mirror of
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5dfd67a22a
* copy in, get building, add some basic tests * complete the testing Except for regiosiomers, which do not work * regioisomers work now * backup commit; things work * remove last of NM macros from hashfunctions.cpp * remove last of NM macros from hashfunctions.cpp * remove dependency on the abstraction layer * typo * start using namespaces clang-format * switch to using enums for the HashFunctions and StripTypes * Add initial python wrapper (and tests) * move the new hashing code to the MolHash library still may want to revise the naming of this * Setup deprecation of the older hashing code * better release notes text * change in response to review
4669 lines
195 KiB
Markdown
4669 lines
195 KiB
Markdown
# Release_2019.09.1
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(Changes relative to Release_2019.03.1)
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## Important
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- The atomic van der Waals radii used by the RDKit were corrected/updated in #2154.
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This leads to different results when generating conformations, molecular volumes,
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and molecular shapes.
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## Backwards incompatible changes
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- See the note about atomic van der Waals radii above.
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- As part of the enhancements to the MolDraw2D class, we changed the type of
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DrawColour from a tuple to be an actual struct. We also added a 4th element to
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capture alpha values. This should have no affect on Python code (the alpha
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value is optional when providing color tuples), but will require changes to C++
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and Java/C# code that is using DrawColour.
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- When reading Mol blocks, atoms with the symbol "R" are now converted into
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queries that match any atom when doing a substructure search (analogous to "*"
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in SMARTS). The previous behavior was to only match other dummy atoms/
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- When loading SDF files using PandasTools.LoadSDF(), we now default to
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producing isomeric smiles in pandas tables. To reproduce the original
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behavior, use isomericSmiles=False in the call to the function.
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- The SMARTS generated by the RDKit no longer contains redundant wildcard
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queries. This means the SMARTS strings generated by this release will generally
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be different from that in previous releases, although the results produced by
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the queries should not change.
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## Highlights:
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## Acknowledgements:
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## Bug Fixes:
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## New Features and Enhancements:
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## Deprecated code (to be removed in a future release):
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- The old MolHash code should be considered deprecated. This release introduces
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a more flexible alternative. Specifically the following pieces will be removed in a future release:
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- The python functionality `rdkit.Chem.rdMolHash.GenerateMoleculeHashString()`
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- The C++ functionality directly present in the header file `GraphMol/MolHash/MolHash.h`
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# Release_2019.03.1
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(Changes relative to Release_2018.09.1)
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## REALLY IMPORTANT ANNOUNCEMENT
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- As of this realease (2019.03.1) the RDKit no longer supports Python 2. Please
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read this rdkit-discuss post to learn what your options are if you need to
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keep using Python 2:
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https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08354.html
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## Backwards incompatible changes
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- The fix for github #2245 means that the default behavior of the MaxMinPicker
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is now truly random. If you would like to reproduce the previous behavior,
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provide a seed value of 42.
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- The uncharging method in the MolStandardizer now attempts to generate
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canonical results for a given molecule. This may result in different output
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for some molecules.
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## Highlights:
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- There's now a Japanese translation of large parts of the RDKit documentation
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- SGroup data can now be read from and written to Mol/SDF files
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- The enhanced stereo handling has been improved: the information is now
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accessible from Python, EnumerateStereoisomers takes advantage of it, and it
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can be read from and written to CXSmiles
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## Acknowledgements:
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Michael Banck, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke,
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Bakary N'tji Diallo, Guillaume Godin, Anne Hersey, Jan Holst Jensen, Sunhwan Jo,
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Brian Kelley, Petr Kubat, Karl Leswing, Susan Leung, John Mayfield, Adam Moyer,
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Dan Nealschneider, Noel O'Boyle, Stephen Roughley, Takayuki Serizawa, Gianluca
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Sforna, Ricardo Rodriguez Schmidt, Gianluca Sforna, Matt Swain, Paolo Tosco,
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Ricardo Vianello, 'John-Videogames', 'magattaca', 'msteijaert', 'paconius',
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'sirbiscuit'
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## Bug Fixes:
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- PgSQL: fix boolean definitions for Postgresql 11
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(github pull #2129 from pkubatrh)
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- update fingerprint tutorial notebook
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(github pull #2130 from greglandrum)
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- Fix typo in RecapHierarchyNode destructor
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(github pull #2137 from iwatobipen)
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- SMARTS roundtrip failure
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(github issue #2142 from mcs07)
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- Error thrown in rdMolStandardize.ChargeParent
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(github issue #2144 from paconius)
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- SMILES parsing inconsistency based on input order
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(github issue #2148 from coleb)
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- MolDraw2D: line width not in python wrapper
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(github issue #2149 from greglandrum)
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- Missing Python API Documentation
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(github issue #2158 from greglandrum)
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- PgSQL: mol_to_svg() changes input molecule.
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(github issue #2174 from janholstjensen)
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- Remove Unicode From AcidBasePair Name
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(github pull #2185 from lilleswing)
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- Inconsistent treatment of `[as]` in SMILES and SMARTS
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(github issue #2197 from greglandrum)
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- RGroupDecomposition fixes, keep userLabels more robust onlyMatchAtRGroups
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(github pull #2202 from bp-kelley)
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- Fix TautomerTransform in operator=
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(github pull #2203 from bp-kelley)
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- testEnumeration hangs/takes where long on 32bit architectures
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(github issue #2209 from mbanck)
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- Silencing some Python 3 warning messages
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(github pull #2223 from coleb)
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- removeHs shouldn't remove atom lists
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(github issue #2224 from rvianello)
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- failure round-tripping mol block with Q atom
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(github issue #2225 from rvianello)
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- problem round-tripping mol files that include bond topology info
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(github issue #2229 from rvianello)
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- aromatic main-group atoms written to SMARTS incorrectly
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(github issue #2237 from greglandrum)
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- findPotentialStereoBonds() stopping too early
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(github issue #2244 from greglandrum)
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- MinMax Diversity picker seeding shows deterministic / non-random behaviour
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(github issue #2245 from sroughley)
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- Fix to serialize binary strings
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(github pull #2264 from bp-kelley)
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- Recognize N in three-membered rings as potentially chiral
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(github issue #2268 from greglandrum)
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- Failure when parsing mol block with M PXA
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(github issue #2277 from greglandrum)
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- query-query matching failing for atoms constructed from SMARTS
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(github issue #2299 from greglandrum)
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- SMILES parsing fails for dative ring closures
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(github issue #2303 from greglandrum)
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- Missing Dict.h overload: std::string Dict::getVal<std::string>
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(github issue #2308 from greglandrum)
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- fix a problem with the random pickers test
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(github pull #2310 from greglandrum)
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- Some tests still failing on less common platforms.
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(github issue #2311 from giallu)
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- AddHs() using 3D coordinates with 2D conformations
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(github pull #2328 from greglandrum)
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- change to make the SWIG builds work on windows
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(github pull #2340 from greglandrum)
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- uncharger behaves differently on molecules constructed from mol blocks and SMILES
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(github issue #2346 from greglandrum)
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- Memory Error When Writing ToBinary With "AllProps"
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(github issue #2352 from atom-moyer)
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- Seg fault on init if RDBASE is not set
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(github issue #2368 from greglandrum)
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- PandasTools.FrameToGridImage() fails with SVG output
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(github issue #2380 from greglandrum)
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- ClusterMols.GetDistanceMatrix throws a type error in Python 3
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(github issue #2387 from John-Videogames)
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- Uncharging logic reversed: protonate non-acids first
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(github issue #2392 from Anne Hersey)
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## New Features and Enhancements:
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- Allow access to Enhanced Stereochemistry information from Python
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(github issue #2108 from d-b-w)
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- Adopt EnumerateStereoisomers to use extended stereo
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(github issue #2109 from greglandrum)
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- Enable ctest -T memcheck
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(github pull #2113 from ricrogz)
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- Support for parsing/writing SGroups in SD Mol files
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(github pull #2138 from ricrogz)
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- Rename the #define _DEBUG to MMPA_DEBUG in mmpa.cpp
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(github pull #2140 from baoilleach)
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- MolDraw2D: line width should be controlled by MolDrawOptions
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(github issue #2151 from greglandrum)
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- Some refactoring of the distance geometry code
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(github pull #2153 from greglandrum)
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- Less warnings
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(github pull #2155 from UnixJunkie)
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- ShapeTverskyIndex python function
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(github pull #2156 from susanhleung)
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- Skip compound if smiles conversion fails
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(github pull #2168 from msteijaert)
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- Fix #2176: InChI functions should return NULL on un-InChI-able input molecules.
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(github pull #2177 from janholstjensen)
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- Update installation instructions for Linux
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(github pull #2181 from sirbiscuit)
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- Update CMake rules to find external coorgen & maeparser libs
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(github pull #2184 from ricrogz)
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- Update to use the travis Xenial environment
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(github pull #2200 from greglandrum)
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- Do not allow PandasTools to overwrite pandas settings
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(github pull #2206 from sirbiscuit)
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- re-enable (and update) the file parser tests
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(github pull #2208 from greglandrum)
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- Added documentation files written in Japanese into Book directory
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(github pull #2210 from magattaca)
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- Add C++ convenience function for drawing ROMols
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(github issue #2220 from greglandrum)
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- Change boost int types to std types
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(github pull #2233 from bp-kelley)
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- Added exports for SGroup functions
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(github pull #2242 from ricrogz)
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- Use coordMap when starting embedding from random coords
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(github issue #2246 from greglandrum)
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- Improve interactivity of output SVG
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(github pull #2253 from greglandrum)
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- Add options for substructure searching
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(github pull #2254 from greglandrum)
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- keep extra information about bonds from Mol files
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(github pull #2260 from greglandrum)
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- Allow converting mol blocks directly to InChI
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(github pull #2262 from greglandrum)
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- Patch/pains updates
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(github pull #2272 from johnmay)
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- add warning for 2D conformations flagged as 3D
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(github pull #2273 from greglandrum)
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- Store extra CXSMILES data as a property
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(github pull #2281 from ricrogz)
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- Parse enhanced stereo information from CXSMILES
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(github pull #2282 from ricrogz)
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- Robustify parsing of CTABs and SGROUPs
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(github pull #2283 from greglandrum)
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- Write enhanced stereo to cxsmiles
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(github pull #2290 from greglandrum)
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- Allow custom type-handlers in the RDProps interface
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(github pull #2293 from bp-kelley)
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- Add serialization to SubstructLibrary
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(github pull #2295 from bp-kelley)
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- support reading/writing atom props from SD files
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(github pull #2297 from greglandrum)
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- Add test for issue #2285, fix molbundle test
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(github pull #2301 from bp-kelley)
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- Update maeparser & coordgen libraries
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(github pull #2302 from ricrogz)
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- Mem errors clean up
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(github pull #2305 from ricrogz)
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- Add definition of MolFragmentToCXSmiles
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(github pull #2307 from greglandrum)
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- Doc update
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(github pull #2312 from greglandrum)
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- Adds gzstream stream, exposes to swig
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(github pull #2314 from bp-kelley)
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- Remove a bunch of Python2-related warts
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(github pull #2315 from greglandrum)
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- some much-needed optimization work on the new property lists
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(github pull #2317 from greglandrum)
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- Build warnings revisited
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(github pull #2318 from ricrogz)
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- change bogus "3D" to "2D" in a test file
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(github pull #2319 from greglandrum)
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- Allow copying atoms in Python
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(github pull #2322 from d-b-w)
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- fixes an r-group symmetrization problem
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(github pull #2324 from greglandrum)
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- simple docstring fix
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(github pull #2326 from sunhwan)
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- allow using system's catch2 for tests
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(github pull #2327 from giallu)
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- Python wrap DetectAtomStereoChemistry from MolFileStereochem.h
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(github issue #2329 from d-b-w)
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- switch to using cmake to handle the C++ spec
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(github pull #2334 from greglandrum)
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- WIP: optional integration with YAeHMOP
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(github pull #2335 from greglandrum)
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- Exposes substructlibrary to swig
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(github pull #2337 from bp-kelley)
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- Add a skip_all_if_match option to the FragmentRemover
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(github pull #2338 from greglandrum)
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- Dev/general csharp fixes
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(github pull #2341 from bp-kelley)
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- Add a read-only Python wrapper for SGroups
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(github pull #2343 from greglandrum)
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- Expose RGroupDecomposition to SWIG
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(github pull #2345 from greglandrum)
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- update debian build script to python3
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(github pull #2350 from UnixJunkie)
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- add GetStereoIsomerCount() function to EnumerateStereoisomers
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(github pull #2354 from greglandrum)
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- Update coordgenlibs to v1.2.2
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(github pull #2355 from ricrogz)
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- Small fixes to get DLLs to build on Windows
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(github pull #2356 from ptosco)
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- Boost deprecation warning
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(github pull #2357 from d-b-w)
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- Removes an extra debugging cerr statment
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(github pull #2360 from d-b-w)
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- Preserve enhanced stereo in reactions
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(github pull #2366 from d-b-w)
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- improvements to the Uncharge functionality
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(github pull #2374 from greglandrum)
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- Add ExplicitBitVect prop and query
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(github pull #2384 from bp-kelley)
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- Allow components of the MolStandardize code to be initialized from streams
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(github pull #2385 from greglandrum)
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# Release_2018.09.1
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(Changes relative to Release_2018.03.1)
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## Deprecations
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- As part of the changes and cleaning up done for #1836 many of the `#defines`
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used in the RDKit have been renamed.
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- `USE_BUILTIN_POPCOUNT` -> `RDK_OPTIMIZE_NATIVE`
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- `RDK_THREADSAFE_SSS` -> `RDK_BUILD_THREADSAFE_SSS`
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- `BUILD_COORDGEN_SUPPORT` -> `RDK_BUILD_COORDGEN_SUPPORT`
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- `BUILD_AVALON_SUPPORT` -> `RDK_BUILD_AVALON_SUPPORT`
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- `BUILD_INCHI_SUPPORT` -> `RDK_BUILD_INCHI_SUPPORT`
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- `BUILD_SLN_SUPPORT` -> `RDK_BUILD_SLN_SUPPORT`
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- `RDK_CAIRO_BUILD` -> `RDK_BUILD_CAIRO_SUPPORT`
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## Documentation updates
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We have moved to using Sphinx's autodoc to create the Python API documentation.
