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• [Adun-commits] Remove causes of minor compiler warnings to improve clarity when compiling Michael Johnston
• [Adun-commits] Rename some ivars for clarity Michael Johnston
• [Adun-commits] Fix: Forgot to move var delclaration required for MAC when creating clearFloatingPointErrors Michael Johnston
• [Adun-commits] Modified so LogStatus also works for initial minimisation if on. [...] Michael Johnston
• [Adun-commits] Fix: Missing multiplication Michael Johnston
• [Adun-commits] Missing newline Michael Johnston
• [Adun-commits] Minor change to timestamp format Michael Johnston
• [Adun-commits] Also log energies when outputting status [...] Michael Johnston
• [Adun-commits] forgot to free matrices on cleanup nils
• [Adun-commits] fix: changing type1vdw to type2vdw nils
• [Adun-commits] Many changes to do with cleaning up logging/output Michael Johnston
• [Adun-commits] Method definition & docs Michael Johnston
• [Adun-commits] Add description method [...] Michael Johnston
• [Adun-commits] Clear fp exceptions at the start of every new block [...] Michael Johnston
• [Adun-commits] adding missing file nils
• [Adun-commits] Add output-dir options Michael Johnston
• [Adun-commits] FIX: FE_INVALID enabled regardless of DisableInvalid option value [...] Michael Johnston
• [Adun-commits] Add missing returns Michael Johnston
• [Adun-commits] Input data Michael Johnston
• [Adun-commits] Initial files Michael Johnston
• [Adun-commits] fix, firstValidDirectory returned last directory instead of first... nils
• [Adun-commits] preventing InstallPlugin.py infinite loop nils
• [Adun-commits] correcting some tabs. Also, changing some syntax marginally to make it compatible with python3* - even though I had to make some questionable changes... nils
• [Adun-commits] changing intendation to \"tab\" nils
• [Adun-commits] adding special cases for CG nils
• [Adun-commits] Add some extra information on search order Michael Johnston
• [Adun-commits] Add defaults resource file Michael Johnston
• [Adun-commits] Add feature to add log the values of the defaults for a run [...] Michael Johnston
• [Adun-commits] Add new resource file to build Michael Johnston
• [Adun-commits] Add extra category Michael Johnston
• [Adun-commits] File for categorising defaults and providing descriptions. [...] Michael Johnston
• [Adun-commits] typo... nils
• [Adun-commits] adding HIS, HIE and HIP to the 3letterresidue name dictionary nils
• [Adun-commits] Small fix of cl options print-out Michael Johnston
• [Adun-commits] adding AdunCMAPTerm.h nils
• [Adun-commits] adding options to control cmap and mainchainterms nils
• [Adun-commits] Fix synchronization Michael Johnston
• [Adun-commits] removing verbosity restriction for the build output of unidentified atoms. it is as important to know what is too much than it is what is missing nils
• [Adun-commits] adding a python script to perform some pdb reformatting so that ADUN has an easier job to read the pdb. nils
• [Adun-commits] Fix exception message when setting column headers. [...] Michael Johnston
• [Adun-commits] Copy of same script in Scripts dir - for testing purposes. Michael Johnston
• [Adun-commits] Switch to use DataSourceDump script in TestScripts dir - CVS not changing execution permissions of the original script. [...] Michael Johnston
• [Adun-commits] Add a return value [...] Michael Johnston
• [Adun-commits] Some minor clarifications Michael Johnston
• [Adun-commits] Fix: Double retain of pluginDirs ivar Michael Johnston
• [Adun-commits] Add missing include [...] Michael Johnston
• [Adun-commits] Added extra logging function Michael Johnston
• [Adun-commits] Log energies of InitialMinimisation if on Michael Johnston
• [Adun-commits] Make InitialMinimisation OFF by default Michael Johnston
