标题: OpenBabel version 2.4.0 released [打印本页] 作者Author: greatzdk 时间: 2016-9-24 22:16 标题: OpenBabel version 2.4.0 released A major new update to OpenBabel has been released, version 2.4.0 is a significant change and is highly recommended.
New file formats
DALTON output files (read only) and DALTON input files (read/write) (Casper Steinmann)
JSON format used by ChemDoodle (read/write) (Matt Swain)
JSON format used by PubChem (read/write) (Matt Swain)
LPMD's atomic configuration file (read/write) (Joaquin Peralta)
The format used by the CONTFF and POSFF files in MDFF (read/write) (Kirill Okhotnikov)
ORCA output files (read only) and ORCA input files (write only) (Dagmar Lenk)
ORCA-AICCM's extended XYZ format (read/write) (Dagmar Lenk)
Painter format for custom 2D depictions (write only) (Noel O'Boyle)
Siesta output files (read only) (Patrick Avery)
Smiley parser for parsing SMILES according to the OpenSMILES specification (read only) (Tim Vandermeersch)
STL 3D-printing format (write only) (Matt Harvey)
Turbomole AOFORCE output (read only) (Mathias Laurin)
A representation of the VDW surface as a point cloud (write only) (Matt Harvey)
New file format capabilities and options
AutoDock PDBQT: Options to preserve hydrogens and/or atom names (Matt Harvey)
CAR: Improved space group support in .car files (kartlee)
CDXML: Read/write isotopes (Roger Sayle)
CIF: Extract charges (Kirill Okhotnikov)
CIF: Improved support for space-groups and symmetries (Alexandr Fonari)
DL_Poly: Cell information is now read (Kirill Okhotnikov)
Gaussian FCHK: Parse alpha and beta orbitals (Geoff Hutchison)
Gaussian out: Extract true enthalpy of formation, quadrupole, polarizability tensor, electrostatic potential fitting points and potential values, and more (David van der Spoel)
MDL Mol: Read in atom class information by default and optionally write it out (Roger Sayle)
MDL Mol: Support added for ZBO, ZCH and HYD extensions (Matt Swain)
MDL Mol: Implement the MDL valence model on reading (Roger Sayle)
MDL SDF: Option to write out an ASCII depiction as a property (Noel O'Boyle)
mmCIF: Improved mmCIF reading (Patrick Fuller)
mmCIF: Support for atom occupancy and atom_type (Kirill Okhotnikov)
Mol2: Option to read UCSF Dock scores (Maciej Wójcikowski)
MOPAC: Read z-matrix data and parse (and prefer) ESP charges (Geoff Hutchison)
NWChem: Support sequential calculations by optionally overwriting earlier ones (Dmitriy Fomichev)
NWChem: Extract info on MEP(IRC), NEB and quadrupole moments (Dmitriy Fomichev)
PDB: Read/write PDB insertion codes (Steffen Möller)
PNG: Options to crop the margin, and control the background and bond colors (Fredrik Wallner)
PQR: Use a stored atom radius (if present) in preference to the generic element radius (Zhixiong Zhao)
PWSCF: Extend parsing of lattice vectors (David Lonie)
PWSCF: Support newer versions, and the 'alat' term (Patrick Avery)
SVG: Option to avoid addition of hydrogens to fill valence (Lee-Ping)
SVG: Option to draw as ball-and-stick (Jean-Noël Avila)
VASP: Vibration intensities are calculated (Christian Neiss, Mathias Laurin)
VASP: Custom atom element sorting on writing (Kirill Okhotnikov)
Other new features and improvements
2D layout: Improved the choice of which bonds to designate as hash/wedge bonds around a stereo center (Craig James)
3D builder: Use bond length corrections based on bond order from Pyykko and Atsumi (http://dx.doi.org/10.1002/chem.200901472) (Geoff Hutchison)
3D generation: "--gen3d", allow user to specify the desired speed/quality (Geoff Hutchison)
Aromaticity: Improved detection (Geoff Hutchison)
Canonicalisation: Changed behaviour for multi-molecule SMILES. Now each molecule is canonicalized individually and then sorted. (Geoff Hutchison/Tim Vandermeersch)
