#
# Version Stack: Latest version is on top!
# ([numbers] are BioSolveIT internal reference numbers.)
#
---- Version 3.1.4 ----------------------------------------------------------
1. Bug fixes
- After loading a project, FlexX did not notice changes in the first
step of the receptor wizard. This bug is fixed.
- In the graphical user interface, a ring conformation generator is only
used during the docking procedure and not while loading a library [4563].
- FlexX did not read the traditional flexx_settings.dat file even if it was
started with option '-c config.dat'. This bug is fixed.
- Pharmacophores with more than one spatial constraint were not loaded
correctly.
2. Computing
3. Menus and user interface
- New command: DOCKING/ANALYZE/MATCHING: Calculates and writes all
energy and matching scores of a ligand (be it read in previously, or
be it with reference coordinates) into a logfile.
5. Graphics
6. Misc.
7. Documentation
---- Version 3.1.3 ----------------------------------------------------------
1. Bug fixes
- FlexX was not able to read SDF files without stereo info
columns. This bug is fixed now [2710].
- Changing the metal coordination after a docking led to a
segmentation fault. This is fixed now [4543].
- Fixed problem with pdb written by FlexX, which contains
water from hetero group file [4544].
- The 'READPDB' command in menu 'ENSEMBLE/GENRDF' searched
for an external 'generic.edf' file. Now, it uses the
internal file.
- serveral small fixes that are not all listed in detail.
2. Computing
3. Menus and user interface
5. Graphics
6. Misc.
7. Documentation
---- Version 3.1.2 ----------------------------------------------------------
1. Bug fixes
- Fixed problems when using the PPI-scoring. [4450]
- FlexX saves the current tree view settings for 'Library'
and 'Binding Site Surface' in your user settings file
and uses these settings as defaults for the next session [4471]
- Canceling the receptor wizard does not lead to an unnecessary
reload of the entire current project any longer. [4354]
- In the docking definition dialog you can now restore
default settings for the docking [4436]
- It is now possible to remove solutions from projects [4393]
- Reading corrupt pdb files possibly resulted in a segmentation
fault (e.g., if waters were named 'WAT' and not 'HOH')
Now this bug is fixed [4451].
- Reading corrupt pdb files possibly resulted in faulty project files
(e.g., if there were chains or waters with same names)
Now this bug is fixed [4467].
- Starting FlexX under Windows 2000 led to a segmentation
fault. This is fixed now. [4485]
- The pdb download dialog now allows variants of proxy server
names (e.g., with and without 'http://') [4486]
- It is now no longer necessary to start FlexX under MS Vista
in XP SP2 compatibility mode. [4487]
- GUI solutions were exported without formal charges.
This bug is fixed [4504]
- FlexX showed no message when projects were not saved following
missing write permissions. This bug is fixed. [4510]
- The GUI could not display interactions with an energy less than
-8.3. This bug is fixed. [4513]
- Reading a lot of projects in one session possibly resulted in a
segmentation fault. Now, this bug is fixed. [4507/4508]
- serveral small fixes that are not all listed in detail.
2. Computing
3. Menus and user interface
- Now, it is possible to define a spatial pharmacophore constraint
by selecting multiple atoms. The position of the spatial constraint
is the centroid of these atoms. Thus, it is much easier to set a
constraint, e.g, to the center of a ring.
5. Graphics
6. Misc.
7. Documentation
---- Version 3.1.1 ----------------------------------------------------------
1. Bug fixes
- Fixed problems starting FlexX under Fedora.
2. Computing
3. Menus and user interface
5. Graphics
6. Misc.
7. Documentation
---- Version 3.1.0 ----------------------------------------------------------
1. Bug fixes
- a multitude of smaller fixes
2. Computing
2.1 The treatment of water
2.1.1 Place a freely rotatable and displaceable water at
crystallographic O positions
2.1.1 A wizard step to create a fully defined H2O molecule incl.
graphical aids for its orientation
2.2 Metal coordination treatment
Metals are now checked for their environment in a GUI receptor prep.
step; an automated coord. geometry calculation is followed by
automated pharmacophore assignment if applicable (i.e., if
interactions to the metal can be formed).
2.3 Ring conformation generation
2.3.1 Internal Corina: An special version of corina (www.mol-net.com)
has been compiled into this FlexX executable so that a
monolithic architecture is achieved.
2.3.2 MOE as a ring conformer generator: MOE (www.chemcomp.com) can
now be used to perform the ring conformer computation. This
needs an SVL script which is part of the
4. File formats
5. Graphics
6. Misc.
- Sulfur, if deprotonated, has now been added per default to coordinate
to metals
7. Documentation
---- Version 3.0.0 ------------------------------------------------------------
1. Bug fixes
- If a pharmacophore contains a very large amount of constraints, the
mechanism for checking this and changing to mode 2 in FlexX-Pharm did
not work if the number of combinations exceeded INT_MAX! FlexX just
ran out of memory and died. This is fixed.
- serveral small fixes that are not all listed in detail
2. Computing
3. Menus and user interface
- RECEPTOR/READ: the pdb format is not longer supported.
- the molecules files, which are written by command LIGAND/WRITE, can
be merged after the parallel script execution [438].
- the build in batch variable $(PVM_ID) is automatically appended to
the filenames of the commands SELOUTP and DOCKING/PRINTSOL, if the
files are not merged after the parallel script execution [2355].
- In order to speed up reading of mol2 receptor files the
surface is approximated for the active site. For this
approximation the second shell is used, which has the radius
SURF_APPROX_RADIUS. If the flag QUERY_SASTAB is set to 1,
then the surface for whole receptor is generated.
A quality check is performed for the approximated surface of
the active site: At least SURF_APPROX_MIN_NOF_SURFATOMS atoms
have to be marked as surface atoms and the resulting surface
has to consist of at least SURF_APPROX_MIN_NOF_TRIANGLES
triangles. If this quality check fails the surface of the
whole receptor will be calculated [3580].
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 2.2.1 ----------------------------------------------------------
1. Bug fixes
- Writing the receptor to mol2 may result in a segmentation
fault. Now this bug is fixed [3599].
- The command RECEPTOR/ACTIVE had no effect. Now this bug is
fixed [3510].
- Removed confusing error messages, which occurred when pyflexx
is started [3359].
- The problem with too many open files is fixed now [1132].
2. Computing
3. Menus and user interface
5. Graphics
6. Misc.
7. Documentation
---- Version 2.2.0 ----------------------------------------------------------
1. Bug fixes
- serveral small fixes that are not all listed in detail
2. Computing
- new base placement algorithm: single interaction scan (SIS).
This new algorithm can be used with the new option 1 of DOCKING/PLACEBAS
3. Menus and user interface
- command LIGAND/FROMPDB: the structure for the search pattern has
changed
- New flag INIT_MOL2_RECEPTOR.
