diff --git a/CMakeLists.txt b/CMakeLists.txt index 241ceff3e2..33bf2da29e 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -32,7 +32,7 @@ endif() # had too many 1.100.1 releases. :-) set(BABEL_MAJ_VER 3) set(BABEL_MIN_VER 0) -set(BABEL_PATCH_VER 0a2) +set(BABEL_PATCH_VER 0) # This should be phased out in preference for just using the target name set(BABEL_LIBRARY openbabel) diff --git a/NEWS b/NEWS deleted file mode 100644 index 72354395b2..0000000000 --- a/NEWS +++ /dev/null @@ -1,515 +0,0 @@ -Open Babel 2.5.0 (2017-XX-XX) - -Open Babel 2.4.0 (2016-9-15) - -Open Babel 2.3.0 (2010-10-23) - -This release represents a major update and should be a stable upgrade, -strongly recommended for all users of Open Babel. Highlights include a -completely rewritten stereochemistry engine, Spectrophore fingerprint -generation, 2D depiction, improved 3D coordinate generation, conformer -searching, and more. Many formats are improved or added, including -CIF, PDBQT, SVG, and more. Improved developer API and scripting -support and many, many bug fixes are also included. - -What's New from 2.2.3: - -* Completely rewritten stereochemistry perception, including support - for tetrahedral, square planar, and higher-order stereochemistry. -* Dramatically improved canonicalization algorithm (Note that in general, canonical SMILES have changed since the 2.2.x release.) -* 2D depiction, including SVG vector graphics generation using code from MCDL. -* New Spectrophore generation, contributed by Silicos NV. -* New ChargeMethod API including support for partial charge assignment - from Gasteiger, MMFF94, QEq, QTPIE methods and plugin interface for - adding more. -* Improved 3D coordinate generation. -* New conformer generation framework, including support for diverse - conformer generation and genetic algorithm lowest-energy searching. -* Improved user documentation. -* Improved aromaticity / Kekule bond assignment. -* Improved unit test suite using the CMake-based CTest program. -* Improved support for crystallographic unit cells (e.g., in CIF format). -* Improved UFF force field method, including hypervalent 5, 6, 7 and higher coordination numbers. -* Support for the GAFF (Generalized Amber Force Field) method. -* Support for reading geometry optimizations as multiple conformers - from Gaussian, GAMESS-US, and other quantum chemistry packages. -* Support for reading molecular orbital energies from quantum chemistry formats. -* Several memory leaks fixed. -* Fixed many compiler warnings. -* Fixed support for MinGW and Cygwin environments. -* Fixed bugs with Gaussian 09 output files. -* Latest released version of the InChI library (1.0.3) generating standard InChI. -* Many more bug fixes and small feature improvements. - -==New Command-Line Operations== - -* --canonical: Output atoms in canonical order for any file format (i.e., not just SMILES) -* --conformer: Run a conformer search on the input molecules (has many options) -* --gen2D: Generate a 2D depiction of the molecule -* --partialcharge : Use the partial charge model supplied to - generate charges (i.e., instead of default Gasteiger sigma model) -* --sort : Sort molecules by a specified descriptor -* --unique: Only output unique molecules (as determined by InChI generation) - -==New File Formats== - -Import & Export: -- DL-POLY CONFIG -- FHIaims XYZ -- PDBQT - -Import only: -- DL-POLY HISTORY -- GULP output -- PWscf output -- Text - -Export only: -- MNA (Multilevel Neighborhoods of Atoms) -- SVG vector graphics - - -Open Babel 2.2.3 (2009-07-31) - -What's New from 2.2.2: - -This release represents an important bug-fix upgrade, strongly recommended -for all users of Open Babel. - -- Fixed bug in fingerprints in 2.2.2, where the default fingerprint - format and bit length was changed inadvertently. -- Fixed detection of shared_ptr in tr1/memory. -- Fixed additional aromaticity / Kekule assignment bugs. -- Fixed several bugs in the MMCIF format. -- Additional bug fixes. - -Open Babel 2.2.2 (2009-07-04) - -What's New from 2.2.1: - -This release represents a major bug-fix release and is a stable -upgrade, strongly recommended for all users of Open Babel. While there -may not be many new features, many crashes and other bugs have been -fixed since 2.2.1. - -- Upgraded to the new InChI 1.02 release to produce standardized InChI - and InChIKey output. -- Fixed many stereochemistry errors when reading/writing SMILES. This - is part of a larger project which will be finished in the 2.3 - release. -- Fixed compilation and installation on Cygwin and MinGW platforms. -- Significantly improved aromaticity and Kekule bond assignment. -- Improved 2D -> 3D coordinate generation -- Improved coordinate generation using the --gen3d command-line - operation -- Improved performance for coordinate generation. -- New --fillUC command-line operation for babel. -- Fixes to pH-dependent hydrogen addition. -- Added support for reading vibrational data from Molden, Molpro, and - NWChem output files. -- Updated atomic radii from recent theoretical calculations. -- Fixed bug