| 735624b | Ronny Lorenz | 08 February 2016, 18:45:35 UTC | This is version 2.2.3 - Restore backward compatibility of get_alipf_arrays() - Added annotation of motifs found with RNAfold's --motif option - More documentation of constraints features in RNAfold/RNAalifold manpages | 13 February 2016, 18:01:39 UTC |
| ed9db33 | Ronny Lorenz | 08 February 2016, 18:22:33 UTC | Merge branch 'master' into development | 08 February 2016, 18:22:33 UTC |
| d1ff0af | Ronny Lorenz | 08 February 2016, 17:21:42 UTC | Bump to version 2.2.2 This fixes --noLP issue in RNAcofold | 08 February 2016, 17:23:50 UTC |
| 0be51a8 | Ronny Lorenz | 08 February 2016, 17:21:42 UTC | Fix --noLP issue in RNAcofold | 08 February 2016, 17:21:42 UTC |
| 471d405 | Ronny Lorenz | 06 February 2016, 14:35:58 UTC | Merge branch 'master' into development | 06 February 2016, 14:35:58 UTC |
| fcce317 | Ronny Lorenz | 06 February 2016, 14:32:52 UTC | Merge branch 'release_2.2.1' | 06 February 2016, 14:32:52 UTC |
| cbfb8a2 | Ronny Lorenz | 25 January 2016, 10:06:45 UTC | This is version 2.2.1 This version mainly includes bugfixes for various programs, and corrects install target directories for perl and python interface Program fixes: - Fixed potential bug of using uninitialized variable in RNApdist - Use bugfixed version of Kinfold that does allow for loading parameter files again - Bugfix for segfault in RNAcofold -a - Bugfix for segfault in RNAfold -g -p --MEA - Bugfix for miscomputation of MEA structure in RNAfold with activated gquadruplex support Library fixes: - Fix bug in MEA() with gquadruplexes | 06 February 2016, 14:25:41 UTC |
| 5bf996f | Ronny Lorenz | 05 February 2016, 23:28:22 UTC | Force perl path in viennarna.spec for OBS | 05 February 2016, 23:28:22 UTC |
| 6ec701f | Ronny Lorenz | 05 February 2016, 18:14:19 UTC | Fix bug in MEA() with gquadruplexes - For some reason, we computed the unpaired probabilities wrong, when gquadruplex support was activated. This caused MEA() to fail in the backtracking routine for some input sequences. We now remove the paired probability given to some gquadruplex[k,l] encloses i in a post-processing step. | 05 February 2016, 18:14:19 UTC |
| 9cea35d | Ronny Lorenz | 05 February 2016, 17:07:48 UTC | Bugfix for miscomputation of MEA structure in RNAfold with activated gquadruplex support | 05 February 2016, 17:07:48 UTC |
| 2d97a19 | Ronny Lorenz | 05 February 2016, 13:07:52 UTC | Bugfix for segfault in RNAfold -g -p --MEA | 05 February 2016, 13:07:52 UTC |
| ae51a9b | Ronny Lorenz | 05 February 2016, 13:07:25 UTC | Bugfix for segfault in RNAcofold -a | 05 February 2016, 13:07:25 UTC |
| 67ff5d6 | Ronny Lorenz | 02 February 2016, 23:02:55 UTC | packaging/ - Make core + swig interfaces belong to same group/distribution named 'viennarna-package' This makes installation of binary packages easier, by just installing/updating the group, and not each package individually | 02 February 2016, 23:02:55 UTC |
| 0d0f412 | Ronny Lorenz | 02 February 2016, 14:04:54 UTC | Put programs from src/Utils into bindir upon installation, and add manpage for ct2db | 02 February 2016, 14:04:54 UTC |
| c07f3b6 | Ronny Lorenz | 02 February 2016, 14:02:41 UTC | declare main() function in src/Cluster/AD_main.c return int instead of implying it | 02 February 2016, 14:02:41 UTC |
| 3a97bce | Ronny Lorenz | 02 February 2016, 14:01:57 UTC | Updated .gitignores | 02 February 2016, 14:01:57 UTC |
| 5cc9ba1 | Ronny Lorenz | 30 January 2016, 09:26:41 UTC | Moved packaging related files into separate directort packaging/ | 30 January 2016, 09:26:41 UTC |