- The flags USE_TRANSFORMS, TEST_ATOM_TYPES, ADD_HYDROGENS ,
ASSIGN_FORMAL_CHARGES, and ASSIGN_DELOCALIZED are now HIDDEN CONSTANT,
i.e., they are no longer part of the default config.dat and cannot
be changed with the SET command any more. By default they are all
set to 1, i.e., the new initialization is used, which can be
adjusted with LIGAND/SELINIT. For more details please refer to
the user guide.
THE FLAGS WILL BE REMOVED in one of the next versions, so
DO NOT USE them any more!!!!
- The flags AUTO_MINIMIZE, FF_CHARGES ,FF_CONVERGENCE_CRIT,
FF_DIELECTRIC_FUNC, FF_PREOPTIMIZE, FF_USE_INTRA_CUTOFF
are now HIDDEN CONSTANT, i.e., they are no longer part of
the default config.dat and cannot be changed with the SET
command any more.
THE FLAGS WILL BE REMOVED in one of the next versions, so
DO NOT USE them any more!!!!
4. File formats
- Direct import of a receptor MOL2 file (no RDF file needed).
This feature was completly revised, however there is still
a known issue: under certain circumstances (e.g. large protein
structures) reading proteins in mol2 format might last very
long, especially if no active site is defined in the mol2
input file.
We are still working on this problem!!
- amino.dat revised and slightly extended. Major changes are:
- additional tors entry contains typical h_torsion angles
used to check RDF settings
- there are now two templates for protonated ASP: asp1 and asp2 the former
template asp (which was in fact asp1) should no longer be used (but it
is still present in amino.dat as basic template to apply modifiers).
- bugfix in CYS template: The template definition were somewhat
confusing so we change the like this:
name situation / meaning
----------------------------------------------
cys- R-S(-) (charged)
cys R-S-S-R (neutral, in S-bridges)
cysh R-SH (neutral, protonated)
5. Graphics
6. Misc.
7. Documentation
---- Version 2.1.0 ----------------------------------------------------------
1. Bug fixes
- serveral small fixes that are not all listed in detail
2. Computing
- New module FlexX-Screen: This module is an extension of FlexX
which enables a speed-up structure-based virtual screening.
The module comprises three parts:
- the evaluation of molecule properties
- generating of interaction spots for the receptor
- the placebase caching
New menus and commands:
- the evaluation of molecule properties
LIGAND/EVAL : Evalutes the given property for the current ligand
CLIB/SETFILTER : Set resp. reset a filter expression for the library
LIGAND/FILTER: Sub-menu for handling multimol files and scanning to
property
LIGAND/FILTER/READMACRO : load macro definitions of molecule
properties from a file
- generating of interaction spots for the receptor
RECEPTOR/SPOTS : Sub-menu for site interaction spots
DOCKING/SCANMODE : Set flexx scan mode
- the placebase caching
PBC : Sub-menu for placebas caching approach
The static data file filter_macros.dat contains a set of filter
macro definitions. These include a lipinsky like filter rule,
a toxcicty filter, and a filter that rules out reactive groups.
In order to activate these macros, the file must be read with
the command LIGAND/FILTER/READMACRO.
- FlexC can now be combined with FlexX-Pharm
- New commands:
CLIB/CPHARM : Compute the combinatorial library dependency
on pharmacophore constraints
CLIB/DELPHARM: Deleting the dependency on pharmacophore constraints
CLIB/RELEXTCORE: Release an extended core
- geometry*.dat: set surface_mode to 0 for all geometry entries in order
to avoid problems with wrong probe locations [2698].
3. Menus and user interface
- New command: DOCKING/EXPORT: writes all energy and matching scores
of selected docking solutions to a comma separated values (csv) file
- New feature: LIGAND/WRITE resp. CDOCK/WRITESOL
The single/multi SDF-file contains for each placement the score values
as data blocks [2781].
- CLIB/RESETCORE reset the combinatorial library now to its initial
status. And the new command CLIB/RELEXTCORE releases the extended
core [2534].
- new parameter for DOCKING/ANALYZE/SCORE which allows for placing
hydrogens using the local geometry of the fix coordinates [2187].
- command TRIHASH: the command does not ask any longer for the pocket name,
instead the command asks now for the pocket index [1986].
- new flag USE_ACCESS_SCALING for turning on and off access scaling.
4. File formats
- chempar.dat is splitted in two parts:
- the new chempar.dat with the general chemistry knowledge (CHEMPAR)
- flexx_settings.dat with tool specified parameters (SETTINGS)
- Large file support enabled (i.e., file larger then 2 GB can now be handled
(does currently not work for windows)) [735].
5. Graphics
6. Misc.
- logp value module integrated in flexx [2662]
- new programm parameter 'LOGP_CLASS' is added:
- LOGP_CLASS = 1 : Wildmann/Crippen descriptors
- LOGP_CLASS = 2 : Ghose/Crippen descriptors
- new internal variables are available for scripts:
- $(CLIB_READY) is set to 'TRUE', if a combinatorial library is available.
- $(CORE_ID) contains the index of the currently core group.
- $(NOF_CORE_INST) contains the number of instances for the currently core group.
- $(NOF_RGROUPS) contains the number of rgoups (without the core group).
- FlexX can now be accessed via MOE (Molecular Operating Environment).
7. Documentation
---- Version 2.0.3 ----------------------------------------------------------
1. Bug fixes
- incomplete conformations in conformational set builder for rgroup
instances cause a segmentation fault. This bug is fixed now [2865].
- the EDIT commands contained a nasty bug. Now this bug is fixed [2277].
2. Computing
3. Menus and user interface
4. File formats
- RECEPTOR/WRITE: active site atom selections and the full protein
can be written in MOL2 format.
5. Graphics
6. Misc.
7. Documentation
---- Version 2.0.2 ----------------------------------------------------------
1. Bug fixes
- Fixed torsion angles in mol2-files (FIXTORSION) are overwritten.
Now this bug is fixed [2128]
- PHARM/DRAW and PHARM/PICKPH are not available to draw an interactions
on a specific hydrogen of an interacting group. Now this bug is
fixed [2013]
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
- Added support for FlexLM update keys (update from version 1.13)
7. Documentation
---- Version 2.0.1 ----------------------------------------------------------
1. Bug fixes
- segfaults upon SMILES import. Now this bug is fixed [2006]
- wrong molecule counting in multi entry files. Now this bug is fixed [1905]
- If a PVM-Job aborted, the output of this job is deleted from the logfiles.
The deleting was erroneous: the output of other jobs was deleted too.
Now this bug is fixed [1850]
- removing hydrogen and charge at an atom results in wrong atom charge.