Charge models: "--print" writes the partial charges to standard output after calculation (Geoff Hutchison)
Conformations: Confab, the systematic conformation generator, has been incorporated into Open Babel (David Hall/Noel O'Boyle)
Conformations: Initial support for ring rotamer sampling (Geoff Hutchison)
Conformer searching: Performance improvement by avoiding gradient calculation and optimising the default parameters (Geoff Hutchison)
EEM charge model: Extend to use additional params from http://dx.doi.org/10.1186/s13321-015-0107-1 (Tomáš Raček)
FillUnitCell operation: Improved behavior (Patrick Fuller)
Find duplicates: The "--duplicate" option can now return duplicates instead of just removing them (Chris Morley)
GAFF forcefield: Atom types updated to match Wang et al. J. Comp. Chem. 2004, 25, 1157 (Mohammad Ghahremanpour)
New charge model: EQeq crystal charge equilibration method (a speed-optimized crystal-focused charge estimator, http://pubs.acs.org/doi/abs/10.1021/jz3008485) (David Lonie)
New charge model: "fromfile" reads partial charges from a named file (Matt Harvey)
New conversion operation: "changecell", for changing cell dimensions (Kirill Okhotnikov)
New command-line utility: "obthermo", for extracting thermochemistry data from QM calculations (David van der Spoel)
New fingerprint: ECFP (Geoff Hutchison/Noel O'Boyle/Roger Sayle)
OBConversion: Improvements and API changes to deal with a long-standing memory leak (David Koes)
OBAtom::IsHBondAcceptor(): Definition updated to take into account the atom environment (Stefano Forli)
Performance: Faster ring-finding algorithm (Roger Sayle)
Performance: Faster fingerprint similarity calculations if compiled with -DOPTIMIZE_NATIVE=ON (Noel O'Boyle/Jeff Janes)
SMARTS matching: The "-s" option now accepts an integer specifying the number of matches required (Chris Morley)
UFF: Update to use traditional Rappe angle potential (Geoff Hutchison)
Language bindings
Bindings: Support compiling only the bindings against system libopenbabel (Reinis Danne)
Java bindings: Add example Scala program using the Java bindings (Reinis Danne)
New bindings: PHP (Maciej Wójcikowski)
PHP bindings: BaPHPel, a simplified interface (Maciej Wójcikowski)
Python bindings: Add 3D depiction support for Jupyter notebook (Patrick Fuller)
Python bindings, Pybel: calccharges() and convertdbonds() added (Patrick Fuller, Björn Grüning)
Python bindings, Pybel: compress output if filename ends with .gz (Maciej Wójcikowski)
Python bindings, Pybel: Residue support (Maciej Wójcikowski)
Development/Build/Install Improvements
Version control: move to git and GitHub from subversion and SourceForge
Continuous integration: Travis for Linux builds and Appveyor for Windows builds (David Lonie and Noel O'Boyle)
Python installer: Improvements to the Python setup.py installer and "pip install openbabel" (David Hall, Matt Swain, Joshua Swamidass)
Compilation speedup: Speed up compilation by combining the tests (Noel O'Boyle)
MacOSX: Support compiling with libc++ on MacOSX (Matt Swain)
just google https://sourceforge.net/projects/openbabel/作者Author: Daniel_Arndt 时间: 2018-11-11 04:29
我好几次在公交车上遇到了OpenBabel维护者中的Geoff Hutchison，他全程玩Pokemon Go。大神的世界确实不懂。作者Author: Novice 时间: 2019-6-26 20:07
Open Babel 3.0.0即将问世了，手册出来了，可是源文件还没有放出来
Released 2019/nn/nn.
This is a major release. It fixes some long-standing issues affecting performance in terms of chemical accuracy and speed, and all users are recommended to upgrade. It also removes deprecatedcomponents and breaks the API in a few places. For information on migrating from earlier version, please see [REF].
