linux/32bit/inchi-1 creating: INCHI-1-BIN/linux/32bit/so/ inflating: INCHI-1-BIN/linux/32bit/so/libinchi.so.1.07.gz inflating: INCHI-1-BIN/linux/32bit/so/inchi_main inflating: INCHI-1-BIN/linux/32bit/so/libinchi.so.1.07 inflating: INCHI-1-BIN/linux/32bit/so/inchi_main.gz inflating: INCHI-1-BIN/linux/32bit/inchi-1.gz creating: INCHI-1-BIN/linux/64bit/ inflating: INCHI-1-BIN/linux/64bit/inchi-1 creating: INCHI-1-BIN/linux/64bit/so/ inflating: INCHI-1-BIN/linux/64bit/so/libinchi.so.1.07.gz inflating: INCHI-1-BIN/linux/64bit/so/inchi_main inflating: INCHI-1-BIN/linux/64bit/so/libinchi.so.1.07 inflating: INCHI-1-BIN/linux/64bit/so/inchi_main.gz inflating: INCHI-1-BIN/linux/64bit/inchi-1.gz @debian:~/Desktop/inchi_test$ @debian:~/Desktop/inchi_test$ cd INCHI-1-BIN/linux/64bit/ @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ ls inchi-1 inchi-1.gz so @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ chmod 775 ./inchi-1 @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ obabel -:"c1ccncc1" -h --gen3d -O pyridine.sdf -x3 1 molecule converted @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ md5sum ./inchi-1 50ab0180934c33ff8da93a8a7ff05d1b ./inchi-1 @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ cat ./pyridine.sdf OpenBabel09232411263D 0 0 0 0 0 999 V3000 M V30 BEGIN CTAB M V30 COUNTS 11 11 0 0 0 M V30 BEGIN ATOM M V30 1 C 1.43303 0.0515849 0.000998063 0 M V30 2 C 0.687995 1.22595 0.00150645 0 M V30 3 C -0.694235 1.12564 0.00218175 0 M V30 4 N -1.36237 -0.0485314 0.00552039 0 M V30 5 C -0.611969 -1.17189 0.00692408 0 M V30 6 C 0.773792 -1.17331 0.00331962 0 M V30 7 H 2.51852 0.0903642 -0.00112859 0 M V30 8 H 1.17153 2.1963 0.00126842 0 M V30 9 H -1.31976 2.01344 6.15393e-05 0 M V30 10 H -1.17257 -2.10232 0.0114491 0 M V30 11 H 1.32543 -2.10632 0.00269552 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 2 1 6 M V30 3 1 1 7 M V30 4 2 2 3 M V30 5 1 2 8 M V30 6 1 3 4 M V30 7 1 3 9 M V30 8 2 4 5 M V30 9 1 5 6 M V30 10 1 5 10 M V30 11 1 6 11 M V30 END BOND M V30 END CTAB M END $$$$ @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ ./inchi-1 ./pyridine.sdf InChI version 1, Software v. 1.07 (inchi-1 executable) Linux 64-bit Build (gcc 11.4.0) of Aug 10 2024 18:58:34 Opened log file './pyridine.sdf.log' Opened input file './pyridine.sdf' Opened output file './pyridine.sdf.txt' Opened problem file './pyridine.sdf.prb' The command line used: "./inchi-1 ./pyridine.sdf" Generating standard InChI Input format: MOLfile Output format: Plain text Full Aux. info Timeout per structure: 60000 msec Up to 1024 atoms per structure End of file detected after structure #1. Finished processing 1 structure: 0 errors, processing time 0:00:00.00 @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ cat ./pyridine.sdf.txt * Input_File: "./pyridine.sdf" Structure: 1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H AuxInfo=1/0/N:1,2,6,3,5,4/E:(2,3)(4,5)/rA:11nCCCNCCHHHHH/rB:s1;d2;s3;d4;d1s5;s1;s2;s3;s5;s6;/rC:1.43303,.0515849,.00099806;.687995,1.22595,.00150645;-.694235,1.12564,.00218175;-1.36237,-.0485314,.00552039;-.611969,-1.17189,.00692408;.773792,-1.17331,.00331962;2.51852,.0903642,-.0011285;1.17153,2.1963,.00126842;-1.31976,2.01344,6.15393;-1.17257,-2.10232,.0114491;1.32543,-2.10632,.00269552; @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$ lsb_release -a No LSB modules are available. Distributor ID: Debian Description: Debian GNU/Linux trixie/sid Release: n/a Codename: trixie @debian:~/Desktop/inchi_test/INCHI-1-BIN/linux/64bit$
