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ChangeLog
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version 1.9.2
230308 Martin Raden
* licence change (from GNU to MIT) for both latpack and biu
* cleanup for GitHub upload
version 1.9.1
160808 Martin Mann
- biu-2.3.5 : replaced by biu-2.3.7
+ biu-2.3.7 : extended biu version
* configure :
* biu-2.3.7 enabled
* bin/latFold.cc :
* uses now biu::RNG_ARS4x32, a counter-based generator from the
Random123 library (thanks to Victor Zhao)
* parameter "run" info extended
* bin/latFoldVec.cc :
* uses now biu::RNG_ARS4x32, a counter-based generator from the
Random123 library (thanks to Victor Zhao)
* parameter "run" info extended
* now sets the RNG.seed for each run
160722 Martin Mann
* bin/latFold.cc :
* RNG seed set for each run, since LCG produced similar RNG runs for
long simulations with many runs (thanks to Victor Zhao)
-> LCG should be avoided (thanks to Victor Zhao):
http://dx.doi.org/10.1002/jcc.21638
-> maybe integrate Random123
http://www.deshawresearch.com/resources_random123.html
version 1.9.0
100622 Martin Mann
* latNum : space consumption is now close to zero since symmetry exclusion
is now done via the comparison of the move string to its normalized
version instead of storing all normalized structures within a set
container
100621 Martin Mann
+ latNum : number of lattice protein structures of a given length and their
symmetry free enumeration
100312 Martin Mann
* configure :
- latFold default : disabled (since ELL ist not part of the package)
* BIU v2.3.5 is now part of the package
* latFold : FCC folding uses now TRIANGULAR PULL MOVES (new default in BIU)
--> up to now latFold utilized "standard" square pull moves (Lesh et al)
for FCC resulting in larger neighborhoods and unneccesary move
artefacts
version 1.8.1
091120 Martin Mann
* latConv :
* BUGFIX : base scaling for given bond length was wrong for FCC and 210
(thanks to Reda Rawi)
* now "-seq" accepts also non-HP-sequences ...
091117 Martin Mann
* latMap :
+ lowest distance for only backbone or only sidechain data if sidechain
models are given
091103 Martin Mann
* latFit :
* BUGFIX : possible fragment starts (after gap bridging) are now checked
if they are valid nodes in the current lattice used
version 1.8.0
091018 Martin Mann
* latFit :
* SAW bridging of chain gaps now restricted to short chain gaps (currently
up to length 6, see constant MAX_SAW_LENGTH_TO_CONSIDER
+ for long chain gaps the approximate relative position to fit is
determined via a superpositioning of the chain fitted so far. All
lattice points around this position and their lattice neighbors are
considered for the start of the next fragment. A reflection is
checked as well to ensure the correct superpositioning.
091015 Martin Mann
* biu/SuperPos_Kabsch :
+ superpositioning returns now the applied transformation information,
i.e. translation vector, rotation matrix, and scaling factor
091007 Martin Mann
* latFold / latFoldVec :
+ new parameter "final" allows for the specification of a structure that
triggers the end of a folding simulation run
--> this is checked independently of the minimal energy ("minE") request
* latFold :
* final structure printed for each run is now normalized
091005 Martin Mann
* latFold :
+ output of final structure per run
* hit rate output only if "minE" parameter present
* latFoldVec :
* hit rate output only if "minE" parameter present
090929 Martin Mann
* latFoldVec :
* now Boltzmann probabilities of neighbors is calculated based on energy
change to reduce maximal value of the partition function (was exceeding
range of <double> otherwise). still the same probabilities are
maintained since all neighbored structures have the same 'energy anchor'
which is the elongated structure.
