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ChangeLog
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2011-02-15 16:14 joroy
* CMakeLists.txt: See previous commit
Also remove uninstall custom target
2011-02-15 16:13 joroy
* lib/CMakeLists.txt: Update the build system to handle library
version and symlinks on the include directory
2011-02-15 16:12 joroy
* config.h.cmake: Update license header
2011-02-04 20:39 joroy
* cmake/FindMySQLpp.cmake, cmake/cmake_uninstall.cmake.in,
lib/CMakeLists.txt: Fix copyright year and typos
2011-02-04 20:16 joroy
* CMakeLists.txt, config.h.cmake: Update copyright year
2011-02-04 19:32 joroy
* .project, CMakeLists.txt, Makefile.in, cmake,
cmake/FindMySQLpp.cmake, cmake/cmake_uninstall.cmake.in,
config.guess, config.h.cmake, config.h.in, config.sub, configure,
configure.in, install-sh, lib/AbstractModel.cc, lib/Atom.cc,
lib/AtomSet.cc, lib/AtomType.cc, lib/AtomTypeStore.cc,
lib/Binstream.h, lib/CMakeLists.txt, lib/Exception.cc,
lib/ExtendedResidue.cc, lib/Genbankstream.cc, lib/GraphModel.cc,
lib/HBond.cc, lib/HomogeneousTransfo.cc, lib/Makefile.in,
lib/Messagestream.cc, lib/Model.cc, lib/ModelFactoryMethod.cc,
lib/Molecule.cc, lib/PairingPattern.cc, lib/PdbFileHeader.cc,
lib/Pdbstream.cc, lib/PropertyType.cc, lib/PropertyTypeStore.cc,
lib/Relation.cc, lib/ResId.cc, lib/ResIdSet.cc, lib/Residue.cc,
lib/ResidueFactoryMethod.cc, lib/ResidueType.cc,
lib/ResidueTypeStore.cc, lib/Rmsd.cc, lib/RnamlReader.cc,
lib/RnamlWriter.cc, lib/Sequence.cc, lib/ServerSocket.cc,
lib/SqlExtrac.cc, lib/SqlReader.cc,
lib/TypeRepresentationTables.cc, lib/Vector3D.cc, lib/Version.cc,
lib/sockstream.cc, lib/zstream.cc, logo.jpg, mccore-config.in,
mkinstalldirs, stamp-h.in, test/GraphModel.cc,
test/HomogeneousTransfo.cc, test/OrientedGraph.cc,
test/UndirectedGraph.cc: Update the build system to CMake
2011-01-31 23:38 joroy
* .: Create a cmake branch for mccore
2011-01-31 23:34 joroy
* Remove old directory
2011-01-31 23:33 joroy
* Move mccore one directory up
2011-01-31 22:35 joroy
* Remove old CVS stuff
2007-01-14 18:21 larosem
* New modified bases.
2007-01-10 04:17 larosem
* Many new AtomType added.
2007-01-09 01:07 larosem
* Corrected Pairing and BHbond initialisation. Added isBHbond
predicate.
2007-01-09 00:15 larosem
* Deprecated method changed.
2007-01-09 00:14 larosem
* Corrected bug in UndirectedGraph.h.
2007-01-09 00:13 larosem
* All atoms are kept in the regular annotation.
2007-01-09 00:09 larosem
* Added some modified bases. Unstable release.
2007-01-09 00:05 larosem
* *** empty log message ***
2007-01-09 00:02 larosem
* New BHbond mask added.
2007-01-08 23:59 larosem
* New pBHbond type added.
2007-01-08 23:57 larosem
* New pHbond type added.
2007-01-08 23:46 larosem
* Contact cutoff added. Range insertion modified to speed the
process.
2007-01-08 23:44 larosem
* New annotation flag added.
2007-01-08 23:39 larosem
* Range insertion is much faster.
2007-01-08 23:33 larosem
* Extract contact takes a cutoff parameter. It also limits the
observed residues to DNA, RNA and Amino Acids.
2007-01-08 23:30 larosem
* New version.
2007-01-08 19:19 thibaup
* *** empty log message ***
2007-01-08 19:19 thibaup
* Corrected glycosyl restriction in CCM algorithm.
2006-11-20 18:33 larosem
* *** empty log message ***
2006-11-15 19:44 larosem
* PDB headers are read from file and saved in the Molecule. They
are written
in subsequent PDB saves.
2006-11-15 19:43 larosem
* Reduced annotation bounding box to 3A.
2006-11-14 19:01 larosem
* New insertion method added.
2006-11-14 18:58 larosem
* A new extractContacts method added that take the result vector as
an argument.
