Re: [Avogadro-devel] Building avogadrolibs "core" only

On Sun, Sep 16, 2018 at 3:33 PM Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > Hi Marcus, > > I'm working along on the force field code - and wondering if there's > documentation on building the "core" parts of avogadrolibs. > > I have the sense that you do something like this for the

Re: [Avogadro-devel] Working as a programmer on Avagadro

Hi, I updated http://wiki.openchemistry.org/Build#Building with a little more detail on my Windows build, locating the Qt5_DIR location from a binary. In front of the machine if more is needed. Thanks, Marcus On Sun, 15 Jul 2018 at 15:31, Marcus D. Hanwell wrote: > Hi, > > I recen

Re: [Avogadro-devel] Working as a programmer on Avagadro

Hi, I recently build a fresh tree on Windows using Visual Studio 2017. You can download the binary Qt package for VS 2015/2017, and just use that to link to/build against. I can try and write up each step as I do it fresh tomorrow once I am in front of that machine, but it really didn't take too

Re: [Avogadro-devel] Design for Charges and Force Fields in avogadrolibs

On Wed, Apr 25, 2018 at 10:51 AM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > I'm working on an implementation of force field plugins for avogadrolibs > but I have some conceptual questions on where to put some of the code. > > Initially, I'd just put the bits into qtplugins

Re: [Avogadro-devel] PubChem QC in Avogadro

On Tue, Jul 25, 2017 at 3:34 PM, Geoffrey Hutchison < geoff.hutchi...@gmail.com> wrote: > > This sounds great, we can get the optimized structure, and some > properties, but I don't see mention of orbital data - is that possible at > this stage? This sounds like a great resource, and something we

Re: [Avogadro-devel] cannot load PDB into avogadro

On Tue, Jun 6, 2017 at 12:18 PM, Chitrak Gupta wrote: > Dear avogadro users, > > I am relatively new to Avogadro. I am facing problem loading PDB file into > avogadro. > > I created a PDB file using the build feature of Avogadro, but when I try > to load the same file, I am

Re: [Avogadro-devel] Conda builds?

On Wed, Apr 19, 2017 at 7:17 AM, Rick Muller wrote: > I took the easy way out and just uninstalled numpy and boost from my build > environment, so that python wasn't autoconfigured by cmake. The build just > completed successfully. I'll test it out when I get into work this >

Re: [Avogadro-devel] Conda builds?

On Tue, Apr 18, 2017 at 7:09 AM, Rick Muller wrote: > Hi, > > Long time user, first time caller ;-). I'm interested in building avogadro > under conda, but I haven't found any existing projects under the usual > channels. Has anyone started anything like this with either

Re: [Avogadro-devel] Avo2: List of Plugin Repositories

> On Jan 10, 2017, 11:18 PM -0500, Geoffrey Hutchison > , wrote: > I met with Ethan today and he has a working version of the plugin > downloader. > > What’s your thought on a source for the list of repositories? We have the > avogadro.cc domain - but I’d like to make

Re: [Avogadro-devel] CJSON in Open Babel

On Sat, Jan 7, 2017 at 2:56 PM, Geoffrey Hutchison wrote: > As we continue to develop the workflow idea, one obvious help would be to > integrate CJSON into Open Babel. I'm willing to do some of the work, since > there's already other JSON formats (src/formats/json).

Re: [Avogadro-devel] Workflow Scripts (for Avo2)

On Wed, Dec 28, 2016 at 3:04 PM, Gary Kedziora wrote: > Have you looked at pymatgen? It has a lot of useful features for crystal > structures and some also for molecules as well. > > I have been looking at pymatgen, but hadn't thought about it in this context. We should

[Avogadro-devel] Avogadro 1.90.0 released

We are pleased to announce the release of Avogadro 1.90.0, our latest release as we finish up features for a final Avogadro 2.0 release. This release has a lot of new work completed over the last year, including the results of our first Google Summer of Code where two students worked on projects

Re: [Avogadro-devel] 1.90 release..

Geoff, On Tue, Nov 29, 2016 at 4:04 PM, Geoffrey Hutchison wrote: > > You had mentioned spinning the 1.90 release tomorrow. While I have a few > things moving along, they're clearly not ready for 1.90 - I'll target them at > mid-December. Sounds great, the selection code is

Re: [Avogadro-devel] Selection tool progress

On Mon, Nov 21, 2016 at 9:47 AM, Geoffrey Hutchison wrote: >> is much nicer than how we did it before, and it seems like it would be >> simple to add to CJSON. > > I think it's a good idea to add selection to CJSON for a few reasons. One, > the concept of "named

Re: [Avogadro-devel] Roadmap for 1.91?