| 2177df1 | Ronny Lorenz | 30 January 2016, 08:43:03 UTC | Updated ViennaRNA.spec.in and PKGBUILD.in for proper package generation | 30 January 2016, 08:43:03 UTC |
| 6859924 | Ronny Lorenz | 29 January 2016, 10:53:48 UTC | Use bugfixed version of Kinfold that does allow for loading parameter files again | 29 January 2016, 10:53:48 UTC |
| 9afcf9d | Ronny Lorenz | 29 January 2016, 10:53:09 UTC | Use libRNA convenience library for programs in src/Cluster | 29 January 2016, 10:53:09 UTC |
| a0c4763 | Ronny Lorenz | 28 January 2016, 17:55:30 UTC | Fixed misc/ViennaRNA.spec to build RPMs on platforms other than fedora | 28 January 2016, 17:55:30 UTC |
| bdcf387 | Ronny Lorenz | 28 January 2016, 17:50:20 UTC | Fixed bug in backtrack() in mfe.c that returned arbitrary data This bug was only effecting the return value of the new function vrna_backtrack_from_intervals() in mfe.c, since it is the only one that uses, and passes along the return value of backtrack(). Nevertheless, this was a bug, so we fixed this by setting the return type of both functions to void. | 28 January 2016, 17:50:20 UTC |
| fc79509 | Ronny Lorenz | 28 January 2016, 17:49:29 UTC | Fixed potential bug of using uninitialized variable in RNApdist | 28 January 2016, 17:49:29 UTC |
| fade888 | Ronny Lorenz | 28 January 2016, 17:39:48 UTC | Updated misc/PKGBUILD.in | 28 January 2016, 17:39:48 UTC |
| be88883 | Ronny Lorenz | 28 January 2016, 14:25:22 UTC | ViennaRNA.spec file now splits the package into binaries, development, perl, and python2 | 28 January 2016, 14:25:22 UTC |
| 2e255cb | Ronny Lorenz | 28 January 2016, 14:24:59 UTC | Let the user specify the perl interpreter at configure time | 28 January 2016, 14:24:59 UTC |
| 03f7849 | Ronny Lorenz | 26 January 2016, 20:27:35 UTC | Remove automake rule to build .pyc for swig python interface - We don't need this, this is all automagically handled by automake itself upon install, whenever some .py script is listed under _PYTHON | 26 January 2016, 20:27:35 UTC |
| 88d25db | Ronny Lorenz | 25 January 2016, 21:20:32 UTC | Account for proper installation directories for Perl and Python extensions - architecture dependent and independent files may now be installed into different directories - perl extensions may use 'site' or 'vendor' targets. The default is 'site', and can be set to 'vendor' using the INSTALLDIRS environment variable at configure time, e.g.: ./configure --prefix=/path/to/install INSTALLDIRS=vendor Ideas for the applied changes came from studying: http://perldoc.perl.org/Config.html https://wiki.archlinux.org/index.php/Perl_package_guidelines https://lists.gnu.org/archive/html/autoconf-archive-maintainers/2014-02/msg00015.html http://www.gnu.org/savannah-checkouts/gnu/automake/manual/html_node/Python.html | 25 January 2016, 21:32:38 UTC |
| af5bc4c | Ronny Lorenz | 25 January 2016, 11:47:40 UTC | Merge branch 'master' into development | 25 January 2016, 11:47:40 UTC |
| 95779b1 | Ronny Lorenz | 25 January 2016, 10:06:45 UTC | Fixed minor packaging stuff | 25 January 2016, 10:06:45 UTC |
| 723f1ef | Ronny Lorenz | 24 January 2016, 17:59:45 UTC | Merge branch 'master' into development | 24 January 2016, 17:59:45 UTC |
