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FlexS – changes
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# (numbers in square brackets [ ] are BioSolveIT internal references numbers)
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---- Version 2.1.2 ----------------------------------------------------------
1. Bug fixes
- Added batch variable $(PVM_ID).
- [37337417] Fixed termination with node-locked license keys.
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 2.1.1 ----------------------------------------------------------
1. Bug fixes
- RIF alignment: write the correct normed flexs score to molecule files
- Fixed an issue loading molecules with the 32 bit executable on a 64
bit system.
2. Computing
3. Menus and user interface
RIF alignment: added an intra molecular clash filter for optimized
conformations. If the Lennard-Jones potential of an aligned solution
is greater than the value of the parameter RIF_LJPOT_FILTER the
solution will be skipped.
4. File formats
5. Graphics
6. Misc.
- the output of the RIF/ALIGN command extended.
For more details please refer to the user guide.
7. Documentation
---- Version 2.1.0 ----------------------------------------------------------
1. Bug fixes
- [12511] Avoid endless license searching in case of not responding servers.
- [12473] Fixed checking license keys on different servers.
2. Computing
3. Menus and user interface
- the interface to Python no longer exists.
4. File formats
5. Graphics
6. Misc.
- the output of the RIF/ALIGN command changed. For more details please
use the user guide.
7. Documentation
---- Version 2.0.0 ----------------------------------------------------------
1. Bug fixes
- Molecule interactions with more as one reference atom, where the given
reference coordintates are collinear, will be skipped now.
2. Computing
3. Menus and user interface
- New command RIF/ALIGN computes an alignment which based on a given
matching, e.g. FTrees matching. For more details please refer to
the user guide.
- New variable PCGENERATOR contains the path and name of an external
partial charge generator, to add missing partial charges.
- New flags USE_RL_TRANSFORM and USE_TL_TRANSFORMS: To switch between
the new and the old molecule initialization for the reference and
test ligands.
- The flags 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_sp.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 TEST_LIG/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 removed.
- New commands: REF_LIG/SELINIT, TEST_LIG/SELINIT and CLIB/SELINIT
To adjust the various initialization levels for reference, test
ligands and combinatorial fragments.
- SUPERPOS/EVALUATE/SCORE is scoring the alignment of the test and
reference ligand for the loaded coordinates. The command is
replacing the command MATCH_LS, which will be removed in one of
the next versions.
4. File formats
- reading: (single/multi-) sdf-files (test lig, reference lig)
- static data file amino.dat is removed. The necessary data are
taken now from contact_sp.dat.
5. Graphics
6. Misc.
7. Documentation
---- Version 1.30.1 ----------------------------------------------------------
1. Bug fixes
- Windows: fixed some problems with FlexV
- fixed problems with license version numbers
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.30.0 ----------------------------------------------------------
1. Bug fixes
2. Computing
- New commands:
CLIB/EXTENDCORE expands a single core instance and rgroup instances to a
extended core, which will be used as a "core instance"
CLIB/RELEXTCORE release the extended core
CLIB/RESETCORE reset the combinatorial library to its initial status.
Important note: If an extended core defined (with CLIB/EXTENDCORE), commands
like CSUPER/PLACEC, CSUPER/EXTENDR and CSUPER/EXTENDMR take automatically
the expanded core and do not ask for a core id. Other commands like
CSUPER/PLACER and CSUPER/PLACESEQ are not available, if a core instance is
extended.
LIGAND/SMARTS matches a given SMARTS-pattern on the test ligand
- SMARTS: In FlexS 1.30 SMARTS can be used to match molecules substructures.
In addition SMARTS subgraphs can be used to assign properties with
static data information.
3. Menus and user interface
- 3D_GEN_FORMAT
Select a file-format that should be used as input/output for the
3DGENERATOR executable: 0 = SDF, 1 = MOL2
4. File formats
- reading: (single/multi-) mol2-files (test lig, reference lig)
- writing sdf files is available for the following commands:
TEST_LIG/WRITE and TEST_LIG/CONFORM/WRITONE
- chempar_sp.dat is splitted in two parts:
- the new chempar.dat with the general chemistry knowledge (CHEMPAR)
- flexs_settings.dat with tool specified parameters (SETTINGS)
- chempar contains sybyl bond length table
5. Graphics
6. Misc.
7. Documentation
---- Version 1.20.3 ----------------------------------------------------------
1. Bug fixes
- incomplete conformations in conformational set builder for rgroup
instances cause a segmentation fault. This bug is fixed now [2865].