2006-11-08 20:43 thibaup
* Dummy rule for accurate library version info: Version.cc is
complied whenever any object is compiled, including itself.
Therefore it can be compiled twice ... :-(
2006-11-08 14:42 thibaup
* *** empty log message ***
2006-11-08 14:25 thibaup
* grouped rule 'mccore-config' in variable SCRIPTS
2006-11-08 14:24 thibaup
* added rule 'before-all' that forces compilation of Version.cc to
include accurate compilation info in library.
2006-11-08 14:23 thibaup
* new logo!
2006-11-08 14:22 thibaup
* configure cleanup: AC_OUTPUT is no longer used as obsolete
2006-10-31 20:11 thibaup
* forced dependency between mcore-config and mccore-config.in
2006-10-26 19:09 larosem
* insert method should return an exception when the string isn't
formatted correctly so that the application know what is
happening.
2006-10-24 19:11 thibaup
* - Corrected method ResidueType::generalizeBase to return the root
type ResidueType* if
unable to find a closer ancestor.
- Added new static type member ResidueType::rResidue of root type
ResidueType.
2006-10-11 18:40 thibaup
* corrected error in rule 'dist'
2006-10-11 17:55 thibaup
* static constant cannot be initialized in header file.
2006-10-11 17:35 thibaup
* - new constructor with version string parameter "x.x.x"
- new method version() returns version string only
- new method compatibleWith() verify if a version is compatible
with
another (by their first two version numbers)
2006-10-11 17:33 thibaup
* -f passed to gunzip
2006-10-04 14:57 larosem
* *** empty log message ***
2006-10-04 14:46 larosem
* *** empty log message ***
2006-09-26 12:31 thibaup
* corrected rnaml test
2006-09-22 18:12 thibaup
* Removed option --libs-static :-S
Option --libs now take optional argument CLASS to specify class
of
library to include:
all: all libs (default)
mccore: -lmccore
ext: extension libraries, if enabled (-lrnamlc++ if --with-rnaml)
std: standard libraries (-lz)
2006-09-22 15:45 thibaup
* - Added rnamlc++ in libs if configured to include it.
- New option '--libs-static' using linker '-B' switches to link
against static mccore (and rnamlc++) lib and dynamic z lib.
2006-09-22 15:42 thibaup
* New static method createSymbolic(). Returns a new Relation object
with
only symbolic members initialized (ref/res faces and labels).
2006-09-19 22:47 larosem
* Clear bug corrected.
2006-08-28 18:06 thibaup
* (re-)correction of method fillMoleculeWithCyles: both edge
direction
are saved in cycle with no vertex overwritting.
2006-08-28 17:51 thibaup
* new overload for reassignResiduePointers that takes already
determined
'ref' and 'res' addresses.
2006-08-28 17:50 thibaup
* method reassignResiduePointers() now throws
NoSuchElementException, in
sync with class Relation.
2006-08-18 16:26 larosem
* Reference bugs corrected.
2006-08-14 14:43 thibaup
* FileNotFoundException automatically reports system error message
(via
strerr()).
2006-08-02 18:29 larosem
* Typo.
2006-08-02 18:25 larosem
* Version 1.6.2
2006-08-02 18:01 larosem
* Final merge from 1.5.
2006-07-26 17:52 thibaup
* removed class namespace in header prototype.
2006-07-26 15:58 thibaup
* New static method parseAnnotationMask() that parses a string into
a
bitmask.
2006-06-29 19:12 thibaup
* * Version 1.6.1
** HomogeneousTransfo class reimplemented
New implementation of HomogeneousTransfo class. Replaced the 16
float
array by 12 independent float variables for first three row of
the 4X4
matrix. Last row is implicit (always {0,0,0,1}). The interface is
unchanged.
Using default gcc optimization (-O2), matrix multiplication is
now
100X faster and matrix inversion is near 200X faster.
Multiplication
by a 3D point (Vector3D) at same speed, however.
New implementation of matrix inversion. Previous implementation
was
using the analytical simplification applicable to rigid body
transformation. However, this method shows unstable numerical
error. Therefore it was replaced by a general inversion method
applicable to any invertible matrix. This method isn't more
precise
than the latter method as a one-shot, but numerical errors are
stable. Even if more floating point operations are needed to do
so,
performance with default gcc optimization (-O2) is not
affected. Previous implementation was still conserved and renamed
invert_unstable().