| 142e193 | Ronny Lorenz | 24 January 2016, 17:57:38 UTC | Merge branch 'release_2.2.0' into 'master' This is version 2.2.0 Many new features have been implemented, among them are: - hard and constraints for MFE, suboptimals, partition function, and base pair probability computations for single sequences, sequence alignments, and sequence dimers - new ViennaRNA-perl submodule that augments the Perl interface to RNAlib - removed partition function option from RNALalifold since it is NOT IMPLEMENTED - made RNAcofold able to omit base pair probability computations (-p0) - include RNAforester version 2.0 - RNAplex now allows for computation of interactions without length limitation - bump libsvm version to 3.20 - made stochastic backtracking in part_func.c faster using Boustrophedon scheme - restructured unit test framework with libcheck to use checkmk - added polymorphic functions vrna_mfe(), vrna_pf, and vrna_pbacktrack() - started object oriented SWIG interfaces for several data structures in RNAlib - started documenting scripting interface in reference manual - added a reference implementation for generic soft constraints feature to incorporate binding energy of ligands to aptamer motif, e.g. theophylline aptamer - fixed numerical instability in RNAheat - use Link Time Optimization (LTO) to allwo for cross-object function inlining - removed src/Utils/Fold script - removed src/Readseq - fix segfault in simple plotlayout, when hairpin loop size is 0 - store SHAPE reactivity pseudo-energies gap-free for RNAalifold, and apply them only if there is no gap position in a stack - convert FLT_OR_DBL macro into an actual typedef - switch to libtool for library generation - added configure switch to turn-on deprecated symbol warnings See merge request !33 | 24 January 2016, 17:57:38 UTC |
| 610c3bd | Ronny Lorenz | 24 January 2016, 13:36:41 UTC | Merge branch 'release_2.2.0' into development | 24 January 2016, 13:36:41 UTC |
| eaafeea | Ronny Lorenz | 11 May 2015, 15:08:17 UTC | This is version 2.2.0 Many new features have been implemented, among them are: - hard and constraints for MFE, suboptimals, partition function, and base pair probability computations for single sequences, sequence alignments, and sequence dimers - new ViennaRNA-perl submodule that augments the Perl interface to RNAlib - removed partition function option from RNALalifold since it is NOT IMPLEMENTED - made RNAcofold able to omit base pair probability computations (-p0) - include RNAforester version 2.0 - RNAplex now allows for computation of interactions without length limitation - bump libsvm version to 3.20 - made stochastic backtracking in part_func.c faster using Boustrophedon scheme - restructured unit test framework with libcheck to use checkmk - added polymorphic functions vrna_mfe(), vrna_pf, and vrna_pbacktrack() - started object oriented SWIG interfaces for several data structures in RNAlib - started documenting scripting interface in reference manual - added a reference implementation for generic soft constraints feature to incorporate binding energy of ligands to aptamer motif, e.g. theophylline aptamer - fixed numerical instability in RNAheat - use Link Time Optimization (LTO) to allwo for cross-object function inlining - removed src/Utils/Fold script - removed src/Readseq - fix segfault in simple plotlayout, when hairpin loop size is 0 - store SHAPE reactivity pseudo-energies gap-free for RNAalifold, and apply them only if there is no gap position in a stack - convert FLT_OR_DBL macro into an actual typedef - switch to libtool for library generation - added configure switch to turn-on deprecated symbol warnings | 24 January 2016, 13:09:31 UTC |
| f39a3a9 | Ronny Lorenz | 22 January 2016, 20:02:03 UTC | Merge branch 'dev_merge_comparative' into 'development' Switch to libtool and merge new API consensus structure functions into single sequence functions (polymorphism) This merge will introduce polymorphism for all relevant function like vrna_mfe(), vrna_pf(), and vrna_pbacktrack() such that they can deal with the polymorphism of vrna_fold_compound_t. Furthermore, from now on, compilation and linking of libraries and programs will be done by libtool. This makes many things much easier and portable. See merge request !32 | 22 January 2016, 20:02:03 UTC |