Now this bug is fixed [1840]
- the command TRANSFORM contained same nasty bugs. These bugs are
fixed [1829]:
- current fragmentation is removed
- TRANSFORM is not available for combinatorial molecules
- inconsistent pharmacophore-ligand-dependencies are removed
and new dependencies are generated
- buggy template _ca in amino.dat/amino_pcharges.dat corrected [1823]
2. Computing
3. Menus and user interface
4. File formats
- static data file chempar.dat
new parameter for base selection: MAX_NOF_COMP_TO_DOCK [1939]
# maximum number of components allowed per molecule. docking a
# molecule with more components will be time-consuming, the
# chance of correct prediction is extremely low. Therefore FlexX
# aborts the docking of molecules with more components.
5. Graphics
6. Misc.
- path entry for the temporary filesin config.dat: TEMP shows
to /tmp/ [1916]
7. Documentation
---- Version 2.0.0 ----------------------------------------------------------
1. Bug fixes
- during covalent docking there were not enough of the atoms
around the covalent bond excluded from the receptor/ligand clash
tests - [902] fixed.
- Pharmacophore constraints can now be used with scoring schemes
other than the standard FlexX scoring function - [613] fixed.
- [526] fixed with the integration of the new pharm interface (see point
under graphics below)
- \bf format not parsed-out of the .hlp sources - fixed [552]
- Fixed internal string handling when opening files [420]
- Reading pdf files on PC written on SUN/HP/SGI (and vise versa)
was partially broken. This is fixed now by the introduction of
pdf version 2.0. Old pdfs are still read by the application [282]
- Highly improved numerical stability in function smallest_enclosing_sphere [418]
- Fixed computation of torsion angles. Old code might have crashed the
executable [572]
- If a combinatorial molecule complete extracted, the behaviour of the command
CLIB/EXTEND was inconsistent. Now this bug is fixed [653].
- flexx-pvm recognises the enviroment variables PVM_TMP resp. PVM_VMID now
and if PVM_TMP and/or PVM_VMID are used, flexx-pvm uses these enviroment
variables, too. [730/734]
- Memory leak in minimization of ligand internal energy with the Tripos force
field (AUTO_MINIMIZE). Now this bug is fixed [793].
2. Computing
- Improved and reworked chemistry
- New commands:
ACTIVE
The extended ACTIVE command and new ATLIST command for interactive selection of
an active site
MOLINF: a new command for outputting all docking-relevant information annotated
to the ligand
CLIB/EXTENDCORE expands a single core instance and rgroup instances to a
core molecule, which will be used as a "core instance"
CLIB/RESETCORE resets an extended core
Important note: If an extended core defined (with CLIB/EXTENDCORE), commands
like CDOCK/PLACEC, CDOCK/EXTENDR and CDOCK/EXTENDMR take automatically the
expanded core and do not ask for a core id. Other commands like CDOCK/PLACER
and CDOCK/PLACESEQ are not available, if a core instance is extended.
DOCKING/SELBAS: A new base selection routine allows for the selection of base
fragments with more than three components. All parameters controlling the base
selection mechanism can be controlled within chempar.dat.
SELBAS gets two new modes for selection by reference (f and c). f freezes the
conformational degrees of freedom to the given reference structure. c limits
the conformational degrees of freedom to the given reference structure and
two alternatives (+-10 deg) per rotatable bond.
- added handling of pseudo stereo centers like O.3 or S (with three single
bonds) [379]
- added handling of e/z stereo centers with three resp. two patterns [379]
- Encrypting and decrypting of data files is possible
- a new docking algorithm based on a single interaction search (sis) [545].
- up to 30% speedup for virtual screening on PCs
- FlexLM incorporated
- RPM-based installation under Linux
- Improved and more robust PVM interface
- virtual machine IDs
- parallelisation of nested loops
- simultaneous usage of multiple PVM daemons
- SMARTS: In FlexX 2.0, SMARTS can be used to match and alter molecules.
- aromaticity perception, intelligent protonation and much more based on SMARTS
rules
- extended FlexX-Pharm constraint definitions
- Buriedness
Awarding deeply buried interactions; implemented after a publication by M. Stahl
(JMGM 16, 121-132, 1998)
- Scoring parameter adjustment: now accessible from the command line.
This means a project such as target-based tuning of a scoring function becomes
much easier.
MODULE EXTENSIONS and NOVELTIES
FlexX-Pharm
- Multiple scoring function compatibility
Pharmacophore constraints can be used in conjunction with all available scoring
functions in FlexX 2.0.
- Improved constraint definition
Molecular substructures may be defined as spatial pharmacophore constraints using
the new SMARTS functionality, while complex relationships between constraints can
be defined as logical expressions e.g. (A and B) or (C and D).
- Supported constraint generation
A pharmacophore input file can be automatically generated using FlexV:
launch FlexV with the new PICKPH command and interactively pick and set your
constraints using the pharmacophore manager, and save to file.
- GRID field type constraints
Grid data (ACNT, GRID), e.g. drugscore fields, can be imported into FlexX and used
as hotspots ("fuzzy" pharmacophore type constraints) during docking or as a filter
following docking.
- Buriedness constraints
Based on the computation of buriedness, deep points within the active site can be
converted into fuzzy pharmacophore constraints using the RECEPTOR/GAUSS menu.
Fuzzy constraints created in this way can then be further converted into standard
FlexX-Pharm spatial constraints.
- Compatibility with FlexE
FlexC
- Import from CSLN: FlexXC is now able to import combinatorial libraries directly from
cSLN.
- EXTENDCORE: This command enables a single core fragment to be joined with the
fragments of an R-group in order to improve core placement.
This method overcomes difficulties FlexX may have had when docking particularly small
or featureless core fragments.
- Compatibility with FlexE
In FlexX 2.0 combinatorial libraries may be docked while simultaneously considering
an ensemble of active site conformations.
- ENUMFILE: The enumeration of combinatorial libraries can now be exported directly
into a multi-mol2 file.
FlexE
- Compatibility with FlexXC (see above)
- Compatibility with FlexX-Pharm (see above)
FlexV
- Improved defaults for drawing docking solutions
- Interactive picking of pharmacophore features (see above under FlexX-Pharm)
- Scriptable drawing mode
The representation (or drawing mode) used for drawing molecules (lines, balls and
sticks, etc.) can now be selected (and thus scripted) from within FlexX.
3. Menus and user interface
- renamed DATABASE/RELOAD to DATABASE/RELOADDAT
- as far as the user is concernemol objects are now referred to more
generically as graphics objects
- SELBAS: new automatic base selection (see comments above)
- new SELBAS options f (freeze) and c (cool down) (see comments above)
- new parameter LIGAND/MAPREF which allows to explicitly exclude hydrogens from
being part of the reference structure.
- LIGAND/WRITE: additional value for "dock entry selection": 'c' for current
coords.
