Changes in Release 1.7
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* Removed Qt dependency for non-GUI compilation and fixed issues with recent
gcc and boost versions
* Added Quaternary Structure (QS) scoring module
* Fixed mmCIF parser to work with mmCIF dictionary version 5 (now with useful
revision data) and add r_free, r_work and entity.id to MMCifInfo
* Added fast accessibility and secondary structure (mimicking naccess & dssp)
computation (Accessibility & AssignSecStruct in mol.alg)
* Changed behaviour of mol.alg.Superpose with match = 'local-aln' or
'global-aln' which used to fail for chains without peptide bonds (e.g.
CA-only)
* Large updates for documentation
* Several minor bug fixes, improvements, and speed-ups
Changes in Release 1.6
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* Added code to compare structures attached to a multiple seq. aln.
* Incorporated Antechamber based force-field parameter generation for mm mod.
Changes in Release 1.5
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* Added binding to 3DComb (structural alignment)
* Added functions to predict contacts from multiple sequence alignments
* Added some functions to analyze MD trajectories (pairwise distance matrices,
pairwise distance fluctuations, RMSD matrix etc.)
* Support of non-orthogonal unit cells for wrapping entities
* Flexible implementation of HBPlus
* Updated dependencies (Eigen2 to Eigen3, Boost 1.47 to 1.53)
* Wrapper for OpenMM. This allows for direct access to molecular mechanics
functionality from within OST.
* The compoundslib now features InChI and InChIKeys (machine readable InChI
hash)
* Names of compounds are also stored in the compoundslib now
* Added seq.ProfileHandle class and io.LoadSequenceProfile to work with
sequence profiles.
* Added a wrapper to HHblits.
* Removed levenberg_marquardt.h in img/alg
Changes in Release 1.4
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* Feasibility check set to off by default, atoms in compounds are now
connected by the Builder irrespective of the distance between them
* Speed improvement for bracketed within selections up to a factor of 20
* refactored and streamlined the conop interface. The builder classes
have been replaced by processors (HeuristicProcessor, RuleBasedProcessor)
Changes In Release 1.3.3
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* fix context menu/main menu for newer Qt versions
* CreateEntityFromView remembers chemical type (BZDNG-430)
* fix gfx.PrimList.SetLineWidth
* Fix remote=true for MMCIF loader (BZDNG-449)
* made CreateViewFromAtoms more flexible (BZDNG-408)
Changes In Release 1.3.2
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* Fixed atom ordering in the GetFrameFromEntity() function in the
structure_analysis.py module.
* Fix atom indices generated by CoordGroup::Filter()
* small tweaks to lDDT output
* small tweaks to molck
* Repaired bio unit parsing from mmCIF file/ PDBizing bio units, before
chains with different transformations were ignored
* use new remote loader written in Python to work around crash on Mountain
Lion
Changes In Release 1.3.1
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* Export missing default argument for AligmentHandle.ToString
* Automatically attach entity view in SequenceFromChain
* Export GetMatchingBackboneViews to Python
* Fix compilation with boost 1.33.1
* Allow renumbering of single chain
Changes In Release 1.3.0
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* Scene background can now be set to a gradient or an image
* Better Handling of HSV colors
* Table: direct access to columns tab['x'] is also available as tab.x
* Table: Export to ConTeXt and HTML tables
* Table: Barplot interface
* The BLAST binding supports newer versions of BLAST
* Bindings for CAD score
* Update directory layout of OST to be more conformant with the site-package
system of Python: Instead of storing the modules in lib{64}/ost/ost, they
are now in lib{64}/python{{VERSION}}/site-packages/ost
* Added molck, the molecular checker. A small command-line tool to clean PDB
files, e.g. remove atoms with zero occupancy, "virtual atoms", hydrogens
etc.
Changes In Release 1.2.3
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* PDBWriter: Prevent writing of out-of-bounds atom coordinates.
Changes in Release 1.2.2
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* Fixed loop indentation in the PDBize function for bio units, leading to
exponential running time/ memory consumption. This problem only affected a
fraction of PDB entries.
Changes in Release 1.2.1
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* Use RPATH for linux bundles. No longer requires LD_LIBRARY_PATH to be set
for chemdict_tool and lddt [BZDNG-385]
* "install command line tools" also symlinks lddt, and chemdict_tool
[BZDNG-386]
* Fixed broken the_hammer.py example [BZDNG-387]
* MacOS X: Make sure to use python2.6, not python as pyexec [BZDNG-388]
* Fix example directory path for MacOS X bundle [BZDNG-389]
* PDBWriter: Insert newline after END [BZDNG-391]
* Added missing documentation for a few AlignmentHandle methods
* Workaround for naccess which was failing when directory contains dots.
* Fixed superposition dialog for unnamed chains
* Fixed byte-swapping issue for DCD trajectories
* Fixed FFT panel update after switching data in main viewer
* Added missing pdbx_struct_assembly.id export
* lDDT: Updated default angle and bond tolerance parameters from 8 stddev to 12
stddev.
Changes in Release 1.2 (since 1.1)
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* added mmCIF parser to enable loading of mmCIF files. The following categories
are currently understood:
atom_site, entity, entity_poly, citation, citation_author, exptl, refine,
pdbx_struct_assembly, pdbx_struct_assembly_gen, pdbx_struct_oper_list,
struct, struct_conf, struct_sheet_range, pdbx_database_PDB_obs_spr,
struct_ref, struct_ref_seq, struct_ref_seq_dif
* trajectory analysis support
* better intergration with numpy
* added Smith-Waterman local align and Needleman-Wunsch global align algorithms
* static linking of C++ executables
* support for building OST library with no gfx, gui, info libraries. This leads
to a compact application bundle that can easily be deployed
* work around compiler bugs in gcc-4.1 enabling compilation with CentOS 5.5's
default compiler and libraries
* introducing the new table class, supporting all kinds of analyses on tabular
data, including plotting and statistical analyses.
* added stereochemical plausibility checks and support for multiple references
to lDDT
* new superposition dialog in DNG