Highlights
New file formats
Add basic support for RInChI (Reaction InChI) (by baoilleach, PR#1667)
Added basic ADF Band and ADF DFTB readers (by psavery, PR#1793)
Add support for COF format (Culgi object file) plus tests (by pbecherer, PR#1944)
New file format capabilities and options
Improve svg ball and stick (by ghutchis, PR#360)
Add an option to the canonical SMILES format to specify the timeout. (by timvdm, PR#386)
Allow to set space group origin in PDB CRYST1 section (by afonari, PR#1558)
Parse _space_group_symop_operation_xyz in mmcif (by afonari, PR#1578)
Improve performance of SMILES parser (by baoilleach, PR#1589)
Handle undervalent atoms and radicals in Mol files and Smiles (by baoilleach, PR#1626)
Add support for agents to RXN file format (by baoilleach, PR#1656)
Allow RSMI format to read partial reactions (by baoilleach, PR#1660)
Add support for %(NNN) notation for SMILES ring closures (by baoilleach, PR#1677)
By default, don’t perceive stereo when reading SMILES, but have the option (by baoilleach, PR#1696)
Speed up the SMILES writer (by baoilleach, PR#1699)
Faster SMILES: Replace std::endl by “n” (by baoilleach, PR#1706)
Speed up SMILES writer by replacement of SSSR in SMILES writer with a bounded BFS (by baoilleach, PR#1715)
Speed up SMILES reading: don’t pre-scan the SMILES string for illegal characters (by baoilleach, PR#1716)
Minor speedup in SMILES: avoid repeated calls to IsOption by caching some options (by baoilleach, PR#1718)
Read reaction map from ChemDraw CDX files (by CamAnNguyen, PR#1720)
Two minor SMILES speed improvements (by baoilleach, PR#1725)
Speed up SMILES reading: Moved more inside the switch statement for SMILES parsing (by baoilleach, PR#1727)
Speed up SMILES reading: In the SMILES reader, avoid allocating a BUFSIZE buffer, and the associated string copy (by baoilleach, PR#1728)
Speed up SMILES writing: Make generation of the SMILES atom order vector optional (by baoilleach, PR#1712)
Add support for using atom classes as Tinker atom types. (by ghutchis, PR#1734)
Gaussformat reading electrostatic potentials (by mmghahremanpour, PR#1748)
Reading Exact Polairzability from Gaussian log file (by mmghahremanpour, PR#1751)
Gaussformat reading multiple charge models (by mmghahremanpour, PR#1752)
Write atom occupancy (if present) to PDB (by afonari, PR#1799)
Update reaction support in ChemDraw (by baoilleach, PR#1878)
ADF DFTB: Add new detection string for ADF 2018 (by psavery, PR#1888)
Update Gaussian format (by e-kwsm, PR#1969)
Update URLs of specification of gromacs (by e-kwsm, PR#1974)
Other new features and improvements
Include original when there are zero rotatable bonds in confab (by cowsandmilk, PR#370)
Improve thread safety for global objects (by baoilleach, PR#381)
Change the OBAromTyper from using SMARTS patterns to a switch statement (rebased) (by baoilleach, PR#1545)
Keep count of implicit hydrogens instead of inferring them (by baoilleach, PR#1576)
Obthermo update patch (by mmghahremanpour, PR#1598)
Improve performance of element handling (by baoilleach, PR#1601)
Implement the Daylight aromaticity model as described by John Mayfield (by baoilleach, PR#1638)
Allow multiple agents in OBReaction (by baoilleach, PR#1640)
Clarify python examples (by theavey, PR#1657)
Add support for wrapping GetRGB() call to return r, g, b params. (by ghutchis, PR#1670)
Adding missing manpages (by merkys, PR#1678)
Expose obfunctions api through python bindings (by cstein, PR#1697)
Avoid logging messages that are taking time (by baoilleach, PR#1714)
warning/error messages for fastindex when the structure file is compressed (by adalke, PR#1733)
Refactor atom class to being data on an atom rather than on a molecule (by baoilleach, PR#1741)
Add Molecule.make2D function (by eloyfelix, PR#1765)
Change the behavior of OBMol.Separate so that it preserves atom order (by baoilleach, PR#1773)
