Recent changes to bugs

#760 incorrect treatment of aromatic with explicit bond

Noel O'Boyle — Wed, 26 Jul 2017 08:28:33 -0000

This bug is closed. See https://github.com/openbabel/openbabel/issues/1140 and the notice about this SourceForge bug tracker at the top of https://sourceforge.net/p/openbabel/bugs/. If you have found a new bug, please file it on Github as described in that notice.

#760 incorrect treatment of aromatic with explicit bond

Termo — Wed, 26 Jul 2017 08:19:35 -0000

And more weird stuff when looking at bond orders for the input inchi molecule:

[b.GetBondOrder() for b in ob.OBMolBondIter(mol)]
Out[40]: [2, 1, 1, 2, 2, 2, 1, 1, 1, 1]

and the output of a small function I have made to give a bond dict:

getbsum('InChI=1S/C6H4/c1-2-4-6-5-3-1/h1-4H', term='inchi')
Out[43]: [defaultdict(int, {'[C]-1-[C]': 2, '[C]-1-[H]': 4, '[C]-2-[C]': 4}), #C    6 #H    4
 dtype: int64]

So 4 double bonds (should be 2) and no triple bonds (should be 1) ??

#760 incorrect treatment of aromatic with explicit bond

Termo — Wed, 26 Jul 2017 07:51:36 -0000

How can this bug still stick around? I just ran into it with Benzyne 'c1ccccc#1', which I suddenly found had wrong atomic count in my database...

obabel -ismi -:'c1ccccc#1' -oreport -h
FILENAME:
FORMULA: C6H6
MASS: 78.1118

obabel -iinchi -:'InChI=1S/C6H4/c1-2-4-6-5-3-1/h1-4H' -oreport -h
FILENAME:
FORMULA: C6H4
MASS: 76.0960

Test

Noel O'Boyle — Fri, 24 Mar 2017 13:45:40 -0000

Test

Noel O'Boyle — Fri, 24 Mar 2017 13:44:48 -0000

Test

#994 obminimize gives warnings

Noel O'Boyle — Fri, 24 Mar 2017 13:39:36 -0000

status: open --> wont-fix
assigned_to: Noel O'Boyle

#994 obminimize gives warnings

Pent — Fri, 24 Mar 2017 13:36:39 -0000

Ah, it works in a new command prompt without warnings!
Please close.

#994 obminimize gives warnings

Noel O'Boyle — Fri, 24 Mar 2017 13:32:51 -0000

The environment variable BABEL_DATADIR is either not set, or pointing to a location that does not contain those files. It should be set, by the installer. If you could open a new command prompt and check whether it's set correctly, that'd be appreciated. echo %BABEL_DATADIR% will do the job. I don't have a Win 10 machine to hand, so I can't help much beyond this.

obminimize gives warnings

Pent — Fri, 24 Mar 2017 12:19:15 -0000

To reproduce:

obminimize 4047.mol
It reports

==============================
*** Open Babel Warning  in OpenBabel::OBGlobalDataBase::Init
  Cannot initialize database 'types.txt' which may cause further errors.
==============================
*** Open Babel Warning  in OpenBabel::OBTypeTable::Translate
  Cannot perform atom type translation: table cannot find requested types.
==============================
*** Open Babel Warning  in OpenBabel::OBTypeTable::Translate
  Cannot perform atom type translation: table cannot find requested types.

However, then it continues with

A T O M   T Y P E S

IDX TYPE    RING
1   12  NO
2   11  NO
3   39  AR
4   9   AL
5   66  AR
6   37  AR
7   63  AR
8   37  AR
9   4   AL
10  3   AL
11  63  AR
12  64  AR
13  37  AR
14  37  AR
15  37  AR
16  37  AR
17  37  AR
18  37  AR
19  37  AR
20  37  AR
21  37  AR
22  37  AR
23  60  NO

and outputs seemingly-correct optimized structure.

obabel -V
Open Babel 2.4.1 -- Oct 10 2016 -- 21:23:29

I'm on Windows 10. Reproducible with both 32-bit and 64-bit binaries.

obminimize gives warnings

Pent — Fri, 24 Mar 2017 12:19:15 -0000

Ticket 994 has been modified: obminimize gives warnings
Edited By: Noel O'Boyle (baoilleach)
Status updated: u'open' => u'wont-fix'
Owner updated: None => u'baoilleach'