- new RUNTTESTS command to perform some internal validation of the
executable and modules [268]
- Command Completion: Hitting the [tab] key cycles through the list of
possible menu commands with a given prefix [267]
- FlexX-Pharm fix [588] - avoid reading constraints over and over
- CLIB/SELECT: new param. [select mode] (o)verwrite, (e)xtend or (d)elete [800]
- new flag in config.dat: USE_PVM_FEATURE [790]
If equals 1, the execution of a parallel batch file is available. Otherwise,
if equals 0, a batch script is executed only sequentially.
- Tab completion of menu commands on the command line interface
is now supported (Windows excluded)
4. File formats
- Support of all major file formats: mol2, SD, smiles, sln, csln; protein as pdb and
mol2 input
- reading of CLSN revised [2018]
- new parameters in chempar.dat for controlling the base selection process:
MAX_NOF_CONF_PER_FRAG, NOF_FRAGMENTATIONS, MAX_NOF_FRAGMENTATIONS,
MAX_COMP_COVER, MAX_IA_FRAGSCORE: see user guide or comments in chempar.dat for
a description of the parameters.
- placement description file: new version 2.0 (compatible 1.98)
- support for reading any combination combination of newlines in text
data and config files generated on PC, Unix, or Mac [208]
- Unify FLEXX_FIXTORSION resp. FLEXX_FIXRING to FIXTORSION resp. FIXRING for all tools
[1471].
5. Graphics
- new drawing defaults for the DOCKING/DRAW and MDRAW commands. By default
the receptor is drawn with the current receptor settings into its own
graphics object (default is object 4). The object contains a slider with
three instances:
instance 0: the receptor with the current settings
instance 1: as in instance 1 plus the Connolly surface
instance 2: as in instance 2 plus hydrogen bonding interaction geometries
The receptor is drawn with the "lines" representation.
The docked ligand conformations are drawn to the docking graphics object
(default is fifo between objects 6 and 7) along with the dotted lines showing
interactions. The ligand is drawn using the "sticks" representation.
- drawing of docking conformations: coloring of ligands according to total
score and coloring of interaction dotted lines according to energy was
wrong - [870] fixed
- FlexV-Pharm interface integrated into FlexX code PHARM menu PICKPH command.
FlexV is started in pharm mode with the pharm control panel (see flexv ug
and pharm module in flexx ug).
Code: PHARM_IF ifdefs removed whereever possible and elsewhere converted to
PHARMs so that interface becomes part of standard FlexX-Pharm.
- as a consequence of the above for standard receptor draws, the interaction
surfaces are given an identifying string as default label
- view centered for new calls to FlexV (i.e. first call and restarts): bug 223
6. Misc.
- Debug log [220]
Any FlexX session creates a debug log in /tmp to be aware of current
settings and static data to make it easier to reproduce reported errors.
- new path entry in config.dat: PVM_TEMP contains the temporary batch
files of a FlexX-PVM run.
- XFlexX removed from package. XFlexX will no longer be maintained.
- removed the the flag FILTER_PHARM from flexx and chempar.dat.
- new: PVM-based parallelization of nested loops [809]
- new command line option: -i put the processor id
7. Documentation: Fully reworked, index created.
---- Version 1.20.0 ----------------------------------------------------------
Minor version of 2.0: slower and not so extensive and large as version 2.0
---- Version 1.13.5 ----------------------------------------------------------
1. Bug fixes
- if placemets of combinatorial docking will be read from a pdf file,
sometimes the orientation for the conformation are inconsistent.
Now this bug is fixed [567].
2. Computing
3. Menus and user interface
- Updated Tripos FlexLM library on Linux, Irix, HP-ia64
- PMF/DrugScore Module temporarily disabled
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.13.4 ----------------------------------------------------------
1. Bug fixes
- If a ligand with one atom loaded, the manual base selection of SELBAS
caused a segmentation fault. Now this bug is fixed [455].
- The change of scaling factors for the G_ff_* energy parameters in geometry.dat
had no effect. Now this bug is fixed [458].
- Under specific conditions fragments of the some instances of the rgoups
will be placed twice in the combinatorial docking algorithms. Now this
bug is fixed [489].
- Workaround to avoid FATAL ERROR in function smallest_enclosing_sphere [418]
- Win32: Fixed problems with config paths beginning with a driver letter [424]
2. Computing
3. Menus and user interface
- The number of pvm slave processes is now limited to 8192 [492].
- Upgraded to Tripos FlexLM 9.2 on Linux, Irix, HP-ia64
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.13.3 ----------------------------------------------------------
1. Bug fixes
- CDOCK/OPTC
the command does not handle correct a list of selected placements. Now this
bug is fixed.
- CDOCK/EXTENDR
If a R-group x switch to core, EXTENDR will not add the R-group 0 for
a combinatorial docking. Now this bug is fixed.
- reading mol2 files which include molecule names larger than
80 characters no longer crashes the executable [364]
- in the win32 environment the hostname may be larger than
15 characters now [371]
- fixed stream i/o problems running flexx in a cygwin32 shell [389]
- write CONECT entries to PDB file
if hetero groups are included in the receptor description, it might be useful to
find the according connectivity in the resulting PDB file written by receptor/write.
This functionality has been added.
- FlexX-Pharm FILTER command: this did not work properly if used when
ligand was only partially docked.
- If a molecule would be read, which contains an allene structure C=C=C/S,
FlexX chrashed. Now this bug is fixed. FlexX determines now, if an
allene structure is a stereo center or not. [379]
- Fixed crash bugs related to CSLN parsing [106,107,305]
- If different scaling factors for the scoring parameters (final/partial)
will be used in geometry.dat, FlexX scores mostly only the last fragment
with final scoring parameters, but not the whole placement.
Now this bug is fixed. [421]
- Bugfix: Added work around code for broken enclosing spheres [418]
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
- Tag feature not distributed by Tripos
7. Documentation
---- Version 1.13.2 ----------------------------------------------------------
1. Bug fixes
- command : DOCKING/PRINTSOL
the command didn't work accuratly during a flexx-pvm run, if a slave
process crashed. The crashed slave process will be restarted and the
printsol-file of this process will be overwritten. So, some results
are lost. Now this bug is fixed.
- Flag SECONDARY_TORSION_MODE:
If equals 1 and no torsion angles for a rotatable bond are defined in
torsion db, the torsional potential is calculated by a force field and
appropriate angles are selected.
If the ligand has a bad 3D structure, a never-ending loop may be
generated. Now this bug is fixed.
- placement description files (*.pdf)
If the energy values are written "uncoded" in the pdf file, the order of
values was wrong. Now this bug is fixed.
- command: DOCKING/ANALYZE/SASTAB
the command inclosed a memory leak. Now this bug is fixed.
- command: DOCKING/ANALYZE/SCORE
in the line format the rmsd value was missing. Now this bug is fixed.