On Mon, Nov 21, 2016 at 12:01 AM, Geoffrey Hutchison wrote: > You mentioned previously wanting to get out a new release fairly soon (1.91). > Do you have a target date? Dec. 1st? > I would like to tag 1.90 pretty soon, and then move to C++11/14 being required. I added

Re: [Avogadro-devel] CJSON format proposal

On Sun, Nov 20, 2016 at 11:57 AM, Boone, Paul wrote: > Can you explain more how BSON fits in here? If CJSON were supposed to be a > file format for internal interchange, then I have nothing against storing > coords as one array and then processing them when you read it in or

Re: [Avogadro-devel] Plugin Repositories & Archives

Stuck on a plane most of the day traveling back from a conference, but like Dave said CMake just reuses several libraries and adds a little API on top. Very limited access to Internet, but I would rather not make CMake a runtime dependency. If we need to add a new dependency let's keep it as

Re: [Avogadro-devel] Avogadro2 Tool Priorities

The current default is navigate when loading a molecule, and edit when the molecule is empty. I think that should be preserved, and merging the toolbars back together with priority ordering is the right way to go. On Wed, Nov 16, 2016 at 4:25 PM, Jens wrote: > > I agree.

Re: [Avogadro-devel] VS2015 Build

On Thu, Nov 10, 2016 at 1:14 PM, Marcus D. Hanwell <marcus.hanw...@kitware.com> wrote: > On Tue, Nov 8, 2016 at 1:47 PM, Marcus D. Hanwell > <marcus.hanw...@kitware.com> wrote: >> On Wed, Oct 12, 2016 at 10:22 AM, Marcus D. Hanwell >> <marcus.hanw...@kitware.co

Re: [Avogadro-devel] VS2015 Build

On Tue, Nov 8, 2016 at 1:47 PM, Marcus D. Hanwell <marcus.hanw...@kitware.com> wrote: > On Wed, Oct 12, 2016 at 10:22 AM, Marcus D. Hanwell > <marcus.hanw...@kitware.com> wrote: >> On Sun, Oct 9, 2016 at 5:39 PM, Pavolik, Ethan Thomas <et...@pitt.edu> wrote: >>

Re: [Avogadro-devel] VS2015 Build

On Wed, Oct 12, 2016 at 10:22 AM, Marcus D. Hanwell <marcus.hanw...@kitware.com> wrote: > On Sun, Oct 9, 2016 at 5:39 PM, Pavolik, Ethan Thomas <et...@pitt.edu> wrote: >> I was wondering if you'd made any progress getting VS2015 up and running on >> your machine. I'm st

Re: [Avogadro-devel] Chemical JSON Spec

On Wed, Oct 19, 2016 at 9:20 PM, Geoffrey Hutchison wrote: > I know as part of the GSOC project there were some questions about a more > formal spec for CJSON. Considering that I'd like to start adding pieces into > Open Babel (and maybe RDKit?) it would be really

Re: [Avogadro-devel] Avo2 - Paste & Python Dialogs

On Wed, Oct 12, 2016 at 1:21 PM, Geoffrey Hutchison wrote: >>> - I'm going to take the InputGeneratorWidget out of avogadrolibs / >>> molequeue and put it into qtgui/ as InterfaceWidget. It will handle both >>> input generators and the new action scripts (i.e.,

Re: [Avogadro-devel] Make Package for Avogadro

On Wed, Oct 12, 2016 at 1:09 PM, Geoffrey Hutchison wrote: >> Geoff has some custom scripts he runs that are not in the build >> system, I wasn't able to generate a DMG last time I tried in Avogadro >> 1, but as Geoff always made the DMG I didn't look into it much more

Re: [Avogadro-devel] Make Package for Avogadro

On Tue, Oct 11, 2016 at 4:01 PM, Patrick Avery wrote: > Hi there, > > I've been working on adding yaehmop features to Avogadro. The work for Dr. > Jochen Autschbach's class is pretty much complete (they are going to be > trying it out), and I wanted to package the program on

