File: NEWS

package info (click to toggle)
openbabel 2.0.2-1
  • links: PTS
  • area: main
  • in suites: etch, etch-m68k
  • size: 15,652 kB
  • ctags: 15,998
  • sloc: cpp: 128,176; ansic: 86,170; sh: 8,920; perl: 1,847; python: 1,369; pascal: 793; makefile: 381; xml: 97
file content (221 lines) | stat: -rw-r--r-- 9,281 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
Open Babel 2.0.2 (2006-07-24)

What's New from 2.0.1:

This release represents a bug-fix release and should be a stable upgrade,
recommended for all users of Open Babel. A large number of bugs have
been fixed, so even users who have not had problems with 2.0.1 are
encouraged to upgrade.

- Substantial fixes to the SMILES and SMARTS parsing support, thanks
  to a variety of bug reports.
- A variety of fixes to aromaticity perception and Kekule form
  assignment.
- Fixed gzip support, broken in version 2.0.1 inadvertantly.
- Output a warning when a multi-molecule files is converted to a
  single-molecule format.
- Better support for command-line tools such as obgrep on Cygwin.
- Fixed a variety of crashes.
- Countless other bug fixes.

Open Babel 2.0.1 (2006-04-17)

What's New from 2.0.0:

This release represents a bug-fix release and should be a stable upgrade,
recommended for all users of Open Babel.

- Support for dynamic building on the Cygwin environment. This fixes a
  long-standing problem that made Open Babel useless to Cygwin users.
- Fixed a variety of memory leaks and improved overall memory use. 
  More work to reduce memory consumption is underway for the 2.1 release.
- Improved Perl and Python scripting wrappers, including many
  bug-fixes.
- Fixes to the "make check" test suite, which should prevent problems
  running before babel is installed.
- Fixes compilation problems with AIX, Fedora Core 4, and the
  newly-released GCC-4.1.
- Fixed several reported compilation problems with Windows builds
  using VisualC++.
- Fixed several reported crashes.
- Fixed problems with the Turbomole format, thanks to Mikael
  Johansson.
- Fixed a bug with PDB files with coordinates < -1000 Ang.
- Improved support for the Sybyl mol2 format, thanks to Kevin Parkes.
- Fixed a variety of typos in the API documentation.
- Countless bug fixes.


Open Babel 2.0 (2005-11-26)

What's New from 1.100.2:

This release represents Open Babel's fourth "birthday" and a milestone for
a stable, flexible interface for developers and users alike.

- New conversion framework. The new framework allows dynamic
   loading/unloading of file translator modules (i.e., shared
   libraries, DLLs, DSO, etc.). More importantly, it facilitates adding
   new formats, since each format is self-contained and no editing of
   other files is required.
- Improved support for XML chemistry formats, including CML, PubChem XML, 
- Support for fingerprinting and calculation of Tanimoto coefficients for 
   similarity consideration. 
   (A flexible fingerprint framework is available for developers.)
- New support for Perl and Python "wrappers" of the Open Babel library.
- Many enhancements to the Open Babel API: See the Developers API Notes for
   more information. Some code will require updating, see the 
   Developer's Migration Guide for details.
- Support for automatically reading .gz compressed files.
   (e.g., 1abc.pdb.gz is uncompressed and treated as a PDB file)
   Use of the -z flag creates gzip-compressed output files.
- Support for the new IUPAC InChI identifiers.
- Improved bond order typing, including flexible SMARTS matching in
   bondtyp.txt.
- New Kekulization routine -- improves aromaticity detection in aromatic amines
   like pyrroles, porphyrins, etc.
- Improved support for radicals and spin multiplicity, including
   assignment of hydrogens to radicals.
- Improved support for 2D vs. 3D file formats.
- New error logging framework keeps an "audit log" of changes to files
   (hydrogen addition, bond order assignment) and different levels of
   error reporting / debugging.
   Use the "---errorlevel 4" flag to access this information.
- Improved atom typing and hydrogen addition rules.
- Improved obfit utility will output RMSD and find matches with the
   best RMSD.
- Updated isotope data from 2003 IUPAC standard.
- Updated elemental data from the Blue Obelisk Data Repository.
   (project started, in part, to validate the old Open Babel data)
- Improved z-matrix code (CartesianToInternal / InternalToCartesian).
- Countless bug fixes.