2006-06-29 18:39 thibaup
* *** empty log message ***
2006-06-29 16:50 thibaup
* *** empty log message ***
2006-06-29 16:49 thibaup
* *** empty log message ***
2006-06-22 21:10 thibaup
* *** empty log message ***
2006-06-22 20:08 thibaup
* Added logo.jpg to dist files
2006-06-22 18:13 thibaup
* *** empty log message ***
2006-06-22 18:07 thibaup
* Makefile.in
2006-06-22 18:06 thibaup
* removed rule 'release'
2006-06-22 17:58 thibaup
* Updated rule 'dist'
Removed rule 'release'
2006-05-31 13:32 thibaup
* Added output for long long integer
2006-05-24 13:01 thibaup
* rule mccore-config corrected
2006-05-15 19:52 thibaup
* *** empty log message ***
2006-05-15 18:10 thibaup
* - Added one bit to annotation mask for backbone pairing:
msb-ASPB-lsb.
- Optional parameter to annotate(): ASPB mask bit.
- In Relation: areAdjacent(), areStacked, arePaired and
areHBonded now
public.
2006-05-15 17:59 thibaup
* (same as below)
2006-05-15 17:59 thibaup
* Added (resurrected...) C1' atom in nuclebases' theoretical
coordinates. A bool parameter controls its addition (default is
no
addition).
2006-05-15 17:56 thibaup
* Correction in operator= from a Residue object. Local and global
coordinates being the same, the new referential is set
to identity.
2006-05-04 20:21 larosem
* Merge from rel-1-5-patch-5.
2006-05-04 13:59 thibaup
* Added mccore-config script to package.
2006-05-03 21:11 larosem
* Patch merge from rel-1-5.
2006-05-02 20:54 larosem
* Merge with rel-1-5-patch-4.
2006-05-02 20:03 larosem
* Merge with rel-1-5-patch-3.
2006-05-02 19:52 larosem
* *** empty log message ***
2006-05-02 19:51 larosem
* evaluate include base orientation for a better classification.
2006-05-02 19:48 larosem
* cis/trans uses _pyrimidine_ring_center rather than average hbonds
orientation. translatePairing include base orientation for a
better classification.
2006-05-02 19:41 larosem
* Lifted output level for hydrogens and lone pair warnings.
2006-05-02 19:33 larosem
* Corrected xmlcpg include directories.
2006-05-02 19:32 larosem
* Added LGPL license headers.
2006-04-18 15:31 thibaup
* - new install-doc and uninstall-doc rule, installing doc in
share/mccore/1.6.0/doc (including html)
- logo now shows 1.6.0
2006-04-13 18:05 thibaup
* changed header include directory from xmlcpg/ to rnamlc++/
2006-04-13 18:03 thibaup
* added warning message if type is unknown
2006-04-13 18:02 thibaup
* added copy constructor and assignation operator for base class
Vector3D (slicing not explicitly prevented).
2006-02-24 15:38 larosem
* Merge from rel-1-5-patch-1.
2006-02-23 16:35 gendrop
* Removed O2' and HO2' from arePaired since they are not base atoms
2006-01-26 21:22 thibaup
* Modified topology graph type: edges are now pair of atom types
representing the linked vertices
2006-01-26 21:19 thibaup
* Renamed class attributes ... apparently "minor" and "major" are
replaced by cpp!
2006-01-26 21:18 thibaup
* print the matrix on scale factor error when trying to invert.
2006-01-24 16:56 larosem
* *** empty log message ***
2006-01-23 23:05 larosem
* Version 1.6.0.
2006-01-23 22:06 larosem
* Type punning bug.
2006-01-19 20:09 larosem
* Bug corrected in sort. The code was rewritten to preserve it's
independence with the super class.
2005-12-19 17:51 thibaup
* Updated for new stacking property types and parallel/antiparallel
2005-12-16 17:38 thibaup
* Bug in floating value I/O ..
Replaced former use of float aliasing to int by type punning.
However
it is still to be proven what is the appropriate way to pass a
float
in htonl() and ntohl().
2005-12-15 16:46 thibaup
* new global operator<< to print an Exception object in an
Exception
stream.
2005-12-12 21:40 thibaup
* temporary boolean parameter "backbone" passed to method
Relation::annotate() and GraphModel::annotate():
true (default) => annotate everything.
false => don't annotate pairing with backbone (O2P and O2').
2005-12-09 22:47 larosem
* Bug correction.
2005-12-09 18:47 thibaup
* comment update in stacking annotation
2005-12-09 18:46 thibaup
* Bug corrected in Residue and ExtendedResidue object copy.
2005-12-09 18:28 larosem
* Model assignment bug corrected.
2005-11-25 20:07 thibaup
* corrected a double-delete bug (grrr...)