• [Adun-commits] Changed error description when cell space exceed maximum to be more informative Michael Johnston
• [Adun-commits] Update to use MatrixColumnDiff.st to compare interaction matrices. [...] Michael Johnston
• [Adun-commits] Script for comparing matrices using column headers to identify equivalent columns [...] Michael Johnston
• [Adun-commits] typo nils
  • [Adun-commits] typo nils
• [Adun-commits] getting additional paths from IOManager nils
• [Adun-commits] Regression tests of system building for various force-fields [...] Michael Johnston
• [Adun-commits] Regression test files for Charmm27 builds Michael Johnston
• [Adun-commits] Update: test-script output no longer deleted automatically. Michael Johnston
• [Adun-commits] Updated to take account of ability to have multiple checks per test Michael Johnston
• [Adun-commits] Extend so multiple checks can be specified for a single test-script Michael Johnston
• [Adun-commits] Fix exit status [...] Michael Johnston
• [Adun-commits] Added updateDataSourceConfiguration before reloadData Cesar Avila
• [Adun-commits] Removed unnecesary log lines. Added [system reloadData] after coordinates update Cesar Avila
• [Adun-commits] CMAP data for AmberCG Cesar Avila
• [Adun-commits] Fix compile line Michael Johnston
• [Adun-commits] Update min SDK Michael Johnston
• [Adun-commits] Replace use of deprecated cString method Michael Johnston
• [Adun-commits] Use existing ivar ioManager to ULIOManager related calls. [...] Michael Johnston
• [Adun-commits] Moved registration of BuildOutput default to ULIOManager. [...] Michael Johnston
• [Adun-commits] Add prototype and docs for AdFirstValidFile. [...] Michael Johnston
• [Adun-commits] Bash scripting for testing if a file exists Michael Johnston
• [Adun-commits] Change scope of some new AdunKernel headers to public Michael Johnston
• [Adun-commits] Added new atom types CT2 and CTP for Gly and Pro C-alpha respectively as a way [...] Cesar Avila
• [Adun-commits] Change logs to debug logs Michael Johnston
• [Adun-commits] Do not checkpoint topology after exchange Michael Johnston
• [Adun-commits] Update with some information on installing xcode docs on lion Michael Johnston
• [Adun-commits] Alternative Replica Exchange Molecular Dynamics plugin Cesar Avila
• [Adun-commits] CMAP data for Charmm27 forcefield Cesar Avila
• [Adun-commits] Included CMAP as a compilation target Cesar Avila
• [Adun-commits] Hopefully, CMAP implementation is fully debugged. Cesar Avila
• [Adun-commits] Modified ULAmberCGInformation correcting the order of the parameters for bond, angles and torsions. [...] Cesar Avila
• [Adun-commits] Advances on debugging CMAP term for Charm27 and AmberCG ff Cesar Avila
• [Adun-commits] Minor fix to makefile when compiling in parallel. [...] Michael Johnston
• [Adun-commits] Fix typo Michael Johnston
  • [Adun-commits] Fix typo Michael Johnston
• [Adun-commits] Switch to NSLog for the moment Michael Johnston
• [Adun-commits] Rename sort functions to avoid conflict with those in AdParameterDictionary Michael Johnston
• [Adun-commits] Fix: init method should return object Michael Johnston
• [Adun-commits] Fix some memory problems. [...] Michael Johnston
• [Adun-commits] _buildMainChainTorsionsForAtoms is now debugged and working. Cesar Avila
• [Adun-commits] Implemented new method for generating main chain torsion interactions. Cesar Avila
• [Adun-commits] Hopefully, the full code. Needs debugging though. Cesar Avila
• [Adun-commits] removed interpolation functions from here Cesar Avila
• [Adun-commits] Added interpolation functions for use in CMAP Cesar Avila
• [Adun-commits] Added forces. Debugging still needed. Cesar Avila
• [Adun-commits] Missing forces Cesar Avila
• [Adun-commits] Still missing methods to load CMAP table Cesar Avila
• [Adun-commits] Added Energy term - Still missing forces Cesar Avila
