adun-commits  

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• [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
• [Adun-commits] Fix signed/unsigned comparisons Michael Johnston
  • [Adun-commits] Fix signed/unsigned comparisons Michael Johnston
• [Adun-commits] Relying preprocessor macro not defined under gnustep Michael Johnston
• [Adun-commits] Fix: Missing explicit return value in two methods [...] Michael Johnston
• [Adun-commits] Move parallel variables inside ifdef Michael Johnston
• [Adun-commits] Fix Signed/unsigned Michael Johnston
• [Adun-commits] Remove unused variables Michael Johnston
  • [Adun-commits] Remove unused variables Michael Johnston
  • [Adun-commits] Remove unused variables Michael Johnston
  • [Adun-commits] Remove unused variables Michael Johnston
• [Adun-commits] Brackets Michael Johnston
  • [Adun-commits] Brackets Michael Johnston
• [Adun-commits] Add init brackets, remove unused vars Michael Johnston
• [Adun-commits] Use ProgramDirectoryLocation default to find where the adun dir is Michael Johnston
• [Adun-commits] there was a semicolon missing Nils Drechsel
• [Adun-commits] debugged, but untested Nils Drechsel
• [Adun-commits] completed LIE implementation; un-debugged, nonfunctional for sure Nils Drechsel
• [Adun-commits] fixed an issue with selectionstrings Nils Drechsel
• [Adun-commits] Make function var unsigned Michael Johnston
• [Adun-commits] Fix formatting in error string Michael Johnston
• [Adun-commits] Use absolute paths in reindexAll Michael Johnston
• [Adun-commits] Internal Update: add _checkClass method. [...] Michael Johnston
• [Adun-commits] BugFix: Sending message to array instead of object in array. Michael Johnston
• [Adun-commits] Grammar Michael Johnston
• [Adun-commits] Tighten reporting of errors when accessing a remote store Michael Johnston
• [Adun-commits] Add error code related to simulation storages Michael Johnston
• [Adun-commits] More coding updates Michael Johnston
• [Adun-commits] Store URL as string rather than NSURL object. [...] Michael Johnston
• [Adun-commits] Script for adding objects to a database from the CL Michael Johnston
• [Adun-commits] Another update to URLByAppendingPathComponent: Michael Johnston
• [Adun-commits] Missing retain Michael Johnston
• [Adun-commits] Fix for NSDate encoding problem Michael Johnston
• [Adun-commits] Remove index lock/unlock when updating the index. [...] Michael Johnston
• [Adun-commits] Add remote sim storage Michael Johnston
• [Adun-commits] Logs of remote simulations can now be displayed. Michael Johnston
• [Adun-commits] Update to handle when user tries to export a remote simulation. Michael Johnston
• [Adun-commits] Update to use URLByAppendingPathComponent. Michael Johnston
• [Adun-commits] Update to use URLByAppendingPathComponent. [...] Michael Johnston
• [Adun-commits] Fix misformatted log Michael Johnston
• [Adun-commits] Minor update. Michael Johnston
• [Adun-commits] API Change: location method returns location as URL instead of string. Michael Johnston
• [Adun-commits] Fix: Instances not being dealloced due to the way the request processing thread was started/stopped. [...] Michael Johnston
• [Adun-commits] Allow max size of each http request to be customised via defaults. Michael Johnston
• [Adun-commits] Update to use \"prepareForCheckpointRequests\" method. [...] Michael Johnston
• [Adun-commits] Fixes: Wasn't handling multipart headers in multiframe requests. [...] Michael Johnston
• [Adun-commits] http/ftp updates Michael Johnston
• [Adun-commits] Fix: Retaining storage twice in both AdTrajectory and AdMutableTrajectory Michael Johnston
• [Adun-commits] Convert some logs to debug logs, remove others Michael Johnston
• [Adun-commits] Add AdRemoteSimulationStorage Michael Johnston
• [Adun-commits] Fix number in macro: has to be octal Michael Johnston
• [Adun-commits] Temporary change to handle differences in API between GS pre 1.18, OSX 10.4 and everything else. [...] Michael Johnston
• [Adun-commits] Updates to allow accessing simulations stored on remote servers. [...] Michael Johnston
• [Adun-commits] API Extension: Add dataURL and unarchiveFromLocation: methods. [...] Michael Johnston
• [Adun-commits] Removed cause of \"did you send finishEncoding:\" warning. Michael Johnston
• [Adun-commits] Add convenience method URLByAppendingPathComponent: to NSURL for non 10.6 API versions. [...] Michael Johnston