2005-11-17 19:26 thibaup
* New labeling:
- sub-families "straight" and "reverse" no longer inherit from
"stack". They are now root families (inherit PropertyType only)
- "stacking" sub-family upward renamed "up"
- "stacking" sub-family downward renamed "down"
- "upward" replaces "straight_upward" (inherits both up and
straight)
- "downward" replaces "straight_downward" (inherits both down and
straight)
- "inward" replaces "reverse_upward" (inherits both up and
reverse)
- "outward" replaces "reverse_downward" (inherits both down and
reverse)
- new type "parallel" inherits both "pairing" and "straight"
(replaces
"straight" in pairing annotation)
- new type "antiparallel" inherits both "pairing" and "reverse"
(replaces "reverse" in pairing annotation)
- Removed sub-family "BaseOrientation"
2005-11-15 16:10 thibaup
* using an explicit level for warning output
2005-11-15 16:09 thibaup
* moved non-integral type float constant from class member static
constant to global constant in .cc files
2005-11-04 19:46 larosem
* Corrections on templates for gcc 4.0
2005-10-25 15:36 thibaup
* Residue::setReferential() recomputes pseudo atoms to avoid
numerical
instability.
Cannot be done in getReferential() because of constness, but a
call to
finalize() also recomputes pseudo atoms.
2005-10-19 14:52 thibaup
* Added RNA and DNA flavour for Phosphate residue type.
2005-09-30 20:24 larosem
* areHBonded lives again!!!
2005-09-30 19:21 thibaup
* new general type static instance rRibose for a nucleic acid
ribose
(RNA or DNA)
2005-09-30 19:20 thibaup
* inverting phosphate tfo only if relation is annotated as adjacent
2005-09-30 19:19 thibaup
* Implementation modification:
- no redefinition of operator<< from ostream
- inhibition of ouput controlled by a temporary redirection of
streambuf to NULL (is this legal?)
2005-09-21 22:14 larosem
* No headers are witten in Pdbstream::AMBER mode.
2005-09-14 18:33 thibaup
* *** empty log message ***
2005-09-14 16:57 thibaup
* - new multiline writing method that doesn't breakup words
2005-09-09 22:02 larosem
* O2P and O2' annotations are added, a simple distance metric is
used. For this purpose, 2 new properties are added pRibose and
pPhosphate.
2005-09-06 15:32 larosem
* H-bond maximum distance value constant put in a constant
variable.
2005-08-30 19:51 larosem
* Amber terminals added to ResidueTypeStore table.
2005-08-30 17:58 thibaup
* added operator<< for short and long long integer types
2005-08-30 13:16 thibaup
* removed static strings
2005-08-30 13:16 thibaup
* new IntLibException "FileNotFoundException"
2005-08-26 20:22 larosem
* Inserted atoms should be put back in local coordinates even if
the placed flag is false.
2005-08-23 13:17 thibaup
* corrected error in getFuranoseType()
2005-08-19 20:24 thibaup
* *** empty log message ***
2005-08-19 20:22 thibaup
* correction for binstream i/o compatibility accross 32b and 64b
arch
2005-08-19 19:17 larosem
* Binstream type corrections for 32/64 bits compatibility (not
complete).
2005-08-19 19:00 thibaup
* bug correction in class AtomSetAtom
2005-08-19 15:26 thibaup
* slightly reduced compilation time...
2005-08-19 15:24 thibaup
* modified method getFuranoseType(): now using 16 propertytype
labels
named "{alpha,beta}-{L,D}-{lyxo,ribo,arabino,xylo}furanoside",
where
"beta-D-ribofuranoside" is the canonical type in RNA
2005-08-18 18:07 larosem
* Binary dump for GraphModel, Relations and HBond added.
2005-08-15 21:28 larosem
* Added Binstream to I/O.
2005-08-05 16:01 larosem
* *** empty log message ***
2005-08-05 16:00 larosem
* ResidueType pointers singletons are const.
2005-08-05 15:59 larosem
* String explicitely allocated on stack.
2005-08-05 15:58 larosem
* Pseudo constants changed to real constants.
2005-08-05 15:55 larosem
* Path and cycle stuff removed until completed. Relations are
deleted before the Residues (more logical).
2005-08-05 15:53 larosem
* Path and cycle stuff removed until completed.
2005-08-05 15:51 larosem
* *** empty log message ***
2005-07-26 21:46 larosem
* memcpy is not posix.
2005-07-26 20:25 larosem
* Bug correction: the size of an object cannot be known until it's
class is fully defined.
2005-07-18 20:17 thibaup
* - Modified ribose optimization methods objective function return
value: now returning the RMSD between length of implicit C5'-O5'
and
C3'-O3' bonds and their theoretical length (1.440 and 1.431
Angstroms respectively).