- the acceptor interaction points of type N(amino) point into nirvana
instead of surface. This bug is fixed now [2283].
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.20.2 ----------------------------------------------------------
1. Bug fixes
- the command TEST_LIG/WRITE contained a nasty bug: e.g.
WRITE test n n c 1-2
This command should write two sets of coordinates: test_001 and test_002
with separate coordinate sets. Instead, the command writes the file, test,
twice and only the second coordinate set survives. Now this bug is
fixed [2345].
- if filename for the command TEST_LIG/WRITEOPT contains a non existing
directory, then the file is written to the current directory. Now this
bug is fixed. Now the command aborts with a error messag [2345].
- the EDIT commands contained a nasty bug. Now this bug is fixed [2277]
2. Computing
3. Menus and user interface
- removed the flag 3D_GEN_FORMAT from config_sp.dat [2476]
4. File formats
5. Graphics
6. Misc.
- the output of 'LIST mol' satisfies now the FlexS standard.
7. Documentation
---- Version 1.20.1 ----------------------------------------------------------
1. Bug fixes
- the command SUPERPOS/EVALUATE/MATCH_LS used possibly inconsistent
coordinates. Now this bug is fixed [2345]
- The changing of the EXECUTABLE variables like EDITOR is now
available [2277]
- the command TEST_LIG/READC caused a segmentation fault, if partial
charge is loading from a seperate mol2-file. Now this bug is
fixed [2208]
- the option "heteroatom bonded only" of the command SELGRA was not
availble. Now this bug is fixed [2208]
- the option 'q' of the command TEST_LIG/WRITE did not work. Now
this bug is fixed [2208].
- no consistence, if test ligands and a combinatorial library are
contemporaneously used. Now this bug is fixed [2108]
2. Computing
3. Menus and user interface
4. File formats
- contact_sp.dat: the subgraph of acceptor_N(terminal) is modified [463]
5. Graphics
6. Misc.
- Added support for FlexLM update keys (update from version 1.11)
7. Documentation
---- Version 1.20.0 ----------------------------------------------------------
1. Bug fixes
- 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]
- If the generating of triangle hash table failed, the command PLACEBAS does
not switch automatically to the overlap method. Now this bug is fixed [852].
- Memory leak in minimization of ligand internal energy with the Tripos force
field (AUTO_MINIMIZE). Now this bug is fixed [793].
- flexs-pvm recognises the enviroment variables PVM_TMP resp. PVM_VMID now
and if PVM_TMP and/or PVM_VMID are used, flexs-pvm uses these enviroment
variables, too. [730/734]
- If a combinatorial molecule complete extracted, the behaviour of the command
CLIB/EXTEND was inconsistence. Now this bug is fixed [653].
2. Computing
- add handling of pseudo stereo centers like O.3 or S (with three single
bonds) [379]
- add handling of e/z stereo centers with three resp. two patterns [379]
3. Menus and user interface
- renamed DATABASE/RELOAD to DATABASE/RELOADDAT
- The number of pvm slave processes is now limited to 8192 [492].
- CLIB/SELECT: new param. [select mode] (o)verwrite, (e)xtend or (d)elete [800]
- new flag in config_sp.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.
- 3D_GEN_FORMAT
Select a file-format that should be used as input/output for the
3DGENERATOR executable: 0 = SDF, 1 = MOL2
- renamed flags in config_sp.dat:
CLEANUP_PROG renamed to 3DGENERATOR
MOL_CLEANUP renamed to 3D_GEN
KEEP_CLEANUP_FILES renamed to KEEP_3DGEN_FILES
- removed command flag in config_sp.dat: CONV_SMILES
3DGENERATOR is used instead of CONV_SMILES
- Updated Tripos FlexLM library on Linux, Irix, HP-ia64
4. File formats
- multi-(mol2/sdf/sln/smi)-files (test lig, reference lig)
you read a single ligand, a list of ligands or 'all' ligands.
- reading of CLSN disabled [2018]
- placement description file: new version 2.01 (compatible 1.98)
- the command SUPERPOSE/EVALUATE/ALIGN can now read sdf files.
- Unify FLEXX_FIXTORSION resp. FLEXX_FIXRING to FIXTORSION resp. FIXRING for all
tools [1471].
