Public bug reported: When running the command "obabel -L descriptors", the output contains garbage characters: # obabel -L descriptors abonds `�V atoms bonds p� cansmi Canonical SMILES cansmiNS Canonical SMILES without isotopes or stereo ,S formula Chemical formula HBA1 Number of Hydrogen Bond Acceptors 1 (JoelLib) HBA2 Number of Hydrogen Bond Acceptors 2 (JoelLib) HBD Number of Hydrogen Bond Donors (JoelLib) InChI IUPAC InChI identifier InChIKey InChIKey abonds InChIKey InChIKey logP octanol/water partition coefficient MP Melting point MR molar refractivity MW Molecular Weight filter nF Number of Fluorine Atoms s SMARTS filter sbonds SmartsDescriptor smarts SMARTS filter tbonds iptor is definable title For comparing a molecule's title TPSA topological polar surface area
In particular, the descriptors "cansmi", "formula", and "title" are corrupted (it appears on the line above each of these names). The corruption appears to be in the names themselves because when I use the openbabel library (C++ code) in my own application and try to use any one of these descriptors, it fails to even find the descriptor, presumably because the name does not match (due to the corruption). All other available descriptors work fine. I have compiled the upstream source code from openbabel directly on the same machine and the output does not contain any corruption and my C++ code finds these descriptors without problem. Here is the output with the upstream version: # obabel -L descriptors cansmi Canonical SMILES cansmiNS Canonical SMILES without isotopes or stereo formula Chemical formula HBA1 Number of Hydrogen Bond Acceptors 1 (JoelLib) HBA2 Number of Hydrogen Bond Acceptors 2 (JoelLib) HBD Number of Hydrogen Bond Donors (JoelLib) InChI IUPAC InChI identifier InChIKey InChIKey logP octanol/water partition coefficient MR molar refractivity MW Molecular Weight filter nF Number of Fluorine Atoms s SMARTS filter smarts SMARTS filter title For comparing a molecule's title TPSA topological polar surface area I tried downloading the source package of openbabel from Ubuntu and building the package myself, which I was able do successfully, but the corrupt output remained. System Info ------------- # lsb_release -rd Description: Ubuntu 16.04 LTS Release: 16.04 # apt-cache policy openbabel openbabel: Installed: 2.3.2+dfsg-2.2build1 Candidate: 2.3.2+dfsg-2.2build1 Version table: *** 2.3.2+dfsg-2.2build1 500 500 http://archive.ubuntu.com/ubuntu xenial/universe amd64 Packages 100 /var/lib/dpkg/status # apt-cache policy libopenbabel4v5 libopenbabel4v5: Installed: 2.3.2+dfsg-2.2build1 Candidate: 2.3.2+dfsg-2.2build1 Version table: 2.3.2+dfsg-2.2build1 500 500 http://archive.ubuntu.com/ubuntu xenial/universe amd64 Packages *** 2.3.2+dfsg-2.2build1 100 100 /var/lib/dpkg/status ** Affects: openbabel (Ubuntu) Importance: Undecided Status: New -- You received this bug notification because you are a member of Kubuntu Bugs, which is subscribed to openbabel in Ubuntu. https://bugs.launchpad.net/bugs/1597525 Title: data corruption in unbutu package version To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/openbabel/+bug/1597525/+subscriptions -- kubuntu-bugs mailing list kubuntu-b...@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/kubuntu-bugs