- Modified range of acceptable omega value in estimation: now
accepting omega in [-1.25,1.25].
- Exterminated a bug in estimation method.
- Clarification of header comments.
2005-07-18 20:14 thibaup
* Changed default value for alpha_square static variable to
2.632^2, and
temporary removed its constness.
2005-07-18 20:12 thibaup
* Using AC_CANONICAL_HOST variables instead of calling uname
2005-07-08 00:25 larosem
* A GraphModel is clearly an oriented graph and not a undirected
graph.
2005-06-23 19:06 larosem
* front and back method added.
2005-06-21 13:48 thibaup
* - bug correction in _build_ribose_preprocess()
- new methods getFuranoseAmplitude() and getFuranoseType()
2005-06-20 15:14 thibaup
* warning when residue number < -999 (along with > 9999)
2005-06-16 15:55 thibaup
* - warning messages issued when ATOM record format is not
respected in
ouput stream.
2005-06-16 15:53 thibaup
* - correct value now returned by buildRiboseByEstimation()
2005-06-10 18:09 thibaup
* PSO atom was missing in obligatory sets.
2005-06-09 15:01 larosem
* New file.
2005-06-09 14:41 thibaup
* new filter methods keepRNA(), keepDNA and keep(ResidueType*)
2005-06-07 22:15 larosem
* Defined variable KERNEL created conflict with Darwin's global
variable.
2005-06-07 20:42 larosem
* long double types removed to accomodate Darwin compilation.
2005-06-07 19:59 larosem
* *** empty log message ***
2005-05-31 20:28 thibaup
* using uname -s instead of uname -o for compatibility with Darwin
2005-05-31 20:05 thibaup
* Modified I/O methods of primitive types to be compatible between
32b
and 64b architectures. Type sizes are written and read as follow:
16b: char, unsigned char, signed char, short, unsigned short.
32b: int, unsigned, float.
64b: long int, unsigned long int, long long int, unsigned long
long int, double.
Strings (char* or std::string) support is unchanged, i.e. the
length
integer precedes the character buffer. There is no support for
long
double or long long double.
Switch between 32b and 64b was tested sucessfully in both
directions,
but endianess is still to be tested...
2005-05-31 19:55 thibaup
* output standard string instead of C-style char* string.
2005-05-31 19:52 thibaup
* New method safeFind() that throws NoSuchElementException when
residue
isn't found.
2005-05-20 15:28 thibaup
* New utility class Version to output package version and building
information.
2005-04-27 16:44 thibaup
* Copy constructor correction: atoms are copied from source object
using
the class interface in case the source object is an
ExtendedResidue
and needs to be placed (see class ExtendedResidue).
2005-04-13 16:04 thibaup
* PDB file title section is cut at 70 characters for read and write
2005-04-12 20:14 larosem
* Sequence annotation is added in the rnaml output.
2005-04-12 19:56 larosem
* 'good' flag is used instead of eof.
2005-04-12 19:55 thibaup
* corrected string "RRU33" to "RRU3"
2005-04-12 19:55 larosem
* Bug correction: GraphModel was not able to stop at the ENDMDL.
2005-04-07 21:09 larosem
* mccore models will be placed in separate rnaml Molecule.
Sequences may not be the same between models.
2005-04-07 19:20 larosem
* Saenger and Gautheret types written in base-pair comment.
2005-04-07 19:19 larosem
* Dependency flag changed to -M to catch library changes.
2005-04-06 16:21 thibaup
* type helix now inherits from type stack
2005-04-06 16:21 thibaup
* New pseudo atom PSO at nucleotide frame's origin (N1 in
pyrimidines,
N9 in purines).
2005-04-04 23:08 larosem
* gcc 3.4 types update.
2005-03-31 22:33 larosem
* Type correction.
2005-03-31 22:32 larosem
* -fPIC added for 64bits compilation.
2005-03-30 19:01 larosem
* strand-orientation added.
2005-03-30 18:59 larosem
* Initialisation moved to header file.
2005-03-30 18:57 larosem
* ResidueType and not Residue should be included.
2005-03-29 23:41 larosem
* Empty remark string ranges from 12 to 70.
2005-03-22 01:10 larosem
* Structure annotations are saved.
2005-03-17 22:15 larosem
* Annotation setter added.
2005-03-14 21:19 thibaup
* minor correction
2005-03-10 22:58 larosem
* Output operator redirects the call to the virtual method.
2005-03-10 19:18 thibaup
* *** empty log message ***
2005-03-10 19:03 thibaup
* Added missing Binstream I/O operators in header file
2005-03-10 18:36 thibaup