Open Babel 2.1.1 (2007-07-07) What's New from 2.1.0: This release represents a bug-fix release and should be a stable upgrade, highly recommended for all users of Open Babel. A large number of bugs have been fixed, so even users who have not had problems with 2.1.0 are encouraged to upgrade. - Improved scripting support, including dictionary-support for OBGenericData in pybel, casting from OBUnitCell, etc. Improved access to OBRings from OBMol.GetSSSR(). - Added support for descriptors (e.g., PSA, logP) from scripting interfaces. - Added support for reading all PDB records (beyond current atom and bond connections). Records not handled directly by Open Babel are added as key/value pairs through OBPairData. - Added a new configure flag --with-pkglibdir to allow Linux package distributors to define version-specific directories for file format plugins. - Fixed a bug which would not output chirality information for canonical SMILES with 3D files. - Fixed problems with new line-ending code. Now correctly reads DOS and old Mac OS files with non-UNIX line endings. - Correctly rejects SMILES with incorrect ring closures. Thanks to Craig James for the report. - Fixed a crash when output to canonical SMILES. - Fixed a crash when converting from SMILES to InChI. - Fixed a crash when reading some PDB files on Windows. - Fixed a crash when reading invalid MDL/SDF files. - Fixed a bug which made it impossible to read some GAMESS files. - Fixed a problem when reading ChemDraw CDX files on Mac OS X. - A large number of additional fixes, including some rare crashes. Open Babel 2.1.0 (2007-04-07) This release continues the Open Babel version 2 series, introducing new features and file formats without breaking compatibility. What's New from 2.0.2: - Now handles molecules with >65536 atoms or bonds. Some PDB entries, in particular have such large molecular systems. - New features for molecular mechanics force fields, including energy evaluation and geometry optimization. Ultimately, this will enable coordinate generation and refinement for SMILES and other formats. (A flexible force field framework is available for developers.) - Implementation of the open source Ghemical all atom force field. - Framework for canonical atom numbering, including a new canonical SMILES format. - New support for Ruby and Java interfaces to the Open Babel library. - Improved scripting interfaces through Perl and Python, including the new "pybel" module with a more Python-like syntax. - Automatically handles reading from text files with DOS or Mac OS 9 line endings. - Many enhancements to the Open Babel API: See the Developers API Notes for more information. - New obenergy tool - evaluate the energy of a molecule using molecular mechanics. - New obminimize tool - optimize the geometry of structures using molecular mechanics. - Improved obprop tool - outputs a variety of molecular properties including Topological Polar Surface Area (TPSA), Molar Refractivity (MR), and logP. - The babel tool can now setting program keywords for some quantum mechanics formats from the command-line, including: GAMESS, Gaussian, Q-Chem, and MOPAC. (This feature can also be accessed by developers and expanded to other formats.) - New options for babel tool, including: -e for continuing after errors -k for translating computational keywords (e.g., GAMESS, Gaussian, etc.) --join to join all input molecules into a single output --separate to separate disconnected fragments into separate molecular records -C (combine mols in first file with others having the same name) --property to add or replace a property (e.g., in an MDL SD file) --title to add or replace the molecule title --addtotitle to append text to the current molecule title --addformula to append the molecular formula to the current title - Many more bug fixes and small feature improvements. New File Formats: Import & Export: Carine's ASCII Crystal (ACR) ChemDraw CDX & CDXML Crystallographic Interchange Format (CIF) Fasta Sequence Thermo Format Import: Gaussian fchk InChI Export: Open Babel MolReport Titles 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: - 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