- static data file chempar_sp.dat
new parameter for base selection: MAX_NOF_COMP_TO_ALIGN [1939]
# maximum number of components allowed per molecule. superposing a
# molecule with more components will be time-consuming, the
# chance of correct prediction is extremely low. Therefore FlexS
# aborts the superposing of molecules with more components.
5. Graphics
6. Misc.
- Debug log [220]
Any flexs 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_sp.dat: PVM_TEMP contains the temporary batch
files of a FlexS-PVM run.
- new: PVM-based parallelization of nested loops [809]
- new command line option: -i put the processor id
- path entry for the temporary filesin config.dat: TEMP shows
to /tmp/ [1916]
7. Documentation
---- Version 1.11.4 ----------------------------------------------------------
1. Bug fixes
- Through a postoptimization of alignments (SUPERPOS/POPT) the est. score
of a placement will be doubled. Now this bug is fixed [617].
- if placemets of combinatorial alignment will be read from a pdf file,
sometimes the orientation for the conformation are inconsistent.
Now this bug is fixed [567].
2. Computing
2. Computing
3. Menus and user interface
- Updated Tripos FlexLM library on Linux, Irix, HP-ia64
4. File formats
5. Graphics
6. Misc.
---- Version 1.11.3 ----------------------------------------------------------
1. Bug fixes
- the command SUPERPOSE/EVALUATE/ALIGN caused a segmentation fault, if no
alignment computable. Now this bug is fixed [451]. Output message if no
alignment is also given.
- the command SUPERPOSE/EVALUATE/ALIGN generated a virtual atom for
reference ligand without removing this virtual atom after score computing.
Now this bug is fixed [452].
- A interaction geometry without discrete interaction points caused a
segmentation fault. Now this bug is fixed [463].
- the command SUPERPOSE/EVALUATE/ALIGN had memory leak. Now this bug is fix [464]
- Trying to draw a ref ligand with the SELGRA settings "1 1 1 1 0 0" caused
a seg fault (this could have been a ligand specific problem) - fixed [471]
- If a test ligand with one atom loaded, the manual base selection of SELBAS
caused a segmentation fault. Now this bug is fixed [455].
- Under specific conditions fragments of the some instances of the rgoups
will be placed twice in the combinatorial alignment algorithms. Now this
bug is fixed [489].
- nasty bug in the combinatorial alignment routines fixed: after PLACEC the
the next fragment, which will be added (through EXTENDMR resp. EXTENDR),
will be added first in the next iteration. Now this bug is fixed [534].
2. Computing
3. Menus and user interface
- SUPERPOSITION/LIST*: If test ligand read out a multi file, the commands
use the molecule name instead of the filename in the header line of solution
table [127].
- Upgraded to Tripos FlexLM 9.2 on Linux, Irix, HP-ia64
4. File formats
5. Graphics
6. Misc.
7. Documentation
- COMBISUPER command aliases put in #application definition
- Output improved for the SUPERPOS/EVALUATE> ALIGN command (see [451])
---- Version 1.11.2 ----------------------------------------------------------
1. Bug fixes
- reading mol2 files which include molecule names larger than
80 characters no longer crashes the executable [364]
- CDOCK/EXTENDR
If a R-group x switch to core, EXTENDR will not add the R-group 0 for
a combinatorial alignment. Now this bug is fixed.
- If a molecule would be read, which contains an allene structure C=C=C/S,
FlexS chrashed. Now this bug is fixed. FlexS determines now, if an
allene structure is a stereo center or not. [379]
- Bugfix: Added work around code for broken enclosing spheres [418]
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.11.1 ----------------------------------------------------------
1. Bug fixes
- command : SUPERPOS/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.
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- Version 1.11.0 ----------------------------------------------------------
1. Bug fixes
- command : SUPERPOS PRINTSOL
the command didn't worked accurate during a flexs-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 feature: TEST_LIG/WRITE
The single/multi MOL2-file contais for each placement, which will be
written, three new line :
# @<TRIPOS>FLEXS_SCORE
# 'header line'
# 'score line'
- New flag in config_sp.dat: SECONDARY_TORSION_MODE]
If equals 1 and no torsion angles for a rotatable bond are defined in
torsion db, the torsion potential is calculated in force field and
appropriate angles are selected.