• [Adun-commits] Updated makefile Michael Johnston
• [Adun-commits] Add method for searching all interactions of a certain type Michael Johnston
• [Adun-commits] Added methods to query and search the collection Michael Johnston
• [Adun-commits] Another attempt to fix path problem Michael Johnston
• [Adun-commits] Update to ensure paths are absolute before creating file URLS [...] Michael Johnston
• [Adun-commits] Add missing method (dictionaryOfParameters) Michael Johnston
• [Adun-commits] Added dictionaryOfParameters method. [...] Michael Johnston
• [Adun-commits] Some extra docs Michael Johnston
• [Adun-commits] Move AdParameterDictionary to FFML framework (renamed to FFParameterDictionary) [...] Michael Johnston
• [Adun-commits] Added methods for extracting new types of interaction information from ffml parameter files. [...] Michael Johnston
• [Adun-commits] Add methods for retrieving element property information from FFML file. [...] Michael Johnston
• [Adun-commits] Corrected some typos. Cesar Avila
• [Adun-commits] Corrected some typos. It is able to compile now. Cesar Avila
• [Adun-commits] added missing headers for ambercg nils
• [Adun-commits] build output file is now controlled by IOManager nils
• [Adun-commits] Minor updates Michael Johnston
  • [Adun-commits] Minor updates Michael Johnston
• [Adun-commits] Added some extra info on parallel compilation Michael Johnston
• [Adun-commits] Add information on building without gui Michael Johnston
• [Adun-commits] A couple of scripts for extracting information for ffml files. [...] Michael Johnston
• [Adun-commits] Remove unused vars and add parentheses Michael Johnston
• [Adun-commits] Updates due to linked list API change [...] Michael Johnston
• [Adun-commits] Updates due to linked list API change Michael Johnston
• [Adun-commits] API Change: Remove unused index parameter for linked list add functions [...] Michael Johnston
• [Adun-commits] Fix: decodeBoolForKey: doesn't work correctly in gs-base 1.22 if the key doesn't exist. Michael Johnston
• [Adun-commits] Class implamentation for CMAP. Version 0.000001 Cesar Avila
• [Adun-commits] Add information on libreadline Michael Johnston
• [Adun-commits] r19 - in /website: _adun_harmonic_constraint_term_8h_source.html class_ad_harmonic_constraint_term-members.html class_ad_harmonic_constraint_term.html Michael Johnston
• [Adun-commits] r18 - /website/ Michael Johnston
• [Adun-commits] r16 - /website/ Michael Johnston
• [Adun-commits] GUI script for outputting the information in a system as a set of csv files Michael Johnston
• [Adun-commits] GUI script for calculating the energy of a system Michael Johnston
• [Adun-commits] Print a dividing line between the output of different scripts Michael Johnston
• [Adun-commits] Add logDivider method Michael Johnston
• [Adun-commits] More detailed description line Michael Johnston
• [Adun-commits] r15 - /website/index.html Michael Johnston
• [Adun-commits] r14 - /website/index.html Michael Johnston
• [Adun-commits] Add link to home page in docs Michael Johnston
• [Adun-commits] BugFix: Not providing correct filename for in-memory downloads Michael Johnston
• [Adun-commits] solvation molecules Nils Drechsel
• [Adun-commits] Update some comments Michael Johnston
• [Adun-commits] missing file Nils Drechsel
• [Adun-commits] recommitting... Nils Drechsel
• [Adun-commits] another missing file Nils Drechsel
• [Adun-commits] was apparently missing.. Nils Drechsel
• [Adun-commits] changing a line and testing the commit (after some months) Jordi Villà-Freixa
• [Adun-commits] Projects updates Michael Johnston
• [Adun-commits] r13 - /website/index.html Michael Johnston
• [Adun-commits] r12 - /website/index.html Michael Johnston
• [Adun-commits] Update documentation Michael Johnston
• [Adun-commits] r11 - /website/svn-commit.tmp Michael Johnston