| e7af646 | Ronny Lorenz | 22 January 2016, 18:25:36 UTC | Made vrna_pbacktrack polymorphic | 22 January 2016, 18:25:36 UTC |
| 98a2c09 | Ronny Lorenz | 22 January 2016, 13:07:47 UTC | Made vrna_pf() isomorphic, and implemented simple-interface convenience functions The simple interface convenience functions allow one to use vrna_pf() without the need of creating a vrna_fold_compound_t | 22 January 2016, 13:07:47 UTC |
| 15f8e00 | Ronny Lorenz | 21 January 2016, 17:54:32 UTC | Make sure to add SHAPE bonuses only for real stacks in alifold | 21 January 2016, 18:49:28 UTC |
| 1e5e654 | Ronny Lorenz | 21 January 2016, 16:26:27 UTC | Make sure to use the correct linker and linker flags with libtool andi SVM feature | 21 January 2016, 16:26:27 UTC |
| daef17d | Ronny Lorenz | 21 January 2016, 16:25:32 UTC | Some cleanup in header files in src/ViennaRNA | 21 January 2016, 16:25:32 UTC |
| 9584094 | Ronny Lorenz | 21 January 2016, 16:24:29 UTC | Added return type to main() in src/Cluster/AS_maint.c | 21 January 2016, 16:24:29 UTC |
| 56e5720 | Ronny Lorenz | 20 January 2016, 16:12:33 UTC | Made deprecated symbol warnings optional Preprocessor warnings about deprecated symbols are now optional and may be activated with the --enable-warn-deprecated configure switch | 20 January 2016, 16:12:33 UTC |
| 5654096 | Ronny Lorenz | 03 January 2016, 22:23:16 UTC | Switch to libtool We use a libtool convenience library for internal static linking to RNAlib This also ensures that PIC level is correct for shared libraries of the SWIG interfaces. For LTO compilation/linking, we let the user specify ar/ranlib/nm commands via configure script | 20 January 2016, 11:59:42 UTC |
| f484c55 | Ronny Lorenz | 13 December 2015, 21:24:40 UTC | Make floatpf configure switch working again This patch re-introduces the --enable-floatpf switch for the configure script. It also changes the FLT_OR_DBL macro to an actual typedef. One important thing has to be noted: Soft constraints are most likely to not work properly with single precision floating points. The Boltzmann factors in sc->exp_en_up are increasing way too fast for longer sequence stretches. Thus, they actually require a scaling mechanism, similar to that used for regular partition function! | 20 January 2016, 11:59:40 UTC |
| a30b824 | Ronny Lorenz | 11 December 2015, 09:49:07 UTC | Store hard constraints matrix into row-wise accessed array in base pair probability computation This is necessary for a large speedup due to fewer cache-misses | 20 January 2016, 11:59:39 UTC |
| 54c070d | Ronny Lorenz | 11 December 2015, 09:48:32 UTC | Split interior loop evaluation again (single vs. comparative) | 20 January 2016, 11:59:39 UTC |
| ca34adf | Ronny Lorenz | 04 December 2015, 19:07:00 UTC | Store Deigan pseudo energies for SHAPE data in alifold gapfree Now we still have the problem that pseudo energies for gap nucleotides will be added to a stack, where the energy is taken from next base 5' of the gap. This should be fixed! | 20 January 2016, 11:59:38 UTC |
| 023296a | Ronny Lorenz | 01 December 2015, 10:39:07 UTC | Fixed potential issues with negative loop lengths in comparative evaluation of hairpins and interior loops | 20 January 2016, 11:59:38 UTC |