4. File formats
- static data file chempar_sp.dat: new parameters for FlexS-C
SCORE_TABLE_SIZE 5
# number of placement energies stored for each combinatorial library
# molecule during a superposition run
STORE_PLACEMENT_THRESHOLD 0.0 # kJ/mol
# determines the energy threshold for writing combinatorial superposition
# results in placement files
STORE_PLACEMENT_MODE 0
# the way placements are stored in combinatorial superposition runs:
# 0 : no files -1: PDF files (FlexS internal format)
# >0: store first k placements in a multi mol2 file
MAX_NOF_FILE_WRITE 0
# the number of files maximally generated during a combinatorial run:
# -1: a file for each molecule placed
# 0: a single multi-mol2 file for all molecules and placements (only
# if STORE_PLACEMENT_MODE > 0, else like -1)
# k: store files of k highest scoring molecules
KEEP_ALL_SCORES_ACHIEVED 0
# If KEEP_ALL_SCORES_ACHIEVED is set to 1, FlexS-C keeps the scores achieved
# for all placements (only for the placement solutions of EXTENDMR and
# PALCESEQ)
TORSION_MINIMA_CUTOFF 30.0 # % of maximum pseudo energy around torsion
# Cut-off for assigning low pseudo energy torsions
5. Graphics
6. 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
- New modul for FlexS: FlexS-C (alignment of combinatorial libraries)
CLIB : Sub-menu for handling combinatorial libraries
CLIB/READ : Read core fragments/R-groups from multi-MOL2 resp. csln
(combinatorial Sybyl Line Notation) files to FlexS' main memory
CLIB/READREF : Read reference coordinates for comparing the docking results
CLIB/SETREF : Set reference coordinates to the coordinates from the input file
CLIB/MAPREF : Load a mol2 mapping file for reference
CLIB/CLOSE : Substitute all open R-groups by hydrogens
CLIB/DELETE : Delete a combilib from FlexS' main memory
CLIB/INFO : Print information about the combilib currently loaded
CLIB/RGROUP : List molecules, active/inactive flag for an R-group
CLIB/SELECT : Selects subsets of R-group molecules to be active/inactive
CLIB/EXTRACT : Generates a molecule from the combinatorial library
CLIB/RELEASE : Deletes the last (k) added R-group from the extracted molecule
CLIB/EXTEND : Adds an R-group to the already extracted molecule
CLIB/SWITCH : Switches an R-group to a core and the previous core to an R-group
CLIB/ENUM : Enumerates a subset of the combilib molecules
CLIB/MINFO : Prints information about a specific molecule of the combilib
CLIB/SELADM : Select administration defaults for combinatorial library graphics
CLIB/SELGRA : Select defaults for drawing combinatorial libraries
CLIB/SELCOL : Select colors for drawing combinatorial libraries
CLIB/SELLAB : Select labels for drawing combinatorial libraries
CLIB/DRAW : Draw a combinatorial library (use DISPLAY to execute)
CLIB/GRAINF : Shows the settings of the combinatorial library graphic context
CSUPER : Sub-menu for superposition and analyzing combinatorial libraries
CSUPER/DELETE : Delete combilib placements from FlexS main memory
CSUPER/LISTP : List placement results (score) for an R-group
CSUPER/SELINS : Select a set of Core/R-group molecules for base placement
CSUPER/PLACEC : Place core molecules directly
CSUPER/POPTC : Postoptimization of core placements
CSUPER/READC : Read a set of placements for a core instance from a pdf file
CSUPER/WRITEC : Write the current placements of a core instance into a pdf file
CSUPER/EXTRACT : Extract a combilib molecule and loads the corresponding placement
file
CSUPER/RELEASE : Release the combilib molecule and deletes the placement data
CSUPER/PLACER : Place a single R-group directly
CSUPER/EXTENDR : Extend a core placement by a single R-group
CSUPER/SELECTR : Select R-groups by placement results
CSUPER/EXTENDMR : Extend a core placement by multiple R-groups
CSUPER/PLACESEQ : Place combilib molecules sequentially and independent from each
other
CSUPER/WRITESOL : Reads the best placements form the pdf files and writes to
(a multi) mol2/sdf file(s)
CSUPER/EXTRACTTOP : Extract the combilib molecule with the best alignment score
and loads the corresponding placement file
- Python-extension : PyFlexS
New commands:
pyflexs.get_noftlig() :
Get the number of the currently loaded test igands.
pyflexs.get_nofrlig() :
Get the number of the currently loaded reference ligands.
pyflexs.get_torsion_status() :
Get the torsion status of the currently loaded test ligand.
pyflexs.get_nof_placement() :
Get the number of currently placements.