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`epydoc`, the tool we used to use, is no longer actively developed and only supports
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Python2. There will undoubtedly be problems associated with the change; if you notice
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anything missing in the documetation or something that's really badly formatted,
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please either let us know or submit a PR with a fix.
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## Backwards incompatible changes
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This release includes a set of changes to make the default arguments to common
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functions less error prone (github #1679).
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- GetAtomSmiles() now generates isomeric SMILES by default.
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- The ringMatchesRingOnly option to the FindMCS() function now applies to
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atom-atom matches as well as bond-bond matches.
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- The Python functions EmbedMolecule() and EmbedMultipleConfs() now use the
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ETKDG algorithm by default instead of standard distance geometry.
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## Highlights:
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- This release includes two contributions from the Google Summer of Code:
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- A new generalized fingerprint generator.
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- An integration/port of MolVS to the core RDKit.
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The API on both of these may change a bit with future releases.
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- The rdkit.Chem.Draw module now includes functions for depicting fingerprint
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bits. Morgan and RDKit fingerprints are currently supported.
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## Acknowledgements:
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Boran Adas, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke, Guillaume Godin,
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Brice Hoff, Brian Kelley, Karl Leswing, Susan Leung, Pat Lorton, Josh Meyers, Hirotomo Moriwaki,
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Dan Nealschneider, Noel O'Boyle, Pavel Raiskup, Sereina Riniker, Ricardo Rodriguez Schmidt,
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Stephen Roughley, Roger Sayle, Takayuki Serizawa, Rim Shayakhmetov, Gregory Simm, Jon Sorenson,
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Matt Swain, Kiran Telukunta, Paulo Tosco, Alain Vaucher, Maciej Wójcikowski, '0xDECAFC0FFEE',
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'jaechanglim', 'paconius'
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## Contrib updates:
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- The FastCluster code has been updated.
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## New Features and Enhancements:
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- expose MolChemicalFeature.{get,set}ActiveConformer() to python
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(github issue #1636 from greglandrum)
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- added Scripts/create_deb_packages.sh
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(github pull #1655 from UnixJunkie)
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- Start to use Catch2 for new tests
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(github pull #1732 from greglandrum)
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- Switch DbCLI scripts from optparse to argparse
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(github issue #1778 from greglandrum)
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- Add EEM partial charges
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(github pull #1828 from greglandrum)
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- Add header file providing access to RDKit compile time flags
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(github issue #1836 from greglandrum)
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- add control over the coordinate precision to coordgen
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(github pull #1847 from greglandrum)
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- Add Properties interface to ChemicalReactions
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(github pull #1848 from greglandrum)
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- Switch Python API documentation generation over to Sphinx autodoc
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(github pull #1849 from greglandrum)
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- expose MolOps::assignStereochemistryFrom3D() to Python
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(github issue #1850 from greglandrum)
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- bivariate_normal deprecation in mlab.py of matplotlib
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(github issue #1851 from telukir)
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- Expose minAtomRingSize() and minBondRingSize() to Python wrappers
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(github pull #1859 from mwojcikowski)
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- enable building DLLs on Windows
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(github pull #1861 from ptosco)
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- Fix compatibility with Boost 1.67+
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(github pull #1864 from mcs07)
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- Don't manually set RDConfig paths in conda env
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(github pull #1865 from mcs07)
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- Make svg xmlns prefix use more consistent
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(github pull #1866 from mcs07)
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- Add custom 3D Descriptors
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(github pull #1867 from greglandrum)
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- Add initial Maestro format Supplier using maeparser library
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(github pull #1872 from lorton)
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- add queryAtomNonHydrogenDegree() query operation
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(github issue #1873 from greglandrum)
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- Add an auto-populated file with cmake config options
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(github pull #1874 from greglandrum)
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- Custom property VSA
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(github pull #1884 from sriniker)
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- Swap maeparser and coordgen dependencies to use releases
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(github issue #1887 from greglandrum)
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- expose MolDraw2DSVG.tagAtoms() to python
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(github pull #1897 from greglandrum)
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- allow the cleanup step of Mol2 parsing to be disabled
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(github pull #1898 from greglandrum)
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- Allow Atom.GetAtomSmarts() to return isomeric SMILES
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(github pull #1902 from greglandrum)
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- Allow coordgen and maeparser to be built as static libraries
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(github pull #1909 from ptosco)
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- Support reaction_to_svg() in cartridge
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(github issue #1916 from greglandrum)
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- Addresses several minor warning messages during the build
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(github pull #1935 from d-b-w)
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- Some optimization of the queries constructed from SMARTS
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(github pull #1940 from greglandrum)
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- Add ring/chain match constraints options to AdjustQueryParameters()
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(github issue #1943 from greglandrum)
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- roc calculation naming problem
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(github pull #1975 from 0xDECAFC0FFEE)
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- Fingerprinting functions should call assignStereochemistry() when necessary
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(github issue #1993 from bricehoff)
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- Dev/GSOC2018_MolVS_Integration
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(github pull #2002 from susanhleung)
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- GSoC 2018 - Fingerprints
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(github pull #2005 from Boranadas)
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- port fingerprint bit rendering code from CheTo
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(github pull #2008 from greglandrum)
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- PgSQL: add support for PostgreSQL_CONFIG cmake var
|
|
(github pull #2014 from praiskup)
|
|
- Add missing boost header for v1.64
|
|
(github pull #2016 from gncs)
|
|
- Enhanced stereo read/write support in SDF files.
|
|
(github pull #2022 from d-b-w)
|
|
- IPythonConsole hooks should copy the original docstring
|
|
(github issue #2025 from adalke)
|
|
- Allow dumping interchange information into SVG files
|
|
(github pull #2030 from greglandrum)
|
|
- MCS: add test for ring--non-ring matches at the atom level
|
|
(github issue #2034 from greglandrum)
|
|
- Ability to generate a list of possible smiles representation for a given molecule
|
|
(github issue #2042 from thegodone)
|
|
- add scoring test (relevant to #1975)
|
|
(github pull #2064 from greglandrum)
|
|
- actually run the SmilesWriterNoNames() test
|
|
(github pull #2067 from greglandrum)
|
|
- Add a default for maximum products generated by a reaction (maxProduc…
|
|
(github pull #2069 from bp-kelley)
|
|
- Add user-defined literals for parsing SMILES and SMARTS
|
|
(github pull #2070 from greglandrum)
|
|
- move rdInfoLog to stderr
|
|
(github pull #2073 from greglandrum)
|
|
- add confId argument to MolChemicalFeatureFactor::getFeaturesForMol()
|
|
(github issue #2077 from greglandrum)
|
|
- Expose a CMake flag to build RDKit with -rpath
|
|
(github pull #2084 from coleb)
|
|
- Dev/expose setquery to python
|
|
(github pull #2088 from bp-kelley)
|
|
- Updated .gitignore with files generated outside of build directory.
|
|
(github pull #2095 from ricrogz)
|
|
- Address compile warnings & trivial improvements
|
|
(github pull #2097 from ricrogz)
|
|
- Coordgen: stop printing Templates location
|
|
(github pull #2102 from greglandrum)
|
|
- Update Docs For CalcBEDROC
|
|
(github pull #2103 from lilleswing)
|
|
|
|
## Bug Fixes:
|
|
- Cannot find rings for ChEBI 50252
|
|
(github issue #299 from greglandrum)
|
|
- Feature request: #defines to test RDKit version
|
|
(github issue #1454 from baoilleach)
|
|
- Atoms in residue read from pdb lose their AtomPDBResidueInfo after reaction (Bug)
|
|
(github issue #1632 from hjuinj)
|
|
- SMARTS parse failure for some queries involving Hs
|
|
(github issue #1719 from greglandrum)
|
|
- Conformer indexing bug in RDFreeSASA.cpp?
|
|
(github issue #1786 from paconius)
|
|
- allow libs to not be installed
|
|
(github pull #1832 from greglandrum)
|
|
- RWMol::addAtom(Atom,bool) missing from Java wrappers
|
|
(github issue #1837 from greglandrum)
|
|
- RWMol::clear now calls ROMol::initMol
|
|
(github pull #1844 from bp-kelley)
|
|
- Allow types.h to be included in applications that use /D_USE_MATH_DEFINES
|
|
(github pull #1846 from d-b-w)
|
|
- Fixes failing Python tests on Windows
|
|
(github pull #1855 from ptosco)
|
|
- Allow building on cygwin using -std=c++11
|
|
(github pull #1856 from greglandrum)
|
|
- Stop using the cmake Boost:: targets
|
|
(github pull #1858 from greglandrum)
|
|
- R-group Decomposition: allow H replacements when matchOnlyAtRgroups is set
|
|
(github pull #1871 from bp-kelley)
|
|
- Mark cartridge functions as being parallel safe
|
|
(github issue #1886 from greglandrum)
|
|
- Fixes locale handling on Windows
|
|
(github pull #1892 from ptosco)
|
|
- get the pandas tests working with pandas 0.23
|
|
(github pull #1896 from greglandrum)
|
|
- "make install" appears to miss RDBoost/export.h
|
|
(github issue #1903 from baoilleach)
|
|
- Fix curl fallback for downloading files
|
|
(github pull #1904 from d-b-w)
|
|
- Bond stereo information not output to SMARTS
|
|
(github issue #1906 from greglandrum)
|
|
- Library .so names missing RDKit?
|
|
(github issue #1913 from baoilleach)
|
|
- Negated atom number queries in SMARTS should not set atomic number of query atom
|
|
(github issue #1920 from greglandrum)
|
|
- memory leak in Get3DDistanceMatrix
|
|
(github issue #1924 from jaechanglim)
|
|
- Atom with bond to itself is accepted by the SMILES parser.
|
|
(github issue #1925 from tblaschke)
|
|
- Possibly incorrect aromatic SMILES generated for structure
|
|
(github issue #1928 from baoilleach)
|
|
- Using the coordgen library seems to cause a seg fault
|
|
(github issue #1929 from JoshuaMeyers)
|
|
- Aromaticity failure in 7-ring with charged radical carbon
|
|
(github issue #1936 from bp-kelley)
|
|
- Fix embarassing bug, check the counter each iteration
|
|
(github pull #1939 from bp-kelley)
|
|
- RuntimeError when importing rdkit.Chem.Descriptors with Python 3.7
|
|
(github issue #1948 from drkeoni)
|
|
- Query features in products of rxn files not properly handled
|
|
(github issue #1950 from greglandrum)
|
|
- ReactionToSmarts broken for multi-component templates
|
|
(github issue #1955 from bp-kelley)
|
|
- update knime urls in overview.md
|
|
(github pull #1966 from greglandrum)
|
|
- CXN extended SMILES labels are not applied to the correct atom in SMILES with explicit H
|
|
(github issue #1968 from baoilleach)
|
|
- MolFromSmarts MolToSmarts fails to roundtrip on patterns with chirality
|
|
(github issue #1985 from bp-kelley)
|
|
- QueryAtoms with atom list queries should not have the atomic number set
|
|
(github issue #1988 from greglandrum)
|
|
- RemoveHs not properly updating double bond stereoatoms
|
|
(github issue #1990 from shayakhmetov)
|
|
- Error while parsing empty atom list in Mol files.
|
|
(github issue #2000 from drkeoni)
|
|
- Cleanup step of sanitization sometimes sets undesired formal charges
|
|
(github issue #2020 from avaucher)
|
|
- GetBondSmiles() returns nothing for wedged bonds when allBondsExplicit is true
|
|
(github issue #2029 from greglandrum)
|
|
- PMIs and NPRs return same value between different conformer
|
|
(github issue #2037 from philopon)
|
|
- Failure to parse V3K mol file with bonds to multi-center linkage points
|
|
(github issue #2040 from greglandrum)
|
|
- patch a memory allocation problem in the maeparser v1.0.0
|
|
(github pull #2044 from greglandrum)
|
|
- CIPRank values from JSONDataToMols are not unsigned
|
|
(github issue #2046 from greglandrum)
|
|
- switch to v1.0.1 of the maeparser
|
|
(github pull #2048 from greglandrum)
|
|
- Update fastcluster code
|
|
(github pull #2051 from greglandrum)
|
|
- Fix memory leak in Dict operator=
|
|
(github pull #2061 from bp-kelley)
|
|
- Atom mapping lost after call to MergeQueryHs()
|
|
(github issue #2062 from greglandrum)
|
|
- Drawing racemic bond stereo as crossed bonds should be the default
|
|
(github issue #2063 from coleb)
|
|
- Moved test.h from RDBoost to RDGeneral for consistency with export.h
|
|
(github pull #2074 from ptosco)
|
|
- CTABs behave differently than before regarding stereo
|
|
(github issue #2082 from bp-kelley)
|
|
- BitInfo not complete for RDKFingerprint
|
|
(github issue #2115 from greglandrum)
|
|
|
|
## Removed code:
|
|
- Remove the deprecated MolDrawing code
|
|
(github pull #2111 from greglandrum)
|
|
|
|
|
|
# Release_2018.03.1
|
|
(Changes relative to Release_2017.09.1)
|
|
|
|
## C++11 notes
|
|
|
|
Starting with this release, the RDKit core C++ code is written in modern C++;
|
|
for this release that means C++11. This means that the compilers used to build
|
|
it cannot be completely ancient. Here are the minimum tested versions:
|
|
- g++ v4.8: though note that the SLN parser code cannot be built with v4.8. It
|
|
will automatically be disabled when this older compiler is used.
|
|
- clang v3.9: it may be that older versions of the compiler also work, but we
|
|
haven't tested them.
|
|
- Visual Studio 2015: it may be that older versions of the compiler also work,
|
|
but we haven't tested them.
|
|
|
|
## Backwards incompatible changes
|
|
|
|
This release includes a set of changes to make the default arguments to common
|
|
functions less error prone (github #1679).
|
|
- MolToSmiles() now generates isomeric SMILES by default.
|
|
- The embedding code now uses the ETKDG method by default.
|
|
- MolToMolBlock() will now by default generate a set of 2D coordinates for
|
|
molecules when the includeStereo option is set to True. The changes are made
|
|
to a copy of the molecule; the molecule itself will not be modified.
|
|
- The Mol file (and SDF) parser now determines atomic stereochemisty based on
|
|
the 3D coordinates provided (if 3D coordinates are provided).
|
|
- The SMILES parser now supports CXSMILES by default (assuming that additional
|
|
text that looks like CXSMILES extensions is there).
|
|
|
|
In every case the old behavior can be obtained by providing an optional argument
|
|
to the function(s) mentioned.
