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# Version Stack: newest version on top!
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---- Version 2.2.0 -------------------------------------------------------------
Improvements:
- Aromaticity detection: Fixed various problems in the aromaticity
detection of ring systems. Modified valence states in chempar.dat.
- SMILES notation:
Now, using the localized (Kekule) smiles notation.
Only if the input molecule already contains aromatic bonds,
the delocalized smiles notation is used.
- If fragment labels are given for a fragment space, the reaction/library
label is printed to the first column instead of the last column. The
command 2MOLS resolves unique hash key names in order to retrieve the
original fragment names for each hit, too.
Please note, that this feature is only available, if the fragment
space is also generated with this new version.
Bug fixes:
The SDF file writer produced invalid files under certain
circumstances conjunction with charges [5301].
---- Version 2.1.3 -------------------------------------------------------------
Bug fixes:
- Fixed small issue with fragment labels
- The charge of single atoms and sulfur are not longer neutralized
by applying the transformation rules in transform.dat
---- Version 2.1.2 -------------------------------------------------------------
Bug fixes:
- Fixed a problem in MCREATE that occurred if link types
are defined in the fragment space which are actually not
used by any fragment
- Fixed a segmentation fault in FTreesFS when the reading
of feature trees failed [4858].
New feature:
- Reading of a fragment label file when loading a fragment
space in order to resolving unique hash key names and
retrieve the original fragment names for each hit.
---- Version 2.1.1 -------------------------------------------------------------
Bug fixes:
- Problems parsing SD files with missing columns (commonly generated
by Pipeline Pilot) fixed
---- Version 2.1.0 -------------------------------------------------------------
Improvements:
- Input for Fragment Spaces now also in SMILES and SDF format
- New format of the fragment space file (fsf) (see the user guide
for more detail)
- Merged the link description file (ldf) to the feature tree
description file (fdf): fragment spaces with ldf and (old) fdf are
still readable.
Bug fixes:
- Problems parsing SD files with missing columns (commonly generated
by Scitegic tools) fixed
- Seg fault when applying the SELOUTP command to the GENERATE command
is fixed
- Fixes for Fragment Spaces (FTrees-FS):
- added the "#end_of_file" to fdf files in order to recognize
incomplete fragment space input files
- fixed some bugs in reading fdf files
- if reading of fdf failed, then the fragment space load is aborted
- during recreation of fdf files sometimes the files were not
recreated in full, this is now fixed
- problems recognizing fragments with only one terminal single
non-hydrogen atom are fixed
---- Version 2.0.2 (bug fix patch) ---------------------------------------------
Bug fixes:
- Missing license status information -- especially when the license could not
be found -- has been restored
- Seg fault when using the DATABASE> DECRYPT command is fixed on Windows
- MOL> COMPMOLS command had difficulty with 0D/2D molecules if these needed
protonating, this has been fixed
---- Version 2.0.1 (bug fix patch) ---------------------------------------------
Improvements:
- Large file (>2GB) support now also for Windows platforms
Bug fixes:
- Correct printing of explicit H's for aromatic N in SMILES output
- On Windows platforms, files with paths beginning '\\' can now be read
- defaults offered for FFSEARCH menu (FS module) commands: MDRAW, 2FTREES,
2MOLS and 2SMILES
- default value for MOL menu READ command parameter (file index) now only
increments after serial reads from the *same* mol file
+++++++++++++++
---- + Version 2.0 + -----------------------------------------------------------
+++++++++++++++
Main features:
- Wizards to guide users through the most crucial steps of molecule
conversion, comparison and clustering
- New comparison algorithm Dynamic Matchsearch including subgraph matching
feature
- Conformation independent molecule handling giving full SMILES and SD format
support
- User accessible molecule preparation tools managed via SMARTS
- Stablized windows version plus an installer script
- Output of molecule-based alignment information
- Similarity threshold filtering of results
- Hierarchical clustering module
- Increased in-memory feature tree capacity and large file support
For details of changes and features for Release 2.0 please refer to the
User Guide.
---- Version 1.5.5 (bug fix patch) ---------------------------------------------
Bug fixes:
- Changing the parameter FFS_TOTAL_DIVERSITY now has an effect on the
results of the fragment space search for FTrees-FS
---- Version 1.5.4 (bug fix patch) ---------------------------------------------
Improvements:
- FTrees-FS works now with up to 10 000 linkers
Bug fixes:
- mol2 file reading: associating substructure data to the atoms fixed
---- Version 1.5.3 -------------------------------------------------------------
Improvements:
- Fragment space searching (FTrees-FS): Disallow termination of certain links
by using the new keyword "None" for the terminal atom type
Details:
It is now possible to enter the keyword "None" instead of an atom type in
the second column of the @link_terminals section of an fsf file (the
following columns are then skipped). If you use the keyword "None", FTrees
is not allowed terminate at this linker but must add another fragment
instead.
