#42 Wikidata entry grey out, cannot type anything.Hi

[Andy the Great]

Hi,

I use openSUSE Tumbleweed KDE.
Install molsketch with sudo zypper in molsketch.
The version downloaded is 0.7.2 not 0.5.3 in the ticket.

Wikidata query url is https://query.wikidata.org/sparql

I tried clicking and typing but nothing happen.

Not sure if it help but this is out put when running on the command line.

Debug: ((null):0, (null)) System locale: QLocale(English, Latin, United States) Translation loaded: false for library: false
Info: ((null):0, (null)) Transferring settings data:
Debug: ((null):0, (null)) Transferring key "arrow-tip-width" with value QVariant(QString, "10")
Debug: ((null):0, (null)) Transferring key "arrow-width" with value QVariant(QString, "1.5")
Debug: ((null):0, (null)) Transferring key "atom-font" with value QVariant(QFont, QFont(Noto Sans,10,-1,5,50,0,0,0,0,0))
Debug: ((null):0, (null)) Transferring key "auto-add-hydrogen" with value QVariant(QString, "true")
Debug: ((null):0, (null)) Transferring key "auto-save-time" with value QVariant(QString, "300000")
Debug: ((null):0, (null)) Transferring key "bond-angle" with value QVariant(QString, "30")
Debug: ((null):0, (null)) Transferring key "bond-length" with value QVariant(QString, "40")
Debug: ((null):0, (null)) Transferring key "bond-separation" with value QVariant(QString, "4")
Debug: ((null):0, (null)) Transferring key "bond-wedge-width" with value QVariant(QString, "4")
Debug: ((null):0, (null)) Transferring key "bond-width" with value QVariant(QString, "2")
Debug: ((null):0, (null)) Transferring key "carbon-visible" with value QVariant(QString, "false")
Debug: ((null):0, (null)) Transferring key "charge-visible" with value QVariant(QString, "true")
Debug: ((null):0, (null)) Transferring key "default-color" with value QVariant(QColor, QColor(ARGB 1, 0, 0, 0))
Debug: ((null):0, (null)) Transferring key "electron-systems-visible" with value QVariant(QString, "false")
Debug: ((null):0, (null)) Transferring key "frame-line-width" with value QVariant(QString, "1.5")
Debug: ((null):0, (null)) Transferring key "grid-color" with value QVariant(QColor, QColor(ARGB 1, 0.627451, 0.627451, 0.643137))
Debug: ((null):0, (null)) Transferring key "grid-linewidth" with value QVariant(QString, "1")
Debug: ((null):0, (null)) Transferring key "horizontal-grid-spacing" with value QVariant(QString, "10")
Debug: ((null):0, (null)) Transferring key "last-save-path" with value QVariant(QString, "/home/andy/Desktop/test")
Debug: ((null):0, (null)) Transferring key "latest-release-notes" with value QVariant(QString, "0.7.2.0")
Debug: ((null):0, (null)) Transferring key "libraries" with value QVariant(Invalid)
Debug: ((null):0, (null)) Transferring key "lone-pair-length" with value QVariant(QString, "7")
Debug: ((null):0, (null)) Transferring key "lone-pair-line-width" with value QVariant(QString, "1")
Debug: ((null):0, (null)) Transferring key "lone-pairs-visible" with value QVariant(QString, "false")
Debug: ((null):0, (null)) Transferring key "mouse-cycle-mode" with value QVariant(QString, "0")
Debug: ((null):0, (null)) Transferring key "obabel-formats-dir" with value QVariant(QString, "")
Debug: ((null):0, (null)) Transferring key "obabel-iface-path" with value QVariant(QString, "\"/usr/lib64/molsketch/libobabeliface.so\"")
Debug: ((null):0, (null)) Transferring key "pixel-scaling-factor" with value QVariant(QString, "10")
Debug: ((null):0, (null)) Transferring key "radical-diameter" with value QVariant(QString, "3")
Debug: ((null):0, (null)) Transferring key "show-terminal-methyls" with value QVariant(QString, "true")
Debug: ((null):0, (null)) Transferring key "size" with value QVariant(QSize, QSize(891, 747))
Debug: ((null):0, (null)) Transferring key "tool-bar-icon-style" with value QVariant(QString, "0")
Debug: ((null):0, (null)) Transferring key "vertical-grid-spacing" with value QVariant(QString, "10")
Debug: ((null):0, (null)) Transferring key "wikidata-query-url" with value QVariant(QString, "https://query.wikidata.org/sparql")