When calling OBMol.Separate, preserve whether aromaticity has been perceived (by baoilleach, PR#1800)
Add OBMol::CopySubstructure (by baoilleach, PR#1811)
Add OBMol::SetChainsPerceived(false) (by baoilleach, PR#1813)
Add stereo + obfunctions + kekulize to ruby binding (by CamAnNguyen, PR#1824)
Generate useful error messages if plugins can’t be found. (by dkoes, PR#1826)
Allow public access to retrieve gradients (by ghutchis, PR#1833)
Re-enable vector.clear() to allow wrapped std::vectors to be reused (by baoilleach, PR#1834)
Implement reaction handling as part of OBMol (by baoilleach, PR#1836)
Added rotors as a descriptor/filter. (by ghutchis, PR#1846)
Keep aromaticity in EndModify() (by baoilleach, PR#1847)
Fragment-based coordinate generation (by n-yoshikawa, PR#1850)
Rebuild OBMM tool for interactive MM optimization (by ghutchis, PR#1873)
Update fragment based builder (by n-yoshikawa, PR#1931)
Refactor python bindings so that openbabel.py and pybel.py are within an openbabel folder (by baoilleach, PR#1946)
Tidy setting/unsetting of molecule perception flags (by baoilleach, PR#1951)
Remove outdated stereo code (by baoilleach, PR#1967)
Remove OBBond::GetBO() and SetBO() (by baoilleach, PR#1953)
Remove OBRandom from the public API (by baoilleach, PR#1954)
Remove miscellanous headers from mol.h, atom.h and bond.h (by baoilleach, PR#1958)
enhancements to obrms to support optimization of pose alignment (by dkoes, PR#1961)
Remove GetGenericValueDef from OBGenericData (by baoilleach, PR#1964)
Remove low-hanging deprecated methods (by baoilleach, PR#1968)
Improve python script (by e-kwsm, PR#1970)
Make pybel.Outputfile compatible with with statment (by yishutu, PR#1971)
Obrms enhancement (by dkoes, PR#1978)
Development/Build/Install Improvements
Change default build type to RELEASE and add -O3 switch (by baoilleach, PR#352)
Add a default issue template for Open Babel - Suggestions welcome (by ghutchis, PR#383)
Compile position independent code for shared libraries. (by susilehtola, PR#1575)
Introduce std:isnan for older versions of MSVC (by mwojcikowski, PR#1586)
Prepend to LD_LIBRARY_PATH instead of overwrite (by barrymoo, PR#1588)
Changes needed to compile with C++17 (by arkose, PR#1619)
Compiler version parsing and comparison from CMake 2.8 (by cowsandmilk, PR#1630)
Create CODE_OF_CONDUCT.md (by ghutchis, PR#1671)
Clarify option needed to generate SWIG bindings. (by jeffjanes, PR#1686)
Correct spelling of file name for Perl bindings (by jeffjanes, PR#1687)
In the Python bindings, avoid adding methods from the iterated object to the iterator itself (by baoilleach, PR#1729)
Ensure portability to ARM platforms (by baoilleach, PR#1744)
Switch to rapidjson library for JSON parsing/writing (by mcs07, PR#1776)
Fix linking of python bindings on Mac (by mcs07, PR#1807)
Using pillow instead of PIL (by hille721, PR#1822)
Ignore compile warnings on inchi directory. (by ghutchis, PR#1864)
Compile project in Cygwin without xtcformat (by bbucior, PR#1894)
Hyperlink DOIs to preferred resolver (by katrinleinweber, PR#1909)
For Travis builds, include output for build failures (by baoilleach, PR#1959)
Add __init__.py to gitignore (by yishutu, PR#1972)
Bug Fixes
Fix for missing ZLIB on win32 (by philthiel, PR#357)
Depict headers were missing in the installation (by tgaudin, PR#359)
Avoid IndexError for plugins with empty names (by langner, PR#361)
Fixed a few errors in space-groups.txt (by psavery, PR#367)
SF #909 - Fix segfault when ReadMolecule() called with PubChem document but file extension was generic .xml (by derekharmon, PR#369)
Preserve triple bond when reading SMILES with a triple bond in an aromatic ring (by baoilleach, PR#371)
Fix bug #368: Python3.6 openbabel: No module named ‘DLFCN’ (by hseara, PR#372)
Fastsearch 64 fix (by dkoes, PR#1546)
Don’t try to install aromatic.txt as it is no longer present (by baoilleach, PR#1547)