New File Formats:
  Import & Export: 
	  ChemDraw CT (Connection Table)
	  CML Reaction files
	  MDL Molfile V3000
	  MDL Rxn files
	  Open Babel free-form fractional (crystallographic coordinates)
	  Open Babel fastsearch database format
	  Open Babel fingerprint formats
	  PCModel format
	  YASARA.org YOB format
	  Turbomole
          Improved CML support
  	  Improved Gaussian 98/03 support
	  Improved SMILES import / export
  Import-Only:
          PubChem XML
  Export-Only: 
 	  MPQC input
	  Open Babel "copy" format (i.e., copy the raw input file)
	  Sybyl MPD descriptor format
	  IUPAC InChI descriptor

  Changed formats:
          MMADS - eliminated
	  bin - OpenEye binary v 1, eliminated
	  GROMOS96 - changed from separate g96a & g96nm types to a
	    unified g96 type. Defaults to output Angstroms, Use -xn
	    to output nm.
	  Titles - eliminated -- can be produced with SMILES -xt

Open Babel 1.100.2 (2004-02-22)

What's New from 1.100.1:

 -Shared library (version 0:0:0) built by default on POSIX systems
  (e.g. Linux, BSD, Mac OS X...)
 -Fixed installation of header files. The headers in the math/
  subdirectory were not installed alongside the other headers.
 -Added tools/ directory with small examples of using libopenbabel:
   * obgrep: Use SMARTS patterns to grep through multi-molecule files.
   * obfit:  Use SMARTS patterns to align molecules on substructures.
   * obrotate: Rotate a torsional bond matching a SMARTS pattern.
 -Improved PDB support: uses HETATM records more appropriately, attempts to
  determine chain/residue information if not available.
 -Fixed a variety of bugs in ShelX support.
 -Added support for handling atom and molecule spin multiplicity.
 -Updated documentation -- not yet complete, but significantly improved.
 -Fixed major omissions in CML readers and writers. All versions of CML are now
  supported (CML1/2 and array/nonArray). Also added *.bat
  file for roundtripping between these formats for both 2- and 3-D data.
  Fixed bugs in test/cmltest/cs2a.mol.cml.
 -Building and running the test-suite in a build-directory other than the
  source-directory is now fully supported.
 -Support for the Intel C++ Compiler on GNU/Linux.
 -Miscellaneous fixes to make it easier to compile on non-POSIX machines.

New File Formats:

  -Export: Chemtool
           Chemical Resource Kit (CRK) 2D and 3D
           Parallel Quantum Solutions (PQS)
  -Import: CRK 2D and 3D
           PQS

Open Babel 1.100.1 (2003-6-24)

What's New from 1.100.0:

 -Much better bond typing overall for files converted from formats
  without bond information (e.g. XYZ, QM codes). Fixed some bugs in
  1.100.1 and added additional improvments.
 -Support for the command-line "babel" program to convert some or
  all structures in a file with multiple molecules. By default this
  version will convert all molecules in a file. To change this, use
  the -f and -l command-line options as documented in the man page.
 -Isotope support, including exact masses in the "report" file
  format and SMILES data.
 -Updated API documentation.
 -Support for the Borland C++ compiler.
 -Fixed a variety of bugs in the PDB file format support, including
  better bond typing.
 -Support for output of residue information in the Sybyl Mol2 file
  format.
 -Some support for conversion of unit cell information, both in the
  library and in some file formats (i.e. DMol3, Cacao).
 -Coordinates now use double-precision floating point libraries for
  greater accuracy in conversions.
 -Fixed a variety of bugs uncovered in roundtrip testing.
 -Fixed a bug when attempting to perceive bond information on 2D
  structures.
 -Fixed several rare bugs that could cause segmentation faults.

New File Formats:

  -Import: ShelX
  -Export: ZINDO input

A big thanks to all who helped contribute to this release,
especially those reporting bugs, suggesting features, and donating
files to the test suite. All of this is greatly appreciated!


Open Babel 1.100.0 (2002-12-12)

What's New from 1.99:

 -Bond order typing is performed when importing from formats with no notion of
  bonds (quantum chemistry programs, XYZ, etc.).  -Now better conforms to the ISO
  C++ standard, should compile on most modern C++ compilers.
 -Improved test suite, including "roundtrip" testing, ensuring more accurate translations.
 -Support for the Chemical Markup Language (CML) and other file formats. (see below)
 -Improved PDB support -- should read PDB files more accurately and hew closer to the current PDB standard for export.
 -Improved Gaussian input generation.
 -Added support for the Chemical MIME standards, including command-line switches.
 -Added support for using the babel program as a pipe for a "translation filter" for other programs.
 -Can add hydrogen atoms based on pH.
 -Fixed a variety of memory leaks, sometimes causing other bugs.
 -Fixed a wide variety of bugs in various file formats.
 -Faster SMARTS matching and some overall speedups across the program.
 -API documentation using the Doxygen system.
 -Of course there are *many* other bug-fixes and improvements.

New File Formats:

  -Import: NWChem Output
  -Export: POV-Ray, NWChem Input
  -Both: CML, ViewMol, Chem3D