| d8e7147 | Ronny Lorenz | 29 November 2015, 21:42:33 UTC | Merged hairpin and interior loop handling for consensus MFE predictions IMPORTANT: 1. SHAPE handling for alifold does not work for now, since pseudo energies are now taken sequence position wise, while they had been alignment columnwise before 2. Make sure, that loop sizes are NEVER < 0. This might be the case when a2s[p] == a2s[i] and u = a2s[p] - a2s[i] - 1 | 20 January 2016, 11:59:37 UTC |
| 18eb095 | Ronny Lorenz | 29 November 2015, 14:09:35 UTC | Free fold compound in RNAalifold.c at correct place | 20 January 2016, 11:59:37 UTC |
| c1dbfcd | Ronny Lorenz | 29 November 2015, 14:08:34 UTC | Separated Stochastic backtracking related functions into boltzmann_sampling.[c,h] | 20 January 2016, 11:59:36 UTC |
| 2a89d8f | Ronny Lorenz | 20 January 2016, 11:39:41 UTC | Fixed segfault in simple plotlayout, when hairpin loop size is 0 | 20 January 2016, 11:39:41 UTC |
| a4d7c4a | Ronny Lorenz | 23 December 2015, 10:35:25 UTC | Fixed cofold bug in multibranch_loops.c | 23 December 2015, 10:35:25 UTC |
| 63b6f31 | Ronny Lorenz | 22 December 2015, 21:28:49 UTC | Fixed output of pf_scale in RNAfold | 22 December 2015, 21:28:49 UTC |
| dcf836c | Ronny Lorenz | 22 December 2015, 21:27:59 UTC | Fix misusage of jindx in interior loops partition function | 22 December 2015, 21:27:59 UTC |
| 5f1e744 | Ronny Lorenz | 17 December 2015, 16:08:32 UTC | Merge branch 'dev_llvm_lto' into 'development' Enable LTO support for Linux with clang/clang++ The trick is to call clang/clang++ with -fuse-ld=gold for linking and set the corresponding tool prefixes, i.e. llvm-ar, llvm-ranlib, and llvm-nm. This, however, required several changes in the autotools mess. We now pass several variables to the subpackages to make them actually compile and link to our static RNAlib with LTO support. How this should be done for OS X remains unsolved for now. This commit also sets RNAforester to a version that actually builds with clang See merge request !31 | 17 December 2015, 16:08:32 UTC |
| d66972c | Ronny Lorenz | 15 December 2015, 15:40:59 UTC | Enable LTO support for Linux with clang/clang++ The trick is to call clang/clang++ with -fuse-ld=gold for linking and set the corresponding tool prefixes, i.e. llvm-ar, llvm-ranlib, and llvm-nm. This, however, required several changes in the autotools mess. We now pass several variables to the subpackages to make them actually compile and link to our static RNAlib with LTO support. How this should be done for OS X remains unsolved for now. This commit also sets RNAforester to a version that actually builds with clang | 17 December 2015, 15:50:27 UTC |
| b24e063 | Ronny Lorenz | 11 December 2015, 13:46:31 UTC | Let MakeMaker honour the CC environment variable settings This enables making the perl interface with clang or icc | 11 December 2015, 13:46:31 UTC |
| 178b26a | Ronny Lorenz | 28 November 2015, 15:24:27 UTC | Reverted deprecated function constrain_ptypes() to original state This ensures that snofold runs as intended. The function will be removed in the future anyway. | 28 November 2015, 15:24:27 UTC |
| 0aeff6e | Ronny Lorenz | 28 November 2015, 12:27:12 UTC | Stay backwards compatible in pkg-config file for RNAlib | 28 November 2015, 12:27:12 UTC |
| f906fed | Ronny Lorenz | 27 November 2015, 19:09:31 UTC | Fixed issue of slow function calls in in eval.c and findpath.c in repetetive old API calls | 27 November 2015, 19:09:31 UTC |
| 6469fdf | Ronny Lorenz | 25 November 2015, 16:41:52 UTC | Added missing .i files in interfaces/ makefiles | 25 November 2015, 16:41:52 UTC |
| 92137b8 | Ronny Lorenz | 25 November 2015, 16:41:12 UTC | Removed src/Readseq and src/Utils/Fold These things are obsolete and will not be distributed anymore | 25 November 2015, 16:41:12 UTC |
