[Open Babel] openbabel + confab
Hi all, For some internal purposes, I wanted a combined openbabel/confab code base, so I merged them. If anyone else is interested, I've posted the merge with openbabel HEAD on a fork at https://github.com/cowsandmilk/openbabel/commit/3b782c0d726ad1e35b508cda29abb6bebfe527bb Additionally, if you want openbabel-2.3.2 with confab, I put that version here: http://cowsandmilk.net/pub/openbabel-2.3.2_with_confab.tar.bz2 -David -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
> For some internal purposes, I wanted a combined openbabel/confab code > base, so I merged them. Thanks. Noel (cough, cough) said he'd do this ages ago. :-) Can you remind me the differences that went into confab? I seem to remember that Noel thought I might have some issues with certain changes and I'd prefer to review them before the merge. I do see one clear issue, with tree.hh, which is covered under the GPL v3. Despite the naming, Open Babel (GPv2) is not compatible with GPLv3 code. If there's a version of tree.hh covered under Boost (as suggested by the comments) I think we'd be OK. Thanks very much, -Geoff > Additionally, if you want openbabel-2.3.2 with confab, I put that version > here: > http://cowsandmilk.net/pub/openbabel-2.3.2_with_confab.tar.bz2 > > -David > > -- > Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester > Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the > endpoint security space. For insight on selecting the right partner to > tackle endpoint security challenges, access the full report. > http://p.sf.net/sfu/symantec-dev2dev > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
That's true. One of those things I've never gotten around to. Maybe this is the spur I need. According to tree.hh's website, it says that it's now available under GPL v2 also. My mistake with Confab was to alter Open Babel rather than write a separate application that used the library. I didn't feel confident enough with C++ to do this at that stage. I think that tree.hh and one or two other files should be moved into a Confab project and the rest merged with OB. There were a couple of improvements to the torsion handling (the code in OB ignores currently graph symmetry, e.g. torsions involving phenyls), and I don't know what else. The key code that is somewhat specific to Confab is the on-the-fly RMSD filtering. - Noel On 12 March 2013 01:15, Geoffrey Hutchison wrote: >> For some internal purposes, I wanted a combined openbabel/confab code >> base, so I merged them. > > Thanks. Noel (cough, cough) said he'd do this ages ago. :-) Can you remind me > the differences that went into confab? I seem to remember that Noel thought I > might have some issues with certain changes and I'd prefer to review them > before the merge. > > I do see one clear issue, with tree.hh, which is covered under the GPL v3. > Despite the naming, Open Babel (GPv2) is not compatible with GPLv3 code. > > If there's a version of tree.hh covered under Boost (as suggested by the > comments) I think we'd be OK. > > Thanks very much, > -Geoff > >> Additionally, if you want openbabel-2.3.2 with confab, I put that version >> here: >> http://cowsandmilk.net/pub/openbabel-2.3.2_with_confab.tar.bz2 >> >> -David >> >> -- >> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester >> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the >> endpoint security space. For insight on selecting the right partner to >> tackle endpoint security challenges, access the full report. >> http://p.sf.net/sfu/symantec-dev2dev >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > -- > Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester > Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the > endpoint security space. For insight on selecting the right partner to > tackle endpoint security challenges, access the full report. > http://p.sf.net/sfu/symantec-dev2dev > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
According to current webpage of tree.hh it's released on GPL3 OR 2 [ http://tree.phi-sci.com/] Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/3/12 Geoffrey Hutchison > > For some internal purposes, I wanted a combined openbabel/confab code > > base, so I merged them. > > Thanks. Noel (cough, cough) said he'd do this ages ago. :-) Can you remind > me the differences that went into confab? I seem to remember that Noel > thought I might have some issues with certain changes and I'd prefer to > review them before the merge. > > I do see one clear issue, with tree.hh, which is covered under the GPL v3. > Despite the naming, Open Babel (GPv2) is not compatible with GPLv3 code. > > If there's a version of tree.hh covered under Boost (as suggested by the > comments) I think we'd be OK. > > Thanks very much, > -Geoff > > > Additionally, if you want openbabel-2.3.2 with confab, I put that > version here: > > http://cowsandmilk.net/pub/openbabel-2.3.2_with_confab.tar.bz2 > > > > -David > > > > > -- > > Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester > > Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the > > endpoint security space. For insight on selecting the right partner to > > tackle endpoint security challenges, access the full report. > > http://p.sf.net/sfu/symantec-dev2dev > > ___ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > > -- > Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester > Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the > endpoint security space. For insight on selecting the right partner to > tackle endpoint security challenges, access the full report. > http://p.sf.net/sfu/symantec-dev2dev > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