* latFit :
+ output of superpositioned original chain for dRMSD optimization
reenabled
090925 Martin Mann
* latFit :
* dRMSD optimization
+ all chain fragments are now placed in same lattice (no independent
placements and orientation)
+ distance between successive fragment ends are constrained by an
according selfavoiding walk in the lattice, i.e. they could be
connected via a backbone on the lattice
+ progress bar output
* BUGFIX : dRMSD calculation of two point sets used wrong normalization
090917 Martin Mann
* latFoldVec :
+ new parameter "-maxStepsIncrease" to trigger a linear increase of the
simulation length based on "maxSteps" times current sequence length
+ PivotMoveSet enabled again
090915 Martin Mann
* doc : latfold-manual : fix of "-kT" parameter docu thanks to Rada Rawi
* latFoldVec :
* energy calculation fixed
090826 Martin Mann
* energy files now installed to INSTALLDIR/share/latpack/
* latFoldVec :
* BUGFIX : now only final structure/energy output for successful runs
090825 Martin Mann
* latFoldVec :
* BUGFIX : chain elongation selection was uniform selection since all
elongations were restricted to 1.0! now replaced with full Boltzmann
weight
+ per default final structure and energy printed to STDOUT
* longer output buffering : only a few std::endl that trigger a flush()
090824 Martin Mann
* DEPENDENCY UPDATE : ELL 3.1.2 and BIU 2.3.2
* latFold :
* beta --> kT
* latFoldVec :
* BUGFIX : memory leak fixed
* initial structure CT based (not streched one)
* beta --> kT
+ rerun of a folding simulation if a chain is not elongatable anymore
* time measurement updated such that each co-translational folding
simulation is measured and the overall time does not count for aborted
simulations
090822 Martin Mann
* manuals of latFold and latVec : removed some inconsistencies and C&P
errors
+ latFoldVec : simulates co-translational/vectorial folding via a
combination of a chain growth algorithm (as in latVec) and a global
folding simulation (as in latFold) for the intermediate protein chains
+ manual for latFoldVec
version 1.7.2
090729 Martin Mann
* latFit :
* dRMSD mode : independent subchain superpositioning for output
090728 Martin Mann
* latFit :
* dRMSD mode : independent subchain superpositioning for cRMSD calculation
version 1.7.1
090727 Martin Mann
* latFit : added support for empty side chain id using the '_' char
090701 Martin Mann
* latFit : added optimization mode to verbose output
version 1.7.0
090630 Martin Mann
* LatticeDescriptorCKW :
+ getBaseScale : calculates the base vector multiplicator to scale all
neighboring vectors to a given length
* SuperPos_Kabsch
+ source file includes the basic C function of Arno Formella
* LatticeProteinUtil :
+ toMoveSequence : IPointVec to MoveSequence
* latFit :
+ output of absolute move string of each subchain in verbose mode
090629 Martin Mann
+ LatticeProteinUtil : utilitiy class for conversion between lattice
protein structure representations and structural distance calculations
+ toMoveSequence : string to MoveSequence
+ toString : MoveSequence to string
+ toIntPoint : MoveSequence to IPointVec
+ toDblPoint : MoveSequence to DPointVec
+ structural distance measures formerly part of SuperPos_Kabsch class
(cRMSD, dRMSD, GDT_TS, GDT_HA)
* SuperPos_Kabsch
- structural distance measures (now part of LatticeProteinUtil interface)
090626 Martin Mann
+ SuperPos_Kabsch : utility class that allows for
+ superpositioning of point vectors utilizing the algorithm by Kabsch
(1976) and its implementation by Arno Formella
+ cRMSD : coordinate root mean square deviation
+ dRMSD : distance root mean square deviation
+ GDT_TS : global distance test - total score
+ GDT_HA : global distance test - high accuracy score
* latFit :
+ full dRMSD support including side chain models
+ final cRMSD evaluation when doing dRMSD optimization
+ PDB output adapted for dRMSD optimization
* manual updated
* RENAME : CKW --> 210 : lattice parameter value changed
* configure.ac : GSL check added
090624 Martin Mann
- bin/latSeF : renamed to latVec
+ bin/latVec : renamed latSeF
090623 Martin Mann
* latFit : dRMSD optimization enabled (for backbone-only models)
090311 Martin Mann
* manual update (citation of LatPack publication)
version 1.6.4
090310 Martin Mann
* LatSeF manual : structure normalization explained
* latFit:
+ PDB parsing support for negative amino acid indices (strange case ...)