when reading gzip-compressed Mol2 or XML files. -- Close files after an error. Fixes a bug with Pybel where files would - remain open. -- Many more bug fixes and small feature improvements. - -==New File Formats== - -Import & Export: -- Molpro input and output. -- VASP coordinate files (CONTCAR and POSCAR). - -Open Babel 2.2.1 (2009-03-01) - -What's New from 2.2.0: - -This release represents a major bug-fix release and is a stable -upgrade, strongly recommended for all users of Open Babel. While there -may not be many new features, many crashes and other bugs have been -fixed since 2.2.0. - -- Improved scripting interfaces, including Python 3 support and improved - Java and C# support. -- Added support for MACCS fingerprints. Thanks to the RDKit project. -- Many fixes and enhancements to the force field code. In particular, - the UFF force field implementation should handle many more molecules. -- Improved 3D coordinate generation, particularly with ring - fragments. You can give this a try with the obgen utility. -- Fixed a variety of PDB import errors with atom types. -- Added support for reading charges and radii from PQR file formats. -- Added support for reading and writing unit cells in PDB formats. -- New "output" file format for taking generic ".out", ".log", and - ".dat" files and reading with appropriate file type based on - contents. Currently works extremely well for quantum chemistry - packages. -- Added improved error handling and reporting when unable to load file - formats. -- Improved CIF file format support. -- Many, many, many additional bug fixes and small enhancements. - - -Open Babel 2.2.0 (2008-07-04) - -What's New from 2.1.1: - -- New support for 3D coordinate generation using the OBBuilder class. - Note that this code directly supports non-chiral compounds - Stereochemistry may or may not be supported in this release -- Significantly faster force fields (up to 200x faster) and support - for constrained optimization. -- New force fields, including complete UFF, MMFF94, and MMFF94s implementations. -- Monte Carlo conformer search support, including a new obconformer tool. -- Unified framework for plugin classes, including easy-to program file - formats, descriptors, filters, force fields, fingerprints, etc. -- A new "descriptor" plugin framework for QSAR descriptors, etc. - Initial descriptors include hydrogen-bond donors, acceptors, - octanol/water partition, topological polar surface area, molar - refractivity, molecular weight, InChI, SMARTS, titles, Lipinski - Rule of Five, etc. -- A new "filter" plugin framework for selecting molecules by title, - molecular weight, etc. -- Facility to add new "ops", commandline options or operations on the - conversion process as plugin code. - Initial operations include 3D coordinate generation, tautomer - standarization, and addition of polar hydrogens. -- Code for integrating Open Babel and the BOOST graph library. -- Improved scripting support, including new bindings for C# and - improved Java, Ruby, Python, and Perl bindings. -- Space group support and thoroughly revised and improved CIF format. -- Initial support for 3D point group symmetry perception. -- Improved support for "grids" or "cubes" of molecular data, such as - from quantum mechanics programs. (See below for supported file - formats.) -- Initial support for reading trajectories and animations. -- Improved support for reaction formats, including CML, RXN, and - Reaction SMILES. -- Improved residue handling in PDB and Mol2 formats. -- Improved pH-dependent hydrogen addition. -- Latest released version of the InChI library, including use of the - latest "preferred" options for InChI generation. -- Support for the cross-platform CMake build system. -- File format modules are now installed in a version-specific - directory on unix, preventing problems between 2.2.x and 2.1.x (or - older) plugin libraries. -- Framework to support "aliases" for group abbreviations, partially - implemented for MDL formats. -- Many more bug fixes and small feature improvements. - -==New File Formats== - -Import & Export: - Chemkin - Gaussian Cube - Gaussian Z-matrix - GROMACS xtc trajectories - MCDL - mmCIF - OpenDX cube (e.g., from APBS) - Reaction SMILES -Import only: - Accelrys/MSI Cerius II MSI text format - ADF output - ADF Tape41 ASCII data - GAMESS-UK input and output - Molden structure - PNG (for embedded chemical data) - PQR -Export only: - MSMS input - ADF input - InChI Keys - -Open Babel 2.1.1 (2007-07-07) - -What's New from 2.1.0: - -- 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) - -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: - -- 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 - - -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 - diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index eccb1e04d9..7c83ca3558 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,6 +1,6 @@ # Library versioning -set(SOVERSION 5) -set(LIBRARY_VERSION 5.0.0) +set(SOVERSION 6) +set(LIBRARY_VERSION 6.0.0) find_package(Boost 1.45.0 COMPONENTS system)