While the tree.hh website says GPLv2 or GPLv3, the downloaded code says GPLv3. Looking at the history of tree.hh, there are older versions that say v2 or v3, but then at some point he switched to specifying GPLv3 in his code files, a change that makes me uncomfortable with listening to the website. I dug up old versions of tree.hh from Cadabra . Luckily, it actually has the exact same files as Confab, but with a GPLv2-compliant license. Since the author of Cadabra is the same person as the author of tree.hh, I think these files should be considered cleanly under GPLv2. changeset at https://github.com/cowsandmilk/openbabel/commit/d27bb24dd2efa4304b369f4c3923c0ce43de97bb -David On Tue, Mar 12, 2013 at 6:15 AM, Noel O'Boyle wrote: > That's true. One of those things I've never gotten around to. Maybe > this is the spur I need. According to tree.hh's website, it says that > it's now available under GPL v2 also. > > My mistake with Confab was to alter Open Babel rather than write a > separate application that used the library. I didn't feel confident > enough with C++ to do this at that stage. I think that tree.hh and one > or two other files should be moved into a Confab project and the rest > merged with OB. There were a couple of improvements to the torsion > handling (the code in OB ignores currently graph symmetry, e.g. > torsions involving phenyls), and I don't know what else. The key code > that is somewhat specific to Confab is the on-the-fly RMSD filtering. > > - Noel > > On 12 March 2013 01:15, Geoffrey Hutchison wrote: >>> For some internal purposes, I wanted a combined openbabel/confab code >>> base, so I merged them. >> >> Thanks. Noel (cough, cough) said he'd do this ages ago. :-) Can you remind >> me the differences that went into confab? I seem to remember that Noel >> thought I might have some issues with certain changes and I'd prefer to >> review them before the merge. >> >> I do see one clear issue, with tree.hh, which is covered under the GPL v3. >> Despite the naming, Open Babel (GPv2) is not compatible with GPLv3 code. >> >> If there's a version of tree.hh covered under Boost (as suggested by the >> comments) I think we'd be OK. >> >> Thanks very much, >> -Geoff >> >>> Additionally, if you want openbabel-2.3.2 with confab, I put that version >>> here: >>> http://cowsandmilk.net/pub/openbabel-2.3.2_with_confab.tar.bz2 >>> >>> -David >>> >>> -- >>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester >>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the >>> endpoint security space. For insight on selecting the right partner to >>> tackle endpoint security challenges, access the full report. >>> http://p.sf.net/sfu/symantec-dev2dev >>> ___ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> >> -- >> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester >> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the >> endpoint security space. For insight on selecting the right partner to >> tackle endpoint security challenges, access the full report. >> http://p.sf.net/sfu/symantec-dev2dev >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
> I dug up old versions of tree.hh from Cadabra . Luckily, it actually > has the exact same files as Confab, but with a GPLv2-compliant > license. Since the author of Cadabra is the same person as the author > of tree.hh, I think these files should be considered cleanly under > GPLv2. If the file header is labeled as GPLv2, the file is released (to the wild) under GPLv2. Thanks for the investigation. > changeset at > https://github.com/cowsandmilk/openbabel/commit/d27bb24dd2efa4304b369f4c3923c0ce43de97bb If Noel gives the go-ahead, I'd be happy to merge this into openbabel master. I think it's much better to avoid an unmaintained confab fork. Thanks! -Geoff -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
Looks good, but not all the Confab code is in there. If it going to be called Confab I want to make sure it works the same as the original. So...what do you think about merging this onto a branch? I hereby commit to sorting it out :-) - Noel On 15 March 2013 19:26, Geoffrey Hutchison wrote: >> I dug up old versions of tree.hh from Cadabra . Luckily, it actually >> has the exact same files as Confab, but with a GPLv2-compliant >> license. Since the author of Cadabra is the same person as the author >> of tree.hh, I think these files should be considered cleanly under >> GPLv2. > > If the file header is labeled as GPLv2, the file is released (to the wild) > under GPLv2. Thanks for the investigation. > >> changeset at >> https://github.com/cowsandmilk/openbabel/commit/d27bb24dd2efa4304b369f4c3923c0ce43de97bb > > If Noel gives the go-ahead, I'd be happy to merge this into openbabel master. > I think it's much better to avoid an unmaintained confab fork. > > Thanks! > -Geoff -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