+ PDB parsing support for incomplete leading and tailing amino acid
coordinates (e.g. N atom only present)
+ PDB parsing support for different models (new parameter "pdbModel")
* changed default parameter value for "pdbChain" from " " to "A"
* changed default parameter value for "outMode" from "CML" to "PDB"
version 1.6.3
090307 Martin Mann
+ biu/Rotator3D : rotation handler for 3D biu::DblPoint objects around
X, Y, and Z axis
* latFit:
* BUGFIX : dRMSD calculation for gapped sequences
* BUGFIX : rotation matrix for Y axis rotation was partially initialized
using the X rotation angle (C&P error)
+ usage of Rotator3D
090305 Martin Mann
* latFit :
* BUGFIX : no rotation and rescaling done for distance calculation
of two double coordinates.
* BUGFIX : output coordinates were not correct when rotated and shifted
090303 Martin Mann
* latFit :
* BUGFIX : best fit was not copied but reference was set to local
variable : segfault
* BUGFIX : it was not checked if the last extension was successful or not
* sideChainFit : check extension if PDB information is complete, i.e.
same number of coordinates for side chain and backbone extracted
090302 Martin Mann
+ biu/LatticeDescriptorCWK : descriptor for Chess Knight Walk lattice
but NO relative move conversion matrices stated!
090226 Martin Mann
* Miyazawa-Jernigan (MJ) energy table added to package
090224 Martin Mann
+ added package version information output to all binaries
* source updated to be compilable with g++ 4.3.*
version 1.6.2
081112 Daniel Maticzka
* added <limits.h> header where needed for newest g++ support
version 1.6.1
081112 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
* LatFold :
* parameter 'beta' to 'kT' changed (including internal handling)
+ manual-latFold
version 1.6.0
080624 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
+ LatConv : Conversion of different structure representations into each
other. Supported types are:
+ absolute move string
+ relative move string
+ CML (chemical markup language = XML)
+ XYZ
+ PDB
+ move string normalization for symmetry breaking
version 1.5.0
080624 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
* local biu updated to 2.0.0
080623 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
BIU >= 2.0.0
ELL >= 2.3.0
* LatFold:
+ support for distance interval based energy functions
- parity lattice support disabled
version 1.4.0
080620 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
BIU >= 1.7.0
ELL >= 2.2.0
* LatSeF:
+ support for distance interval based energy functions
version 1.3.0
080618 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
* BUGFIX : LatFit : temporary test program exit removed
080617 Daniel Maticzka
* LatFold: Pivot Moves support added
080616 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
* local BIU library only compiled if '--with-BIU' is not specified
version 1.2.1
086011 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
* LatFit:
+ chain gap support for side chain models
version 1.2.0
080610 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
* LatFit:
+ new option "pdbChainGaps" adds the support for non-consecutive position
data in PDB files --> currently for backbone fit only
version 1.1.0
080522 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
+ optional ELL check and usage
+ LatFold: folding simulations of lattice backbone models based on HPfold
by Daniel Matizcka 2008
+ arbitrary energy function and alphabet via text file
+ output guidance
+ different verbose output levels
080502 version 1.0.2
080426 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
LatSeF:
+ output: number of best CT structures in storage
080502 version 1.0.1
080426 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
* documentation completed
LatSeF:
+ maximal storage size can be set to restrict maximal memory consumption
080424 version 1.0.0
080424 Martin Mann http://www.bioinf.uni-freiburg.de/~mmann/
LatSeF:
+ chain growth algorithm for backbone lattice protein models
+ arbitrary energy function and alphabet via text file
+ lattice models = 2D-square, 3D-cubic, 3D-face-centered-cubic
+ extensibility check for last monomer (if one free neighbor is available)
+ output of up to k structures with increasing energy
+ output of up to k structures with minimal energy only
+ minimal memory consumption via compression of move string representation
+ progress bar, silent or verbose output