Activity for Hendrik Vennekate
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Hendrik Vennekate created a blog post
Version 0.8.1 -- Fluorine-13
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Sync properties widget and atom
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Charges get cropped when exporting to image
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Hi Alex! Finally released a new version 0.8.0, which fixes this issue. Had to completely rewrite the atom label rendering logic (and got distracted quite a few times by other things); sorry for the delay!
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Version 0.8.0 Fluorine
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Oxygen-18 0.7.3
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Windows build failing
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Oxygen-18 0.7.3
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Testing the build pipeline
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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
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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...)
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Oh, good catch: its being set during build in settings.pri lines 25/26, respectively.
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Ok, that's interesting -- where in particular? If you have found something in the code, I'd be more than happy about a PR ;)
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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...
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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...
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Hi Andy! Alright, I'll look into it (I used to offer appimages, but it got a little unwieldy). But what is flathub? Or does the link you provided indicate that Kevin already created a flatpak in the flathub repo? I'm a little confused... ;)
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Hi Alex! You really mean the "text tool", i.e. not the atom labels, right?
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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
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Hello Jenkins
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Oxygen-17 0.7.2
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Hi Yuri! Ok, thanks -- probably missed that in your original post. The key difference is the use of Ninja, though, as you wrote in the cmake bug report. Indeed with the make backend, the same target is generated, but it is not executed as the file (here: the *.ts file) already exists. And so, yes, Craig is also correct in pointing out that I did use the wrong function here: it should have been qt_add_translation instead of qt_create_translation (or qt5_... for the version-dependent pendant). But...
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Hi Yuri! Quick question: which version of Qt are you using? There seems to have been a change to Qt5LinguistToolsMacros.cmake for instance https://github.com/qt/qttools/commit/a9790627873d17f91f29c9bd8be0fb609ec29f03, but reverting that particular change does not appear to lead to the error you observed, so I'm still not quite able to reproduce it...
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Oxygen-16 0.7.1
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Ah, ok, thanks a lot for spotting this, Craig. I'll check it out. Interestingly enough, this seems to have worked both on my machine (OpenSUSE), as well as, e.g. Fedora. Probably depends on the version of qt_create_translation() used then? In the mean time two hints: * you can always alternatively use qmake (in fact I use it myself during development, so there is somewhat of a chance that I might have missed some things in the cmake build, as I only check that occasionally) * unfortunately, when...
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Ah, ok, thanks a lot for spotting this, Craig. I'll check it out. Interestingly enough, this seems to have worked both on my machine (OpenSUSE), as well as, e.g. Fedora. Probably depends on the version of qt_create_translation() used then? In the mean time two hints: you can always alternatively use qmake (in fact I use it myself during development, so there is somewhat of a chance that I might have missed some things in the cmake build, as I only check that occasionally) unfortunately, when removing...
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Hi Yuri! That is a bit confusing as those files are indeed part of the package (*.tar.gz). Which build system are you using? Also: Why is there an @ after /usr/local/lib/qt5/bin/lupdate?
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Oxygen-16 0.7.1
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Oxygen-16 0.7.1
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Oxygen-16 0.7.1
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Hi Matthias! After merging your fixes, I also reworked some other aspects of the cmake-based build process. Would you be so kind as to let me know if those changes (on the main branch of the github repo) cause any trouble on your end? Many thanks in advance and kind regards!
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0.6.0 has many clang compiler warnings
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Just a quick update: 0.7.0 has been released in the meantime and hence I'm going to close this -- assuming that clang does not generate any more warnings.
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Oh, and one more note -- should probably be added in one of the readme files -- the repo is at https://github.com/hvennekate/Molsketch
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Thanks for reporting and sorry, my bad. I'm working with Tumbleweed, so my Qt version is more recent and while fixing some deprecation warnings, I just used what they recommended (e.g. the constructor for QSet with the begin and end iterators) without checking the docs of those methods (it appears that said constructor was introduced only in Qt 5.14). Let me see if we can use some macros to sort this out -- or maybe just live with the deprecation warning as Qt 6 seems to be around the corner. What...
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Oxygen 0.7.0
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Guiding points remain visible
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Export includes hover highlight
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Hi Alex, thanks for reporting this. It is an issue that relates to one of your earlier reports about bonds colliding with charges (and an old sin in the code): The bounding rectangle is limited to the atom and does not include the charge label. After re-designing the bond shapes and - bounding rectangles (those are the two concepts that Qt knows) in the last version, I guess it would be appropriate to give a major overhaul to the way atoms are drawn next... Best, Hendrik
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Probably only going to do this for mouse hover for now; otherwise the drawing area might get somewhat crowded.
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Infobox not synced
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This essentially is a duplicate of #25 (https://sourceforge.net/p/molsketch/feature-requests/25/) now, so I'm going to close this as #25 is more recent.
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Ok, can I close this then and we'll see if I missed anything in the next release? (I only enabled the corresponding compiler option for gcc and did not actually try with clang...)
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Context menu not possible for covered items
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Seems to be solved in Nitrogen 0.6.0
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0.6.0 has many clang compiler warnings
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Whoa that was > 9k warnings... Fixed them and pushed to GitHub. Thanks for reporting! Do you need me to do a re-release?
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Sum formulae: Implemented, shown in status bar for selection and as tool tip for molecules when hovering mouse over them.
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Calculations of molecular masses, sum formulas
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New Version 0.6.0 Nitrogen
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Use MIME types instead of file extensions
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Also: limit the z-level for the increment/decrement actions
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Add z-level indicator to selection highlight
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Performance issues with large molecules
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Fixed by improving the bond collision detection.
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Crash when the the molecule is loaded and "Automatically add hydrogen atoms" is turned off
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Crash when the the molecule is loaded and "Automatically add hydrogen atoms" is turned off
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No obvious way to add individual atoms
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Ok, I'll close it then, thanks! Please keep maintaining that FreeBSD build, though, and a happy new year!
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Performance issues with large molecules
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Hi Yuri! Is this still an open problem? Best, Hendrik
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Hi Yuri! As I'm having some time to code for Molsketch again and would like to see what needs to be done: Is this ticket effectively still open? Best, Hendrik
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Since sum formula has meanwhile been implemented, This ticket essentially still requires the molar mass.
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Calculations of molecular masses, sum formulas
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Implemented, shown in status bar for selection and as tool tip for molecules when hovering mouse over them.
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Showing a bond is behind another
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Solved by using clipping, should not require addressing background colors.
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Charges don't work
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Can't reproduce.
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Build breaks on FreeBSD because of the 'major()' function conflict
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Ok, thanks a lot.
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Hi Yuri! Thanks for reporting, but I can't reproduce this crash. Could you provide some details on what you did? Thanks in advance and kind regards, Hendrik
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Hi Yuri, yes, we should definitely add/update the docs. Tim's videos have gotten somewhat out of date. What you want to do is use the "draw" action (the button shows the currently active element symbol (Default: C) and the currently active bond type (Default: single bond)). Then just click anywhere on the drawing area and it will insert an atom of the selected type. Click and drag to add two atoms connected by the selected bond type (or add a bond, if you start by clicking on an existing atom and...
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Build breaks on FreeBSD because of the 'major()' function conflict
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One more thing: could you please let me know if this works for you (i.e. is compilable) so that I can close the tickt?
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