Re: [Avogadro-devel] Avo2 - Paste & Python Dialogs

On Wed, Oct 12, 2016 at 11:52 AM, Geoffrey Hutchison wrote: > Hi Marcus, > > As I've mentioned before, I'm working with Paul Boone here at Pitt on a new > script interface in Avogadro 2. Scripts (not just Python) will have a similar > API to the input generators, but

Re: [Avogadro-devel] VS2015 Build

On Sun, Oct 9, 2016 at 5:39 PM, Pavolik, Ethan Thomas wrote: > I was wondering if you'd made any progress getting VS2015 up and running on > your machine. I'm still stuck with the previous link errors when trying to > build Avogadro-libs. This week I tried rebuilding QT5 from

Re: [Avogadro-devel] CMake Error building MoleQueue on OSX 10.9.5

On Tue, Oct 11, 2016 at 10:44 PM, Geoffrey Hutchison wrote: > I've installed Qt (5.6.0) and Cmake (3.3.1) using anaconda, and followed the > instructions here: > > > That may be the problem. I've had trouble with anaconda (or homebrew) > versions of the Qt packages. > >

Re: [Avogadro-devel] CMake error (Avo2)

On Sun, Oct 9, 2016 at 11:33 AM, Marcus D. Hanwell <marcus.hanw...@kitware.com> wrote: > On Sun, Oct 9, 2016 at 11:32 AM, Marcus D. Hanwell > <marcus.hanw...@kitware.com> wrote: >> On Sun, Oct 9, 2016 at 12:04 AM, Geoffrey Hutchison >> <geoff.hutchi...@gmail.com>

Re: [Avogadro-devel] CMake error (Avo2)

On Wed, Oct 5, 2016 at 10:10 PM, Geoffrey Hutchison wrote: > I upgraded my laptop to Mac OS Sierra and the new Xcode. I'm now having > trouble getting AvogadroApp to compile. I get a weird CMake error when > BUILD_MOLEQUEUE is enabled: > > CMake Error at >

Re: [Avogadro-devel] VS 2015 Progress

On Tue, Sep 20, 2016 at 8:38 PM, Pavolik, Ethan Thomas wrote: > I'm (bravely) trying to build Avogadro 2 using Visual Studio 2015 and I > wanted to post on some issues I've resolved so far as well as try to get > some help on the issues I'm currently facing. > Thanks for posting a

Re: [Avogadro-devel] Progress this Week

On Fri, Sep 9, 2016 at 9:28 AM, Geoffrey Hutchison wrote: > > I have an undergrad student, who will be working on some features in Avogadro > v2. Has there been success at VS2015 compilation? I haven't even tried VS 2015, I thought you had a student who had managed to

Re: [Avogadro-devel] Extending Avo2 "Input Generators" to "Modify" scripts

On Tue, Aug 2, 2016 at 5:52 PM, Geoffrey Hutchison wrote: > I’ve been talking with Paul Boone, an experienced Python programmer on staff > here at Pitt (and soon to be PhD student) about the Python interface to > Avo2. > > Short message - we think it's easy to add

Re: [Avogadro-devel] Avogadrolibs Roadmap

On Wed, Jun 15, 2016 at 3:44 PM, Geoffrey Hutchison wrote: > > - Are there general or specific “loose threads” in the code? It seems like > there are some needs for batch undo/redo in RWMolecule, for example. I would like to investigate grouping commands, and naming

Re: [Avogadro-devel] Avo2 - Downloading from GitHub

On Thu, Jun 9, 2016 at 1:25 PM, Geoffrey Hutchison wrote: >> GNU Octave can download and compile its C++ packages automatically. >> Perhaps it can serve as an example? > > My concern is this requires a C++ compiler from the end-user. On Mac and > Windows in particular,

Re: [Avogadro-devel] Avo2 - Downloading from GitHub

On Thu, Jun 9, 2016 at 1:57 PM, Geoffrey Hutchison wrote: >> I wonder if we might either use the GitHub APIs > > We can definitely use the GitHub API via HTTP. The catch is this ties us to > GitHub a bit more, while using Git directly makes it easier to point at >

Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

On Fri, May 27, 2016 at 11:22 AM, Marcus D. Hanwell <marcus.hanw...@kitware.com> wrote: > On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison > <geoff.hutchi...@gmail.com> wrote: >>> I thought that ideally HydrogenTools would operate on the RWMolecule, >>>

Re: [Avogadro-devel] Getting an Atom from an RWAtom (Avo2)

On Tue, May 24, 2016 at 11:54 AM, Geoffrey Hutchison wrote: >> I thought that ideally HydrogenTools would operate on the RWMolecule, >> but RWMolecule is now a lightweight class. There is not currently a >> way to get the Atom from an RWAtom, but the code would be very

Re: [Avogadro-devel] avogadro-super custom targets?