This is specially relevant when the fragment space is created from a
COMBINATORIAL LIBRARY. In these spaces the termination of molecules is
already ensured by the library's linkage rules and it is undesirable to
have FTrees terminate these links with other terminal groups. The new
functionality can now be used to force FTrees to build up molecules
that come from these libraries completely.
It follows therefore that this new keyword should only be applied carefully
for fragment spaces that are generated by shredding compound libraries.
Using "None" in this case may cause FTrees to build up huge
molecules because the only termination criterion will be the maximum
number of allowed fragments!!
---- Version 1.5.2 (bug fix patch) ---------------------------------------------
Improvements:
- extended the output formats of the 2SMILES command:
- table format : previous format (default)
- csv file format : csv format
- smiles file format : smiles format
Bug fixes:
- Fixed the output of smiles linker components (in the style 7*) from
the 2SMILES output in the FFSEARCH command
- Feature Trees file (fdf) was always overwritten by the MOL> CONVERT
command even if the user requested 'append' to file - this is now
fixed.
- The MOL> CONVERT command continued asking for further command options
even though it reported that it could not find the molecule file - fixed.
---- Version 1.5.1 (bug fix patch, removal of obsolete MTREES menu) ------------
Improvements:
- Removal of obsolete MTrees functionality to avoid confusion with new,
not yet available functionality, as seen in recently published papers.
See also: http://www.biosolveit.loc/news/mtrees_clarf.html
- New batch script variable $(LAST_SLOT) returns last *filled* FTree slot
Bug fixes:
- read of molecules with command MOL> READ despite invalid parameter input
for molecule number -> fixed
- assignment of vdw radii to molecules from sdf file was not complete
- nodes with infinite volume were calculated for molecules with 0.0 coords
- if an error occurred reading the desired FTree from file, the next was
simply loaded instead - fixed: if an error occurs for the wanted FTree
then no FTree is loaded
- ranking for enrich command did not show true ranks of positives: fixed
---- Version 1.5 ---------------------------------------------------------------
new licensing scheme, low level new functionality and bug fix release
Improvements
- new FlexLM licensing scheme for Linux version: floating licenses handled
by license server now possible
- new menu: DATABASE
This menu contains commands for e.g. editing the static data files
- improved error logs for failed FTree conversion (CONVERT command)
- fix for long comparisons using MATCHSEARCH 1 (match search algorithm)
new changes show amazing speed up: comparisons that ran over hours
now all run in a matter of seconds
- improved error logging during molecule/FTree conversion (see CONVERT
command)
- new control flags for filtering unwanted molecules from the conversion
- debug logging: all FTrees sessions create a debug log in /tmp. This
log records all current settings and static data along with the command
log to make it easier for BioSolveIT support to track your problem
Bug fixes
- Stablize FFSEARCH/MREAD and MWRITE commands (various crashes
have been fixed [1741,1742,1749]
- bug fix for continuing crash with FFSEARCH/2MOLS command [1469,1747,1748]
- bug fix: FTrees (rarely) used the wrong FTree for comparisons etc. [1758]
this was particularly a problem for FTrees generated from the
results of a fragment space search and other FTrees with very
long names (eg. when the file path is included in the name)
---- Version 1.4.4(bugfix release version) -------------------------------------
PATCH:
- ftrees-pvm recognises the enviroment variables PVM_TMP resp. PVM_VMID now
and if PVM_TMP and/or PVM_VMID are used, ftrees-pvm uses these enviroment
variables, too. [730/734]
- bug fixes around the FFS module 2FTREES command. The generated FTrees
contained spurious nodes that led to:
- differences in similarity between a 2FTREE FTree and the same FTree
created via 2MOLS and CONVERT in the MOL menu.
- segmentation fault when quitting FTrees
- segmentation fault when working with the MPL descriptor together with
2FTREES generated FTrees
- bug fix for segmentation fault on double load of a Fragment Space (FFS)
- some improvements in the SD file reader
- some improvements in avoiding FATAL_ERROR complete stop of the FTrees
program
- fix for the ranking of results with the ENRICH command if active and
inactive FTrees have exactly the same sim value
---- Version 1.4.3(bugfix release version) -------------------------------------
PATCH:
- could only read in 499,999 FTrees instead of 500,000 BUG432 - fixed
- the help given when starting FTrees with the -h option was incomplete,
fixed
- small fixes in program output: eg. list all command showed also exes.