• [Adun-commits] Removed implementation of methods now in AdSimulationStorageWriting protocol. [...] Michael Johnston
• [Adun-commits] Conforms to AdSimulationStorageReading protocol Michael Johnston
• [Adun-commits] Added two protocols defining methods for reading/writing stored trajectory data. [...] Michael Johnston
• [Adun-commits] Moved storage reading/writing methods to new protocols. [...] Michael Johnston
• [Adun-commits] Update to use AdTrajectory::location() instead of deprecated dataPath method. Michael Johnston
• [Adun-commits] Add advanced frame caching mechanism Michael Johnston
• [Adun-commits] New class for accessing trajectory data over http. [...] Michael Johnston
• [Adun-commits] Add URLRequest method Michael Johnston
• [Adun-commits] Regroup methods for clarity. Michael Johnston
• [Adun-commits] Correct some spelling Michael Johnston
• [Adun-commits] Raul's latest changes Nils Drechsel
• [Adun-commits] Add Size metadata key when object is archived. Michael Johnston
• [Adun-commits] BugFix: In last commit - not retaining model-object if supplied. [...] Michael Johnston
• [Adun-commits] Update domain mapping function to map Annotations to user domain. Michael Johnston
• [Adun-commits] Update warn log Michael Johnston
• [Adun-commits] Changed ivar to be instance of NSDate. Michael Johnston
• [Adun-commits] BugFix: Using unintialised variable in warn log Michael Johnston
• [Adun-commits] BugFix: Was re-adding existing script menu items on each update. Michael Johnston
• [Adun-commits] Add metadataForSelectedObject: - convenience method for scripts interacting with current selection. Michael Johnston
• [Adun-commits] Using incorrect key-path to get source pdb name Michael Johnston
• [Adun-commits] Update to use objectMetadataForType: where possible [...] Michael Johnston
• [Adun-commits] Add temporary function for dividing the keys in a combined metadata dictionary into domains. [...] Michael Johnston
• [Adun-commits] Implement objectMetadataForType: Michael Johnston
  • [Adun-commits] Implement objectMetadataForType: Michael Johnston
• [Adun-commits] Add objectMetadataForType: method to ULPasteboardDataSource protocol. [...] Michael Johnston
• [Adun-commits] Update metadata method so the returned dictionary includes volatile metadata Michael Johnston
• [Adun-commits] Add declaration of new method to category interface Michael Johnston
• [Adun-commits] Fix variable type Michael Johnston
• [Adun-commits] Add metadata and combinedMetadata methods [...] Michael Johnston
• [Adun-commits] Regroup methods Michael Johnston
• [Adun-commits] Remove deprecated method Michael Johnston
• [Adun-commits] Update to handle http and ftp URLs. Michael Johnston
• [Adun-commits] Upgrade stored client configurations. [...] Michael Johnston
• [Adun-commits] Remove stray object creation Michael Johnston
• [Adun-commits] BugFix: Not retaining ivar on initialisation Michael Johnston
• [Adun-commits] Define some more constants for use with the databases property dictionary. Michael Johnston
  • [Adun-commits] Define some more constants for use with the databases property dictionary. Michael Johnston
• [Adun-commits] Update old client configurations to use ULDatabaseIdentifier. [...] Michael Johnston
• [Adun-commits] Update due to change in names of methods for creating AdunServer URLs Michael Johnston
• [Adun-commits] Set name of databases accessed via http/ftp to have a specific color in the browser Michael Johnston
• [Adun-commits] Internal update: conditionally update indexes where possible. [...] Michael Johnston
• [Adun-commits] Use new initialiser to create backends. Michael Johnston
• [Adun-commits] Added initialiser with same form as new ULFilesystemDatabaseBackend initialiser. [...] Michael Johnston
• [Adun-commits] Add new designated initialiser with scheme and port parameters [...] Michael Johnston
• [Adun-commits] Minor formatting Michael Johnston
• [Adun-commits] Update due to change in key in ULFilesystemDatabaseBackend properties dict. Michael Johnston
• [Adun-commits] ULFileSystemDatabaseBackend can now read data from URLs with different schemes (file://, http:// etc). [...] Michael Johnston
• [Adun-commits] Don't pass host parameter for default filesystem db. Michael Johnston
• [Adun-commits] Added URLResponse method - returns the NSURLResponse object corresponding to an URL request. [...] Michael Johnston

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