Debug: ((null):0, (null)) Transferring key "window-state" with value QVariant(QByteArray, "\x00\x00\x00\xFF\x00\x00\x00\x00\xFD\x00\x00\x00\x01\x00\x00\x00\x00\x00\x00\x02\x1D\x00\x00\x02\x88\xFC\x02\x00\x00\x00\x03\xFB\x00\x00\x00*\x00w\x00i\x00k\x00i\x00""d\x00""a\x00t\x00""a\x00-\x00q\x00u\x00""e\x00r\x00y\x00-\x00w\x00i\x00""d\x00g\x00""e\x00t\x01\x00\x00\x00L\x00\x00\x00\xF9\x00\x00\x00\x99\x01\x00\x00\x03\xFB\x00\x00\x00$\x00t\x00o\x00o\x00l\x00""b\x00o\x00x\x00-\x00""d\x00o\x00""c\x00k\x00w\x00i\x00""d\x00g\x00""e\x00t\x01\x00\x00\x01""F\x00\x00\x00\xC8\x00\x00\x00`\x01\x00\x00\x03\xFB\xFF\xFF\xFF\xFF\x01\x00\x00\x02\x0F\x00\x00\x00\xC5\x00\x00\x00y\x01\x00\x00\x03\x00\x00\x01]\x00\x00\x02\x88\x00\x00\x00\x04\x00\x00\x00\x04\x00\x00\x00\b\x00\x00\x00\b\xFC\x00\x00\x00\x01\x00\x00\x00\x02\x00\x00\x00\x06\x00\x00\x00\x18\x00""f\x00i\x00l\x00""e\x00-\x00t\x00o\x00o\x00l\x00""b\x00""a\x00r\x01\x00\x00\x00\x00\xFF\xFF\xFF\xFF\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x18\x00""e\x00""d\x00i\x00t\x00-\x00t\x00o\x00o\x00l\x00""b\x00""a\x00r\x01\x00\x00\x00\xE2\xFF\xFF\xFF\xFF\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x18\x00z\x00o\x00o\x00m\x00-\x00t\x00o\x00o\x00l\x00""b\x00""a\x00r\x01\x00\x00\x01\xAA\xFF\xFF\xFF\xFF\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x1E\x00""d\x00r\x00""a\x00w\x00i\x00n\x00g\x00-\x00t\x00o\x00o\x00l\x00""b\x00""a\x00r\x01\x00\x00\x02H\xFF\xFF\xFF\xFF\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x1C\x00m\x00o\x00""d\x00i\x00""f\x00y\x00-\x00t\x00o\x00o\x00l\x00""b\x00""a\x00r\x01\x00\x00\x02\xD3\xFF\xFF\xFF\xFF\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\"\x00""a\x00l\x00i\x00g\x00n\x00m\x00""e\x00n\x00t\x00-\x00t\x00o\x00o\x00l\x00""b\x00""a\x00r\x01\x00\x00\x03'\xFF\xFF\xFF\xFF\x00\x00\x00\x00\x00\x00\x00\x00")
Warning: ((null):0, (null)) Could not create image from "/home/david/Oxygen/trunk/32x32/actions/edit-copy.png"
Warning: ((null):0, (null)) Could not create image from "/home/david/Oxygen/trunk/32x32/actions/edit-paste.png"
Warning: ((null):0, (null)) Could not create image from "/home/david/Oxygen/trunk/32x32/actions/edit-copy.png"
Warning: ((null):0, (null)) Could not create image from "/home/david/Oxygen/trunk/32x32/actions/edit-paste.png"
Debug: ((null):0, (null)) Clipboard types available: ("TIMESTAMP", "TARGETS", "MULTIPLE", "SAVE_TARGETS", "text/html", "text/_moz_htmlcontext", "text/_moz_htmlinfo", "text/plain", "COMPOUND_TEXT", "text/plain;charset=utf-8", "text/x-moz-url-priv")
Warning: ((null):0, (null)) :icons/document-new.svg:602:58: Could not resolve property: #linearGradient5167
Warning: ((null):0, (null)) :icons/document-new.svg:602:58: Could not resolve property: #linearGradient5167
Warning: ((null):0, (null)) :icons/document-open.svg:4289:6: Could not resolve property: #pattern5614
Warning: ((null):0, (null)) :icons/document-open.svg:4289:6: Could not resolve property: #pattern5626
Warning: ((null):0, (null)) :icons/document-open.svg:4289:6: Could not resolve property: #pattern5614
Warning: ((null):0, (null)) :icons/document-open.svg:4289:6: Could not resolve property: #pattern5626
Warning: ((null):0, (null)) :icons/preferences-system.svg:1712:6: Could not resolve property: #linearGradient4636
Warning: ((null):0, (null)) :icons/preferences-system.svg:1712:6: Could not resolve property: #linearGradient4592
Warning: ((null):0, (null)) :icons/preferences-system.svg:1712:6: Could not resolve property: #linearGradient4247
Warning: ((null):0, (null)) :icons/preferences-system.svg:1712:6: Could not resolve property: #linearGradient4636
Warning: ((null):0, (null)) :icons/preferences-system.svg:1712:6: Could not resolve property: #linearGradient4592
Warning: ((null):0, (null)) :icons/preferences-system.svg:1712:6: Could not resolve property: #linearGradient4247
Warning: ((null):0, (null)) QGraphicsScene::removeItem: item 0x55e3e055afc0's scene (0x0) is different from this scene (0x55e3e047a8e0)
Warning: ((null):0, (null)) :icons/help-contents.svg:7091:6: Could not resolve property: #linearGradient3592
Warning: ((null):0, (null)) :icons/help-contents.svg:7091:6: Could not resolve property: #linearGradient7999
Warning: ((null):0, (null)) :icons/help-contents.svg:7091:6: Could not resolve property: #radialGradient2943
Warning: ((null):0, (null)) :icons/help-contents.svg:7091:6: Could not resolve property: #linearGradient3592