Make sure to add conformers after performing bond perception. (by ghutchis, PR#1549)
Set default coordinates before doing bond perception. (by ghutchis, PR#1550)
Ignore some non-functioning python SWIG bindings. (by djhogan, PR#1554)
Remove delete statement. (by djhogan, PR#1556)
Link libinchi with math library (by nsoranzo, PR#1564)
Fix segfault in OBMol::GetSpacedFormula (by bbucior, PR#1565)
Fix regression + minor cppcheck report (by serval2412, PR#1567)
Convert tabs to spaces in testpdbformat.py (by adamjstewart, PR#1568)
cppcheck: Condition ‘1==0’ is always false (by serval2412, PR#1572)
UFF: Fix conversion constant (by aandi, PR#1579)
Remove the change in resonance structure from the vinylogous carboxylic acid pH model (by kyle-roberts-arzeda, PR#1580)
Fix wedge/hash in cyclopropyl (by fredrikw, PR#1582)
Fix multifragment depiction (by fredrikw, PR#1585)
Fix wrong spin multiplicity assignment (by nakatamaho, PR#1592)
Change silicon to correct MM3 atom type (by keipertk, PR#1593)
Fix pubchem JSON handling of enum types as ints (by mcs07, PR#1596)
Correct MM3 carboxyl oxygen atom type definition (by keipertk, PR#1599)
Fix for calculating implicit H count when reading SMILES (by baoilleach, PR#1606)
Fix some small misspellings in the csharp bindings (by cmanion, PR#1608)
Tweak the handling of implicit Hs when reading SMILES (by baoilleach, PR#1609)
Fix underflow causing a noticeable delay when e.g. writing a molfile (by baoilleach, PR#1610)
Fix install regression with element data (by bbucior, PR#1617)
Added some missing formats to the static build (by psavery, PR#1622)
In SiestaFormat, print warnings to cerr (by psavery, PR#1623)
For SIESTA format, use obErrorLog instead of cerr (by psavery, PR#1627)
Correct the spelling of the Frerejacque number in a comment (by baoilleach, PR#1629)
Lowercase second element letter in PDB and test (by cowsandmilk, PR#1631)
Remove erroneous -1 in switch statement (by baoilleach, PR#1632)
Make sure to handle molecular total charge by default for keywords (by ghutchis, PR#1634)
Added fix for OBMolAtomBFSIter in Python3 (by oititov, PR#1637)
space-groups.txt: correct Hall symbol for C -4 2 b (by wojdyr, PR#1645)
Reset path to empty in kekulization code (potential segfault) (by baoilleach, PR#1650)
Correct handling of stereo when writing InChIs (by baoilleach, PR#1652)
ECFP Fixup (by johnmay, PR#1653)
Fix “folding” for fingerprints to larger bit sizes - #1654. (by ghutchis, PR#1658)
Fix reading atom symbols from XSF file (by sencer, PR#1663)
Minor fixes in the nwchem format reader (by xomachine, PR#1666)
use isinstance to test if filename is bytes (by cowsandmilk, PR#1673)
Fix bug found due to MSVC warning (by baoilleach, PR#1674)
Fix MSVC warning about unused variable (by baoilleach, PR#1675)
Correct handling of atom maps (by baoilleach, PR#1698)
Fix #1701 - a GCC compiler error (by baoilleach, PR#1704)
Remove some audit messages (by baoilleach, PR#1707)
Fix bug when copying stereo during obmol += obmolB (by baoilleach, PR#1719)
Fix uninitialized read in kekulize.cpp found by Dr Memory. (by baoilleach, PR#1721)
Fixes for ring closure parsing (by baoilleach, PR#1723)
Make sure that OBAtom::IsInRing always triggers ring perception if not set as perceived (by baoilleach, PR#1724)
Fix code error found from @baoilleach compiler warnings (by ghutchis, PR#1736)
Fix Python3 compatibility (by ghutchis, PR#1737)
Fix ChemDraw CDX incremental value (by CamAnNguyen, PR#1743)
Fix error in VASPformat found by static code analysis (by baoilleach, PR#1745)
Fix for 1731. Store atom classes in CML atomids by appending _ATOMCLASS. (by baoilleach, PR#1746)
Fix GCC warnings (by baoilleach, PR#1747)
Fix warning in fastsearch substructure fingerprint screen (by baoilleach, PR#1749)
Fix #1684 - string comparison does not work with numeric sd titles (by cowsandmilk, PR#1750)