|
|
|
|
## Acknowledgements:
|
|
Boran Adas, José Emilio Sánchez Aparicio, Patrick Avery, Jason Biggs, Brian
|
|
Cole, Andrew Dalke, JW Feng, Peter Gedeck, Guillaume Godin, Richard Hall, Thomas
|
|
Heavy, Gareth Jones, Brian Kelley, Karl Leswing, Susan Leung, Chris Morris, Dan
|
|
Nealschneider, Noel O'Boyle, Axel Pahl, Pavel Polishchuk, Sereina Riniker, Jeff
|
|
van Santen, Roger Sayle, Martin Šícho, Matt Swain, Paolo Tosco, Sam Webb, Maciej
|
|
Wójcikowski, Nicola Zonta, 'clinntt', 'hjuinj', 'iwatobipen',
|
|
|
|
## Highlights:
|
|
- An initial version of an integration with Schrodinger's coordgen library is
|
|
included. This produces much better 2D coordinates for complex molecules.
|
|
- Thanks to the move to modern C++ the RDKit is now faster and uses less
|
|
memory
|
|
- A number of improvements were made to the PDB reader
|
|
- v2 of the ETKDG torsions and potentials is now available
|
|
|
|
## Contrib updates:
|
|
- Implementation of Peter Ertl's IFG method for identifying functional groups
|
|
from Guillaume Godin and Richard Hall
|
|
(github pull #1813 from thegodone)
|
|
|
|
## New Features and Enhancements:
|
|
- Support InChi 1.05
|
|
(github issue #1533 from greglandrum)
|
|
- Update CPack to create .deb files correctly
|
|
(github pull #1580 from psavery)
|
|
- Initial commit of EnumerateHeterocycles
|
|
(github pull #1588 from coleb)
|
|
- Version 2 of ETKDG
|
|
(github pull #1597 from sriniker)
|
|
- GetMolFrags now optionally returns atom indices along with mols
|
|
(github pull #1602 from ptosco)
|
|
- NP Likeness with confidence value
|
|
(github pull #1608 from apahl)
|
|
- Adding an option to EnumerateStereoisomers to only return unique isomers
|
|
(github pull #1612 from coleb)
|
|
- Add function wedgeBond()
|
|
(github issue #1615 from greglandrum)
|
|
- Dev/substructlibrary docs
|
|
(github pull #1620 from bp-kelley)
|
|
- Turns off exception throwing for certain classes Rlabel sanitization.
|
|
(github pull #1621 from bp-kelley)
|
|
- Add an "MDL" aromaticity model
|
|
(github issue #1622 from hjuinj)
|
|
- Add support for %(NNN) notation for ring closures
|
|
(github pull #1624 from baoilleach)
|
|
- Enable windows build that uses cairo
|
|
(github pull #1628 from greglandrum)
|
|
- [MRG] Fix PDB reader + add argument to toggle proximity bonding
|
|
(github pull #1629 from mwojcikowski)
|
|
- Improve AddHs for molecules read from PDB
|
|
(github pull #1647 from mwojcikowski)
|
|
- Improved regression test for ETKDG version 2
|
|
(github pull #1640 from sriniker)
|
|
- RDKit interpretation of atom stereo SMILES is different from 4 other toolkits
|
|
(github issue #1652 from coleb)
|
|
- Treat bonds in PDB CONECT records explicitly, but make blacklisted ones zero-order.
|
|
(github pull #1658 from mwojcikowski)
|
|
- There is no need to enforce that (i, j) and (k, l) be bonded when setting a i, j, k, l dihedral
|
|
(github pull #1673 from ptosco)
|
|
- Make default arguments to common functions less error prone
|
|
(github issue #1679 from greglandrum)
|
|
- Add Fast cluster script
|
|
(github pull #1683 from iwatobipen)
|
|
- Update embedded InChI to v1.05
|
|
(github pull #1684 from mcs07)
|
|
- Add `AllChem.MMFFGetMoleculeForceField().CalcGradient()` to Python wrappers
|
|
(github issue #1688 from theavey)
|
|
- Play nice with naughty MOL blocks
|
|
(github issue #1689 from jw-feng)
|
|
- Make the defaults for some functions less error prone.
|
|
(github pull #1690 from greglandrum)
|
|
- implemented Python wrappers for computing PMI axes and moments
|
|
(github pull #1700 from ptosco)
|
|
- Enable range-based for loops for molecules
|
|
(github pull #1701 from bp-kelley)
|
|
- Support some cactvs extensions to SMARTS
|
|
(github pull #1704 from greglandrum)
|
|
- Integrate Coordgen
|
|
(github pull #1708 from greglandrum)
|
|
- Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
|
|
(github pull #1713 from greglandrum)
|
|
- Set atomic properties from SMARTS
|
|
(github pull #1716 from greglandrum)
|
|
- Allow installation of Python tests to facilitate testing installations
|
|
(github pull #1724 from greglandrum)
|
|
- setAromaticity() should work even if there are aromatic atoms present
|
|
(github issue #1730 from greglandrum)
|
|
- Use uint32 atom and bond indices
|
|
(github pull #1742 from greglandrum)
|
|
- Switch from boost::thread to std::thread
|
|
(github pull #1745 from greglandrum)
|
|
- switch to using std::regex in the SLN parser
|
|
(github pull #1746 from greglandrum)
|
|
- replace the usage of rdk_auto_ptr with std::unique_ptr
|
|
(github pull #1752 from greglandrum)
|
|
- getMolBoundsMatrix() should do triangle bound smoothing by default
|
|
(github issue #1763 from greglandrum)
|
|
- Added Morgan feature fingerprints to Java API
|
|
(github pull #1764 from jones-gareth)
|
|
- Reaction fingerprints not exposed in Java wrapper
|
|
(github issue #1776 from webbres)
|
|
- add Tversky index calculation for shapes
|
|
(github pull #1777 from susanhleung)
|
|
- Add MolToInchiKey function()
|
|
(github pull #1784 from greglandrum)
|
|
- speedup the NumBitsInCommon operation
|
|
(github pull #1785 from greglandrum)
|
|
- Stop putting brackets around * atoms in SMILES
|
|
(github pull #1788 from greglandrum)
|
|
- Support for a JSON-based molecule interchange format
|
|
(github pull #1798 from greglandrum)
|
|
|
|
## Bug Fixes:
|
|
- Fixes Java wrapper build error with Boost 1.64
|
|
(github pull #1613 from ptosco)
|
|
- AssignStereochemistry cleanIt=True incorrectly removing new CIS/TRANS bond stereo
|
|
(github issue #1614 from coleb)
|
|
- switch to using a specific freesasa version
|
|
(github pull #1619 from greglandrum)
|
|
- Add support for %(NNN) notation for ring closures
|
|
(github pull #1624 from baoilleach)
|
|
- Draw._moltoSVG() raises an exception
|
|
(github issue #1625 from greglandrum)
|
|
- MolDrawCairo2D does not build on windows
|
|
(github issue #1627 from greglandrum)
|
|
- Enable windows build that uses cairo
|
|
(github pull #1628 from greglandrum)
|
|
- don't always download the FreeSASA source
|
|
(github issue #1630 from greglandrum)
|
|
- Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0
|
|
(github pull #1635 from coleb)
|
|
- from rdkit.Chem import AllChem has grown a six dependency
|
|
(github issue #1637 from bp-kelley)
|
|
- Fixing bug in IPythonConsole SVG rendering introduced in 1027d4469545653180fff9a38dc8224bd50e8b0d
|
|
(github pull #1641 from coleb)
|
|
- changes required to allow replacing the obsolete __conda_version__ in conda-rdkit
|
|
(github pull #1644 from ptosco)
|
|
- GetConformerRMSMatrix does not work if some conformers were removed
|
|
(github issue #1650 from DrrDom)
|
|
- EnumerateLibrary with initFromString called twice doesn't clear the reaction
|
|
(github issue #1657 from bp-kelley)
|
|
- Missed symmetrization in R-Group decomposition
|
|
(github issue #1659 from greglandrum)
|
|
- Use numpy not numeric for boost 1.65+ - fixes #1581
|
|
(github pull #1664 from mcs07)
|
|
- Support valence 7 for As, Sb, and Bi
|
|
(github issue #1668 from greglandrum)
|
|
- Fix: GetDonor2FeatVects heavy atoms confusion
|
|
(github pull #1676 from josan82)
|
|
- Acetylenic hydrogens not given appropriate 2D coordinates
|
|
(github issue #1691 from jasondbiggs)
|
|
- Warning on import of rgroup decomposition package
|
|
(github issue #1695 from greglandrum)
|
|
- AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required
|
|
(github issue #1702 from baoilleach)
|
|
- Dative bonds interfere with kekulization and the perception of aromaticity
|
|
(github issue #1703 from greglandrum)
|
|
- Fix/rgroup prefer matching nonhs over hs
|
|
(github pull #1707 from bp-kelley)
|
|
- bonds that are STEREOCIS or STEREOTRANS cannot be depickled
|
|
(github issue #1710 from greglandrum)
|
|
- Get queries from the new cactvs SMARTS extensions to pickle correctly
|
|
(github pull #1712 from greglandrum)
|
|
- fix an irritating cmake problem
|
|
(github pull #1715 from greglandrum)
|
|
- Added dependency from Boost headers to PgSQL CMakeLists.txt
|
|
(github pull #1717 from ptosco)
|
|
- Updates python test runner to always use sys.executable
|
|
(github pull #1721 from bp-kelley)
|
|
- - make bond stereo detection in rings consistent
|
|
(github pull #1727 from ptosco)
|
|
- xlocale.h not needed to compile with clang
|
|
(github issue #1728 from adalke)
|
|
- BreakBRICSBonds() not preserving stereochemistry
|
|
(github issue #1734 from greglandrum)
|
|
- rdmolfiles.CanonicalRankAtoms segfaults on 0 atom molecules
|
|
(github issue #1735 from lilleswing)
|
|
- deprecated apply() function causes GetRDKFingerprint to fail in Python 3
|
|
(github issue #1747 from clinntt)
|
|
- Stop dereferencing end() iterators
|
|
(github pull #1748 from greglandrum)
|
|
- out of range fromAtom causes GetMorganFingerprintAsBitVect to segfault
|
|
(github issue #1749 from adalke)
|
|
- Generated SMARTS does not contain atomic chiral tags
|
|
(github issue #1756 from greglandrum)
|
|
- make the build work even if boost::serialization is disabled
|
|
(github pull #1767 from greglandrum)
|
|
- Fix typo in GetBoolProp documentation
|
|
(github pull #1770 from jvansan)
|
|
- Fingerprint segfaults with branchedPaths=False and useHs=False
|
|
(github issue #1793 from chrishmorris)
|
|
- Fix python linkage (primarily for conda builds)
|
|
(github pull #1808 from greglandrum)
|
|
- removeHs() should not remove H atoms that are contributing to the definition of a stereo bond
|
|
(github pull #1810 from d-b-w)
|
|
- global EmbedParameters objects should not be writeable in SWIG wrappers
|
|
(github issue #1826 from greglandrum)
|
|
- RDKit crashes when MolsToGridImage function is called with an empty iterable.
|
|
(github issue #1829 from martin-sicho)
|
|
|
|
|
|
# Release_2017.09.1
|
|
(Changes relative to Release_2017.03.1)
|
|
|
|
## Important
|
|
- The fix for bug #1567 changes the way fragment SMILES are canonicalized.
|
|
MolFragmentToSmiles() and canonicalizeFragment() will now often return
|
|
different results
|
|
- The fix for bug #1604 changes the behavior of QueryAtom::setQuery(), which
|
|
now deletes the current query before setting the new value. If you are using
|
|
QueryAtom::setQuery() from C++ (or possibly Java), be sure that you are not
|
|
also deleting that memory.
|
|
|
|
## Acknowledgements:
|
|
Brian Cole, Peter Gedeck, Guillaume Godin, Jan Halborg Jensen, Malitha Kabir,
|
|
Tuomo Kalliokoski, Brian Kelley, Noel O'Boyle, Matthew O'Meara, Pavel
|
|
Polishchuk, Cameron Pye, Christian Ribeaud, Stephen Roughley, Patrick Savery,
|
|
Roger Sayle, Nadine Schneider, Gregor Simm, Matt Swain, Paolo Tosco, Alain
|
|
Vaucher, Sam Webb, 'phenethyl', 'xiaotaw'
|
|
|
|
## Highlights:
|
|
- The new R-Group decomposition code provides a flexible and powerful tool for
|
|
building R-group tables or datasets look in $RDBASE/Docs/Notebooks for
|
|
example notebooks showing how to use this.
|
|
- Drawing of chemical reactions has been greatly improved and is now done using
|
|
the C++ rendering code.
|
|
- The MaxMinPicker is dramatically faster.
|
|
- New descriptors: the QED descriptor has been added as have a large collection
|
|
of new 3D descriptors and implementations of the USR and USRCAT fingerprints.