Warning: ((null):0, (null)) :icons/help-contents.svg:7091:6: Could not resolve property: #linearGradient7999
Warning: ((null):0, (null)) :icons/help-contents.svg:7091:6: Could not resolve property: #radialGradient2943
Debug: ((null):0, (null)) Updating UI from setting: "Change bond line width"
Debug: ((null):0, (null)) setting to control: 2
Debug: ((null):0, (null)) Updating UI from setting: "Change arrow line width"
Debug: ((null):0, (null)) setting to control: 1.5
Debug: ((null):0, (null)) Updating UI from setting: "Change arrow tip width"
Debug: ((null):0, (null)) setting to control: 10
Debug: ((null):0, (null)) Updating UI from setting: "Change frame line width"
Debug: ((null):0, (null)) setting to control: 1.5
Debug: ((null):0, (null)) Updating UI from setting: "Change default bond length"
Debug: ((null):0, (null)) setting to control: 40
Debug: ((null):0, (null)) Updating UI from setting: "Change default bond angle"
Debug: ((null):0, (null)) setting to control: 30
Debug: ((null):0, (null)) Updating UI from setting: "Change default double bond separation"
Debug: ((null):0, (null)) setting to control: 4
Debug: ((null):0, (null)) Updating UI from setting: "Change default stereo bond wedge width"
Debug: ((null):0, (null)) setting to control: 4
Debug: ((null):0, (null)) Updating UI from setting: "Toggle automatic hydrogens for new atoms"
Debug: ((null):0, (null)) Updating UI from setting: "Toggle carbon visibility"
Debug: ((null):0, (null)) Updating UI from setting: "Toggle visibility of terminal methyl groups"
Debug: ((null):0, (null)) Updating UI from setting: "Toggle automatic lone pairs"
Debug: ((null):0, (null)) Updating UI from setting: "Toggle electron systems"
Debug: ((null):0, (null)) Updating UI from setting: "Toggle charges"
Debug: ((null):0, (null)) Updating UI from setting: "Change default atom font"
Debug: ((null):0, (null)) Updating UI from setting: "Change default color"
Debug: ((null):0, (null)) Updating UI from setting: "Change grid color"
Debug: ((null):0, (null)) Updating UI from setting: "Change grid line width"
Debug: ((null):0, (null)) setting to control: 1
Debug: ((null):0, (null)) Updating UI from setting: "Grid horizontal spacing"
Debug: ((null):0, (null)) setting to control: 10
Debug: ((null):0, (null)) Updating UI from setting: "Change vertical grid spacing"
Debug: ((null):0, (null)) setting to control: 10
Debug: ((null):0, (null)) Updating UI from setting: "Change default lone pair line width"
Debug: ((null):0, (null)) setting to control: 1
Debug: ((null):0, (null)) Updating UI from setting: "Change default lone pair length"
Debug: ((null):0, (null)) setting to control: 7
Debug: ((null):0, (null)) Updating UI from setting: "Change default radical diameter"
Debug: ((null):0, (null)) setting to control: 3
Debug: ((null):0, (null)) Loaded OpenBabel functions. Available Functions: load: false save: false toSmiles: false fromSmiles: false inputFormats: false outputFormats: false fromInChI: false gen2dAvailable: false optimizeCoordinates: false inChIAvailable: false callOsra: false
Debug: ((null):0, (null)) OpenBabel available:  "0" Library location: "\"/usr/lib64/molsketch/libobabeliface.so\""
Debug: ((null):0, (null)) InChI available:  "0" gen2d available:  "0"
Debug: ((null):0, (null)) OpenBabel available:  "0" Library location: "\"/usr/lib64/molsketch/libobabeliface.so\""
Debug: ((null):0, (null)) InChI available:  "0" gen2d available:  "0"
Debug: ((null):0, (null)) Starting assistant with arguments: "/usr/share/doc/molsketch/doc/en/molsketch.qhp" "/usr/lib64/qt5/bin/assistant-qt5"
Warning: ((null):0, (null)) QIODevice::write (QProcess): device not open
Warning: ((null):0, (null)) QGraphicsScene::removeItem: item 0x55e3e055afc0's scene (0x0) is different from this scene (0x55e3e047a8e0)
Warning: ((null):0, (null)) QGraphicsScene::removeItem: item 0x55e3e055afc0's scene (0x0) is different from this scene (0x55e3e047a8e0)
Warning: ((null):0, (null)) QGraphicsScene::removeItem: item 0x55e3e055afc0's scene (0x0) is different from this scene (0x55e3e047a8e0)
Warning: ((null):0, (null)) QGraphicsScene::addItem: item has already been added to this scene
Debug: ((null):0, (null)) Clipboard types available: ("text/plain", "text/html", "TARGETS", "MULTIPLE", "TIMESTAMP", "SAVE_TARGETS")