- There was an unreasonalbe large overlap between hetero group in united
protein structure and docked ligand => fixed.
2. Computing
3. Menus and user interface
- FlexE- or FlexX-Pharm-license
A Tripos-license for FlexE or FlexX-Pharm will be used only after
calling the menus ENSEMBLE (FlexE) or PHARM (FlexX-Pharm).
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.13.1----------------------------------------------------------
1. Bug fixes
- fixed import/export of hydrogen atoms
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.13.0 ----------------------------------------------------------
1. Bug fixes
- windows path errors
- Covalent Docking:
Covalent docking is always associated with the formal separation of water
or similar compounds. The respective atoms have to be removed from the clash test.
On the receptor side, such atoms could still make interactions.
fixed
- command : DOCKING PRINTSOL
the command didn't worked accurate during a flexx-pvm run. Each work process
created the printsol-file. So some results are lost. Now the bug is fixed.
Each work process create a printsol-file and the master process merges the
files.
2. Computing
3. Menus and user interface
- New Command:
RECEPTOR/ACTIVE
defines the active site by a reference ligand or by a sphere
DOCKING/ANALYZE/SASTAB
a table with the sas of receptor, ligand and receptor-ligand-complex for
the docking solutions
- New commandline option "-q" for quiet startup
- New feature: LIGAND/WRITE
The single/multi MOL2-file contais for each placement, which will be
written, three new line :
# @FLEXX_SCORE
# 'header line'
# 'score line'
- New parameter: DOCKING/SELBAS: f
Base fragments are selected via an rms fit to the reference structure
loaded previously with the LIGAND/MAPREF command.
- New command:
CDOCK/WRITESOL
Reads the best placements form the pdf files and writes to (a multi) mol2/sdf
file(s)
CDOCK/EXTRACTTOP
Extract the combilib molecule with the best docking score and loads the
corresponding placement file
4. File formats
- CLIB/READ is able to handle *.csln (combinatorial Sybyl Line Notation)
files
- static data file chempar.dat
new parameter for combinatorial docking: KEEP_ALL_SCORES_ACHIEVED
# If KEEP_ALL_SCORES_ACHIEVED is set to 1, FlexX-C keeps the scores achieved
# for all placements (only for the placement solutions of EXTENDMR and
# PALCESEQ)
5. Modul
- PVM : Revision of the modul
- limited re-starts of aborted commissions (pvm-jobs)
- in the end of a flexx-pvm run:
- status report of hosts
- status report of executed commissions (pvm-jobs)
- new merge routine for the result files
- Python-extension: PyFlexX
New commands:
pyflexx.get_torsion_status() Get the torsion status of the currently loaded
ligand.
pyflexx.get_nof_placement() Get the number of currently placements.
6. Graphics
7. Misc.
A new version of the license manager FLEXlm (version 9.0) will be used
to check the TRIPOS license keys. TRIPOS supports Linux, SGI and HP-UX
Itanium64.
8. Documentation
Updated
---- Version 1.12.2 ----------------------------------------------------------
1. Bug fixes
dynamical linc libraries substituted by statical libraries
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.12.1 ----------------------------------------------------------
1. Bug fixes
long host name causes segmentation fault. FIXED!
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.12.0 ----------------------------------------------------------
1. Bug fixes
CLIB/DRAW:
trying to plot an R-group that has previously been switched
to a core instance leads to a segfault.
in global command SELOUTP:
The command 'SELOUTP outfile o n' didn't overwrite the file 'outfile'.
The option 'o' didn't work. Now the bug is fixed.
2. Computing
PVM
- old: If FlexX-PVM can't start a workprocess of one host, switch to the
sequentiell modus
- now: If FlexX-PVM can't start a workprocess of one host, FlexX avoids
this host but starts the other hosts
- new: Killing a single work process is now possible
Filterfunctions can be used:
filter for polarity (parameter: FILTER_POLARITY)
filter for 1,5-repulsions-atoms (parameter: FILTER_1_5_REPULSION)
pharm-filter (modul PHARM) (parameter: FILTER_PHARM)
tag-filter (modul TAG) (parameter: FILTER_TAG)
Soring parameters (geometry.dat)
The parameters of the scoring terms will scaling now with two factors.
The first scaling factor only used in the final score calculation and
the second scaling factor only used for partially built ligands.
3. Menus and user interface
New keyword in config.dat: @license_files
@license_files
/home/license/flexx/lic1.dat
/home/license/flexx/lic2.dat
The files lic1.dat and lic2.dat contain the license keys for flexx.
New program flag in config.dat:
PDF_VIEWER
# PDF_VIEWER : must be defined if you want to use the manual online
New Flag in config.dat: MOL_NAME
MOL_NAME: switches between different output name strings
1 : mol2 molecule name (from input file)
2 : mol2 molecule name
mol2 molecule name + solution number (placement solution)
3 : output filename or
output filename + solution number (placement solution)
New Command:
DOCKING/PRINTSOL
prints the result values from tables of LISTALL for every placement
in a file line.
Gobal/MANUAL
view User Guide with your local PDF viewer
New options for command:
CDOCK/EXTENDMR + CDOCK/PLACESEQ:
- quit an extendmr/placeseq-run
- continue of a stopped/arborted extendmr/placeseq-run
4. File formats
chempar.dat:
Switches for the filter functions
FILTER_POLARITY
FILTER_1_5_REPULSION
FILTER_PHARM
FILTER_TAG
Value: 0/1 = Filter deactive/active
rename:
torsion.dat => torsion_standard.dat
new:
torsion_fine.dat
5. Modul
FlexX-PVM is now a standard modul of FlexX. No additional license is
necessary.
FlexX is as a python extension modul available (currently only for
Linux and IRIX architectures). No additional license is necessary.
6. Graphics
7. Misc.
8. Documentation
---- Version 1.11.1 ----------------------------------------------------------
1. Bug fixes
2. Computing
3. Menus and user interface
New Flag: SECONDARY_TORSION_MODE
SECONDARY_TORSION_MODE: calculation of torsion angles
0 : off
1 : on, if no torsion angles for a rotatable bond defined in torsion db
the torsion potiantial is calculated in force field and appropriate
angles are selected
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.11.0 ------------------------------------------------------------
1. Bug fixes
- FlexX-C crashed if bond to rgroup was the last bond in the input file
- FlexX-C bond count in clib molecule was wrong
- drawing of paired interactions used wrong energy cutoff
- read/write pdf files didn't work properly (read/write incompatibility)
- some bug fixes in protein surface computation, metals are excluded from
the calculation now and always belong to the surface
- FlexX-PVM scheduler bug caused max. frequence of one request per second
2. Computing
- mimumba torsion energy can be used as part of the scoring scheme
3. Menus and user interface
- PVM executable name for work processes is the program name defined in
FLEXX (config.dat) or the name of the master process if FLEXX is undefined.