|
|
|
|
## New Features and Enhancements:
|
|
- Bring back USR and USRCAT descriptors
|
|
(github pull #1417 from greglandrum)
|
|
- Generate a warning for conflicting bond directions
|
|
(github issue #1423 from greglandrum)
|
|
- expose and test GetDrawCoords()
|
|
(github pull #1427 from greglandrum)
|
|
- Improvement suggestions for SaltRemover
|
|
(github issue #1431 from ribeaud)
|
|
- Remove obsolete scripts from Scripts dir
|
|
(github pull #1440 from greglandrum)
|
|
- Support drawing reactions from C++
|
|
(github pull #1444 from greglandrum)
|
|
- QED code with unit test file
|
|
(github pull #1445 from gedeck)
|
|
- Add support for other datatypes to ConvertToNumpyArray
|
|
(github issue #1447 from pyeguy)
|
|
- - updated FindCairo.cmake
|
|
(github pull #1455 from ptosco)
|
|
- - fixes PgSQL CMakeLists.txt to enable conda build on Windows
|
|
(github pull #1457 from ptosco)
|
|
- Some cleanups to make Travis builds faster
|
|
(github pull #1464 from greglandrum)
|
|
- ExplainPairScore does not support includeChirality=True
|
|
(github issue #1466 from xiaotaw)
|
|
- Add a collection of new 3D descriptors
|
|
(github pull #1467 from greglandrum)
|
|
- Update cartridge documentation to use ChEMBL 23
|
|
(github issue #1491 from greglandrum)
|
|
- First entry of the SubstructLibrary module
|
|
(github pull #1493 from bp-kelley)
|
|
- assorted fixes to get the current master branch to build on Windows
|
|
(github pull #1495 from ptosco)
|
|
- Support assignment of stereochemistry tags to bonds from 3D structure
|
|
(github issue #1497 from gncs)
|
|
- Support black and white molecule drawing
|
|
(github issue #1510 from greglandrum)
|
|
- Missing def_readwrite for backgroundColour in rdMolDraw2D.cpp
|
|
(github issue #1519 from goraj)
|
|
- Adds canonicalization of atom maps
|
|
(github pull #1521 from bp-kelley)
|
|
- Implement stereoisomer enumeration
|
|
(github pull #1531 from greglandrum)
|
|
- Add a MolBundle class
|
|
(github pull #1537 from greglandrum)
|
|
- Provide support for color palettes in MolDraw2D
|
|
(github pull #1546 from greglandrum)
|
|
- A few reaction drawing tweaks
|
|
(github pull #1549 from greglandrum)
|
|
- R group improvements
|
|
(github pull #1552 from greglandrum)
|
|
- Add a canned Atom query for heavy atom degree
|
|
(github issue #1563 from greglandrum)
|
|
- Adds FreeSASA adapter
|
|
(github pull #1565 from bp-kelley)
|
|
- Added C++ version of getBestRMS()
|
|
(github pull #1568 from psavery)
|
|
- SMILES lexer optimization/enhancement
|
|
(github pull #1575 from greglandrum)
|
|
- Update IPythonConsole and PandasTools to use new drawing code
|
|
(github pull #1577 from greglandrum)
|
|
- Squashes warnings on cygwin
|
|
(github pull #1578 from bp-kelley)
|
|
- Support continuous highlighting in drawMolecules().
|
|
(github pull #1579 from greglandrum)
|
|
- Enhanced Similarity Maps depiction
|
|
(github pull #1594 from gerebtzoff)
|
|
|
|
## Bug Fixes:
|
|
- RDKit gets stuck on PubChem CID 102128817
|
|
(github issue #1281 from TuomoKalliokoski)
|
|
- MMP code not including molecules with no cuts
|
|
(github issue #1406 from greglandrum)
|
|
- Fixes PandasTools to also work with pandas 0.20
|
|
(github pull #1410 from bp-kelley)
|
|
- csharp input files out of date
|
|
(github issue #1413 from greglandrum)
|
|
- Fix cxsmiles parse on VS2008
|
|
(github pull #1415 from mcs07)
|
|
- MaxMinPicker picking non-existent element
|
|
(github issue #1421 from greglandrum)
|
|
- _isCallable clashes with Celery
|
|
(github issue #1434 from momeara)
|
|
- Impossible to build the RDKit from source without Python installed
|
|
(github issue #1435 from greglandrum)
|
|
- RemoveHs() removes H atom attached to dummy if it came from AddHs()
|
|
(github issue #1439 from DrrDom)
|
|
- fix a couple failing windows tests related to temp file removal
|
|
(github pull #1446 from greglandrum)
|
|
- SanitizeRxn fails with a runtime exception when unused Rlabels are in product
|
|
(github issue #1448 from bp-kelley)
|
|
- String module conversion bug
|
|
(github pull #1452 from coleb)
|
|
- GetConformerRMS() documentation is misleading
|
|
(github pull #1459 from greglandrum)
|
|
- URANGE_CHECK not doing its job in RWMol::addBond
|
|
(github issue #1461 from baoilleach)
|
|
- ExplainPairScore does not support includeChirality=True
|
|
(github issue #1466 from xiaotaw)
|
|
- MolToSmarts does not include atom-map or isotope info for molecules built from SMILES
|
|
(github issue #1472 from greglandrum)
|
|
- AdjustQueryProperties() removing properties from dummy atoms
|
|
(github issue #1474 from greglandrum)
|
|
- Fixes lookup for HELM Monomer 'D'
|
|
(github pull #1477 from bp-kelley)
|
|
- Aromatic rings composed solely of dummy atoms should not be kekulized
|
|
(github issue #1478 from bp-kelley)
|
|
- Directly specify rotor model used in QED.
|
|
(github pull #1483 from bp-kelley)
|
|
- Unicode problem with pidPS tests on Mac
|
|
(github issue #1490 from greglandrum)
|
|
- Pattern fingerprint setting bad bits with degree zero atoms
|
|
(github issue #1496 from greglandrum)
|
|
- Remove xlocale header
|
|
(github pull #1501 from greglandrum)
|
|
- Fixes atom documentation
|
|
(github pull #1505 from bp-kelley)
|
|
- TypeError from PandasTools.SaveXlsxFromFrame
|
|
(github issue #1507 from pyeguy)
|
|
- Removes trailing spaces after \ to fix windows compilation errors
|
|
(github pull #1516 from bp-kelley)
|
|
- prepareMolForDrawing() not in SWIG wrappers
|
|
(github issue #1522 from greglandrum)
|
|
- Bond is missing IsInRing methods in Java wrapper
|
|
(github issue #1535 from sroughley)
|
|
- Fixes blanking of non-query atom data when QueryAtomData was being pi…
|
|
(github pull #1541 from bp-kelley)
|
|
- ChemicalReaction code not calling setNoImplicit() when H counts are set.
|
|
(github issue #1544 from greglandrum)
|
|
- Fixes failing build with MSVC
|
|
(github pull #1547 from ptosco)
|
|
- Kekulization error with cores from R-Group Decomposition
|
|
(github issue #1550 from greglandrum)
|
|
- Fixes double free for Dict::update
|
|
(github pull #1571 from bp-kelley)
|
|
- QueryAtom::setQuery() should delete the old query first
|
|
(github pull #1604 from greglandrum)
|
|
|
|
|
|
# Release_2017.03.1
|
|
(Changes relative to Release_2016.09.1)
|
|
|
|
## Important
|
|
- The fix for bug #879 changes the definition of the layered fingerprint.
|
|
This means that all database columns using layered fingerprints as well as
|
|
all substructure search indices should be rebuilt.
|
|
- All C++ library names now start with RDKit (see #1349).
|
|
|
|
## Acknowledgements:
|
|
Brian Cole, David Cosgrove, JW Feng, Berend Huisman, Peter Gedeck, 'i-tub',
|
|
Jan Holst Jensen, Brian Kelley, Rich Lewis, Brian Mack, Eloy Felix Manzanares,
|
|
Stephen Roughley, Roger Sayle, Nadine Schneider, Gregor Simm, Matt Swain,
|
|
Paolo Tosco, Riccardo Vianello, Hsiao Yi
|
|
|
|
## Highlights:
|
|
- It's now possible (though not the default) to pickle molecule properties
|
|
with the molecule
|
|
- There's a new, and still in development, "Getting started in C++" document.
|
|
- A lot of the Python code has been cleaned up
|
|
|
|
## New Features and Enhancements:
|
|
- Add removeHs option to MolFromSmiles()
|
|
(github issue #554 from greglandrum)
|
|
- support a fixed bond length in the MolDraw2D code
|
|
(github issue #565 from greglandrum)
|
|
- Pattern fingerprint should set bits for single-atom fragments.
|
|
(github issue #879 from greglandrum)
|
|
- Reviewed unit tests of rdkit.ML - coverage now 63.1%
|
|
(github pull #1148 from gedeck)
|
|
- Reviewed unit tests of rdkit.VLib - coverage now 67.1%
|
|
(github pull #1149 from gedeck)
|
|
- Removes exponetial numBonds behavior
|
|
(github pull #1154 from bp-kelley)
|
|
- Exposes normalize option to GetFlattenedFunctionalGroupHierarchy
|
|
(github pull #1165 from bp-kelley)
|
|
- Expose RWMol.ReplaceBond to Python
|
|
(github pull #1174 from coleb)
|
|
- Review of rdkit.Chem.Fraggle code
|
|
(github pull #1184 from gedeck)
|
|
- Add support for dative bonds.
|
|
(github pull #1190 from janholstjensen)
|
|
- Python 3 compatibility (issue #398)
|
|
(github pull #1192 from gedeck)
|
|
- 1194: Review assignments of range in Python code
|
|
(github pull #1195 from gedeck)
|
|
- Moved GenerateDepictionMatching[23]DStructure from Allchem.py to C++
|
|
(github pull #1197 from DavidACosgrove)
|
|
- Review rdkit.Chem.pharm#D modules
|
|
(github pull #1201 from gedeck)
|
|
- Find potential stereo bonds should return any
|
|
(github pull #1202 from coleb)
|
|
- Gedeck coverage sim div filters
|
|
(github pull #1208 from gedeck)
|
|
- Gedeck review unit test inchi
|
|
(github pull #1209 from gedeck)
|
|
- Coverage rdkit.Dbase
|
|
(github pull #1210 from gedeck)
|
|
- Coverage rdkit.DataStructs
|
|
(github pull #1211 from gedeck)
|
|
- UnitTestPandas works on Python3
|
|
(github pull #1213 from gedeck)
|
|
- Cleanup and improvement to test coverage of PandasTools
|
|
(github pull #1215 from gedeck)
|
|
- Cleanup of rdkit.Chem.Fingerprints
|
|
(github pull #1217 from gedeck)
|
|
- Optimization of UFF and MMFF forcefields
|
|
(github pull #1218 from ptosco)
|
|
- Support for ChemAxon Extended SMILES/SMARTS
|
|
(github issue #1226 from greglandrum)
|
|
- Improved test coverage for rdkit.Chem.Fingerprints
|
|
(github pull #1243 from gedeck)
|
|
- Adding a few tests for coverage utils
|
|
(github pull #1244 from gedeck)
|
|
- Make Pandastools modifications to generic RDkit functionality more obvious
|
|
(github pull #1245 from gedeck)
|
|
- Rename test file and cleanup
|
|
(github pull #1246 from gedeck)
|
|
- Review of rdkit.Chem.MolKey
|
|
(github pull #1247 from gedeck)
|
|
- Review tests in rdkit.Chem.SimpleEnum
|
|
(github pull #1248 from gedeck)
|
|
- Move execution of DocTests in rdkit.Chem into a UnitTest file
|
|
(github pull #1256 from gedeck)
|
|
- Review code in rdkit.Chem.Suppliers
|
|
(github pull #1258 from gedeck)
|
|
- Add python wraps
|
|
(github pull #1259 from eloyfelix)
|
|
- Rename file UnitTestDocTests in rdkitChem
|
|
(github pull #1263 from gedeck)
|
|
- Gedeck rdkit chem unit test surf
|
|
(github pull #1267 from gedeck)
|
|
- cleanup rdkit.Chem.Lipinski and rdkit.Chem.GraphDescriptors
|
|
(github pull #1268 from gedeck)
|
|
- Address Issue #1214
|
|
(github pull #1275 from gedeck)
|
|
- Dev/pickle properties
|
|
(github pull #1277 from bp-kelley)
|
|
- Remove unused test boilerplate
|
|
(github pull #1288 from gedeck)
|
|
- Refactored the script SDFToCSV
|
|
(github pull #1289 from gedeck)
|
|
- Dev/rdmmpa api update
|
|
(github pull #1291 from bp-kelley)
|
|
- Fix/rogers fixes
|
|
(github pull #1293 from bp-kelley)
|
|
- Remove expected (error) output during unit tests
|
|
(github pull #1298 from gedeck)
|
|
- Refactor FeatFinderCLI and add unittests
|
|
(github pull #1299 from gedeck)
|
|
- Refactor BuildFragmentCatalog - 1
|
|
(github pull #1300 from gedeck)
|
|
- Review of rdkit.Chem code - 1
|
|
(github pull #1301 from gedeck)
|
|
- Minor cleanup in rdkit.Chem
|
|
(github pull #1304 from gedeck)
|
|
- Start using py3Dmol in the notebook
|
|
(github pull #1308 from greglandrum)
|
|
- Add the option to match formal charges to FMCS
|
|
(github pull #1311 from greglandrum)
|
|
- Review of rdkit.Chem.Subshape
|
|
(github pull #1313 from gedeck)
|
|
- Review rdkit.Chem.UnitTestSuppliers
|
|
(github pull #1315 from gedeck)
|
|
- Add cis/trans tags to double bonds
|
|
(github pull #1316 from greglandrum)
|
|
- MolDraw2D: make custom atom labels easier
|
|
(github issue #1322 from greglandrum)
|
|
- MolDraw2D: allow DrawMolecules() to put all molecules in one pane
|
|
(github issue #1325 from greglandrum)
|
|
- Refactoring rdkit.Chem.SATIS
|
|
(github pull #1329 from gedeck)
|
|
- Minor cleanup of rdkit.Chem.SaltRemover
|
|
(github pull #1330 from gedeck)
|
|
- Review rdkit.chem.FunctionalGroups and rdkit.Chem.UnitTestSuppliers
|
|
(github pull #1331 from gedeck)
|
|
- Get the tests working with python 3.6
|
|
(github pull #1332 from greglandrum)
|
|
- add "RDKit" to the beginning of all library names
|
|
(github pull #1349 from greglandrum)
|
|
- Fix/sanitizerxn merge hs
|
|
(github pull #1367 from bp-kelley)
|
|
- Update AllChem.py
|
|
(github pull #1378 from BerendHuisman)
|
|
|
|
## New Java Wrapper Features:
|
|
|
|
## Bug Fixes:
|
|
- python2 code in python3 install
|
|
(github issue #1042 from kcamnairb)
|
|
- Fixes #1162 (resMolSupplierTest failing with boost 1.62)
|
|
(github pull #1166 from ptosco)
|
|
- add missing $RDKLIBS to cartridge build
|
|
(github pull #1167 from rvianello)
|
|
- Include <boost/cstdint.hpp> for uint64_t
|
|
(github pull #1168 from mcs07)
|
|
- replace std::map::at with std::map::find
|
|
(github pull #1169 from mcs07)
|
|
- Fix Trajectory GetSnapshot behaviour after Clear
|
|
(github pull #1172 from mcs07)
|
|
- Add Contrib dir to RDPaths
|
|
(github pull #1176 from mcs07)
|
|
- RDThreads.h: No such file or directory
|
|
(github issue #1177 from gncs)
|
|
- this now builds with vs2008
|
|
(github pull #1178 from greglandrum)
|
|
- Add information on building RDkit on macOS using conda
|
|
(github pull #1180 from gedeck)
|
|
- new sequence capabilities not available from either Python or Java
|
|
(github issue #1181 from greglandrum)
|
|
- Gets the reaction sanitization code working correctly on 32bit systems
|
|
(github pull #1187 from greglandrum)
|
|
- Adds RDProps to c# wrapper
|
|
(github pull #1188 from bp-kelley)
|
|
- fix compatibility with PostgreSQL 9.2
|
|
(github pull #1189 from greglandrum)
|
|
- Fixes memory leak in closeCheckMolFiles, fixes valgrind read issue in…
|
|
(github pull #1200 from bp-kelley)
|
|
- Support valences of 4 and 6 for Te
|
|
(github issue #1204 from hsiaoyi0504)
|
|
- Stereochemistry not output to SMILES when allHsExplicit=True
|
|
(github issue #1219 from greglandrum)
|
|
- Remove deprecated string module functions
|
|
(github pull #1223 from gedeck)
|
|
- Turns on -fpermissive for gcc >= 6 and boost < 1.62
|
|
(github pull #1225 from bp-kelley)
|
|
- all-atom RMSD used to prune conformers in embedding code, docs say heavy-atom RMSD is used
|
|
(github issue #1227 from greglandrum)
|
|
- FindPotentialStereoBonds() failure
|
|
(github issue #1230 from greglandrum)
|
|
- make the Pandas version checking more robust
|
|
(github pull #1239 from greglandrum)
|
|
- Failure to embed larger aromatic rings
|
|
(github issue #1240 from greglandrum)
|
|
- fixed build failure on Windows due to missing link to library
|
|
(github pull #1241 from ptosco)
|
|
- fixed a test failure on Windows due to CR+LF encoding
|
|
(github pull #1242 from ptosco)
|
|
- MolFromMolBlock sanitizing when it should not be
|
|
(github issue #1251 from greglandrum)
|
|
- PMI descriptors incorrect
|
|
(github issue #1262 from greglandrum)
|
|
- Reactions don't modify isotope unless chemical element is specified for the product
|
|
(github issue #1266 from i-tub)
|
|
- Do not include the 3D descriptors in rdkit.Chem.Descriptors.descList
|
|
(github issue #1287 from greglandrum)
|
|
- ring stereochemistry perception failing for spiro centers
|
|
(github issue #1294 from greglandrum)
|
|
- Property pickling test failing on windows
|
|
(github issue #1348 from greglandrum)
|
|
- Fixes overflow error in boost when compiler chooses int for enum type
|
|
(github pull #1351 from bp-kelley)
|
|
- Hybridization type of group 1 metals
|
|
(github issue #1352 from richlewis42)
|
|
- bad python docs for some distance geometry functions
|
|
(github issue #1385 from greglandrum)
|
|
- Bond from reactant not added to product
|
|
(github issue #1387 from greglandrum)
|
|
- int32_t with no namespace in MolPickler.h
|
|
(github issue #1388 from greglandrum)
|
|
|
|
## Contrib updates:
|
|
- Chemical reaction role assignment code from Nadine Schneider
|
|
(github pull #1185 from NadineSchneider)
|
|
|
|
## Deprecated code (to be removed in a future release):
|
|
- rdkit.Chem.MCS: please use rdkit.Chem.rdFMCS instead
|
|
|
|
# Release_2016.09.1
|
|
(Changes relative to Release_2016.03.1)
|
|
|
|
## Important
|
|
- The adjustQueryParameters structure has been rewritten. If you were using
|
|
this in your code, you'll need to update your code.