| 7d8e67a | Ronny Lorenz | 25 November 2015, 16:02:04 UTC | Removed src/Utils/Fold script from installation We still ship this script but do not install it. It requires the readseq program anyway, which is discontinued since 2005. | 25 November 2015, 16:02:04 UTC |
| 29b1120 | Ronny Lorenz | 25 November 2015, 15:47:24 UTC | Minor changes in doxygen comments | 25 November 2015, 15:47:24 UTC |
| 7d3abc6 | Ronny Lorenz | 25 November 2015, 15:46:15 UTC | Fixed behavior of vrna_subopt_zuker by introducing some magic | 25 November 2015, 15:46:15 UTC |
| 2ed1964 | Ronny Lorenz | 24 November 2015, 16:23:30 UTC | Removed vrna_mfe_comparative(), since vrna_mfe() can distinguish single sequences and alignments now | 24 November 2015, 16:23:30 UTC |
| bfd9779 | Ronny Lorenz | 24 November 2015, 16:21:35 UTC | Default to add hidden instead of visible global model details to new fold compound | 24 November 2015, 16:21:35 UTC |
| d22ab2f | Ronny Lorenz | 24 November 2015, 16:17:55 UTC | Always allocate memory for cofolding when cutpoint > 0 | 24 November 2015, 16:17:55 UTC |
| acbe3c7 | Ronny Lorenz | 24 November 2015, 16:16:52 UTC | Fixed RNAsubopt -z | 24 November 2015, 16:16:52 UTC |
| 9f4c7ec | Ronny Lorenz | 16 November 2015, 18:05:37 UTC | Fixed static library build in Fedora due to missing plugin parameter for ar/ranlib/ld | 16 November 2015, 18:05:37 UTC |
| da6233e | Ronny Lorenz | 16 November 2015, 15:18:17 UTC | Fixed issues with hard constraints | 16 November 2015, 15:18:17 UTC |
| 22d783d | Ronny Lorenz | 14 November 2015, 14:41:52 UTC | Merge branch 'dev_loop_objects' into 'development' Put (almost) all loop evaluations into separate compilation units instead of header files To counteract compiler optimization loss due to removing evaluations from header files, we add link time optimization flags for the compiler and linker to autotools framework See merge request !30 | 14 November 2015, 14:41:52 UTC |
| 8581e7d | Ronny Lorenz | 11 November 2015, 21:16:50 UTC | Put (almost) all loop evaluations into separate compilation units instead of header files To counteract compiler optimization loss due to removing evaluations from header files, we add link time optimization flags for the compiler and linker to autotools framework | 14 November 2015, 14:29:03 UTC |
| 6665c45 | Ronny Lorenz | 13 November 2015, 15:23:32 UTC | Fixed numerical instability in RNAheat | 13 November 2015, 15:23:32 UTC |
| 733c5a1 | Ronny Lorenz | 11 November 2015, 13:01:06 UTC | Removed unused decomposition flag in constraints.h and added stdio.h to mfe.h | 11 November 2015, 13:01:06 UTC |
| d9c0e38 | Ronny Lorenz | 11 November 2015, 11:13:01 UTC | Cleanup attribute names in vrna_sc_t and added some more comments for reference manual | 11 November 2015, 11:13:01 UTC |
| a8f1a6e | Ronny Lorenz | 10 November 2015, 22:26:48 UTC | Split large functions in dp_matrices.c into smaller ones | 10 November 2015, 22:26:48 UTC |
| 8b7040d | Ronny Lorenz | 10 November 2015, 22:26:30 UTC | Fixed usage of uninitialized value in Lfold.c | 10 November 2015, 22:26:30 UTC |
| f7abf1a | Ronny Lorenz | 10 November 2015, 21:46:26 UTC | Fixed segfault in RNA2Dfold partition function Due to memory overlap in vrna_mx_pf_t unpredictable memory issues appeared for matrices of type VRNA_MX_2FOLD. This is fixed now. | 10 November 2015, 21:46:26 UTC |
| a50b362 | Ronny Lorenz | 09 November 2015, 14:47:14 UTC | Export an object oriented interface for vrna_path_t (and all its typename aliases) | 09 November 2015, 14:47:14 UTC |
| 6530658 | Ronny Lorenz | 09 November 2015, 14:06:37 UTC | Export bp_distance() in scripting interface again... | 09 November 2015, 14:06:37 UTC |