- SAS is part of RECEPTOR/INFO now
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.10.2 -----------------------------------------------------------
1. Bug fixes
- optimization of hydrogen torsions in 'SCORE ref' didn't work properly
2. Computing
- new flag TEST_ATOM_TYPES: performs a check of sybyl atom type assignment
- new flag ADD_HYDROGENS: automatically adds hydrogens to unprotonated mol2
or msi files
- new flag AUTO_MINIMIZE: automatically optimizes the ligand input
geometry, mode 2: on, only if intra-ligand force-field score is on
- new flag USE_FLEXIBLE_OPTIMIZE: mode 0: off mode 1: used in post-
optimization mode 2: used during incremental construction
- force field scoring added to set of scoring functions (Tripos force
field)
- numerical BFGS optimizer using pseudo gradient of current scoring function
is used for postoptimization (in principle, it can also be used during
incremental buildup, this is not tested yet)
- force field scoring terms, still under construction
3. Menus and user interface
- old whatif related code removed (WHATIF_AUTORETURN, etc.)
- PVM interface: scheduler can be aborted at every time
- PVM interface: scheduler immediate abort is possible now
- PVM interface: scheduler checks for dead slaves from time to time
and reinitates new processes
4. File formats
- LIGAND/READ is able to handle *.msi files. Conversion to sybyl mol2 atom
types is done automatically
- RECEPTOR/READ is able to handle *.mol2 files as input
- amino.dat file format changed (contains sybyl atom types and formal
charges now)
- charges.dat is changed to amino_pcharges containing partial charges
for amino acids
- geometry.dat contains new entries for Tripos forcefield scoring
G_ff_intra, G_ff_inter_vdw, G_ff_inter_elec
5. Graphics
6. Misc.
- new licensing key scheme (in addition to old one)
- new linux processor id calculation
7. Documentation
- documentation in pdf
---- Version 1.10.0 -----------------------------------------------------------
1. Bug fixes
- Linux version crashed if a script contained a SELINP command
- Complex-buildup had a minor bug in handling local transformations
after transformation optimization in the removal of distance violating
matches
2. Computing
- interaction accessability scaling implemented
- manual base placement: is performed whenever at least three atoms
of the base fragment do have coordinates
- particles are considered in contact_energy and pmf_energy (DrugScore)
- sybyl standard bond lengths are used in FlexX-C virtual synthesis
3. Menus and user interface
- Interaction surfaces can be colored by accessibility
4. File formats
- chempar contains sybyl bond length table
5. Graphics
6. Misc.
- Text output of base placement algorithms redesigned
- two new internal variables are available for scripts:
$(BEST_SCORE) = score of rank 1 solution
$(BEST_RMSD) = RMSD of solution closest to the crystal structure
7. Documentation
---- Version 1.9.0 ------------------------------------------------------------
1. Bug fixes
- conformation selection during manual base placement is done with larger
tolerances concerning the min RMSD to reference
- FlexX-C crashed under certain circumstances during deleting the combilib.
Fixed.
- FlexX-C handles the case of core fragments with different number of
components now (caused a crash previously)
- Number of interaction points is correctly displayed on SGIs (compiler
bug)
- Batch programming internal variables were deleted in FlexX-PVM runs
Fixed.
- mol2 bond types are written with small letters
2. Computing
- scoring: PLP scoring terms included
- scoring terms can be individually switched on/off in the geometry.dat
file. In addition, scoring terms can be specified as partial (not
evaluated for the final placement) and final (only evaluated for the final
placement)
- the RMS threshold for the final clustering step can be controlled
independently now
- new static data file DELOC (delocalized.dat) and corresponding flag
ASSIGN_DELOCALIZED allows the automatic correction of localized to
delocalized systems (for example C(=O)[O-] --> C(O)O with both O's
having a formal charge of -0.5)
- extended tolerances for interaction search (ADDMATCH2_A_EPS, etc.)
to avoid differences between scoring and rescoring
- modified interaction model for testing and scoring: angle tolerances
are calculated from the closest point of the interaction surface
instead of from the interaction main direction
- wider search for interactions forces different handling during
ligand placement optimization: the ligand is now optimized only on
interactions close to optimal distances (within ADDMATCH1_D_EPS)
- DrugScore function included. This function has to be switched
explicitly switched. The implementation differs from the original
in the SAS calculation. The parametrization was redone with the
FlexX SAS algorithm.
3. Menus and user interface
- smiles output at LIGAND/INFO and DOCKING/ANALYZE/SCORE
- smiles input at LIGAND/READ and LIGAND/IMPORT. Both routines call a
3D generator like Corina as defined in config.dat (CONV_SMILES)
- write ligand mol2 files of set printed with query (basf-980901) done.
- output of score at verb level 5 and 7 changed: using 5 allows printing
of matched interactions only
- auto-start of sequential scripts runing on the master if no loop is
contained
- PVM scheduling protocol output improved
- Result tables (matching) are limited to matches with score > 0.0
- automatic assignment of delocalized formal charges (see switch
ASSIGN_DELOCALIZED in config.dat)
- ANALYZE/SCORE can be called directly with a flexx placement
4. File formats
- minor changes in geometry.dat due to new interaction model. see comments
in the file (angle_scaling)
- new static data file delocalized.dat containing subgraphs for automatic
assignment of delocalized systems
- mol2 output contains the input file name, molecule id, and sybyl molecule
name as comments.
5. Graphics
- Drawing matches is limited to matches with score > 0.0
- Surface drawing of highly regular structures improved
6. Misc.
- static data file contact.dat:
- phenyl_center is now also assigned to 6-membered rings with atom
types C.2 instead of C.ar
- new subgraph acceptor_COOH
- COO group is assigned to all terminal COO groups including C(=O)[O-]
- static data file geometry.dat: angle scaling values adapted to new
interaction model.
7. Documentation
---- Version 1.8.0 ------------------------------------------------------------
1. Bug fixes
- missing interactions if the ligand consists out of a base fragment only
(interactions with larger deviations but still contribute to the score)
- file names and numbering for multi-file ligand write with file names
containing more than a single dot.
- FlexX^c: several minor bugs in combinatorial library handling and docking
fixed.
2. Computing
- scoring function parameters are externally changeable: @scoring_parameters,
@lipo_contact_scaling, @ambig_contact_scaling
- parameters for perturbation mode can be changed externally
- new scoring function ChemScore
- N.3 acceptor functions parametrized
- new scoring function PMF scoring (DrugScore)
- MAPREF takes R/S-stereo chemistry into account
- MAPREF is able to handle multiple alternatives which are considered
as alternatives during placement (tripos-990303)
- MAPREF works also with element matching only (instead of exact sybyl
atom type matching)
- FlexX-PVM: recover functionality after crashing the scheduler, manual
merge and removal of commission markers in output files, sorted output
even over a script restart.