|
|
|
|
## Acknowledgements:
|
|
Brian Cole, Piotr Dabrowski, Jan Domanski, Peter Gedeck, Richard Hall, Brian
|
|
Kelley, Joos Kiener, 'maddogcz', John Mayfield, 'michalsta', Michal Nowotka,
|
|
'philopon', Nico Pulver, Sereina Riniker, Stephen Roughley, Roger Sayle, Nadine
|
|
Schneider, Gianluca Sforna, Peter Shenkin, Paolo Tosco, David Turbert, Riccardo
|
|
Vianello, Maciek Wojcikowski
|
|
|
|
## Highlights:
|
|
- New AdjustQueryProperties() (adjustQueryProperties() in C++) for fine-tuning substructure queries.
|
|
- ReactionEnum functionality adds significant new capabilities for doing library enumeration
|
|
- Similarity searches with the PostgreSQL cartridge are substantially faster
|
|
- New 3D descriptors (requires Eigen3 if you are building them yourself)
|
|
|
|
## New Features and Enhancements:
|
|
- Trajectory/Snapshot objects
|
|
(github pull #863 from ptosco)
|
|
- Adds Avalon fingerprints to default set
|
|
(github pull #871 from bp-kelley)
|
|
- Adds the default index to the building block templates
|
|
(github pull #873 from bp-kelley)
|
|
- Pandas: Allow reading just the properties from SDF file
|
|
(github pull #883 from mwojcikowski)
|
|
- Dev/filtercatalog functional groups
|
|
(github pull #885 from bp-kelley)
|
|
- Dev/preprocessrxn cpp
|
|
(github pull #892 from bp-kelley)
|
|
- Rollup of warning squashing (with some tests diagnostics thrown in)
|
|
(github pull #895 from bp-kelley)
|
|
- Adds RDAny (smaller generic holder) Updates all used dictionaries
|
|
(github pull #896 from bp-kelley)
|
|
- expose FPS functions to SWIG
|
|
(github pull #897 from greglandrum)
|
|
- Add SaveFile method to the PyMol wrapper
|
|
(github pull #898 from greglandrum)
|
|
- Add a MultiFPBReader class
|
|
(github pull #909 from greglandrum)
|
|
- Improved Python doc strings for Trajectory/Snapshot objects
|
|
(github pull #912 from ptosco)
|
|
- Added support for building the gzip'd stream test
|
|
(github pull #914 from ptosco)
|
|
- Improved Trajectory Python doc strings
|
|
(github pull #915 from ptosco)
|
|
- improve error reporting for kekulization failures
|
|
(github pull #919 from greglandrum)
|
|
- Feat/github934
|
|
(github pull #939 from greglandrum)
|
|
- Add support for a simplified aromaticity model.
|
|
(github pull #942 from greglandrum)
|
|
- Dev/moldescriptors callables
|
|
(github pull #944 from bp-kelley)
|
|
- Dev/cleanup warnings
|
|
(github pull #948 from greglandrum)
|
|
- Modifications to enable building with MinGW compilers
|
|
(github pull #960 from ptosco)
|
|
- Made DistGeomHelpers test robust against small 3D coordinate variations
|
|
(github pull #961 from ptosco)
|
|
- Adds aromatization and reaction options to AdjustQuery
|
|
(github pull #965 from bp-kelley)
|
|
- Improved planarity for ETKDG
|
|
(github pull #967 from sriniker)
|
|
- Fixes built-in popcount in PgSQL cartridge on Windows
|
|
(github pull #978 from ptosco)
|
|
- A variety of drawing-related changes
|
|
(github pull #986 from greglandrum)
|
|
- Get pango 2D depiction to work with cairocffi
|
|
(github pull #998 from ptosco)
|
|
- Adds Atom atom map and rlabel apis
|
|
(github pull #1004 from bp-kelley)
|
|
- Dev/chemtransforms chirality
|
|
(github pull #1006 from bp-kelley)
|
|
- Added the option to label deuterium and tritium as D and T
|
|
(github pull #1011 from ptosco)
|
|
- Adds replaceCore function that takes a matchVect
|
|
(github pull #1013 from bp-kelley)
|
|
- Add an initial version of wavy bonds
|
|
(github pull #1014 from greglandrum)
|
|
- remove a compiler warning
|
|
(github pull #1019 from greglandrum)
|
|
- Make the Contrib directory available in RDConfig
|
|
(github pull #1024 from NadineSchneider)
|
|
- Adds some additional canned atom and bond query definitions
|
|
(github pull #1047 from greglandrum)
|
|
- Draw crossed bonds
|
|
(github pull #1052 from greglandrum)
|
|
- Alex/struct checker apr15
|
|
(github pull #1054 from bp-kelley)
|
|
- MolDraw2D: allow the amount of padding around atom labels to be adjusted.
|
|
(github issue #1056 from greglandrum)
|
|
- Add multiple molecule drawing to the C++ interface
|
|
(github pull #1059 from greglandrum)
|
|
- add pickle support to FilterCatalog
|
|
(github pull #1063 from greglandrum)
|
|
- Issue #1066: Improved .gitignore file
|
|
(github pull #1068 from gedeck)
|
|
- Cleanup of Scaffolds Python code
|
|
(github pull #1069 from gedeck)
|
|
- Consistent formatting of Python code
|
|
(github issue #1071 from gedeck)
|
|
- Improved test coverage of Python code
|
|
(github pull #1081 from gedeck)
|
|
- Improved test coverage of rdkit.DataStructs
|
|
(github pull #1083 from gedeck)
|
|
- Add some 3D molecular descriptors (requires Eigen3)
|
|
(github pull #1084 from greglandrum)
|
|
- Conformer GetPos returns a numpy array rather than a tuple of tuples
|
|
(github pull #1087 from jandom)
|
|
- make the 3D descriptors available in the Descriptors module
|
|
(github pull #1097 from greglandrum)
|
|
- Documentation update.
|
|
(github pull #1100 from greglandrum)
|
|
- Provide SVG output from the cartridge
|
|
(github pull #1109 from greglandrum)
|
|
- Allow the output of ROMol::debugMol() to show up in jupyter
|
|
(github pull #1110 from greglandrum)
|
|
- Dev/reaction enumeration
|
|
(github pull #1111 from bp-kelley)
|
|
- yapf formatting of recent changes to Python code in rdkit and Code
|
|
(github pull #1120 from gedeck)
|
|
- Add a parameters structure for controlling the embedding options.
|
|
(github pull #1121 from greglandrum)
|
|
- add more detailed error reporting when python tests fail in TestRunner.py
|
|
(github pull #1122 from greglandrum)
|
|
- add support for a default constructor to the python-exposed RWMol class
|
|
(github pull #1129 from greglandrum)
|
|
- The RunStruchk function is not exposed in pyAvalonTools
|
|
(github issue #1130 from pulveni1)
|
|
- SSSR performance improvements to support larger systems
|
|
(github pull #1131 from coleb)
|
|
- Script PythonFormat.py will test the RDkit python code for conformance with the agreed format using yapf
|
|
(github pull #1133 from gedeck)
|
|
- support additional trans-uranic elements
|
|
(github pull #1134 from greglandrum)
|
|
- Expanded sequence support
|
|
(github pull #1140 from greglandrum)
|
|
- add UGM link to documentation
|
|
(github pull #1142 from David-Turbert)
|
|
- Remove iPythonConsole configuration for normal Draw tests
|
|
(github pull #1146 from gedeck)
|
|
- Wrap DetectBondStereoChemistry in python
|
|
(github pull #1156 from coleb)
|
|
|
|
## New Database Cartridge Features:
|
|
- Provide SVG output from the cartridge
|
|
(github pull #1109 from greglandrum)
|
|
- Add cartridge support for adjustQueryProperties()
|
|
(github pull #949 from greglandrum)
|
|
- refactoring of the postgresql cartridge
|
|
(github pull #992 from rvianello)
|
|
|
|
## New Java Wrapper Features:
|
|
- Expose filtermatch to swig
|
|
(github pull #1117 from bp-kelley)
|
|
- adjustQueryProperties()
|
|
- Java wrappers for Trajectory/Snapshot objects
|
|
(github pull #977 from ptosco)
|
|
- Added getAlignmentTransform to ROMol.i to expose in Java SWIG wrapper
|
|
(github pull #1155 from sroughley)
|
|
|
|
## Bug Fixes:
|
|
- initialization of the PeriodicTable object should be made thread-safe
|
|
(github issue #381 from greglandrum)
|
|
- AssignAtomChiralTagsFromStructure() not recognizing chiral S
|
|
(github issue #607 from greglandrum)
|
|
- Fixed a few typos in Code/PgSQL/rdkit/CMakeLists.txt
|
|
(github pull #867 from ptosco)
|
|
- MergeQueryHs explicit H warning when no explicit Hs were actually used
|
|
(github issue #868 from bp-kelley)
|
|
- Fixes regression in python api CalcNumRotatableBonds
|
|
(github pull #870 from bp-kelley)
|
|
- Single atoms setting radius 1 bits in Morgan fingerprints
|
|
(github issue #874 from greglandrum)
|
|
- Providing subImgSize argument to MolsToGridImage() causes drawing failure
|
|
(github issue #876 from greglandrum)
|
|
- javadoc failure on CentOS 7
|
|
(github pull #878 from ptosco)
|
|
- adjust cartridge tests after the fix for #874
|
|
(github pull #884 from greglandrum)
|
|
- bugreport: invalid handling of negation of aromaticity when parsing SMARTS
|
|
(github issue #893 from michalsta)
|
|
- Fixes depictor problem with empty fragments
|
|
(github pull #894 from greglandrum)
|
|
- Fix building with G++ on Mac OS X
|
|
(github pull #900 from johnmay)
|
|
- linked additional libs to fix a build failure on Windows
|
|
(github pull #901 from ptosco)
|
|
- Rdkit 2016_03_1 generate SVG typo in Python bindings
|
|
(github issue #903 from maddogcz)
|
|
- PAINS filters update fails when old Python is installed
|
|
(github issue #904 from greglandrum)
|
|
- rdMolDraw2D.PrepareMolForDrawing() should not default to forceCoords=True
|
|
(github issue #906 from greglandrum)
|
|
- AddHs() using 3D coordinates with 2D conformations
|
|
(github issue #908 from greglandrum)
|
|
- ugly coordinates generated for peptide chains
|
|
(github issue #910 from greglandrum)
|
|
- Cartridge: makefile not using -O2 for C code.
|
|
(github issue #920 from greglandrum)
|
|
- Removes incorrect setting of hasNonPodData
|
|
(github pull #923 from bp-kelley)
|
|
- cleanups of RDLog's tee behavior
|
|
(github pull #926 from greglandrum)
|
|
- initialize boost::once_flag properly
|
|
(github pull #927 from greglandrum)
|
|
- sys not imported in IPythonConsole.py
|
|
(github issue #928 from greglandrum)
|
|
- AddTee is now SetTee
|
|
(github pull #930 from bp-kelley)
|
|
- mistake in SVG generated for wedged bonds
|
|
(github issue #932 from greglandrum)
|
|
- PandasTools AttributeError with pandas-0.18.1
|
|
(github issue #933 from philopon)
|
|
- Jupyter Notebooks: Issue with PyMol.MolViewer on Windows
|
|
(github issue #936 from kienerj)
|
|
- Subshape module: Not Python 3 compatible
|
|
(github issue #937 from kienerj)
|
|
- property dictionaries leaking memory
|
|
(github issue #940 from greglandrum)
|
|
- Bug when removing stereo info?
