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Revision 477 - Directory Listing
Modified Wed Apr 23 10:06:55 2008 UTC (10 years, 5 months ago) by risbud
Added the following features:
1. Show Threshold Spheres
2. Show Neighbour Relationships within the first shell
3. Show second shell

New methods added, are:
1. IntPairSet getfirstShellNbrs(Model, int) (ContactMapPane.java)
2. IntPairSet getfirstShellNbrRels(Model, int) (ContactMapPane.java)
3. void getmousePos() (ContactMapPane.java)
4. void drawSpheres(Model, Model, String, Pair<Integer>) (PyMolAdaptor.java)
5. void drawSpheres(Model, Model, String, IntPairSet) (PyMolAdaptor.java)
6. void showSpheres(Model, Pair<Integer>) (PyMolAdaptor.java)
7. void showSpheres(Model, IntPairSet) (PyMolAdaptor.java)
8. void showSecShell(Model, IntPairSet) (PyMolAdaptor.java)
9. void showShellRels(Model, IntPairSet) (PyMolAdaptor.java)
10. void handleShowSpheres3D() (View.java)
11. void handleShowShellRels() (View.java)
12. void handleShowSecShell() (View.java)

Apart from the new methods, some new variables have been introduces in View.java, to create icons, etc. The names are self-explanatory to correlate them with the above changes.

New icon file is created (spheres.png) for "Show Threshold Spheres"

The backend Python script "cmview.py" has been edited to include method to draw sphere CGOs.
Revision 476 - Directory Listing
Modified Fri Apr 11 12:52:02 2008 UTC (10 years, 6 months ago) by duarte
New feature: now contacts are shown on the actual atoms corresponding to the given contact type instead of always on CAs.
Not fully tested.
Increased massively the time-out for PyMolAdaptor
Revision 475 - Directory Listing
Modified Thu Apr 10 08:15:09 2008 UTC (10 years, 6 months ago) by risbud
Creating dev branch for developing out of the 1.0 release (in trunk)
Revision 284 - Directory Listing
Modified Thu Dec 20 13:40:42 2007 UTC (10 years, 10 months ago) by lpetzo
... backslash at the end of the line doesn't work!
Revision 281 - Directory Listing
Modified Thu Dec 20 13:37:00 2007 UTC (10 years, 10 months ago) by lpetzo
... and also whitespace+backslash at the end of each line
Revision 278 - Directory Listing
Modified Thu Dec 20 13:28:18 2007 UTC (10 years, 10 months ago) by lpetzo
introducing line break in Class-path and putting a whitespace before each line helps to cope with long lines!
Revision 272 - Directory Listing
Modified Thu Dec 20 12:00:56 2007 UTC (10 years, 10 months ago) by lpetzo
getop lib was missing in the classpath
Revision 269 - Directory Listing
Modified Thu Dec 20 11:21:37 2007 UTC (10 years, 10 months ago) by lpetzo
adapted version information for version tag CMView-jung-0.1.2
Revision 267 - Directory Listing
Modified Wed Dec 19 16:36:41 2007 UTC (10 years, 10 months ago) by lpetzo
class Start:
minor change

class View:
- got rid of extra PyMol selection serial for nbh selections
- made pymolSelSerial static as it causes overwriting of previous selections when running more than one View instances
- adapted new naming convention for the nbh selection

class PyMolAdapter:
- implemented new function select(...) which takes the same list of arguments as the corresponding function in PyMol's python API
   -> replaces more or less function createSelectionObject(...) if used in combination with Interval.createSelectionString(TreeSet<Integer>)
   
file make-...:
added jung libraries to the classpath and the classpath as an argument to the javac command line
Revision 266 - Directory Listing
Modified Tue Dec 18 13:22:36 2007 UTC (10 years, 10 months ago) by duarte
Now disabling delete contacts in compare mode
Added getopt to class path in make script
Revision 265 - Directory Listing
Modified Tue Dec 18 11:21:00 2007 UTC (10 years, 10 months ago) by duarte
Fixed bug: CMview doesn't freeze anymore after a pymol connection is lost.
Fixed bug: loading structure into Pymol when pdb code was passed on command line wasn't working
Cleaned debugging output
Revision 264 - Directory Listing
Modified Mon Dec 17 17:33:49 2007 UTC (10 years, 10 months ago) by duarte
New feature: proper command line parameters
New feature: as many as 3 config files are now read from: system-wide file in current dir (as before), user dir and finally the one passed in command line
Now showing waiting cursors in Load dialogs (when clicking on get chains or get models or when clicking ok) and on Needleman-Wunsch sequence alignment
Revision 263 - Directory Listing
Modified Sat Dec 15 13:01:31 2007 UTC (10 years, 10 months ago) by lpetzo
added jung libraries to the class-path and the version to 0.1.1 according to the the CMView builds based on jung
Revision 261 - Directory Listing
Modified Fri Dec 14 16:38:59 2007 UTC (10 years, 10 months ago) by lpetzo
class View:
- even more changes due to the new naming convention for selections and groupings
- constructor increments a View instance counter, dispose() decrements it