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 1.10.2 ----------------------------------------------------------
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 1.10.1 ----------------------------------------------------------
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 1.10.0 ----------------------------------------------------------
1. Bug fixes
in REF_LIG:
WRITEG wrote the gaussians to PATH_TEMP and READG read the gaussians
from PATH_LIGAND: now both use PATH_PREDICT
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 FlexS-PVM can't start a workprocess of one host, switch to the
sequentiell modus
- now: If FlexS-PVM can't start a workprocess of one host, FlexS avoids
this host but starts the other hosts
- new: Killing a single work process is now possible
Filterfunctions can be used:
filter for 1,5-repulsions-atoms (parameter: FILTER_1_5_REPULSION)
Use of Tripos force field for minimization of ligand internal energy.
3. Menus and user interface
Improvements: flag MOL_NAME
MOL_NAME: switches between different output name strings
1 : mol2 molecule name (from input file)
2 : mol2 molecule name + infile number (multi mol file) or
mol2 molecule name + solution number (placement solution)
3 : output filename + infile number (multi mol file) or
output filename + solution number (placement solution)
New keyword (config_sp.dat): @license_files
@license_files
/home/license/flexs/lic1.dat
/home/license/flexs/lic2.dat
The files lic1.dat and lic2.dat contain the license keys for flexs.
New program flag (config_sp.dat):
CLEANUP_PROG
# CLEANUP_PROG: optional, must be defined if you want to clean-up molecule
# structures or if you want to read files in Sybyl Line
# Notation
PDF_VIEWER
# PDF_VIEWER : must be defined if you want to use the manual online
New flags (config_sp.dat):