|
|
(github pull #946 from mnowotka)
|
|
- Distorted aromatic rings from ETKDG
|
|
(github issue #952 from greglandrum)
|
|
- MolDraw2D: default color should not be cyan
|
|
(github issue #953 from greglandrum)
|
|
- GetPropNames() no longer working on Atoms or Bonds
|
|
(github issue #955 from greglandrum)
|
|
- Kekulization issues post successful smiles parsing
|
|
(github issue #962 from bp-kelley)
|
|
- Fixes includes for older boost/gcc
|
|
(github pull #966 from bp-kelley)
|
|
- ugly conformations can be generated for highly constrained ring systems
|
|
(github issue #971 from greglandrum)
|
|
- Cleanup bad conformations
|
|
(github pull #973 from greglandrum)
|
|
- Unnecessary warnings in rxn.validate()
|
|
(github issue #975 from greglandrum)
|
|
- Minor fix to Code/GraphMol/Wrap/testTrajectory.py
|
|
(github pull #979 from ptosco)
|
|
- prepareMolForDrawing(): Do not add Hs to some three-coordinate Cs
|
|
(github issue #982 from greglandrum)
|
|
- MolDraw2D: wedged bonds between chiral centers drawn improperly
|
|
(github issue #983 from greglandrum)
|
|
- Fix format-security GCC warning
|
|
(github pull #984 from giallu)
|
|
- MolDraw2D scaling problems
|
|
(github issue #985 from greglandrum)
|
|
- RIght-justified elements in RCSB SDF files can now be parsed
|
|
(github pull #994 from ptosco)
|
|
- Right-justified elements in RCSB SDF files raise an exception
|
|
(github issue #995 from ptosco)
|
|
- ChemReactions: Bugfix in copy constructor
|
|
(github pull #996 from NadineSchneider)
|
|
- PgSQL README typos
|
|
(github pull #997 from ptosco)
|
|
- Fixes rounding errors in test
|
|
(github pull #1001 from bp-kelley)
|
|
- Fixes middle-justified symbols in sd files, adds M_CHG tests
|
|
(github pull #1002 from bp-kelley)
|
|
- fix compatibility issues with postgres < 9.5 (#1000)
|
|
(github pull #1005 from rvianello)
|
|
- Fixes MMFF94 aromaticity perception and ChemicalForceFields.MMFFHasAllMoleculeParams()
|
|
(github pull #1007 from ptosco)
|
|
- fixes typo which breaks the PostgreSQL cartridge build on Windows
|
|
(github pull #1008 from ptosco)
|
|
- Fix Inchi being hardcoded into PostgreSQL
|
|
(github pull #1009 from ptosco)
|
|
- Support ETKDG from within the SWIG wrappers
|
|
(github pull #1010 from greglandrum)
|
|
- move definition of computedPropName to namespace RDKit::detail
|
|
(github issue #1017 from greglandrum)
|
|
- fix non-inchi build
|
|
(github pull #1018 from greglandrum)
|
|
- Fixes #1018
|
|
(github pull #1020 from ptosco)
|
|
- GetSSSR interrupts by segmentation fault
|
|
(github issue #1023 from PiotrDabr)
|
|
- FMCS fix for Windows DLLs
|
|
(github pull #1030 from ptosco)
|
|
- Cause ImportError from failed dlopen of the rdBase.so shared library to propagate.
|
|
(github pull #1032 from coleb)
|
|
- typos in MMPA hash code
|
|
(github issue #1044 from greglandrum)
|
|
- MolOps::cleanUp() being called by CTAB parser even when sanitization isn't on
|
|
(github issue #1049 from greglandrum)
|
|
- Bond::BondDir::EITHERDOUBLE not exposed to python
|
|
(github issue #1051 from greglandrum)
|
|
- add python3 compatibility
|
|
(github pull #1057 from greglandrum)
|
|
- doc updates from Dave Cosgrove
|
|
(github pull #1060 from greglandrum)
|
|
- Fix leak with renumberAtoms() in the SWIG wrappers
|
|
(github pull #1064 from greglandrum)
|
|
- Timings on Windows with Python 3
|
|
(github pull #1067 from ptosco)
|
|
- computeInitialCoords() should call the SSSR code before it calls assignStereochemistry()
|
|
(github issue #1073 from greglandrum)
|
|
- Remove duplicates doesn't work on first column in rdkit.Dbase.DbUtils.GetData
|
|
(github issue #1082 from gedeck)
|
|
- clear up a bunch of windows warnings
|
|
(github pull #1086 from greglandrum)
|
|
- MolsToGridImage barfs on '&' in labels, at least with useSVG=True
|
|
(github issue #1090 from shenkin)
|
|
- Fixes csharp build for 64 bit systems
|
|
(github pull #1098 from bp-kelley)
|
|
- Cartridge: some C++ functions returning pointers to local storage
|
|
(github issue #1106 from greglandrum)
|
|
- Check for doubles after other integer types when reporting properties
|
|
(github pull #1115 from bp-kelley)
|
|
- Replace has_key use in Python (#issue1042)
|
|
(github pull #1132 from gedeck)
|
|
- fix moldraw2d headers installation path
|
|
(github pull #1143 from giallu)
|
|
- Remove iPythonConsole configuration for normal Draw tests
|
|
(github pull #1146 from gedeck)
|
|
- Adds SWIGWIN definition in WIN32 if not 32bit
|
|
(github pull #1158 from bp-kelley)
|
|
- Fix/java win64 memoryleak
|
|
(github pull #1159 from bp-kelley)
|
|
|
|
## Deprecated code (to be removed in a future release):
|
|
- rdkit.VLib python module
|
|
- SanitizeRxn parameters "ChemDrawRxnAdjustParams" has been renamed to
|
|
"MatchOnlyAtRgroupsAdjustParams". These settings did not reflect
|
|
how integrations with SciQuest or the Perkin Elmer ELN behaved and
|
|
were confusing to users (especially since they were not explicit)
|
|
|
|
## Removed code:
|
|
|
|
## Contrib updates:
|
|
- added an implementation of the Gobbi Atom-Atom-Path (AAP) similarity
|
|
(github pull #1015 from Richard-Hall)
|
|
|
|
## Other:
|
|
|
|
# Release_2016.03.1
|
|
(Changes relative to Release_2015.09.2)
|
|
|
|
## Important
|
|
In order to build the RDKit, it is now necessary to have at least v1.7 of numpy installed.
|
|
|
|
## Acknowledgements:
|
|
Note: The RDKit has the wonderful "problem" that there are a lot of
|
|
contributors and it's tough for me to capture them all to put together release
|
|
notes. I don't even know many of the contributors (which is *awesome!*)
|
|
The names here come largely from what I pull in an automated way from github.
|
|
In cases where there's no real name listed in github, I either guessed
|
|
or used just the github alias in quotes. If I got it wrong, please let me know!
|
|
|
|
Josep Arus, Nik Bates-Haus, Andrew Dalke, 'DoliathGavid', 'elcaceres', Peter
|
|
Gedeck, James Jeffryes, Brian Kelley, Juuso Lehtivarjo, Rich Lewis, Daniel Lowe,
|
|
'maddogcz', Kozo Nishida, Michal Nowotka, Axel Pahl, Steven Roughley, Alexander
|
|
Savelyev, Nadine Schneider, Gianluca Sforna, Teague Sterling, Nik Stiefl, Matt
|
|
Swain, Eric Ting, Paolo Tosco, Samo Turk, Riccardo Vianello
|
|
|
|
## Highlights:
|
|
- Improvements to the build system: it's now much easier to build with InChI
|
|
and/or Avalon support since cmake now knows how to fetch the appropriate
|
|
source code for you. Building the PostgreSQL cartridge is now integrated into
|
|
normal build process.
|
|
- Some improvements to molecule rendering and Jupyter notebook integration: The
|
|
new `Draw.PrepareMolForDrawing()` function takes care of standard tasks like
|
|
wedging bonds, kekulization, and adding chiral Hs. `Draw.MolsToGridImage()`
|
|
can generate SVGs and uses the new molecular drawing code for PNGs when
|
|
possible. The Jupyter notebook integration uses the new drawing code when
|
|
possible.
|
|
- Error and warning messages from the C++ core can now be displayed in the
|
|
Jupyter notebook
|
|
|
|
## Bug Fixes:
|
|
- Sanitizer rejects higher valency halides
|
|
(github issue #115 from dan2097)
|
|
- Bad E/Z assignment from ctab
|
|
(github issue #188 from greglandrum)
|
|
- bad E/Z assignment from ctab
|
|
(github issue #192 from greglandrum)
|
|
- Documentation is still python2 specific.
|
|
(github issue #374 from greglandrum)
|
|
- SVG export - Python 3 support
|
|
(github issue #398 from maddogcz)
|
|
- FragmentOnBonds() producing incorrect chirality
|
|
(github issue #511 from greglandrum)
|
|
- Rings containing all dummy atoms with single bonds are flagged as aromatic
|
|
(github issue #518 from greglandrum)
|
|
- IPython integration broken with latest Jupyter
|
|
(github issue #666 from samoturk)
|
|
- Added missing include/forward declarations
|
|
(github pull #668 from ptosco)
|
|
- Fixes a memory leak in fragmentMol
|
|
(github pull #669 from bp-kelley)
|
|
- resetVect option being ignored by reaccsToFingerprint()
|
|
(github issue #671 from greglandrum)
|
|
- failure in AddHs when addCoords is true and coords are all zero
|
|
(github issue #678 from greglandrum)
|
|
- 404 error for the link to Installation instructions
|
|
(github issue #679 from EricTing)
|
|
- Fix java8 build
|
|
(github pull #681 from greglandrum)
|
|
- Smiles containing "[as]" do not parse.
|
|
(github issue #682 from greglandrum)
|
|
- SMARTS reaction triggers invariant violation on chiral compounds
|
|
(github issue #685 from JamesJeffryes)
|
|
- partially specified chiral substructure queries don't work properly
|
|
(github issue #688 from bp-kelley)
|
|
- ExactMolWt ignoring the mass of the electron
|
|
(github issue #694 from greglandrum)
|
|
- Bad 1-4 bounds matrix elements in highly constrained system
|
|
(github issue #696 from greglandrum)
|
|
- More ChEMBL molecules that fail bounds smoothing
|
|
(github issue #697 from greglandrum)
|
|
- Molecule serialization doesn't read/write atomic numbers above 128
|
|
(github issue #713 from greglandrum)
|
|
- AddHs cip rank is declared <int> should be unsigned int?
|
|
(github issue #717 from bp-kelley)
|
|
- ensure line endings are handled consistently for all users
|
|
(github pull #729 from rvianello)
|
|
- Fixes return type of operator[] (fails on later clangs)
|
|
(github pull #733 from bp-kelley)
|
|
- Fix/thread safe localeswitcher line endings
|
|
(github pull #743 from bp-kelley)
|
|
- Fixes Boost 1.46 issues with type traits
|
|
(github pull #748 from bp-kelley)
|
|
- PR #749 causes seg faults on windows
|
|
(github issue #750 from greglandrum)
|
|
- Fixes notebook problems with newer jupyter installs
|
|
(github pull #753 from bp-kelley)
|
|
- Double bond geometry loss on calling removeHs
|
|
(github issue #754 from sroughley)
|
|
- Bug fix to getShortestPath
|
|
(github pull #757 from JLVarjo)
|
|
- reversed stereochemistry with sulfoxides and ring closures
|
|
(github issue #760 from greglandrum)
|
|
- libRDBoost.so.1: undefined symbol
|
|
(github issue #762 from kozo2)
|
|
- Removed -Xdoclint:none flag when packing org.RDKitDoc.jar
|
|
(github pull #763 from undeadpixel)
|
|
- AnyBond specification treated as single when joining rings in SMARTS
|
|
(github issue #766 from teaguesterling)
|
|
- CanonicalRankAtomsInFragment() leaks when called from Python
|
|
(github issue #769 from greglandrum)
|
|
- MolCanvas2D drawing upside down
|
|
(github issue #774 from greglandrum)
|
|
- Drawing single-atom molecules hangs.
|
|
(github issue #781 from greglandrum)
|
|
- chiral lexical order for ring closure after branch
|
|
(github issue #786 from adalke)
|
|
- surface -> self.surface
|
|
(github pull #787 from mnowotka)
|
|
- Chem.MolToSmarts param misnomer
|
|
(github issue #792 from elcaceres)
|
|
- Fixes MolToSmarts python docs
|
|
(github pull #793 from bp-kelley)
|
|
- npscorer.py: Py3 compat and importable from other locations
|
|
(github #801 from apahl)
|
|
- Pre-condition Violation: bad bond type
|
|
(github issue #805 from nbateshaus)
|
|
- rooted atom fingerprint non identical for the same molecules
|
|
(github issue #811 from nisti74)
|
|
- test60RunSingleReactant() not being run
|
|
(github issue #825 from greglandrum)
|
|
- PostgreSQL bug fixes
|
|
(github pull #835 from ptosco)
|
|
- Crash while running testGithub497() on Windows
|
|
(github pull #842 from ptosco)
|
|
- Return value of NumRadicalElectrons and NumValenceElectrons should be integer
|
|
(github issue #846 from gedeck)
|
|
- Fixed a bug in getUFFAngleBendParams()
|
|
(github pull #850 from ptosco)
|
|
- Lines used to wedge bonds are too thick
|
|
(github issue #852 from greglandrum)
|
|
- Fix out of range dereference in MCS code.
|
|
(github pull #857 from DoliathGavid)
|
|
- Atom symbols in wrong order if bond comes from right
|
|
(github issue #860 from greglandrum)
|
|
|
|
## New Features and Enhancements:
|
|
- switch to using new version of avalon toolkit
|
|
(github issue #382 from greglandrum)
|
|
- MolDraw2D: Expand basic drawing api
|
|
(github issue #417 from greglandrum)
|
|
- MolDraw2D: add options
|
|
(github issue #424 from greglandrum)
|
|
- fixed FutureWarning in PeriodicTable.py
|
|
(github pull #665 from richlewis42)
|
|
- first pass, using google style
|
|
(github pull #672 from greglandrum)
|
|
- Use sets instead of and map. Minor comments cleanup.
