Re: [Open Babel] API for generating 2D coordinates or 3D->2D conversion?
Sorry for the duplicate posting - this question was answered on Dec. 15. -- View this message in context: http://forums.openbabel.org/API-for-generating-2D-coordinates-or-3D-2D-conversion-tp4214535p4214715.html Sent from the General discussion mailing list archive at Nabble.com. -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] [OpenBabel-Devel] Open Babel: 10 Years and Future Directions
On Wed, Dec 21, 2011 at 1:00 AM, Geoffrey Hutchison wrote: > This e-mail has been long delayed. As 2011 draws to a close, Open Babel is > over 10 years old! At this point, it's used by over 40 open source projects, > downloaded over 200,000 times, and been used in over 400 academic papers. And > of course, there have been 15 releases and dozens of contributors. > > > The idea is that an Open Babel v3, and other toolkits, can be built on top of > MolCore. Some level of code modularity will also make it easier to integrate > between multiple toolkits. > > The problem has been to get the ball rolling, particularly since I haven't > had much time to write code myself. The good news is that pieces are falling > into place, so if you're interested in helping out, please let me know. > Thanks for getting the ball rolling on this one Geoff. For any of my contributions they can of course be re-licensed. I moved to Kitware to pursue the further development of open chemistry software, and was recently awarded a Phase II SBIR. Kitware has a long history (over a decade) of developing open toolkits and applications using open permissive licenses. The SBIR gives us a couple of years to really engineer the components needed for cross-platform open chemistry. What we develop will be released under permissive licenses, such as the 3-clause BSD license, and developed in the open. We are also bringing the Kitware software quality process to this work, writing tests and running them daily on multiple platforms and compilers. I want to make these projects community efforts, and MolCore is a very good fit with the project we are working on here. I think we have a real opportunity to build something for the entire community, and it will be better with community participation. I am on the MolCore and Open Babel development lists, among others, please let us know if there are other places we should be subscribed to. In the Quixote work we had weekly Skype meetings, I wonder if that (or Google hangouts) might be useful for people who could make it to them too for a little real time communication. Marcus -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] [OpenBabel-Devel] Open Babel: 10 Years and Future Directions
On Dec 21, 2011, at 2:52 PM, My Th wrote: > My point also was not about version numbering, but rather the project v3 > which has been documented in OB wiki with its goals. I would like to see > them reached. I think you're referring to this: http://openbabel.org/wiki/Roadmap If so, what particular items do you think are needed? While the document hasn't been touched since 2006, you'll note that we have, in fact, been releasing these features as part of the 2.x releases. Removing old API calls would, in fact occur with an Open Babel v3 release (or any similar major release, v4, etc.). That's our numbering scheme. > In our university we have a course on opensource and I'm considering to > use that as an excuse to do some OB programming next semester :) Glad to hear it. We'd be happy to provide any guidance or pointers needed. Cheers, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] GAFF atom assignments
You don't have to use SMARTS -- you could program the atom types with a set of if/else clauses. Essentially all of MMFF94 atom typing is done this way in Open Babel. It's probably more tedious, though. > Sorry, but my question remains as to how can element is assigned its atom > type based solely on bond connectivities. Molecular mechanics implementations like GAFF define a set of atom types determined by humans. So if you have the valence bond structure of a molecule (i.e., atomic numbers, bonded neighbors, and bond types = double, triple, etc.) you should have everything needed for GAFF. The only "other" things I see in the list of GAFF atom types are ring membership and aromaticity. You can, most definitely, assign these based on bond connectivities. So I guess my question is -- what more do you think one would need beyond atomic numbers and bond connectivities? In the organic chemist's view of the world, that's essentially everything. Thanks, -Geoff -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] [OpenBabel-Devel] Open Babel: 10 Years and Future Directions
2011/12/22 Geoffrey Hutchison : > > On Dec 21, 2011, at 2:52 PM, My Th wrote: > >> My point also was not about version numbering, but rather the project v3 >> which has been documented in OB wiki with its goals. I would like to see >> them reached. > > I think you're referring to this: > http://openbabel.org/wiki/Roadmap > > If so, what particular items do you think are needed? While the document > hasn't been touched since 2006, you'll note that we have, in fact, been > releasing these features as part of the 2.x releases. > The roadmap as it is written there is completed, as you say. I was referring to this: http://openbabel.org/wiki/Version_3.0_Projects And in particular to the following points: - Improved Code Quality - Improved Plugin Framework - Indexing from 0, not 1 - Consider using Boost Also I was interested in "SetData and scripting bindings", but that link is broken, so I don't know what it is really about, and in fixing all compiler warnings (API break would be required, so bump to v3). In addition to that I was thinking about these: - Atom index type (size_t) to fix all signed/unsigned int comparison warnings - Decoupling of residue and chain perception, since some formats have defined residues, would be performance win to use that info - Molecule system class or similar thing to group multiple molecules in one unit (useful for modeling file formats) We have discussed the possible improvements to plugin system with Chris Morley, e.g., see the discussion thread "[OpenBabel-Devel] Segfault in OBForceField::MakeNewInstance()", where he proposed the use of Boost's shared pointers for plugin instances, which I think is worth considering. > Removing old API calls would, in fact occur with an Open Babel v3 release (or > any similar major release, v4, etc.). That's our numbering scheme. > As I mentioned, to clean up the code API break would be required, so can't really complete that without v3. All above could and should be done independently of MolCore, IMHO. Reinis P.S. Please consider migrating to Git :) -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Assigning GAFF Torsion Params according to PN value?
In the gaff.dat force field paramater, there are different torsion values of n, gamma, vn_half for c3-c3-c3-c3 chains. I consulted the Amber specification, and it says that if PN is negative, it means that 'additional parameters have to be read'. It was my understanding that the torsional energy of any given bond is calculated in OpenBabel according to: var tor = VectorTorsion(atom A, atom B, atom C, atom D); cosine = Math.cos(DEG_TO_RAD*(n*tor-gamma)); phi1 = 1.0 + cosine; energy = vn_half * phi1; So I have barrier # phase angle PN c3-c3-c3-c3 10.18 0.0-3. Junmei et al, 1999 c3-c3-c3-c3 10.25180.0-2. Junmei et al, 1999 c3-c3-c3-c3 10.20180.0 1. Junmei et al, 1999 so if I have four c3 atoms joined together, how do I determine which one to use? I created a c3-c3-c3-c3 chain and verified in OpenBabel that the torsion uses parameters from the line: c3-c3-c3-c3 10.18 0.0-3. Junmei et al, 1999 and my debugger tells me that n = 3. However I am not sure how this value of n is calculated in the first place, and why it looks up the value for PN = n = -3 when n is supposed to be 3. So to sum up: - how to find n? - how to determine which vn_half, n, gamma values to use? Thanks, Eric -- Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