MOL_CLEANUP
KEEP_CLEANUP_FILES
SDF_MOL_ID_TYPE
SDF_MOL_ID_NUM
AUTO_MINIMIZE
FF_CHARGES
FF_DIELECTRIC_FUNC
FF_USE_INTRA_CUTOFF
FF_CONVERGENCE_CRIT
FF_PREOPTIMIZE
# MOL_CLEANUP: perform clean-up of ligand molecule structure (neccessary
# for ligands from SLN files; useful if ligand has bad geometry).
# 0 : off, no clean-up done
# 1 : on, use clean-up tool defined by CLEANUP_PROG
# KEEP_CLEANUP_FILES:
# 0 : delete cleanup in/out/trace files
# 1 : save all cleanup program files and print files names on the screen
# SDF_MOL_ID_TYPE: determines the field from which the molecule ID in a SD
# File is taken
# 0 : First line of header block
# 1 : Property line with the name given by SDF_MOL_ID_STRING
# 2 : Property line starting/ending with <ID.. / <id.. / ..ID> / ..id>
# 3 : Take the SDF_MOL_ID_NUMth field in the data section
# SDF_MOL_ID_NUM: determines the field from which the molecule ID in a SD
# File is taken, if SDF_MOL_ID_TYPE is set to 3
# x : molecule ID is read from the xth property line of type '> <..>'
# AUTO_MINIMIZE: use Tripos force field for minimization of ligand
# internal energy. Slow! Use only, if initial geometry is bad and
# no structure clean-up program available.
# 0 : off
# 1 : on
# FF_CHARGES: use Coulomb interactions with partial charges in force
# field. Should be switched off for Tripos force field.
# 0 : off
# 1 : on
# FF_CONVERGENCE_CRIT: convergence criterion in force field energy
# minimization. Should be set to 1.
# 1 : normal convergence
# 2 : high convergence (very slow)
# FF_DIELECTRIC_FUNC: handling of dielectric constant in electrostatic
# energy calculation of force field. Should be set to 1.
# 1 : /* FIXME: (ak) comment by ak */
# 2 :
# FF_PREOPTIMIZE: use of a Nelder-Mead simplex minimization for initial
# minimization steps. Should be switched on.
# 0 : off
# 1 : on
# FF_USE_INTRA_CUTOFF: use of intramolecular cut-off in calculation of
# non-bonding force field energy terms. Should be switched off.
# 0 : off, no cut-off
# 1 : on, use a cut-off of FF_NONBOND_CUTOFF (defined in chempar_sp.c)
#
New section (config_sp.dat):
@ID_STRINGS
# --------------------------------------------------------------------------
# DESCRIPTION:
# This optional section is for parsing of SD Files (SDF) and Sybyl Line
# Notation (SLN) only. The field names that determine the molecule-ID
# can be defined here. If they are not defined, "ID" is assumed for SDF
# and "RegID" for SLN. Both values cannot be changed on runtime of FlexS!
# --------------------------------------------------------------------------
SDF_MOL_ID_STRING ID
SLN_MOL_ID_STRING RegID
New Command:
SUPERPOS/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
4. Files
reading Cerius2 MSI-, MDL SDF- and SLN-files (test lig, reference lig)
chempar_sp.dat:
Switches for the filter functions
FILTER_1_5_REPULSION
Value: 0/1 = Filter deactive/active
Paramters for Tripos forcefield handling (auto minimizer)
FF_DIELECTRIC_CONST 1.0
FF_HBOND_RAD_SCALING 0.7
FF_NONBOND_CUTOFF 8.0
FF_ONEFOUR_FACTOR 1.0
5. Static data
rename:
static_data/torsion.dat => static_data/torsion_standard.dat
new:
static_data/torsion_fine.dat
6. Modul
FlexS-PVM is now a standard modul of FlexS. No additional license is
necessary.
FlexS is as a python extension modul available (currently only for
Linux and IRIX architectures). No additional license is necessary.
7. Documentation
- updated
- new layout
---- Version 1.9.2 ----------------------------------------------------------
1. Computing
- FlexS-PVM uses PVM-Version 3.4.4
2. Static data
- contact_sp.dat:
A slot for a fourth atom number is inserted in the data area of the
subgraph-files.
New subgraph-file:
subgraph acceptor_COOH
subgraph center_N(azide)
subgraph acceptor_N(amino)
subgraph acceptor_N(terminal)
renamed subgraph acceptor_N to acceptor_N(aryl)
3. Documentation
- updated
---- Version 1.9.1 ----------------------------------------------------------
1. Bug fixes
- bug in the flexible/rigid-body postoptimization of placements
- bug in info-routine (avoided crash if no placements present)
- bug in computation of superpos energy
- bug in the read of the scoring parameter of base placement
(ignored subset of placements)
2. Menus and user interface
New flag:
- OPTIMIZE:
0 - the similarity-(overlap)-index will be used for the flexible
postoptimization
1 - superpos-energy will be used for the flexible postoptimization
New commands:
- POPT: local postoptimization of flexible/rigide placements;
this command replaces the commands FLEXPOPT and RIGPOPT
- SPOPT: superset of capabilities of local postoptimzation of
flexible/rigide placements including additional flexible
test ligands; this command replaces the command FLEXPOPT
Improvements:
- SCREEN: truncated long filenames to the first 20 characters in the
outputfile
- SWITCHTYPE:
- write coordinates of type 'opt' to coordinates of type 'fix'
- write coordinates of a placement to coordinates of type 'opt'
- write coordinates of type 'fix' to coordinates of type 'opt'
- SETALGO: Optimization-Algorithm for flexible superposition without
reference ligand
New batch variable:
- $(TORSION_STATUS):
-1 : the status is not defined.
0 : torsion angles for all bonds defined on the torsion.dat-data.
1 : torsion angles for all bonds either defined on the torsion.dat-data
or calculated.
2 : non torsion angle found in torsion.dat for at least one rotatable
bound. Taking 30 degree grid with arbitrary reference atom.