|
|
(github pull #675 from DoliathGavid)
|
|
- Dev/squash msvc14 warnings
|
|
(github pull #684 from bp-kelley)
|
|
- Fix/stop unnecessary filtercatalog updates
|
|
(github pull #690 from bp-kelley)
|
|
- Add RDK_USE_BOOST_SERIALIZATION configure option (On by default)
|
|
(github pull #691 from bp-kelley)
|
|
- Minor optimizations of the force field minimization code, fix for issue 696
|
|
(github pull #693 from greglandrum)
|
|
- Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints
|
|
(github issue #695 from greglandrum)
|
|
- Fixed a couple of compilation warnings in Resonance.cpp/Resonance.h
|
|
(github pull #701 from ptosco)
|
|
- Dev/run single reactant
|
|
(github pull #705 from bp-kelley)
|
|
- Updates CMAKE_SOURCE_DIR to CMAKE_CURRENT_SOURCE_DIR
|
|
(github pull #707 from bp-kelley)
|
|
- Make LocaleSwitcher threadsafe
|
|
(github issue #710 from greglandrum)
|
|
- Exposes Get/Set Double, Int, Uint and bool props to molecules
|
|
(github pull #711 from bp-kelley)
|
|
- Speed up molblock generation
|
|
(github pull #712 from greglandrum)
|
|
- Expose generateOneProductSet?
|
|
(github issue #721 from DoliathGavid)
|
|
- Add a reader for FPB files (still experimental)
|
|
(github pull #724 from greglandrum)
|
|
- replace std::map::at with std::map::operator[]
|
|
(github pull #730 from rvianello)
|
|
- Fix/get double prop get props asdict
|
|
(github pull #734 from bp-kelley)
|
|
- Add support for Tversky similarity to the FPB reader
|
|
(github pull #735 from greglandrum)
|
|
- Fix ConformerParser to use const std::string &
|
|
(github pull #737 from mcs07)
|
|
- Fix/expose invariant exception
|
|
(github pull #740 from bp-kelley)
|
|
- Support CTABs where the second letter in atom symbols is capitalized
|
|
(github issue #741 from greglandrum)
|
|
- Adds support for capturing RDLogs in Python StdErr streams
|
|
(github pull #749 from bp-kelley)
|
|
- Allow adding Hs only to atoms matching a query operator
|
|
(github issue #758 from greglandrum)
|
|
- Add argument to addHs allowing only certain Hs to be considered
|
|
(github pull #759 from greglandrum)
|
|
- avoid the multiple definition of rdkitVersion/boostVersion
|
|
(github pull #761 from rvianello)
|
|
- cleanup possible pythonObjectToVect leaks in python wrappers
|
|
(github issue #764 from greglandrum)
|
|
- Stop possible core leaks in pythonObjectToVect()
|
|
(github pull #770 from greglandrum)
|
|
- Add C++ function to prepare mol for rendering
|
|
(github issue #771 from greglandrum)
|
|
- Prefer wedging bonds to Hs
|
|
(github issue #772 from greglandrum)
|
|
- Add prepareMolForDrawing() function to C++
|
|
(github pull #775 from greglandrum)
|
|
- Support blanks in MolsToGridImage()
|
|
(github issue #776 from greglandrum)
|
|
- A number of small additions and features to the drawing code
|
|
(github pull #802 from greglandrum)
|
|
- Support larger isotope deltas in the chirality assignment
|
|
(github issue #803 from greglandrum)
|
|
- Adds option RDK_USE_COMPLEX_ROTOR_DEFINITION
|
|
(github pull #810 from bp-kelley)
|
|
- add Draw.MolsToSVGGrid()
|
|
(github pull #817 from greglandrum)
|
|
- make Hs black instead of gray
|
|
(github pull #819 from greglandrum)
|
|
- Fix alignMols so that it takes into account of QueryAtoms and QueryBonds
|
|
(github pull #821 from DoliathGavid)
|
|
- feat/github831: Add getText() static method.
|
|
(github pull #832 from greglandrum)
|
|
- Add an unfolded count-based version of the RDKFingerprint
|
|
(github pull #838 from NadineSchneider)
|
|
- Add some utils functions to ChemReactions
|
|
(github pull #840 from NadineSchneider)
|
|
- Autodetect boost c++ library and compile with matching one
|
|
(github pull #845 from bp-kelley)
|
|
- Add automatic downloads of junit.jar
|
|
(github pull #859 from greglandrum)
|
|
|
|
## New Database Cartridge Features:
|
|
- support providing InChI (or InChI key) generation options in cartridge
|
|
(github pull #755 from greglandrum)
|
|
- building the cartridge is now integrated with the cmake build system
|
|
(github pull #785 from ptosco)
|
|
|
|
## New Java Wrapper Features:
|
|
- Add a bit more control over the lazy MaxMin picker to the java layer
|
|
(github pull #791 from greglandrum)
|
|
- Ensure reduceProductToSideChains exposed in Java/Swig
|
|
(github issue #744 from bp-kelley)
|
|
|
|
## Deprecated code (to be removed in next release):
|
|
|
|
## Removed code:
|
|
|
|
## Contrib updates:
|
|
|
|
## Other:
|
|
|
|
# Release_2015.09.2
|
|
(Changes relative to Release_2015.09.1)
|
|
|
|
## Acknowledgements:
|
|
Brian Kelley, Paolo Tosco, Riccardo Vianello
|
|
|
|
## Bug Fixes:
|
|
- Fixed a post-decrement which causes a crash when compiling under Windows with MSVC 9
|
|
(from ptosco)
|
|
- Fixes a memory leak in fragmentMol
|
|
(github #669 from bp-kelley)
|
|
- MMPA compile error with Microsoft Visual C++ Compiler for Python 2.7
|
|
(github #655 from rvianello)
|
|
|
|
# Release_2015.09.1
|
|
(Changes relative to Release_2015.03.1)
|
|
|
|
## Acknowledgements:
|
|
|
|
Pierre Bhoorasingh, Gungor Budak, Andrew Dalke, JP Ebejer, Peter Ertl,
|
|
Jan Holst Jensen, Brian Kelley, Joos Kiener, Noel O'Boyle, Axel Pahl,
|
|
Sereina Riniker, Alexander Savelyev, Roger Sayle, Nadine Schneider,
|
|
Andrew Stretton, Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vanello,
|
|
Maciek Wojcikowski
|
|
|
|
## Highlights:
|
|
|
|
- Addition of parsers/writers for sequence notation, FASTA, and basic HELM
|
|
- Improved conformation generation based on experimental torsional parameters
|
|
- Much better filtering of generated conformations to ensure they
|
|
match the chirality of the input structure
|
|
- New method for enumerating molecular resonance structures
|
|
- Addition of a molecular FilterCatalog data structure
|
|
|
|
## Bug Fixes:
|
|
- Draw.MolToImage(mol) does not work for Python 3, because cairo for Python 3 has not yet implemented Surface.create_for_data
|
|
(github issue #460 from apahl)
|
|
- SDWriter.close() fails when the underlying stream has an error
|
|
(github issue #498 from greglandrum)
|
|
- Hexafluorophosphate cannot be handled
|
|
(github issue #510 from greglandrum)
|
|
- Labels of highlighted atoms are invisible
|
|
(github issue #519 from NadineSchneider)
|
|
- MolDraw2D: Fix in highlighting atoms
|
|
(github pull #521 from NadineSchneider)
|
|
- Cartridge: index failing for molecular equality in some circumstances
|
|
(github issue #525 from greglandrum)
|
|
- Bad ring finding in a complex fused ring
|
|
(github issue #526 from greglandrum)
|
|
- Fixed crash upon closing a gzip/bzip2 stream opened in binary mode for use with SDWriter under Python3
|
|
(github pull #531 from ptosco)
|
|
- Regression: _smilesAtomOutputOrder incorrect for dot disconnected molecules
|
|
(github issue #532 from baoilleach)
|
|
- Fix #532 - smilesAtomOutputOrder incorrect
|
|
(github pull #535 from baoilleach)
|
|
- Fix Python3 encoding for FilterCatalog/Entry serialization
|
|
(github pull #537 from bp-kelley)
|
|
- Catalog::setCatalogParams needs to be virtual now
|
|
(github pull #538 from bp-kelley)
|
|
- Bonds in allyl cation are not conjugated
|
|
(github issue #539 from greglandrum)
|
|
- Fixes GitHub issue 539
|
|
(github pull #540 from ptosco)
|
|
- SaltBuilder._initPatterns incorrectly handles SMARTS errors
|
|
(github issue #541 from adalke)
|
|
- merging query Hs failing on recursive SMARTS
|
|
(github issue #544 from greglandrum)
|
|
- Crash in O3A alignment when running multi-threaded
|
|
(github issue #546 from greglandrum)
|
|
- PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
|
|
(github pull #547 from apahl)
|
|
- fix MMPA bugs for some tests
|
|
(github pull #548 from AlexanderSavelyev)
|
|
- TFD fix for single bonds adjacent to triple bonds
|
|
(github pull #550 from sriniker)
|
|
- Canonicalization paper Aug2015
|
|
(github pull #552 from NadineSchneider)
|
|
- Chirality not affected by atom-map index
|
|
(github issue #553 from adalke)
|
|
- Implicit Hs should not appear in depictions for query atoms.
|
|
(github issue #556 from greglandrum)
|
|
- Fix issue with invalid reactions throwing NameError
|
|
(github pull #559 from bp-kelley)
|
|
- InChI radicals not properly converted
|
|
(github issue #562 from pierrelb)
|
|
- MMPA code not python3 compatible
|
|
(github issue #564 from greglandrum)
|
|
- mmpa: fix bug with num_of_cuts > 2 case
|
|
(github pull #566 from AlexanderSavelyev)
|
|
- Incorrect stereochemistry after embedding
|
|
(github issue #568 from greglandrum)
|
|
- changed FrameToGridImage() so that the dataframe index can be used as legend
|
|
(github pull #570 from apahl)
|
|
- MolDraw2DCairo.GetDrawingText() doesn't work with Python3
|
|
(github issue #571 from greglandrum)
|
|
- addBond return value
|
|
(github issue #572 from JLVarjo)
|
|
- Process aborts during ForwardSDMolSupplier gc when the file object is closed
|
|
(github issue #579 from adalke)
|
|
- Fix/update pains filter catalog
|
|
(github pull #581 from bp-kelley)
|
|
- Importing PandasTools on Windows fails due to Salts.txt
|
|
(github issue #583 from baoilleach)
|
|
- renumberAtoms() not setting conformer dimensionality properly
|
|
(github issue #584 from greglandrum)
|
|
- stereo atoms property on double bonds not being updated properly with insertMol
|
|
(github issue #608 from greglandrum)
|
|
- UFF Atom type not properly assigned to lanthanides
|
|
(github issue #613 from greglandrum)
|
|
- segfault from MolToInchi when bad bond stereochem info is present
|
|
(github issue #614 from greglandrum)
|
|
- MQN12 (heavy atom count) seems to be always 0.
|
|
(github issue #623 from kienerj)
|
|
- fmcs: fix issue with initial seed for PR 580
|
|
(github pull #624 from AlexanderSavelyev)
|
|
- fmcs: fixes #631 with chiralirty
|
|
(github pull #634 from AlexanderSavelyev)
|
|
- Fixes sprintf not found on some gcc compiles
|
|
(github pull #635 from bp-kelley)
|
|
- Fix AppVeyor and Travis UnitTests
|
|
(github pull #636 from bp-kelley)
|
|
- Fixes #629 - python GetSubstructureMatch thread safety
|
|
(github pull #637 from bp-kelley)
|
|
- Fix regressions occurring when building with msvc9
|
|
(github pull #638 from rvianello)
|
|
- Fix/python gil release on rdkit threadsafe sss only
|
|
(github pull #639 from bp-kelley)
|
|
- ctest not running some of the python tests.
|
|
(github issue #643 from greglandrum)
|
|
- Issue643
|
|
(github pull #646 from greglandrum)
|
|
- Fix/various bug fixes filtercatalog and bad operator
|
|
(github pull #648 from bp-kelley)
|
|
- unlocking or destroying a locked mutex in the substructure matcher
|
|
(github issue #653 from greglandrum)
|
|
- MMPA compile error with Microsoft Visual C++ Compiler for Python 2.7
|
|
(github issue #655 from rvianello)
|
|
- new canon: fix in special symmetry invariant
|
|
(github pull #663 from NadineSchneider)
|
|
|
|
## New Features and Enhancements:
|
|
- enable popcount by default for cartridge
|
|
(github issue #428 from greglandrum)
|
|
- Added the RSMD calculation over N molecules in the cookbook.
|
|
(github pull #495 from malteseunderdog)
|
|
- Modified force field constraint tests to be more robust
|
|
(github pull #503 from ptosco)
|
|
- Fix mol drawing on Python3 (issue #460)
|
|
(github pull #504 from apahl)
|
|
- mmpa first version was added
|
|
(github pull #505 from AlexanderSavelyev)
|
|
- Forcefield tests now use RDKit::feq() instead of RDKit::round()
|
|
(github pull #506 from ptosco)
|
|
- SDMolSupplier(), setData() and strictParsing
|
|
(github pull #507 from ptosco)
|
|
- Improvements to LoadSDF and WriteSDF
|
|
(github pull #513 from samoturk)
|
|
- updates to mmpa. reduce number of smiles parsing
|
|
(github pull #515 from AlexanderSavelyev)
|
|
- Some enhancements for the new canonicalization
|
|
(github pull #520 from NadineSchneider)
|
|
- mmpa: remove boost_regex dependency at all. Add new test references
|
|
(github pull #527 from AlexanderSavelyev)
|
|
- Support getting atoms involved in Pharm2D bits
|
|
(github issue #530 from greglandrum)
|
|
- Optimized MMFF::MMFFOptimizeMoleculeConfs()
|
|
(github pull #534 from ptosco)
|
|
- RDKit learns how to filter PAINS/BRENK/ZINC/NIH via FilterCatalog
|
|
(github pull #536 from bp-kelley)
|
|
- Expose Conformer's copy constructor to Python
|
|
(github issue #545 from greglandrum)
|
|
- PyMol.py: changed xmlrpc import to have Python2/Python3 compatibility
|
|
(github pull #547 from apahl)
|
|
- Update PAINS smarts to validated set. Always use mergeQueryHs when reading Smarts
|
|
(github pull #549 from bp-kelley)
|
|
- Add a curated set of PAINS filters to the RDKit
|
|
(github issue #555 from greglandrum)
|
|
- Update pains from wehi_pains.csv
|
|
(github pull #560 from bp-kelley)
|
|
- Change MMPA to use CanonicalRankAtoms instead of _CIPRank
|
|
(github issue #561 from adalke)
|
|
- Add adjustQuery() function to make substructure queries more specific.
