#
# Version Stack: Latest version is on top!
# ([numbers] are BioSolveIT internal reference numbers.)
#
---- Version 1.3.0 ----------------------------------------------------------
1. Bug fixes
- several small fixes that are not all listed in detail.
- The SDF file writer produced invalid files under certain
circumstances conjunction with charges [5301].
2. Computing
- Aromaticity detection:
Fixed various problems during the aromaticity detection of ring
systems. Modified the valence states in chempar.dat.
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
- SUBGRAPH-Matching:
[#0] is treated now as a general linker wild card
(before: is treated as [*])
- SMILES notation:
Now, using the localized (Kekule) smiles notation.
Only if the input molecule already contains aromatic bonds,
the delocalized smiles notation is used.
- Flag FAST_SMILES_EXPORT is removed. Thus, CoLibri uses now
the internal USMILES for exporting compounds to a SMILES file.
7. Documentation
---- Version 1.2.0 ----------------------------------------------------------
1. Bug fixes
- serveral small fixes that are not all listed in detail.
2. Computing
3. Menus and user interface
- New menu MLABES:
- defining multi file labels
- writing multi file labels as compound/fragment label to
fragment label files (flf)
- adding a fragment label file to a fragment space file
4. File formats
- New common format of the fragment space file (fsf) for FTrees-FS and
FlexNovo.
5. Graphics
6. Misc.
7. Documentation
---- Version 1.1.4 ----------------------------------------------------------
1. Bug fixes
- Fixed problems with reading and writing of smiles like
[1*H], [1*H1], [1*H2] or [1*H3]. These problems are fixed [4195].
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.1.3 ----------------------------------------------------------
1. Bug fixes
- Fixed a bug in the clipping algorithm. During various clippings
in series, where the source of the next clipping is the result of
the clipping before, multiple fragments vanished and other fragments
occur. This problem is fixed.
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.1.2 ----------------------------------------------------------
1. Bug fixes
- Importing fragments with various linkers, which are treated as
different elements, results in wrong hashkeys. This problem
is fixed [3816].
2. Computing
3. Menus and user interface
- Added a new parameter for the command LIBRARY/CLIP:
the parameter determines if the name of the clipped molecules
will stay unchange or will expand with counter: default: the
name will be expanded
4. File formats
5. Graphics
6. Misc.
7. Documentation
- The problem with missing page numbers is fixed [3720].
---- Version 1.1.1 ----------------------------------------------------------
1. Bug fixes
- FSF/READ: if the fsf file contained more as one line with link types,
the reading of the fsf file was skipped. This bug is now fixed.
- If an atom type of a linker atom or of an adjacent atom is unknown,
then the element type is used now instead of 'Du'.
- the commands EXPORT and UNIFY can have problems with multiple
MOLECULES path. These problems are fixed now [3394].
2. Computing
3. Menus and user interface
- new command LINKER/TYPESTATC implemented: the command generates
as the command TYPESTAT new link-types with an atom type statistic
about linker neighbours as, but uses a faster algorithm.
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.1.0 ----------------------------------------------------------
1. Bug fixes
- LIBRARY/TRANSFORM: the shredder mechanism did not use the last
transform class and their rules: e.g. 'demark1' and 'demark2'
in shred_recap.dat. Now this bug is fixed [3237].
- The rules 'demark1' and 'demark2' in shred_recap.dat modified [3235].
- LIBRATY/ENUM: various problems in the enumeration of molecules are
fixed. Now non terminal linkers will be resolved correctly [2981].
2. Computing
3. Menus and user interface
- new menu DATABASE with the command DECRYPT
the command DECRYPT decrypte the encrypted static data files
- new command EDIT/MERGE implemented: the command merge two
libraries [2361]
- new command LIBRARY/GENNAME implemented: the command generates and
set a new molecule name from name properties
- new command LINKER/TYPESTAT implemented: the command generates new
link-types with an atom type statistic about linker neighbours
- extended the command FSF/WRITE with an additional parameter:
"Add atom type of linker neighbour atom?" (Default: no)
4. File formats
- FlexNovo fsf file format:
- FSF/WRITE 1 writes the new FlexNovo fsf file format
- FSF/WRITE 2 writes the old FlexNovo fsf file format
- FSF/READ reads only the new FlexNovo and the FTrees-FS
fsf file format
- static data file colibri_settings.dat
new parameter in order to limit the number of fragments, which
are built up in enumerated molecules: MAX_NOF_FRAGS [3308]
# maximum numbers of fragments, which are built up in enumerated
# molecules; i.e. the enumerated molecule consists of maximal
# MAX_NOF_FRAGS+1 fragments; if 'MAX_NOF_FRAGS' is set to 0,
# then the upper limit is switch off
- It is now possible to define more than one pair of comptible
linker after a transform rule [3188]
- The file shred_recap.dat is moved to the directory 'static_data'
[3192].