Hi Geoff, On Wed, May 25, 2016 at 2:51 PM, Geoffrey Hutchison wrote: > Hi Marcus, > > There was a request for an “uninstall” target for openbabel. So I added one. > > Now, the avogadro-super build fails because there are duplicate custom > targets.. > > Any suggestions to

Re: [Avogadro-devel] Avo2 - no POVRay menu item?

On Thu, May 12, 2016 at 2:51 PM, Geoffrey Hutchison wrote: > We're trying to port some of the VMRL export code to Avogadro 2 - so I > thought we should start with the POV-Ray export plugin: qtplugins/povray/ > > But it doesn't appear in the interface, at least on Mac?!

Re: [Avogadro-devel] Avogadro 2 release number simplification/jump

On Wed, May 11, 2016 at 3:49 PM, Michael Banck <mba...@debian.org> wrote: > On Wed, May 11, 2016 at 03:43:19PM -0400, Marcus D. Hanwell wrote: >> So I had one or two queries recently that made me realize I should >> have done a better job on less ambiguous version number

[Avogadro-devel] Avogadro 2 release number simplification/jump

Hi, So I had one or two queries recently that made me realize I should have done a better job on less ambiguous version numbering for Avogadro 2 releases. I would like to make the next Avogadro 2 release 1.90, and then after that 1.91, 1.92, 1.93, etc until we feel good with sticking a 2.0

Re: [Avogadro-devel] "Active" Molecules Emit Interface Updates?

On Thu, May 5, 2016 at 2:13 PM, Barry Moore wrote: > All, > > I have been thinking about upgrades to the surfaces interface in Avogadro 2, > but it brought me back to the "Molecules" widget (bottom left). Currently, > it doesn't really do much but I think this would be a

Re: [Avogadro-devel] GitHub issue import test

On Sun, Apr 24, 2016 at 10:27 AM, Geoffrey Hutchison wrote: > I started a test run of importing the Avogadro SourceForge bugs and feature > requests to GitHub issues: > https://github.com/ghutchis/sfimporttest/issues > > * It's very difficult to script importing the

Re: [Avogadro-devel] Avogadro v2 Roadmap

On Wed, Mar 16, 2016 at 4:01 PM, Geoffrey Hutchison wrote: > Since there's more interest in pushing for an Avogadro v2 "full" release in > 2016 (e.g., fall?) I wanted to start a roadmap. > http://wiki.openchemistry.org/Avogadro_Roadmap > > The text came from some

Re: [Avogadro-devel] Hello GSoC-2016

On Mon, Mar 14, 2016 at 10:01 AM, Reinis Danne wrote: > Two questions came up (Python binding project). > > 1. Is it ok to relay on C++11 compiler? A search showed that > there was this discussion before and it was decided that it is ok > to rely on the presence of C++11

Re: [Avogadro-devel] Hello GSoC-2016

On Mon, Mar 7, 2016 at 9:58 AM, Geoffrey Hutchison wrote: >> I'm interested in the project "Python script bindings in Avogadro >> 2". I see that there is already a boost-python branch for >> avogadrolibs. Are you already settled on boost-python or are >> other solutions

Re: [Avogadro-devel] Windows Build for v1.2

Hi Geoff, On Wed, Jan 13, 2016 at 2:21 PM, Geoffrey Hutchison wrote: > Hi Marcus, > > My undergrad this term is working on a Windows build (using VS 2015). He's > had some problems with variable length array declarations and with linking. Some of the topics merged

Re: [Avogadro-devel] Discourse and Translations

On Fri, Jan 1, 2016 at 1:06 PM, Geoffrey Hutchison wrote: > Happy New Year! > > I'm looking into forum options (e.g., Discourse vs. Biostar). Seems like both > can import mbox archives, so I think a key question would be setting up the > Docker instance for Discourse,

Re: [Avogadro-devel] Build Avogadro in Windows from source. MinGW or MSVC?