class Start:
- instance counter for class View -> VIEW_INSTANCES
- only the real owner of the PyMol process is allowed to quit PyMol on exit if that is enabled
- resetting of the PyMol url in case the PyMol port differs from the default port

class PyMolAdaptor:
- added function setting the PyMol-server url
- added functionality to gather all commands in a command buffer and write them to a file at a certain time. PyMol load this file as logfile and executes the commands: flush() -> send commands to PyMol, PyMolAdapter(String,File) -> constructs adapter with url and dump-file
--> HOWEVER: this does not work! kept it for rather sentimental reason.
Revision 259 - Directory Listing
Modified Thu Dec 13 10:14:09 2007 UTC (10 years, 10 months ago) by lpetzo
changed handling of showing selected contacts in pymol. This includes:
- complete refactoring of function View.handleShowSelectedContact3D()
- new function in the PyMolAdapter to send distances, group selection and stuff
Revision 258 - Directory Listing
Modified Wed Dec 12 12:05:05 2007 UTC (10 years, 10 months ago) by stehr
adapted to changes in aglappe (Pdb objects now throwing only PdbLoadErrors instead of GetterErrors)
Revision 254 - Directory Listing
Modified Mon Dec 10 14:18:48 2007 UTC (10 years, 10 months ago) by lpetzo
comments
Revision 253 - Directory Listing
Modified Mon Dec 10 14:18:09 2007 UTC (10 years, 10 months ago) by lpetzo
class Start:
- method runPyMol(): determines port number after starting pymol in server mode. This is due to the fact that pymol tries different port numbers for running the server (starting with 9123 and so on ... )

class View:
- construction of SADPDialog without preferences and start button
Revision 252 - Directory Listing
Modified Fri Dec 7 12:07:40 2007 UTC (10 years, 10 months ago) by lpetzo
class PdbFtpModel:
- added getter function for the cif filename
- added constructor taking a File object pointing to a local copy of the mmCIF file previously loaded from ftp
- new field: cifFile

class View:
- loading from ftp makes use local caching of mmCIF files (refers to changes in doLoadFromFtp() and handleLoadFromFtp() something)

class Start:
- changed type of pdbCode2Filename form <String (-> pdbCode),String (-> filename)> to <String (-> pdbCode),File (->filename)>
Revision 251 - Directory Listing
Modified Wed Dec 5 16:53:46 2007 UTC (10 years, 10 months ago) by lpetzo
added superpositioning for each alignment routine after computing the alignment and constructing the aligned models. the superpositioning is based on the set of common contacts as defined by the alignment.
Revision 250 - Directory Listing
Modified Tue Dec 4 15:29:32 2007 UTC (10 years, 10 months ago) by lpetzo
this class is already needed in revision 248!!!
Revision 249 - Directory Listing
Modified Tue Dec 4 15:27:58 2007 UTC (10 years, 10 months ago) by lpetzo
class Start:
- some changes in function preloadModel(...) due to the new loading scheme for models
- changed default settings for the contact type and the contact distance according to Michael's suggestions

class View:
- adapted new loading scheme for the models
- implemented chain code and model serial Getters for the retrieval of all present chain codes and model serials in the source
Revision 248 - Directory Listing
Modified Tue Dec 4 15:26:06 2007 UTC (10 years, 10 months ago) by lpetzo
class LoadDialog:
- chain code and model serial is implemented as combo box

class *Model:
- separated constructing the objects and loading the structures from the sources
- getChains() and getModels() determine all present chain codes and model serials in the sources

class View:
- adapted new loading scheme for the models
- implemented chain code and model serial Getters for the retrieval of all present chain codes and model serials in the source

class SADPDialog:
- some changes in function main(...) due to the new loading scheme for models

class Start:
- some changes in function preloadModel(...) due to the new loading scheme for models
- changed default settings for the contact type and the contact distance according to Michael's suggestions
Revision 242 - Directory Listing
Modified Wed Nov 28 15:25:08 2007 UTC (10 years, 10 months ago) by lpetzo
added mapping from pdb code to the filename of the local copy of the file containing the structure
Revision 241 - Directory Listing
Modified Wed Nov 28 13:07:53 2007 UTC (10 years, 10 months ago) by duarte
Refactoring of getNbhood methods to match new names in aglappe-jung
Revision 240 - Directory Listing
Modified Wed Nov 28 09:39:52 2007 UTC (10 years, 10 months ago) by duarte
First working version of CMView using the new JUNG framework. Needs more testing. Known bug: showing contacts in 3D in compare mode not working properly.
Fixed 2 bugs/feature requests: computation of common neighborhood sizes now fast (thanks JUNG) and residue types are now shown even for unobserved residues (when sequence is known)
Revision 239 - Directory Listing
Modified Wed Nov 28 09:00:54 2007 UTC (10 years, 10 months ago) by duarte
Branching for development with new JUNG framework (in aglappe-jung branch)
Revision 1 - Directory Listing
Added Wed Mar 14 09:18:10 2007 UTC (11 years, 7 months ago) by dinse
Initial import of the CM2PyMol project