• [Adun-commits] r10 - /website/com.cbbl.Adun.docset/ Michael Johnston
• [Adun-commits] r8 - /website/docs/ Michael Johnston
• [Adun-commits] r7 - /website/index.html Michael Johnston
• [Adun-commits] r6 - /website/docs/index.html Michael Johnston
• [Adun-commits] r5 - /website/docs/ Michael Johnston
• [Adun-commits] Update to enable snapshot and release packages Michael Johnston
• [Adun-commits] Add release_prefix macro Michael Johnston
• [Adun-commits] Add method for computing hat matrix for fit data Michael Johnston
• [Adun-commits] Extra log info Michael Johnston
• [Adun-commits] Add missing method call Michael Johnston
• [Adun-commits] Implement multithread initialisation optimisation for other standard nonbonded term classes Michael Johnston
• [Adun-commits] Clean up divide pairs code Michael Johnston
• [Adun-commits] Optimisation which radically decreases the time required to initialise a multi-threaded nonbonded term. [...] Michael Johnston
• [Adun-commits] Decrease cutoff to 20. [...] Michael Johnston
• [Adun-commits] Small convenience script for creating Adun source-rpms [...] Michael Johnston
• [Adun-commits] Working spec file for building RPMS for Suse and Fedora Michael Johnston
• [Adun-commits] Remove include of non-existent AdMutableIndexSet.h Michael Johnston
• [Adun-commits] Add extra debug info Michael Johnston
• [Adun-commits] changes to output format Nils Drechsel
• [Adun-commits] chaning back AdMutableIndexSet to NSMutableIndexSet Nils Drechsel
• [Adun-commits] changing AdMutableIndexSet back to NSMutableIndexSet Nils Drechsel
• [Adun-commits] bugfixing of the bugfix Nils Drechsel
• [Adun-commits] Documentation Michael Johnston
• [Adun-commits] can now be executed in any directory Nils Drechsel
• [Adun-commits] added the AdunMutableIndexSet Nils Drechsel
• [Adun-commits] infinite performance boost + implicit water Nils Drechsel
• [Adun-commits] unfinished implementation of an index set which is based on c++ maps to accelerate the LIE. It's implementation is somewhat cryptic, so that the c++ includes do not mess with any other classes that include adunkernel.h Nils Drechsel
• [Adun-commits] taking back changes for the LIE, they're not needed anymore Nils Drechsel
• [Adun-commits] Fix for gnustep-base 1.16 Michael Johnston
• [Adun-commits] Fix for compiling with gnustep-base 1.16 Michael Johnston
• [Adun-commits] Not using AdunServerPath default under GNUstep Michael Johnston
• [Adun-commits] Linking fixes Michael Johnston
• [Adun-commits] function for the LIE Nils Drechsel
• [Adun-commits] refactoring so that LIE plugin runs faster Nils Drechsel
• [Adun-commits] bugfixing Nils Drechsel
• [Adun-commits] added function to ensure compatibility with LIE / trajectoryAnalysis plugins Nils Drechsel
• [Adun-commits] Add common warning flags used in suse build service (as part of -Wall) to debug configurations of all targets [...] Michael Johnston
• [Adun-commits] Fix causes of some remaining warnings. Michael Johnston
• [Adun-commits] Remove a lot of unused vars Michael Johnston
• [Adun-commits] Add many suggested parentheses' Michael Johnston
• [Adun-commits] More compiler warning related changes Michael Johnston
• [Adun-commits] Fix assignment Michael Johnston
• [Adun-commits] Fixes for various plugin compiler warnings Michael Johnston
• [Adun-commits] Integer sign fix Michael Johnston
• [Adun-commits] Remove cause of compiler warning (modeForSchema:) Michael Johnston
• [Adun-commits] Fix: Not releasing autorelease pool Michael Johnston
• [Adun-commits] Remove unused vars Michael Johnston
• [Adun-commits] Fix integer types Michael Johnston
• [Adun-commits] Remove unused var Michael Johnston
• [Adun-commits] Use newer gnustep make variables for installation Michael Johnston
• [Adun-commits] NSHostByteOrder() returns int not unsigned Michael Johnston

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