On Mon, Nov 16, 2015 at 7:13 AM, Carlos Salgado wrote: > Dear all, > > I am trying to build the developer version of Avogadro in Windows, but I am > not sure if I have to use MSVC or MinGW, and the corresponding version of > Qt. I have build it in UNIX with

Re: [Avogadro-devel] [Openchemistry-developers] avogadrolibs UHF calculation representation

Adding Avogadro developers list to CC, this is probably most appropriate there. On Mon, Sep 14, 2015 at 9:14 AM, Bryce Anderson wrote: > First of all I should state my motivations: what I want is proper plotting > of UHF wave functions including being able to select

Re: [Avogadro-devel] New Avogadro Manual

On Mon, Aug 31, 2015 at 4:51 PM, Geoffrey Hutchison wrote: > Thanks to support from the University of Pittsburgh Department of Chemistry, > there is a new manual for Avogadro: > http://ghutchis.gitbooks.io/avogadro/ > > You can find the images and Markdown on GitHub,

Re: [Avogadro-devel] Symmetry element rendering

On Wed, Aug 19, 2015 at 11:26 AM, Marcus Johansson mcode...@gmail.com wrote: Hi Was wondering if anyone has some input on rendering symmetry elements in Avogadro v2. There is a need for “disc” (mirror plane) and “vector” (rotation axis) geometries as well as alpha in order to make things

Re: [Avogadro-devel] Require C++11/dropping Boost fallback

On Wed, Jun 3, 2015 at 6:50 PM, Michael Banck mba...@debian.org wrote: On Wed, Jun 03, 2015 at 01:20:01PM -0400, Geoffrey Hutchison wrote: Debian stable (jessie) ahs GCC 4.8 and 4.9, but it got released very recently and many are still on oldstable (wheezy) with GCC 4.7. I guess your

Re: [Avogadro-devel] Volume Rendering

On Thu, Jun 11, 2015 at 1:12 PM, Barry Moore moore0...@gmail.com wrote: Dear All, I recently saw Volume Rendering in the Getting Avo2 to release email and wanted to start some discussion. I recently exposed the Gaussian Cube file type to render MOs (pull request was submitted, including an

Re: [Avogadro-devel] Getting Avo2 to release

On Thu, Jun 4, 2015 at 4:07 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: Selection and residues, along with some rendering features seem most critical to me (we have stick but it has a rendering bug I need to dig into). I'd put selection slightly above residues because I think it's

Re: [Avogadro-devel] subclass QColumnView

On Wed, Jun 3, 2015 at 10:55 AM, Defusco III, Albert A defu...@pitt.edu wrote: Hi everyone, I am nearing completion of my space group dialog. You can see the current state on GitHub https://github.com/AlbertDeFusco/avogadrolibs/tree/spg-rw The next thing I need to do is remove the final

Re: [Avogadro-devel] Getting Avo2 to release

On Wed, May 27, 2015 at 3:55 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: Thoughts? Concerns? Something I've missed? Oh, I forgot color schemes and custom colors. My feeling is that can fall to nice to have for v2.1? I have some time this next couple of weeks to take a stab at

Re: [Avogadro-devel] Avogadro2 Extensions Priorities

On Thu, May 21, 2015 at 3:43 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I'd like to ask about Avogadro2 extensions and priorities. In Avogadro 1, plugins were loaded in alphabetical order (sorted by the filesystem) and then the extension provided an ordered list of commands. This

Re: [Avogadro-devel] Google Summer of Code

Hi, To update the list, we were not selected this year. I got feedback from Google which was very positive and encouraged us to apply again next year. They only accepted 137 organizations this year (down from a high of 190 last year). We had some great ideas, and we will continue to work on links

[Avogadro-devel] Editing, viewing, and making things more fluid again

Hi, So I slacked off a lot over the Christmas break, but have been working on a few patches and thinking about the overall data architecture in the Avogadro 2 application. We spent quite a while thinking about the design, and I looked at a lot of what went well and not so well in Avogadro 1. I

Re: [Avogadro-devel] Editing, viewing, and making things more fluid again

On Tue, Jan 6, 2015 at 12:03 PM, Michael Banck mba...@gmx.net wrote: On Tue, Jan 06, 2015 at 11:05:15AM -0500, Marcus D. Hanwell wrote: What doesn't work at all well is the edit/view GL widget, and the tough/hard line between editing a molecule/viewing it. I am working on merging the two

Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

Albert, I think CML will continue to be very much a first class citizen too. JSON feels much easier to change/augment, and Python support for JSON is very good - it would be great to add it, but I don't think it is critical. We could add some simple Python glue too, the format is super-simple.

Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

On Thu, Dec 11, 2014 at 11:36 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I think Albert was talking about a glue layer for quantum io, not for regular input. Regular input is probably best handled through Open Babel, since that already handles bond perception, typing, etc. Right

Re: [Avogadro-devel] Avogadro-devel Digest, Vol 90, Issue 2

On Thu, Dec 11, 2014 at 4:14 PM, Defusco III, Albert A defu...@pitt.edu wrote: Hi guys, Would good project be to re-wire Avogadro to use cclib instead of relying on the quantumio in Avogadro2? I'm very much in favor of adding visualization capabilities for QuantumEspresso and CP2K. You

Re: [Avogadro-devel] Google Summer of Code

On Mon, Dec 8, 2014 at 3:00 PM, Michael Banck mba...@gmx.net wrote: On Mon, Dec 08, 2014 at 10:53:50AM -0500, Geoffrey Hutchison wrote: The deadline for applying to be a mentoring organization for Google Summer of Code is fast approaching. I'm not sure precisely where to hang our hat (e.g.,

Re: [Avogadro-devel] Migrating Wiki to GitHub Pages

On Thu, Oct 16, 2014 at 4:33 PM, Geoffrey Hutchison geo...@pitt.edu wrote: Hi everyone, Despite the low level of action, I’ve been spending a lot of time *thinking* about Avogadro and the future. There are quite a few exciting things, although it may take a while before they fully appear.

Re: [Avogadro-devel] Migrating Wiki to GitHub Pages

I turned on wiki and issues for the repo if that helps. The GitHub wikis are backed by git, and have editing facilities built in, so that might be the easiest (I haven't used the GitHub wikis much, but willing to give it a try). Marcus On Fri, Oct 17, 2014 at 1:47 PM, Patrick Fuller

Re: [Avogadro-devel] Discourse / Forum Interface

On Tue, Oct 7, 2014 at 12:46 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I've been looking around at web forums, since I see a lot of current undergrads and grad students (i.e., users) don't use e-mail much (much less mailing lists). There are multiple packages and I'm open to

Re: [Avogadro-devel] Switching to GitHub pull requests for review/merge?

On Mon, Oct 6, 2014 at 10:34 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi, Would there be any objections to switching to GitHub pull requests for development? The Kitware instance of Gerrit will be upgraded at some point, removing the topic branch functionality. Gerrit feels

Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

, bigger hard drive too). I will have some time to actually work on this in the coming days though, apologies on the delay - I hadn't factored in spending so much time on real life stuff... Marcus On Thu, Sep 4, 2014 at 9:31 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi Geoff, Sorry

Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

On Mon, Sep 8, 2014 at 10:14 AM, Defusco III, Albert A defu...@pitt.edu wrote: Good morning, Let me add a bit to this discussion as well. I've been working on the crystallography extension in Avogadro2 and I find it exceeding difficult to use the CrystalTools while editing or creating

Re: [Avogadro-devel] Avogadro2 Edit/View Molecule - Code and Interface

Hi Geoff, Sorry, crazy travel schedule, so didn't get this finished as soon as I had hoped. I am working on some changes to make the conversion much simpler, and to alleviate the UI issue. As I said at the time - totally agree, and not pushing to keep the current UI. I think it was a necessary

Re: [Avogadro-devel] Avogadro 1.1.x and Linux Distributions

On Fri, Aug 29, 2014 at 6:58 PM, Michael Banck mba...@debian.org wrote: Hi, On Fri, Aug 29, 2014 at 04:51:49PM -0400, Geoffrey Hutchison wrote: Any progress on this? The Debian freeze is approaching in a couple of months, so I it would be nice to include Avogadro-1.2.0 into the next

Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting

On Tue, Feb 4, 2014 at 5:39 AM, Jure Varlec jure.var...@ki.si wrote: Also, I had to add an include path for Eigen to fix building, do I have to make a separate branch for that single commit? I'm not sure why that (adding an Eigen include path) would be necessary. That should be covered by

Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting

On Tue, Feb 4, 2014 at 10:45 AM, Jure Varlec jure.var...@ki.si wrote: On Tuesday 04 of February 2014 09:56:01 Marcus D. Hanwell wrote: Are you building with Eigen 2 or 3? I just looked at master, and libavogadro/src/CMakeLists.txt adds it to the include directories, the same is not true

Re: [Avogadro-devel] avogadro 1.1.1: Building with Eigen3 fails

On Tue, Dec 31, 2013 at 8:55 AM, Daniel Leidert daniel.leid...@wgdd.de wrote: Hi there, I'm speaking as part of the Debian package maintainers of avogadro. The latest release 1.1.1 fails to build with Eigen3. The reason is, that Eigen2 is still required, e.g. in

Re: [Avogadro-devel] Building Avogadro2 w/o MoleQueue on Arch Linux-64bit

On Sun, Dec 29, 2013 at 5:12 AM, Mark Lee m...@markelee.com wrote: Salutations! I have been trying to build Avogadro2 (to test it out) on my Arch Linux 64 bit system. However, while building avogadrolibs-0.7.2; I get the following error from CMake: snip Is there a way to disable the

Re: [Avogadro-devel] Avogadro Low Resolution Icon in Arch Linux

On Mon, Dec 23, 2013 at 2:19 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I can take a look at this, and will see if I can improve it. The report doesn't reference what version you are referring to, but I presume 1.1.1? We have both a 512x512 icon and an SVG version, so this

Re: [Avogadro-devel] Avogadro Low Resolution Icon in Arch Linux

On Mon, Dec 23, 2013 at 2:41 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: On Mon, Dec 23, 2013 at 2:19 PM, Geoffrey Hutchison geoff.hutchi...@gmail.com wrote: I can take a look at this, and will see if I can improve it. The report doesn't reference what version you are referring

[Avogadro-devel] Avogadro 1.1.1 Released

We are very proud to announce the availability of Avogadro 1.1.1. Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows,

[Avogadro-devel] Avogadro 2 0.7.0 Released

We are very proud to announce the availability of Avogadro 2 0.7.0. Avogadro 2 is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for

Re: [Avogadro-devel] Eigen3 Support

Hi Geoff, On Mon, Sep 30, 2013 at 8:17 PM, Geoffrey Hutchison geo...@pitt.edu wrote: I had a little time to fiddle this afternoon and I've push a patch to Gerrit that allows building against Eigen3 using the support mode. This means that Eigen3's API is not yet supported in Avogadro 1.1.x

Re: [Avogadro-devel] Unable to configure OS X installation directory away from /Applications/Avogadro.app...

On Mon, Sep 2, 2013 at 1:33 AM, Christian Herbig c.her...@me.com wrote: I sincerely hope this is a question that can easily be answered, but I cannot at all figure out how to change the final installation directory from /Applications/Avogadro.app to /Applications/MacPorts/Avogadro.app. I

[Avogadro-devel] CML, NWChem, FoX, Avogadro paper

Hi, I wanted to point out our paper (part of the same special issue as the Avogadro paper) was released recently. It discusses the use of CML produced by NWChem using FoX and visualized in Avogadro. www.jcheminf.com/content/5/1/25 We should hopefully see releases of NWChem soon that can output

Re: [Avogadro-devel] Packmol, Symmol and other Fortran through Webapps

On Fri, May 24, 2013 at 4:49 AM, Jens linuck...@gmail.com wrote: On 23 May 2013 18:15, Geoffrey Hutchison geo...@pitt.edu wrote: I've been silent on the lists, since I'm hard at work getting tenure (the package gets submitted in early August). But I had a brainstorm about some of the

Re: [Avogadro-devel] Avogadro 1.1.0 Released

On Fri, Apr 26, 2013 at 11:13 AM, Michael Banck mba...@debian.org wrote: Hi, On Wed, Sep 12, 2012 at 02:07:21PM -0400, Marcus D. Hanwell wrote: We are very proud to announce the availability of Avogadro 1.1.0. [...] Download: https://sourceforge.net/projects/avogadro/files/avogadro/1.1.0