Hi David, Can you put all of the Confab-related code on a branch so I can get at them without pulling the other unrelated code on your master? Alternatively I can just copy+paste the files locally or if you know some other way I can get these changes using Git I'm happy to hear it. - Noel On 15 March 2013 20:10, Noel O'Boyle wrote: > Looks good, but not all the Confab code is in there. If it going to be > called Confab I want to make sure it works the same as the original. > So...what do you think about merging this onto a branch? I hereby > commit to sorting it out :-) > > - Noel > > On 15 March 2013 19:26, Geoffrey Hutchison wrote: >>> I dug up old versions of tree.hh from Cadabra . Luckily, it actually >>> has the exact same files as Confab, but with a GPLv2-compliant >>> license. Since the author of Cadabra is the same person as the author >>> of tree.hh, I think these files should be considered cleanly under >>> GPLv2. >> >> If the file header is labeled as GPLv2, the file is released (to the wild) >> under GPLv2. Thanks for the investigation. >> >>> changeset at >>> https://github.com/cowsandmilk/openbabel/commit/d27bb24dd2efa4304b369f4c3923c0ce43de97bb >> >> If Noel gives the go-ahead, I'd be happy to merge this into openbabel >> master. I think it's much better to avoid an unmaintained confab fork. >> >> Thanks! >> -Geoff -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
Try cherry-picking a commit. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2013/3/18 Noel O'Boyle > Hi David, > > Can you put all of the Confab-related code on a branch so I can get at > them without pulling the other unrelated code on your master? > Alternatively I can just copy+paste the files locally or if you know > some other way I can get these changes using Git I'm happy to hear it. > > - Noel > > On 15 March 2013 20:10, Noel O'Boyle wrote: > > Looks good, but not all the Confab code is in there. If it going to be > > called Confab I want to make sure it works the same as the original. > > So...what do you think about merging this onto a branch? I hereby > > commit to sorting it out :-) > > > > - Noel > > > > On 15 March 2013 19:26, Geoffrey Hutchison > wrote: > >>> I dug up old versions of tree.hh from Cadabra . Luckily, it actually > >>> has the exact same files as Confab, but with a GPLv2-compliant > >>> license. Since the author of Cadabra is the same person as the author > >>> of tree.hh, I think these files should be considered cleanly under > >>> GPLv2. > >> > >> If the file header is labeled as GPLv2, the file is released (to the > wild) under GPLv2. Thanks for the investigation. > >> > >>> changeset at > https://github.com/cowsandmilk/openbabel/commit/d27bb24dd2efa4304b369f4c3923c0ce43de97bb > >> > >> If Noel gives the go-ahead, I'd be happy to merge this into openbabel > master. I think it's much better to avoid an unmaintained confab fork. > >> > >> Thanks! > >> -Geoff > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_mar > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] openbabel + confab
I added a confab branch to my repository: https://github.com/cowsandmilk/openbabel/tree/confab It has just the confab changes, based on current openbabel/master branch -David On Mon, Mar 18, 2013 at 5:25 PM, Noel O'Boyle wrote: > Hi David, > > Can you put all of the Confab-related code on a branch so I can get at > them without pulling the other unrelated code on your master? > Alternatively I can just copy+paste the files locally or if you know > some other way I can get these changes using Git I'm happy to hear it. > > - Noel > > On 15 March 2013 20:10, Noel O'Boyle wrote: >> Looks good, but not all the Confab code is in there. If it going to be >> called Confab I want to make sure it works the same as the original. >> So...what do you think about merging this onto a branch? I hereby >> commit to sorting it out :-) >> >> - Noel >> >> On 15 March 2013 19:26, Geoffrey Hutchison wrote: I dug up old versions of tree.hh from Cadabra . Luckily, it actually has the exact same files as Confab, but with a GPLv2-compliant license. Since the author of Cadabra is the same person as the author of tree.hh, I think these files should be considered cleanly under GPLv2. >>> >>> If the file header is labeled as GPLv2, the file is released (to the wild) >>> under GPLv2. Thanks for the investigation. >>> changeset at https://github.com/cowsandmilk/openbabel/commit/d27bb24dd2efa4304b369f4c3923c0ce43de97bb >>> >>> If Noel gives the go-ahead, I'd be happy to merge this into openbabel >>> master. I think it's much better to avoid an unmaintained confab fork. >>> >>> Thanks! >>> -Geoff -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