- reading molfiles of MDL MOL format is available [2471]
5. Graphics
6. Misc.
7. Documentation
---- Version 1.0.0 ----------------------------------------------------------
1. Bug fixes
- Counting of output molfiles is inconsistent. This bug is now
fixed [2939].
- The reference molfile is forgotten, if LINKER/UNIFY is
called after LIBRARY/TRANSFORM resp. LIBRARY/CLIP. This bug is
now fixed [2936].
- The internal counter of output molfiles, which counts how
many molecules are written, is inconsistent. This bug is now
fixed [2936].
- Reading a library file without molfile data results in a
segmentation fault. This bug is now fixed [2935].
- colibri failed if it tried to resolve non terminal linkers
in enumerated molecuels. The result was arbitrarily. This bug
is no fixed: if colibri can not resolved non terminal linker(s)
in an enumerated molecule, the molecule is skipped with a
warning [2916]
- If the fragspace file is not exist, then calling FSF/READ resulted
in a segmentation fault. This bug is now fixed [2898].
- If no fragspace available, then calling the command FSF/DELETE
resulted in a segmentation fault. This bug is now fixed [2895].
- Command FSF/WRITE: The name of the fragspace file is always
extended with the suffix 'fsf', even if the filename contained
already the suffix. This bug is now fixed [2895].
- If no linker terminal are defined, then calling the command
FSF/INFO resulted in a segmentation fault. This bug is now
fixed [2893].
- Calling twice the command LINKER/UNIFY in series, resulted in a
segmentation fault. This bug is now fixed [2881].
- Removing linker compatibility from a library resulted in a
segmentation fault, if the command LINKER/CONNECT is called.
This bug is now fixed [2880].
- Calling the command LIBRARY/FILAB for a removed molecule file,
results in a segmentation fault. This bug is now fixed [2873].
2. Computing
3. Menus and user interface
- command LIBRARY/OUTFILE: get a new parameter
OUTFILE []
If the file \pa{outfile} already exists, set
to 'y' for overwriting the data, otherwise the command
is skipped. Default answer is 'no'. [2881]
- the command LINKER/UNIFY: get a new parameter
UNIFY []
If the file \pa{outfile} already exists, set
to 'y' for overwriting the data, otherwise the command
is skipped. Default answer is 'no'. [2881]
- the executable '3D_GENERATOR' in config_clb.dat resp. the executable
'GEN_3D' in colibri.py are renamed to 'GEN_3D_GENERATOR';
the flags '3D_GEN' resp. '3D_GEN_FORMAT' in config_clb.dat are renamed
to 'GEN_3D' resp. 'GEN_3D_FORMAT';
add the flags 'GEN_3D' resp. 'GEN_3D_FORMAT' to colibri.py [2737].
- the command LIBRARY/ENUM:
ENUM []
change the default answer for [] from
'no' to 'yes' [2614].
- flag 'GRAPHIC_MODE' is removed from config file
4. File formats
- Large file support enabled [735].
5. Graphics
6. Misc.
- check of consistence for molecule reference files [2706]
In order to check the consistence of molecule reference files, the md5sum
calculation will not be used anymore. Now the timestamp of the last
modification and the size in bytes are saved for each molecule reference
files. The timestamp and the size are written for each molfile to the
colibri library file. If the colibri library are written, then the internal
saved timestamps and sizes are compared with the current values. If the
colibri library are read from file, then the saved timestamps and sizes in
the library are compared with the current values.
Failed one of these checks for at least one molecule reference file, then
the library is inconsistent and the internal corresponding flag is set.
If a colibri library is inconsistent, then the following commands are
not available: CLIP, ENUM, EXPORT, TRANSFORM and UNIFY
And in pycolibri are the corresponding methods not available.
- logp value module integrated in colibri [2662]
- new programm parameter 'LOGP_CLASS' is added:
- LOGP_CLASS = 1 : Wildmann/Crippen descriptors
- LOGP_CLASS = 2 : Ghose/Crippen descriptors
- implemented short help mechanism for colibri [2617]
7. Documentation
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