Re: [Avogadro-devel] First Avogadro 2 beta release

On Fri, Apr 12, 2013 at 9:29 AM, David Lonie david.lo...@kitware.com wrote: Hi Jens, On Fri, Apr 12, 2013 at 5:00 AM, Jens linuck...@gmail.com wrote: Really great to hear that avogadro2 is now on the scene and I'm excited to see how it develops in the future. It's already looking very

[Avogadro-devel] First Avogadro 2 beta release

Hi, I wanted to let people on these lists know that we just made our first beta release of Avogadro 2, along with MoleQueue and MongoChem. Please see the blog post here, http://blog.cryos.org/archives/265-First-Open-Chemistry-Beta-Release.html We have created binary installers for Windows and

Re: [Avogadro-devel] [Avogadro-Translations] Avogadro in Spanish for Windows

On Fri, Apr 5, 2013 at 2:47 PM, Louis Ricard louis.ric...@polytechnique.edu wrote: Hi all, This is a recurrent problem for Windows users: Windows does not know i18n and, consequently, only english menus are available. Since the Windows version is not compiled with internationalization

Re: [Avogadro-devel] Contributor approval for 3-clause BSD relicensing (YOUR ACTION NEEDED)

On Mon, Mar 18, 2013 at 11:30 AM, Benoit Jacob jacob.benoi...@gmail.com wrote: Dear Avogadro developers, Yes, I agree to have all the code that I contributed to Avogadro relicensed to the 3-clause BSD license. Also, I would suggest moving to Eigen 3 if you haven't already: it is now

[Avogadro-devel] Avogadro relicensing agreement update

Hi, Just a quick update from the replies I have received as far as agreement to relicensing goes. Those who have replied positively (one or two off-list, hopefully they will follow up with on list soon), Marcus D. Hanwell Casper Steinmann David Lonie Geoffrey Hutchison Jens Thomas Matthew

[Avogadro-devel] Contributor approval for 3-clause BSD relicensing (YOUR ACTION NEEDED)

Hi, We have talked about this offline, and at times on the list. As many of you already know we are working on a rewrite of Avogadro, and we are preparing to make an initial alpha release. It features many great new features, but does not yet have feature parity with Avogadro 1.x. Avogadro 2 is a

Re: [Avogadro-devel] painter

On Fri, Mar 1, 2013 at 1:31 PM, Marc-André Dubois ma.dub...@me.com wrote: Hi everyone, I would like to draw a sphere in the molecule render area of avogadro. I simply tried to test this command: gl-painter()-drawSphere(center,13.0); where gl is my GLWidget, but I

Re: [Avogadro-devel] Regarding request for suggestion.

On Sun, Feb 24, 2013 at 11:41 PM, Sujit Tangadpalliwar sujit_tangadpalli...@persistent.co.in wrote: I am using your software Avogadro since a month as it having multiple functionality like visualization, molecule editor, optimization structure

Re: [Avogadro-devel] 300,000 Downloads

On Sun, Jan 27, 2013 at 1:33 PM, Geoffrey Hutchison geo...@pitt.edu wrote: I was pulling up statistics on Avogadro for an NSF proposal, and saw that we finally broke the 300,000 download mark! In 2012, there were ~100,000 downloads alone.

Re: [Avogadro-devel] Avogadro Paper Accesses

On Fri, Sep 14, 2012 at 10:35 AM, Geoffrey Hutchison geo...@pitt.eduwrote: I'll admit I've been very intrigued by the # of accesses statistic from J. Cheminf. I wish more journals showed this -- it's a very interesting way of measuring impact of particular articles. Thanks to Noel O'Boyle's

[Avogadro-devel] Avogadro 1.1.0 Released

We are very proud to announce the availability of Avogadro 1.1.0. Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows,

Re: [Avogadro-devel] Upgrading SourceForge for Avogadro

On Wed, Sep 12, 2012 at 1:32 PM, Geoffrey Hutchison geo...@pitt.edu wrote: One thing we should consider with the release of 1.1.0 is to upgrade Avogadro to the new SourceForge version: https://sourceforge.net/p/upgrade?search=avogadro I think the improved tracker would be great for handling

Re: [Avogadro-devel] Avogadro 1.1.0 tagging

On Tue, Sep 4, 2012 at 1:10 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: On Tue, Sep 4, 2012 at 11:49 AM, Geoff Hutchison ge...@geoffhutchison.net wrote: I think we are more than ready to release once we have the Mac package. This is the first in the beta series to stabilize

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