Fixing minor things for reading ESP from log files (by mmghahremanpour, PR#1753)
Fix #1569 - OB 2.4.1 loses the second molecule in a HIN file (by yishutu, PR#1755)
Fix TESTDIR definition to allow space in path (by mcs07, PR#1757)
Fix regression. Ensure that asterisk is unbracketed when writing a SMILES string (by baoilleach, PR#1759)
Fix MSVC warning about type conversion (by baoilleach, PR#1762)
Fix SMILES parsing fuzz test failures from AFL (by baoilleach, PR#1770)
Fix warning about size_t versus int cast (by baoilleach, PR#1771)
A small improvement of a bugfix solving segfault when reading GAMESS output with vibrations (by boryszef, PR#1772)
In the Python bindings, reset the DL open flags after importing _openbabel (by baoilleach, PR#1775)
fix cdxml stereo bonds (by JasonYCHuang, PR#1777)
Install obabel target if using static build (by torcolvin, PR#1779)
Fix #1769 by correctly handling the mass difference field in MDL mol files (by baoilleach, PR#1784)
Kekulize hypervalent aromatic N and S (by baoilleach, PR#1787)
Pdbqt fix (by dkoes, PR#1790)
Raise a warning when coordinate is NaN (by n-yoshikawa, PR#1792)
Use the InChI values for the average atomic mass when reading/writing isotopes (by baoilleach, PR#1795)
Fix compile failure after recent Molden commit (by baoilleach, PR#1796)
Fix segfault due to running off the start of an iterator in PDBQT format (by baoilleach, PR#1797)
Fix#1768: Segfault upon reading GAMESS outputs of DFTB3 calculations (by serval2412, PR#1798)
Always ensure hybridization (by ghutchis, PR#1801)
Fix #1786 by changing the return value of OBResidue::GetNum() (by baoilleach, PR#1804)
Apply fixes from Benoit Leblanc to address int/double type warnings. (by baoilleach, PR#1806)
Fix#1607: check dynamic cast return (by serval2412, PR#1815)
Fixes #1282: check format input is provided (by serval2412, PR#1818)
Fix#1331: avoid crash with Q-Chem fragment (by serval2412, PR#1820)
Set default to read CIFs with specified coordinates, no wrapping. (by ghutchis, PR#1823)
Fix#1056: remove a debug output (by serval2412, PR#1825)
Get ECFP working (by baoilleach, PR#1829)
Fix cdxml upside down format (by JasonYCHuang, PR#1831)
Fix to CopySubstructure found when running over ChEMBL (by baoilleach, PR#1832)
Fix#192: parse and use ‘-a’ flag for obrotate (by serval2412, PR#1835)
Ensure carbonyl groups are checked at both 0 and 180. (by ghutchis, PR#1845)
Ensure that the check for OBBond::IsInRing obeys the OBMol perception flags (by baoilleach, PR#1848)
Simplify/fix behavior of OBAtom::GetResidue so that it behaves like other lazy properties (by baoilleach, PR#1849)
Fixes #1851: check some limits when converting smi to sdf using –gen2D (by serval2412, PR#1852)
Modify cleaning blank line behaviors (by yishutu, PR#1855)
Ring membership of atoms and bonds was not being reset during perception (by baoilleach, PR#1856)
Update qeq.txt (by mkrykunov, PR#1882)
Support lone pair stereo on nitrogen as well as sulfur (by baoilleach, PR#1885)
Changed indexing of fragments, should fix #1889 (by fredrikw, PR#1890)
Avoid out-of-range access in OBMolBondBFSIter (by baoilleach, PR#1892)
Fix OBChemTsfm wrapping of implicit H counts (by baoilleach, PR#1896)
Updated the coordinate generation from templates. (by fredrikw, PR#1902)
Fix incorrect use of memcpy. (by sunoru, PR#1908)
Add SetChainsPerceived() after EndModify() in formats that add residues (by baoilleach, PR#1914)
define isfinite removed. (by orex, PR#1928)
Teach the isomorphism mapper to respect atom identity (by johnmay, PR#1939)
Fix memory leak in OBSmartsPattern::Init() (by n-yoshikawa, PR#1945)
Address CMake build warning about policy CMP0005 being set to OLD (by baoilleach, PR#1948)
Fix clang warning about in-class init of a non-static data member (by baoilleach, PR#1949)
Update bindings for changes to headers (by baoilleach, PR#1963)
Fix randomly failing Python gradient test (by baoilleach, PR#1966)
