Re: [Avogadro-Discuss] How do I access the Z-matrix tool?
Hi Rick, On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmul...@gmail.com wrote: I'm interested in using the Z-matrix tool in Avogadro. I'm currently using Avogadro v1.1.1, and the tool does not appear in the toolbar or the menus. Can I enable it, or do I need to download a newer build to get it? It is not enabled by default because I never got it working in a robust way. It is enabled by a build flag, I could enable it in the next release builds by default (and would like to revisit this as it would be great to get working). Thanks, Marcus -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees_APR ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] How do I access the Z-matrix tool?
Marcus, Thanks for the reply. What's the probably getting the zmatrix robust? Is it the conversion to cartesian coordinates, or the interaction with the rest of Avogadro? I might be able to help with the former, but probably not the latter. Rick On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi Rick, On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmul...@gmail.com wrote: I'm interested in using the Z-matrix tool in Avogadro. I'm currently using Avogadro v1.1.1, and the tool does not appear in the toolbar or the menus. Can I enable it, or do I need to download a newer build to get it? It is not enabled by default because I never got it working in a robust way. It is enabled by a build flag, I could enable it in the next release builds by default (and would like to revisit this as it would be great to get working). Thanks, Marcus -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees_APR ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Rick Muller rpmul...@gmail.com 505-750-7557 -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] How do I access the Z-matrix tool?
Rick, It is the former (to/from Cartesian, corner cases), it was also in progress as I moved between positions and I never got around to it. I would welcome input on robust implementations, and can handle the Avogadro side. I would gladly update the Avogadro 1.1 version, and am eager to port this to Avogadro 2. Thanks, Marcus On Mon, Apr 7, 2014 at 4:36 PM, Rick Muller rpmul...@gmail.com wrote: Marcus, Thanks for the reply. What's the probably getting the zmatrix robust? Is it the conversion to cartesian coordinates, or the interaction with the rest of Avogadro? I might be able to help with the former, but probably not the latter. Rick On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi Rick, On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmul...@gmail.com wrote: I'm interested in using the Z-matrix tool in Avogadro. I'm currently using Avogadro v1.1.1, and the tool does not appear in the toolbar or the menus. Can I enable it, or do I need to download a newer build to get it? It is not enabled by default because I never got it working in a robust way. It is enabled by a build flag, I could enable it in the next release builds by default (and would like to revisit this as it would be great to get working). Thanks, Marcus -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees_APR ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Rick Muller rpmul...@gmail.com 505-750-7557 -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] How do I access the Z-matrix tool?
I have some python code that I'll start to stress test and maybe commit to the PyQuante2 repository sometime real soon. There's probably nothing valuable in the code right now, but maybe after the debugging process I'll know enough to help out with the process. Guess I should figure out how to build Avogadro... On Mon, Apr 7, 2014 at 2:45 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Rick, It is the former (to/from Cartesian, corner cases), it was also in progress as I moved between positions and I never got around to it. I would welcome input on robust implementations, and can handle the Avogadro side. I would gladly update the Avogadro 1.1 version, and am eager to port this to Avogadro 2. Thanks, Marcus On Mon, Apr 7, 2014 at 4:36 PM, Rick Muller rpmul...@gmail.com wrote: Marcus, Thanks for the reply. What's the probably getting the zmatrix robust? Is it the conversion to cartesian coordinates, or the interaction with the rest of Avogadro? I might be able to help with the former, but probably not the latter. Rick On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi Rick, On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmul...@gmail.com wrote: I'm interested in using the Z-matrix tool in Avogadro. I'm currently using Avogadro v1.1.1, and the tool does not appear in the toolbar or the menus. Can I enable it, or do I need to download a newer build to get it? It is not enabled by default because I never got it working in a robust way. It is enabled by a build flag, I could enable it in the next release builds by default (and would like to revisit this as it would be great to get working). Thanks, Marcus -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees_APR ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Rick Muller rpmul...@gmail.com 505-750-7557 -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Rick Muller rpmul...@gmail.com 505-750-7557 -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] How do I access the Z-matrix tool?
Hi, If you're working on code to create z-matricies, then there is code in the CCP1GUI that might be of interest to you. You can find the CCP1GUI here: http://sourceforge.net/projects/ccp1gui/ The main code to generate the zmatrix is the autoz routine here: http://ccp1gui.cvs.sourceforge.net/viewvc/ccp1gui/ccp1gui/objects/zmatrix.py?view=markup I know that Paul Sherwood (who wrote it) sent a lot of time sorting out various corner cases and it's pretty robust for even quite large molecules. Hopefully this will give you some useful pointers and potentially working code if you're developing something similar yourself. I'm sure that a zmatrix utility that could be used and shared by a variety of codes would be a really welcome addition to the community. Best wishes, Jens On 7 April 2014 21:47, Rick Muller rpmul...@gmail.com wrote: I have some python code that I'll start to stress test and maybe commit to the PyQuante2 repository sometime real soon. There's probably nothing valuable in the code right now, but maybe after the debugging process I'll know enough to help out with the process. Guess I should figure out how to build Avogadro... On Mon, Apr 7, 2014 at 2:45 PM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Rick, It is the former (to/from Cartesian, corner cases), it was also in progress as I moved between positions and I never got around to it. I would welcome input on robust implementations, and can handle the Avogadro side. I would gladly update the Avogadro 1.1 version, and am eager to port this to Avogadro 2. Thanks, Marcus On Mon, Apr 7, 2014 at 4:36 PM, Rick Muller rpmul...@gmail.com wrote: Marcus, Thanks for the reply. What's the probably getting the zmatrix robust? Is it the conversion to cartesian coordinates, or the interaction with the rest of Avogadro? I might be able to help with the former, but probably not the latter. Rick On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell marcus.hanw...@kitware.com wrote: Hi Rick, On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmul...@gmail.com wrote: I'm interested in using the Z-matrix tool in Avogadro. I'm currently using Avogadro v1.1.1, and the tool does not appear in the toolbar or the menus. Can I enable it, or do I need to download a newer build to get it? It is not enabled by default because I never got it working in a robust way. It is enabled by a build flag, I could enable it in the next release builds by default (and would like to revisit this as it would be great to get working). Thanks, Marcus -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees_APR ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Rick Muller rpmul...@gmail.com 505-750-7557 -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Rick Muller rpmul...@gmail.com 505-750-7557 -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees ___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss -- Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test Deployment Start a new project now. Try Jenkins in the cloud.