[Andy the Great]

Screenshot

[Hendrik Vennekate]

Hi Andy!
Thanks for reporting! From the output and from your screenshot it appears that OpenBabel is either not installed or cannot be found (see the "-" (minus) indicators next to "OpenBabel", "InChI", and "gen2d" in the bottom right corner). Did you install OpenBabel?
Cheers,
Hendrik

[Andy the Great]

Hi,
I install openbabel and change the library path in the preference.
But it is still grey out, do I need inchi and gen2d as well?

[Hendrik Vennekate]

Hi!
Well, inchi and gen2d are parts of OpenBabel, actually. This setting was actually only thought for the Windows users, as on Linux the defaults used to just work -- maybe I'll have to check. Also the wording is a bit misleading, frankly: the top value is the one to the obabeliface library (a thin wrapper for OpenBabel, which comes with Molsketch itself). The lower part is the folder where all the OpenBabel format libraries are stored.
So for OpenSUSE Tumbleweed (which I use as well), the upper path needs to be

/usr/lib64/molsketch/libobabeliface.so

The lower box can either be left blank or set to

/usr/lib64/openbabel/2.4.1/

(See screenshot)

[Hendrik Vennekate]

Maybe a bit of background info: obabeliface is loaded as a dynamic library by Molsketch at runtime, somewhat like a plugin. The design idea was to make OpenBabel an optional dependency since it's quite large compared to Molsketch. So Molsketch will try to load this wrapper, which in turn will triggering the loading of OpenBabel. If that works, you have OpenBabel support (meaning mostly the plethora of file formats that it supports). Otherwise, you can still use Molsketch, but will not have access to features that require OpenBabel.
Sometimes (mostly on Windows, I believe), OpenBabel is not easily able to find its format libraries, hence the second box. It essentially sets an environment variable for OpenBabel to locate these libraries. For Wikidata queries, Molsketch fetches InChI strings, which are then converted to structures using OpenBabel (hence you need the InChI format support). Then gen2d (another OpenBabel functionality) is used to generate 2D coordinates (because InChI itself only contains atom connectivity information). gen2d is also used for cleaning up structures (that's the button with the benzene molecule and the broom; you need to select a molecule for it to become active).

[Andy the Great]

Thanks, setting to /usr/lib64/molsketch/libobabeliface.so solve the issue.

In the log above of not working babel, it is
Debug: ((null):0, (null)) OpenBabel available: "0" Library location: "\"/usr/lib64/molsketch/libobabeliface.so\""

Manually re-entering the location yield.

Debug: ((null):0, (null)) OpenBabel available:  "1" Library location: "/usr/lib64/molsketch/libobabeliface.so"

[Andy the Great]

So I think I found the cause.
The quotation marks on the path broke it.
Simply remove the quotation marks around the path fix the issue.

[Hendrik Vennekate]

Ok, that's interesting -- where in particular? If you have found something in the code, I'd be more than happy about a PR ;)

[Andy the Great]

Around openbabel library path in the preference. Im trying to look in the source right now.
Is it something about obabelIfacePath? But I have no clue how it work.

Edit: In the config>SourceForge>Molsketch.conf file. The obabel path is set with quote by default.
obabel-iface-path=\"/app/lib64/molsketch/libobabeliface.so\"

[Hendrik Vennekate]

Oh, good catch: its being set during build in settings.pri lines 25/26, respectively. (would be interesting to know if you can remove the quotes even if the path contains spaces...)

[Andy the Great]

I send a PR on github, but that one change the CmakeList.txt not settings.pri.
But it does fix the issue for me.

[Andy the Great]

I send you a PR

[Hendrik Vennekate]

PR is merged -- I'm still in the process of restoring my build chain (primarily the Windows part is a bit challenging with all the cross-compiling), so it will unfortunately be some time until the next release...
Is that ok for you