3. Documentation
- updated
4. Static data
- new static data file : optpar.dat
optpar.dat replace nspconf.dat and contains
- scoring parameters for the computation of placements
- parameters and stoping criteria for the postoptimization/flexible superposition
- RIGFIT parameter
- geometry_sp.dat adapted in format to geometry.dat
---- Version 1.9 ------------------------------------------------------------
1. Bug fixes
- no crash if molecules with arbitrary atom numbers or unknown atom types
are read. In case of an error while reading from a multi-mol2 file the
error entry is skipped
- TLIG_NAME is now the name of the molecule not the file name
- wrong left boundary detected -> surface computing moved to draw_site
- substructure entry in Mol2-file limited by 20 chars
- bug in placebas p
- bug in formal charge assignment
- minor bugs in batchprog (%, jmp)
- bug in read_placements
- added suffix pvm_mytid() for TEMP files
- corrected estimated scores (EST_SCORE) when placement is read from a pst file
2. Computing
- flexible, multiple orientational and conformational local postoptimization of
FlexS placements/ligands
- transformation of matched atoms (Gaussian fit)
- FlexS-PVM: recover functionality after crashing the scheduler, manual
merge and removal of commission markers in output files, sorted output
even over a script restart
3. Menus and user interface
New commands:
- MATCH: superposition of two test-ligands by a atom matching
- FSUPER: superposition of flexible test-ligands
- FLEXPOPT: local postoptimization of flexible placements
- TRANSFORM: transformation of test-ligand
- SWITCHTYPE: write coordinates of type 1 to coordinates of type 2
- FIX: this should be obsolete!! WRITEN: writing the atom coordinates of type 'opt'
- SWITCHP: energy-parameter for flexible superposition
- SETALGO: optimization-algorithm and parameters for flexible superposition
Improvements:
- FlexS-PVM is now available under Linux
- auto-start of sequential scripts runing on the master if no loop is
contained
- PVM scheduling protocol output improved
- batchprog: consistent handling of quotes, single quotes to avoid substi-
tution of FlexS variables, empty variables can be entered with ""
- SELOUTP: new optional parameter in PVM mode 'pvm_merge' allows to
switch off merging of working process outputs
- replace FlexS variables in unix commands started from the
flexs script language
- allow the execution of an external program and access to the program
output, command EXEC
- 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
- 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.
4. File formats
- mol2 output contains the input file name, molecule id, and sybyl molecule
name as comments.
- mol2 bondtype 'AR' -> 'ar'
- reading SMILES files (test-lig, ref-lig)
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.
- Modul License keys 10000000 for [PVM]
7. Documentation
- updated
---- Version 1.8 ------------------------------------------------------------
first commercial version, only minor changes to v1.7
1. Bug fixes
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
- added TRIPOS license manager
7. Documentation
---- Version 1.7 ------------------------------------------------------------
1. Bug fixes
- read Gaussian and merge Gaussian initiate reinit of several Datastructs
2. Computing
- setting of reference coordinates now substructure matching based
- manual base selection supports now substructure matching
- manual base placement supports now substructure matching
- normed score of superposition available in solution lists
3. Menus and user interface
- reduced output at several places of iterated command execution
(e.g. multi-mol2 read)
- increased readability of output
4. File formats
5. Graphics
6. Misc.
7. Documentation
- updated user guide for FlexS
---- Version 1.6 --------------------------------------------------------------
1. 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)
- No FATAL error if unknown mol2 atom types occur of if the
ligand is too large
2. Computing
- ligand intramolecular clash tests include hydrogen atoms
- PVM interface completely redesigned and debugged
- I/O routines for Gaussian molecular description
- adding, merging, deleting of reference ligand Gaussians
in order to facilitate an `enriched reference'
3. Menus and user interface
- getline library for editing commands
- automated command completion
- cascading execution of superposition commands
(COMPLEX executes PLACEBAS executes SELBAS)
- automated name extension for ?, HELP, and parameter names (SET)
- #application introduced into file_parser
- shorthelp.txt is now separate for each tool (sh_[tool].txt)
- comments after batchlines work now
- batchprog variables can be strings now
- predefined batchprog variables
- IF/BREAK/CONTINUE commands for altering the sequence of commands
in a batch file added
- SCRIPT command has additional argument and keep_batchvar parameter
4. File formats
- .xpl defines a Grid of density values
- .gauss modified mol- or mol2-files defining Gaussians with
the coordinate- and charge-entries
5. Graphics
- internal graphic data handling reimplemented
- more consistent graphic commands
- separate graphic contexts for reference coordinates and placements
of the test ligand
- translucent colors (with flexv)
6. Misc.
- command line options work without ':' now
- n32 for SGI R10000 is now available
- linus fx2wif interface should work now
7. Documentation
- updated user guide for FlexS
--- Version 1.x.x ------------------------------------------------------------
1. Bug fixes
2. Computing
3. Menus and user interface
4. File formats
5. Graphics
6. Misc.
7. Documentation
---- TODO ---------------------------------------------------------------------
© BioSolveIT GmbH, 2013