- SAS calculation for LIGAND, RECEPTOR, DOCKING
- handling of azides in contact.dat
3. Menus and user interface
- Output tables are created depending on the scoring function parameters
(columns for entries != 0.0)
- pocket has to be specified by name now (TRIHASH)
- batchprog: consistent handling of quotes, single quotes to avoid substi-
tution of FlexX variables, empty variables can be entered with ""
- new commands WHILE, INCR
- menus: direct access to submenus of parent menus
- SELADM has a new flag 'APPEND_MODE' deciding whether a graphic file should
be appended or overwritten.
- FlexX-PVM: has now the possibility to stop the scheduler and continue a
parallel calculation later on by reading the summary file (see PVM/RESTART)
- FOREACH-IN Loops can have an additional FROMTO, i.e.
FOREACH $(lig) IN "file.list" FROMTO 10 20
takes only lines 10 to 20 from file.list
- FlexX-PVM: tables are streamlined
- New batchprog buildin variable for number of base fragments $(NOF_BASE_FRAGS)
- columns for ligand names extended to 16 chars
- naming conventions for ring conformation generator changed:
CORINA -> RCGENERATOR, KEEP_CORINA_FILES -> KEEP_RCGEN_FILES. The SCA
interface does not exist any longer, the entries MOLETOPI, SCA, and
ZERLEGE are removed from config.dat.
- RIGID_RINGS is also removed from config.dat. The functionality is moved
to RING_MODE, i.e. RING_MODE 0 means RIGID_RINGS on.
- FlexX-PVM is now available under Linux
- ASSIGN_FORMAL_CHARGES has a third value now which will be the default:
0: off, 1: on, 2: on if loaded charges are likely to be partial charges
- LIGAND/WRITE can write fix coords
- Matching-Table prints protein and ligand name like solutions table
4. File formats
- geometry: format for scoring parameters changed. Additional geometric
parameters can be specified now.
5. Graphics
- flexv also reads gdf and mol2 files without the appropriate appendix
- flexv - POV-Ray interface developed
- flexv: two bugs in rendering of spherical polygons with narrow passes fixed.
6. Misc.
7. Documentation
---- Version 1.7.6 ------------------------------------------------------------
1. Bug fixes
- spherical rectangle interaction geometries, tolerance in direction
of negative azimuth angle was under some circumstances not considered
2. Computing
- new function for calculating the deep part of the active site
- SCORE interaction search radius increased to ADDMATCH2_D_EPS
- final search for interactions of the whole ligand as the last
step of the incremental construction algorithm
- determine last fragments to add via a dummy atom at the end of chain in
order to handle linked ligands, etc (graf-991028)
- enantiomerism can be handled directly as a degree of freedom, see
flag STEREO_MODE (novo-991019)
- intra-ligand clash test: some options allow the user to specify which
tests should be performed (LIGCLASH_*). Especially, there is the choice
to use united atom vdw radii or not.
3. Menus and user interface
- maximum number of allowed conformers per base fragment can be set
externally now
- mol2 molecule names doesn't contain directories and multi-mol2
files have numbered molecule names like name_nnn (tripos-990823)
- replace FlexX variables in unix commands started from the
flexx script langauge (tripos-990823)
- allow the execution of an external program and access to the program
output (tripos-990823), command EXEC
- nearly all FATALs removed during ligand loading, especially with
respect to the torsion angle database
- collinear point set WARNING gives a summary now
- SELOUTP: new optional parameter in PVM mode 'pvm_merge' allows to
switch off merging of working process outputs
- use ligand name instead of file name in log output if a multi-mol2 file
was used (gmd-991029)
- new options: FIXRMSD, FLIPSTER
4. File formats
5. Graphics
6. Misc.
- contact.dat: C.ar == O.2 is considered as a carbonyl (interaction
geometries)
7. Documentation
---- Version 1.7.5 ------------------------------------------------------------
1. Bug fixes
- FlexX crashes if substr_id / charge is missing in mol2 file
- active site selection doesn't work if no file name is given in the rdf file
- lib: site_grid was missing in library
2. Computing
3. Menus and user interface
- new command RECEPTOR/INFO prints list of loaded amino acids
- new command DOCKING/ANALYZE/SCORE calculates a score of a reference
orientation including the optimization of ligand hydrogen torsions
- commands ANALYZE/CONTACT and OVERLAP are completely redesigned and
produce better tables now
- result table: G_lipo is now divided into its three contributions:
G_lipo, G_ambig, and G_clash
- DOCKING/INFO has a new mode (4) showing the scores and rsmd values
during the buildup sequence
4. File formats
- sequence of blanks in PDB files is checked to avoid shift errors
- pdf format changed due to result table changes
5. Graphics
- independent object clipping in FlexV
6. Misc.
7. Documentation
- default.rdf and FlexX User Guide contains pocket definition
---- Version 1.7.0 ------------------------------------------------------------
1. Bug fixes
- pdb ambiguous atom types didn't work correctly
- memory bug during handling with oversized command names fixed
- bond lengths near ring systems have a unique length now, independent
from the ligand build-up direction (this causes differences in results)
- script termination avoided in simple error cases like 'no ligand',
'no receptor', ...
- PVM: config.dat with single @parallel entry cause a segfault if a slave
dies. Also, the a slave is restarted on a wrong machine (Roche-990118).
- autocall of PLACEBAS in COMPLEX is done always if no placements were
found in PLACEBAS
- bug in -a parameter handling in PVM
2. Computing
- redesign of manual and covalent fragment placement
- assignment of reference coordinates by mapping (MAPREF)
- base selection by reference mapping (umar-980910)
- base placement by reference mapping (umar-980910)
- new placement mode (perturbation mode)
3. Menus and user interface
- if/else/endif and break/continue in script language
- last command status as an internal batch variable (tripos-990503)
- write an active site/full protein PDB file containing the hydrogen
locations (tripos-981020)
- particle atom types in mol2 file should be configured in amino.dat
(tripos-981026)
4. File formats
- pdf handles manual placement, perturbation mode and covalent docking now
- flexx writes automatically assigned formal charges in mol2 files
- rdf-file: active_site_filename is changed to pocket. Now, the definition
of subpockets is allowed. Subpockets can be specified in the TRIHASH
command. Therefore, the base placement can be limited to a specific
region of the active site.