- The number of pvm slave processes is now limited to 8192 [492].
---- Version 1.4.2 -------------------------------------------------------------
Improvements/fixes for standalone FTrees:
- Activate ADD_HYDROGENS flag [352]
- error log is now generated at each CONVERT command to record
mols names of failed conversions and reason
Bug fix
- Do not allow use of index files for SD mols
- Temp fix for BUG322 - do not allow use of index files for PVM slaves
---- Version 1.4.1 10.11.2003 SH -----------------------------------------------
PATCH: sdf with index files -> core dump, idx files are now never used for sdf
parsing
---- Version 1.4 17.10.2003 SH -------------------------------------------------
NEW RELEASE: FTrees includes full functionality for running in background of
HTSview. (Functionality at the moment is only available to
HTSview users) This release corresponds to the first HTSview (1.0)
release
Improvements/fixes for standalone FTrees:
- Bug fix in FTREES ENRICH command (correct rank numbers)
- Bug fixes and general improvements for sdf parsing
- New method for calculating node centers that should remove the FATAL_ERRORS
users see specially when working with sdf input
PLEASE NOTE: if FTREES are recalculated with the new version, the .fdf file
entries will now have changed. HOWEVER, if you compare the new FTREE to the
old, the similarity will remain 1.0 (coordinates given to the centers of the
nodes are not used in similarity calculations but only for drawing, superimposing
and for joining fragments in the FFS module).
- New command in MTREES to save the working model in slot 0 to another slot
- Change of command name in MTREES: COMPARE -> COMP2MUL to avoid confusion
with FTREES COMPARE command (MTREES ENRICH = FTREES ENRICH but MTREES COMPARE !=
MTREES COMPARE)
- Bug fixes and small improvements in FFS (fragments spaces module)
- Improved index file facility: ALLOW_IDX_FILES flag in config.dat) allows the user to decide
whether to use indexing. Index files now contain a checksum number to check
whether the index is uptodate with the .fdf file and hence whether it needs
updating itself or can be used directly. Index files now also work with molecule
input files
- Updated and extended docu for the MTREES menu
---- Version 1.3.x ------------------------------------------------------------
1. Bug fixes
2. Computing
3. Menus and user interface
New keyword in config_ft.dat: @license_files
@license_files
/home/license/ftrees/lic1.dat
/home/license/ftrees/lic2.dat
The files lic1.dat and lic2.dat contain the license keys for ftrees.
New program flag in config_ft.dat:
PDF_VIEWER
# PDF_VIEWER : must be defined if you want to use the manual online
New command:
Gobal/MANUAL
view User Guide with your local PDF viewer
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.2.1 22.10.2002 SH ----------------------------------------------
- Bug fixes in ENRICH commands.
- Modules MTREE and HTS separated.
- Name inconsistencies removed: "FTrees" (FTREES,ftrees) replaces
occurences of FTree. FTREE is now only used for the Tool selection
in the makefile (and hence the #ifdef commands)
NB. make ftrees ftrees.dbg !
- User Guides updated.
- Bug fix in FTrees License stuff
- (flexi in download packet for FTrees updated.)
---- Version 1.0 --------------------------------------------------------------
1. Bug fixes
- bug in enclosing sphere algorithm fixed
2. Computing
- new size scaling for the matches included (downscaling of large matches)
- enrichment calculation and sorting by similarity completely redesigned.
The command (ENRICH) works incrementally now and handles much larger data
sets. Also, lists of specified length of most similar molecules (to a
given query) can now be printed
3. Menus and user interface
- ftree array expanded to 250000 molecules
- batchprog variables can be strings now
- predefined batchprog variables
- SCRIPT command has additional argument and keep_batchvar parameter
- if/else/endif and break/continue in script language
- last command status as an internal batch variable (tripos-990503)
4. File formats
5. Graphics
- flexv upgraded to version 1.4.0
- 16 graphic objects -- all with an instance slider -- are now available
in FlexV and can be individually copied
- flexv has a selection browser for imported multi-mol2 files
- flexv takes several (up to 10) gdf and mol2 files in the command line
6. Misc.
7. Documentation
---- Version 1.x.x ------------------------------------------------------------
1. Bug fixes
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
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