[Debichem-devel] Bug#1082109: inchi: support for .sdf (v3000 dialect) is not functional

[Norwid Behrnd]

Package: libinchi1.07
Version: 1.07.1+dfsg-3
Severity: normal
File: inchi
X-Debbugs-Cc: nbehrnd at yahoo.com

Dear Maintainer,

The compiled reference executable of InChI 1.07.1[1] for Linux 64bit assigns
InChI for .sdf in either v2000, or v3000 dialect.  While replying to an issue
report,[2] I noticed `inchi_main` as packaged by DebiChem currently supports
only the elder v2000 style.  I suggest to amend the package's functionality
to allow either input format be accepted.

See the log attached below:

```shell
@debian:~/Desktop/issue_debian$ obabel -:"C" -h --gen3d -O style_2000.sdf
1 molecule converted
@debian:~/Desktop/issue_debian$ inchi_main style_2000.sdf
InChI version 1, Software v. 1.07 (Library call example, classic API)
Linux 64-bit Build (gcc 14.2.0) of Sep  3 2024 05:44:57

Opened log file 'style_2000.sdf.log'
Opened input file 'style_2000.sdf'
Opened output file 'style_2000.sdf.txt'
Opened problem file 'style_2000.sdf.prb'
Generating standard InChI
Input format: MOLfile
Output format: Plain text
Full Aux. info
Timeout per structure: 60000 msec
Up to 1024 atoms per structure

Structure 2 could not be read: Detected end of file.
Processed 1 structure, 0 errors.
@debian:~/Desktop/issue_debian$ cat style_2000.sdf.txt
* Input_File: "style_2000.sdf"
Structure: 1
InChI=1S/CH4/h1H4
AuxInfo=1/0/N:1/rA:5nCHHHH/rB:s1;s1;s1;s1;/rC:.93,-.0596,.0392;2.0222,-.0596,.0392;.5659,-.4666,.9851;.5659,-.6753,-.7862;.5659,.963,-.0813;
@debian:~/Desktop/issue_debian$
@debian:~/Desktop/issue_debian$ obabel -:"C" -h --gen3d -O style_3000.sdf -x3
1 molecule converted
@debian:~/Desktop/issue_debian$ inchi_main style_3000.sdf
InChI version 1, Software v. 1.07 (Library call example, classic API)
Linux 64-bit Build (gcc 14.2.0) of Sep  3 2024 05:44:57

Opened log file 'style_3000.sdf.log'
Opened input file 'style_3000.sdf'
Opened output file 'style_3000.sdf.txt'
Opened problem file 'style_3000.sdf.prb'
Generating standard InChI
Input format: MOLfile
Output format: Plain text
Full Aux. info
Timeout per structure: 60000 msec
Up to 1024 atoms per structure

Error 171 (no INChI; Molfile V3000 input is not supported) inp structure #1.
Structure 2 could not be read: Detected end of file.
Processed 1 structure, 1 error.
@debian:~/Desktop/issue_debian$ cat style_3000.sdf.txt
* Input_File: "style_3000.sdf"
InChI=1S//
@debian:~/Desktop/issue_debian$
```

Regards,

Norwid Behrnd

[1] https://github.com/openbabel/openbabel/releases
[2] https://github.com/IUPAC-InChI/InChI/issues/52


-- System Information:
Debian Release: trixie/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 6.9.10-amd64 (SMP w/4 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages libinchi1.07 depends on:
ii  libc6  2.40-2

libinchi1.07 recommends no packages.

libinchi1.07 suggests no packages.

-- no debconf information