- atom type LP in mol2 files are handled like DU atoms (element UNKNOWN)
5. Graphics
- flexv has a selection browser for imported multi-mol2 files
6. Misc.
- real time measure during parallel execution
7. Documentation
---- Version 1.6.5 ------------------------------------------------------------
1. Bug fixes
- flexv spherical rectangle drawing error if direction vectors are not
orthogonal
- corina interface expects 2 atom shells (even if inside ring system)
- corina interface works correctly with 3-atom rings
- FATAL error if first token in RDF is unknown or not pdb_file
- bug in the assignment of interactions to proteins with missing atoms
- comments at the end of batchprog lines are ignored now
- INPUT can be used in BATCHMODE_FILE also
- memory leak in mol_stereo removed
- handling of dummy atoms and unknown atom types improved
- mol2 file output, bond numbering corrected
- tailing blank in command line caused confusion
- SES computation failed on 4 spheres with cocircular touchpoints
- mol2 writing partial molecules contained undefined data
- spaces were considered as a parameter in script files
- unpacking on LINUX of files packed under SOLARIS works now
2. Computing
- base placement: abort search if a limit for the number of triangles is
exceeded (avoids extremely long run times in the worst case)
- handling of charged particles (consider repulsion, charged interactions)
- PVM interface completely redesigned and debugged.
3. Menus and user interface
- setting of corina options in config.dat
- #system handles OS and OS version now
- #application introduced into file_parser
- shorthelp.txt is now separate for each tool (sh_[tool].txt)
- comments after batchlines work now
- ~ (substituted by $home) can be used in most cases
- new flag io_retry to avoid abort in batchmode_file if server is
temporary unavailable
- introduce leading 0's in enumerated filenames (write ligand) (tripos-0729)
- mol2 files molecule name should be identical with file name (tripos-0729)
- active site selection is optionally be based on monomers (tripos-0814),
-> new parameter in receptor/read
- Tripos license manager added ( version number contains 'T' )
- batch output is streamlined (nearly nothing if verbosity=0) (tripos-0729)
- writing of particle locations in mol2 file (roche-0903)
- flexv: dblclick in object selection switches object on/off
- batchprog variables can be strings now
- predefined batchprog variables
- PVM slaves can be niced
- SCRIPT command has additional argument and keep_batchvar parameter
4. File formats
5. Graphics
- new render options menu
- molecule drawing properties can be defined
- double/aromatic bonds are drawn (flexv import and ligands)
- 16 graphic objects -- all with an instance slider -- are now available
in FlexV and can be individually copied
- graphic objects 1-15 can be used from within FlexX, mdraw is possible to
each graphic object
- SELADM commands: meaning of parameter mol object changed: 0= fifo,
former 9= fifo
- flexv takes several (up to 10) gdf and mol2 files in the command line
- redesign of drawing routines completed
- confusion with particle colors, labels should contain the element name
or particle type (roche-0910)
6. Misc.
- linux fx2wif interface should definitly work now
7. Documentation
---- Version 1.6 --------------------------------------------------------------
1. Bug fixes
- logfile command duplication bug fixed
- drawing interaction points do not consider selection of interaction types
- X-FlexX startup error messages are wrong
- DOCKING/SELECT does not always delete solutions after the entered selection
- manual base placement with highly symmetric base fragments have had
sometimes a wrong atom map
- getline library is switched off if flexx is started with input/output re-
direction
- blank character after abbreviated parameter does not effect argument queue
anymore
- No FATAL error if unknown mol2 atom types occur of if the ligand is too
large
(V 1.6.1)
- xflexx crashes in draw single docking
- xflexx control lights in panels menu were sometimes wrong
- placement reduction during base placement was not exact (find_value_by_rank)
- WHATIF error messages concerning black/white colors corrected
- WHATIF in combination with mdraw commands works now
- assignment of atom equivalence classes ran into problems with bridged
ring systems, corrected
- default energy ranges for energy color modes were wrong (DOCKING/SELCOL)
- xflexx mdraw option uses non-initialized string
- flexv improved rendering of spherical polygons
- order of database messages during start-up corrected
- stereo-consideration in calculation of atom equivalence classes (used
for symmetry-corrected RMSD) improved (cyclohexane-problem)
- cysh template was wrong. All rdf files containing cysh template should
use the cys template instead!
2. Computing
- Calculation of SAS
- surface_mode introduced at interaction geometries (-> phenyl ring
interactions occur even if the atom carrying the interaction is not
part of the surface)
- placement of hydrophobic base fragment
- active site surfaces can be computed in the interior of the protein
(rdf entry @probe_location)
- reduced memory and time requirements due to an earlier match-error test
3. Menus and user interface
4. File formats
- rdf: new entry @probe_location (optional)
- geometry.dat: new entry surface_mode (optional)
5. Graphics
- flexv is able to write GDF files
- flexv has a set-label functionality to allow the users own annotation.
- flexv can change the label font type and size
- mol2-interface: unnecessary caps for sticks mode removed
6. Misc.
- n32 for SGI R10000 is now available
- linux fx2wif interface should work now
7. Documentation
- FlexX User Guide: english language is corrected, extended to new features
- FlexV User Guide: updated to V 1.3.7
- default.rdf is part of the distribution (help)
---- Version 1.5 --------------------------------------------------------------
0. Bug fixes
- memory leaks (at least there should be less than before)
- error handling in scripts (direct termination of script is
avoided at most places)
- PLACEBAS c (covalent docking) input bug fixed
1. Computing
- ligand intramolecular clash tests include hydrogen atoms
- no removal of matches with too short distances
- improved symmetry detection in RMS calculation
2. Particle model
- first version of particle model for placing water molecules
during docking
- integration of metal-water contacts
3. Menus and user interface
- getline library for editing commands
- automated command completion
- cascading execution of docking commands
(COMPLEX executes PLACEBAS executes SELBAS)
- automated name extension for ?, HELP, and parameter names (SET)
- alphabetically sorted parameter lists
4. File formats
- changes in GDF (graphic description file (FlexX->FlexV))
- @chains in RDF (receptor description file) is exchanged by @atoms
with a sequence of exclude/include commands.
- PDB atom names can be defined in chempar.dat
5. Graphics
- internal graphic data handling reimplemented
- more consistent graphic commands
- separate graphic contexts for reference ligand and placements
- translucent colors (with flexv)
- tubes, ribbons, cartoons for protein backbones (with flexv)
- VRML temporary file deletion
- various splines introduced in FlexV
- new GUI for FlexV
6. Misc.
- 2DPLOT command for writing ligplot input files
- command line options work without ':' now
- complete list of elements implemented
- improved error detection and handling in ring conformation interface
7. Documentation
- updated user guide for FlexX, FlexV, X-FlexX
---- TODO ---------------------------------------------------------------------
- predefinition of receptor interaction sites which must be used (zinc, for
example) (umar-980910)
- loop variables included in seloutp filenames produce errors in
PVM runs (gmd-990210)
- switching to automatic selection if MAPREF finds no hits (tripos-990304)
- mol2 fixtorsion entry should allow the definition of preferred torsion
angles.
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