| 6e8bf85 | Ronny Lorenz | 09 November 2015, 09:16:33 UTC | Added base pair probability correction for auxiliary pairs in hairpin loop motifs Also fixed wrong comparison to current decomposition step in ligand.c | 09 November 2015, 11:05:49 UTC |
| 6f79de6 | Ronny Lorenz | 09 November 2015, 09:01:42 UTC | Added base pair probability correction for auxiliary pairs in interior loop motifs | 09 November 2015, 09:01:42 UTC |
| f0822f2 | Ronny Lorenz | 09 November 2015, 07:39:42 UTC | Added failsafe checks for ligand motif binding | 09 November 2015, 07:39:42 UTC |
| 82ed198 | Ronny Lorenz | 08 November 2015, 20:19:07 UTC | Added commandline parameter for ligand motif incorporation into RNAfold | 08 November 2015, 20:19:07 UTC |
| eb846c6 | Ronny Lorenz | 08 November 2015, 20:17:49 UTC | Fixed ligand contribution callback function for partition functions | 08 November 2015, 20:17:49 UTC |
| 12a314c | Ronny Lorenz | 08 November 2015, 18:20:55 UTC | Break computations in RNAfold after first sequence if constraints read from file Users may still process multiple input sequences and apply identical constraints using the --batch option | 08 November 2015, 18:20:55 UTC |
| 7d2858e | Ronny Lorenz | 08 November 2015, 16:15:37 UTC | Merge branch 'dev_aptamer' into 'development' Add convenience function for ligand binding utilizing soft constraints framework See merge request !29 | 08 November 2015, 16:15:37 UTC |
| 8968a41 | Ronny Lorenz | 08 November 2015, 16:10:55 UTC | Removed default application of theophylline aptamer binding in RNAfold | 08 November 2015, 16:10:55 UTC |
| 07a8a03 | Ronny Lorenz | 08 November 2015, 15:54:50 UTC | Removed pre-, and post- callbacks from soft and hard constraints A single callback in vrna_fold_compound_t may now be used to preserve pre-, and post-conditions for the constraints framework, and others. The vrna_fold_compound_t also received a void pointer to store additional user-defined data | 08 November 2015, 15:54:50 UTC |
| 9ad9cc4 | Ronny Lorenz | 08 November 2015, 12:42:51 UTC | Cleanup of ligand.c | 08 November 2015, 12:42:51 UTC |
| fe28560 | Ronny Lorenz | 08 November 2015, 10:52:00 UTC | Added hairpin motifs to ligand.c | 08 November 2015, 10:52:00 UTC |
| 24997d1 | Ronny Lorenz | 06 November 2015, 17:29:58 UTC | Fixed base pair backtracking within ligand binding site | 06 November 2015, 17:29:58 UTC |
| b2a95af | Ronny Lorenz | 06 November 2015, 15:04:49 UTC | Included hi_motif into scripting interface | 06 November 2015, 15:04:49 UTC |
| 7199710 | Ronny Lorenz | 06 November 2015, 14:46:13 UTC | Added backtracking of base pairs in ligand motif | 06 November 2015, 14:46:13 UTC |
| d464396 | Ronny Lorenz | 03 November 2015, 07:02:41 UTC | Honor the options parameter in vrna_sc_add_hi_motif() | 03 November 2015, 07:02:41 UTC |
| d992aa3 | Ronny Lorenz | 02 November 2015, 22:47:05 UTC | Separated ligand binding feature from RNAfold.c to ligand.c This is a crude interface function for adding hairpin or interior loop sequence/strcture motifs that for whatever reason have a (de-)stabilizing effect. For instance, theophylline aptamer binding can be modeled using this interface. See ligand.[c,h] for implementation details. NOTE: hairpin motifs still need implementation | 02 November 2015, 22:47:05 UTC |
| ffd636f | Ronny Lorenz | 12 March 2015, 11:02:13 UTC | Corrected actual implementation of aptamer pocket pseudo energies | 02 November 2015, 20:01:54 UTC |
| 361a54a | Ronny Lorenz | 12 March 2015, 10:45:54 UTC | Use pre- and post- functions of the generalized soft constraints feature | 02 November 2015, 20:01:54 UTC |