|
|
(github issue #567 from greglandrum)
|
|
- changed sascorer.py to enable import from different location
|
|
(github pull #569 from apahl)
|
|
- add export_values() to enums in the python wrapper where it's sensible to do so
|
|
(github issue #573 from greglandrum)
|
|
- Support Sheridan's BT and BP fingerprints
|
|
(github issue #574 from greglandrum)
|
|
- Locale dependent float for _GasteigerCharge
|
|
(github issue #577 from adalke)
|
|
- fmcs: implement adding an initial seed structure
|
|
(github pull #580 from AlexanderSavelyev)
|
|
- Where possible convert docs from RST to MD
|
|
(github issue #585 from greglandrum)
|
|
- [UGM2015] Autodetection of numThreads
|
|
(github issue #586 from mwojcikowski)
|
|
- Generating SVG Images with Transparent Background
|
|
(github issue #587 from gungorbudak)
|
|
- updates to PandasTools.LoadSDF
|
|
(github pull #599 from adalke)
|
|
- Can control mol depiction size with PandasTools.molSize = (200,200).
|
|
(github pull #600 from samoturk)
|
|
- pandas performance and functionality improvements
|
|
(github pull #601 from adalke)
|
|
- Adding documentation for installation with conda.
|
|
(github pull #602 from strets123)
|
|
- Automatic atom reordering in TorsionFingerprints
|
|
(github pull #603 from sriniker)
|
|
- remove bare excepts
|
|
(github pull #606 from adalke)
|
|
- Added option to use SVG rendering in pandas data frames
|
|
(github pull #609 from samoturk)
|
|
- Handle inserting molecules with conformers into molecules without conformers
|
|
(github issue #610 from greglandrum)
|
|
- If wedged bonds are already present, write them to mol blocks
|
|
(github issue #611 from greglandrum)
|
|
- Dev/filter catalog java wrapper
|
|
(github pull #612 from bp-kelley)
|
|
- Support extended reduced graphs
|
|
(github issue #615 from greglandrum)
|
|
- port NumSpiroCenters and NumBridgeheadAtoms descriptors to C++
|
|
(github issue #617 from greglandrum)
|
|
- Add parser/writer for peptide sequences
|
|
(github issue #620 from greglandrum)
|
|
- Add parser/writer for FASTA
|
|
(github issue #621 from greglandrum)
|
|
- Add parser/writer for HELM
|
|
(github issue #622 from greglandrum)
|
|
- Migrate std::string APIs to const std::string &
|
|
(github pull #627 from bp-kelley)
|
|
- Chirality tests
|
|
(github pull #628 from sriniker)
|
|
- Improvements of TFD
|
|
(github pull #630 from sriniker)
|
|
- Added ResonanceMolSupplier
|
|
(github pull #632 from ptosco)
|
|
- Image tostring/fromstring methods replaced by tobytes/frombytes
|
|
(github pull #644 from rvianello)
|
|
- ET(K)DG implementation
|
|
(github pull #647 from sriniker)
|
|
- Build multithreading support by default when boost::threads is present
|
|
(github issue #649 from greglandrum)
|
|
- Minimal SWIG Java wrappers for ResonanceMolSupplier
|
|
(github pull #657 from ptosco)
|
|
|
|
## New Database Cartridge Features:
|
|
- Support for PostgreSQL v8.x has been removed
|
|
- NumSpiroCenters and NumBridgeheadAtoms added
|
|
|
|
## New Java Wrapper Features:
|
|
- Support for FilterCatalogs
|
|
- Support for ResonanceMolSuppliers
|
|
|
|
## Deprecated code (to be removed in next release):
|
|
|
|
## Removed code:
|
|
- rdkit/DataStructs/BitVect.py : a C++ version is used, this was only present for historical reasons
|
|
- rdkit/DataStructs/SparseIntVect.py : a C++ version is used, this was only present for historical reasons
|
|
|
|
## Contrib updates:
|
|
- Addition of Peter Ertl's Natural Product Likeness score.
|
|
|
|
## Other:
|
|
- Much of the documentation has been translated from RST to MD
|
|
|
|
# Release_2015.03.1
|
|
(Changes relative to Release_2014.09.2)
|
|
|
|
## IMPORTANT
|
|
|
|
- This release has a new algorithm for canonical atom ordering. This
|
|
means that canonical SMILES generated with the new version will be
|
|
different from those generated with previous versions.
|
|
|
|
## Acknowledgements:
|
|
|
|
David Cosgrove, Andrew Dalke, JP Ebejer, Niko Fechner, Igor Filippov,
|
|
Patrick Fuller, David Hall, J Bach Hardie, Jan Holst Jensen, Brian
|
|
Kelley, Rich Lewis, John May, Michael Reutlinger, Sereina Riniker,
|
|
Alexander Savelyev, Roger Sayle, Nadine Schneider, Gianluca Sforna,
|
|
Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vianello
|
|
|
|
## Highlights:
|
|
|
|
- A new algorithm for generating canonical atom orders. The new
|
|
algorithm is faster and more robust than the old one.
|
|
- C++-based molecule drawing code, allows consistent molecule
|
|
renderings from C++, Java, and Python. This will become the
|
|
default renderer in the next release.
|
|
- General performance improvements and reduction of memory usage.
|
|
- Torsion Fingerprints for comparing 3D conformations to each other
|
|
- MCS code now available from the PostgreSQL cartridge
|
|
|
|
## Bug Fixes:
|
|
|
|
- fmcs: use the zero bond type instead of other
|
|
(github issue #368 from AlexanderSavelyev)
|
|
- bug fixed in TorsionFingerprints.GetTFDMatrix
|
|
(github issue #376 from sriniker)
|
|
- rdkit.Chem.MolDb.Loader_sa does not work with python3.4
|
|
(github issue #390)
|
|
- ChemReactions: Bugfix/Memleak-fix in runReactants
|
|
(github issue #394 from NadineSchneider)
|
|
- TorsionConstraint bug fix
|
|
(github issue #395 from ptosco)
|
|
- Fixed LoadSDF to keep 3D info
|
|
(github pull #401 from samoturk)
|
|
- Incorrect expected absolute stereochemistries in a test
|
|
(github issue #407)
|
|
- GetSubstructMatches() consumes all available memory
|
|
(github issue #409)
|
|
- Bugfix in the chirality handling of chemical reactions
|
|
(github pull #410 from NadineSchneider)
|
|
- fixed two minor bugs in MMFF code
|
|
(github issue #416 from ptosco)
|
|
- Varied sanitise rejection with hydrogen representation
|
|
(github issue #418)
|
|
- Fixed two trivial bugs
|
|
(github issue #419 from ptosco)
|
|
- RDKit learns how to roundtrip MOLFile values.
|
|
(github issue #420 from bp-kelley)
|
|
- cairoCanvas.py python3 compatibility
|
|
(github issue #426 from bach-hardie)
|
|
- Chem.FragmentOnSomeBonds() should update implicit H count on aromatic heteroatoms when addDummies is False
|
|
(github issue #429)
|
|
- Chem.FragmentOnSomeBonds() crashes if the bond list is empty
|
|
(github issue #430)
|
|
- Increase limit for smallest ring size
|
|
(github issue #431 from cowsandmilk)
|
|
- Problems caused by heteroatoms with radicals in aromatic rings.
|
|
(github issue #432)
|
|
- Conversion from mol to InChI getting ring stereo wrong
|
|
(github issue #437)
|
|
- Metals in mol2 blocks handled incorrectly
|
|
(github issue #438)
|
|
- Fixed a few tests failing when the Windows git client is used
|
|
(github pull #439 from ptosco)
|
|
- Fixed tests failing on Windows when retrieving sources through the Windows git client
|
|
(github pull #440 from ptosco)
|
|
- Conformers not copied correctly in renumberAtoms
|
|
(github issue #441)
|
|
- Radicals are not correctly assigned when reading from SMILES
|
|
(github issue #447)
|
|
- moving RDBoost/Exceptions.h to RDGeneral
|
|
(github pull #458 from rvianello)
|
|
- Add code to accept blank SMILES input.
|
|
(github issue #468 from janholstjensen)
|
|
- Accept empty SMILES and SMARTS
|
|
(github issue #470)
|
|
- Fix MolFile Atom Line List Writer
|
|
(github issue #471 from bp-kelley)
|
|
- Moved 3D ipython renderer to dependency
|
|
(github pull #472 from patrickfuller)
|
|
- Windows build/test failure fixes
|
|
(github issue #473 from ptosco)
|
|
- install missing FMCS/Graph.h header file
|
|
(github pull #478 from rvianello)
|
|
- added const qualifiers to some methods of Atom/Bond iterator classes
|
|
(github pull #479 from rvianello)
|
|
- Bugfix in SmilesWrite and some additional tests for getMolFrags function
|
|
(github issue #482 from NadineSchneider)
|
|
- Removed a while(1) {} in BFGSOpt.h which might result in an infinite loop
|
|
(github issue #484 from ptosco)
|
|
- Gasteiger charge calculation fails with hexavalent sulfur #485
|
|
(github issue #485)
|
|
- SmilesWriter not creating automatic name values for molecules read from CTABs
|
|
(github issue #488)
|
|
- Fix StringType access, remove unused imports
|
|
(github issue #494 from bp-kelley)
|
|
|
|
## New Features:
|
|
|
|
- Isomeric fix in PandasTools
|
|
(github issue #369 from samoturk)
|
|
- added SaveXlsxFromFrame - first version
|
|
(github issue #371 from samoturk)
|
|
- New feature: Torsion fingerprints
|
|
(github issue #372 from sriniker)
|
|
- Add function to extract a molecule with a single (particular) conformer from a multiconf mol
|
|
(github issue #384)
|
|
- Added C++ and Python helpers to retrieve force-field parameters
|
|
(github issue #387 from ptosco)
|
|
- Support providing all options to SWIG-wrapped FMCS
|
|
(github issue #397)
|
|
- Add function to request if calling UpdatePropertyCache is necessary
|
|
(github issue #399)
|
|
- Add function to test if UpdatePropertyCache is necessary
|
|
(github issue #400 from NadineSchneider)
|
|
- Substructure highlighting in pandas dataframe (fixes #362)
|
|
(github issue #403 from nhfechner)
|
|
- Added SDF Export to PandasTools and adjusted SDF Import
|
|
(github issue #404 from nhfechner)
|
|
- support count-based avalon fingerprint
|
|
(github issue #408)
|
|
- New C++ drawing code
|
|
(github issue #412 from greglandrum)
|
|
- RDKit learns how to compute code coverage for tests
|
|
(github issue #413 from bp-kelley)
|
|
- Dictionary access is saniztized and optimized.
|
|
(github issue #414 from bp-kelley)
|
|
- expose MolOps::rankAtoms() and MolOps::rankAtomsInFragment() to python
|
|
(github issue #421)
|
|
- Dev/expose rank atoms to python
|
|
(github issue #422 from bp-kelley)
|
|
- rdkit learns how to wrap a proper RWMol in python
|
|
(github issue #423 from bp-kelley)
|
|
- Docs: document "magic" property values that are used throughout the code
|
|
(github issue #425)
|
|
- MolDraw2D: expose class to Python
|
|
(github issue #433)
|
|
- RDKit learns how to query properties on Atoms
|
|
(github issue #442 from bp-kelley)
|
|
- Issue445: provide helper functions for multithreaded evaluation of some expensive functions
|
|
(github issue #448 from greglandrum)
|
|
- RDKit learns how to release the GIL in python
|
|
(github pull #449 from bp-kelley)
|
|
- Dev/property queries
|
|
(github pull #450 from bp-kelley)
|
|
- Support a confId argument to the atom pair fingerprinting code
|
|
(github issue #453)
|
|
- Save the atom bookmarks so we can deconvolute reaction products.
|
|
(github pull #454 from bp-kelley)
|
|
- Cartridge: Support converting no structs to InChI
|
|
(github issue #455)
|
|
- RDKit learns how to expose ChemicalReaction copy constructor to python
|
|
(github pull #456 from bp-kelley)
|
|
- chirality flag was implemented for fmcs() function
|
|
(github pull #466 from AlexanderSavelyev)
|
|
- Support copy and deepcopy properly for at least Mol and RWMol
|
|
(github issue #467)
|
|
- Cartridge: add qmol_from_smiles() and qmol_from_ctab()
|
|
(github issue #469)
|
|
- restore java and python wrappers. New parameter (matchChiralTag)
|
|
(github issue #477 from AlexanderSavelyev)
|
|
- Added a Python wrapper for getShortestPath()
|
|
(github issue #487 from ptosco)
|
|
- Dev/merge query hs no unmapped atoms
|
|
(github issue #490 from bp-kelley)
|
|
|
|
## New Database Cartridge Features:
|
|
|
|
- The MCS code is now available within the cartridge
|
|
- The functions qmol_from_smiles() and qmol_from_ctab()
|
|
|
|
## New Java Wrapper Features:
|
|
|
|
- The new molecule rendering code is accessible from the SWIG wrappers.
|
|
|
|
## Deprecated code (to be removed in next release):
|
|
|
|
- C++: The functionality in $RDBASE/Code/GraphMol/MolDrawing has been
|
|
superseded by the new drawing code in $RDBASE/Code/GraphMol and will
|
|
be removed in the next release.
|
|
- Python:
|
|
- rdkit/Dbase/Pubmed
|
|
- rdkit/Chem/fmcs (this has been superseded by the C++ implementation)
|
|
- Cartridge: support for v8.x of PostgreSQL (v8.4 is no longer
|
|
supported by the PostgreSQL project team as of July 2014)
|
|
|
|
## Removed code:
|
|
|
|
- the method Atom::setMass() has been removed. Please use setIsotope()
|
|
instead.
|
|
- the methods involving an atom's dativeFlag have been removed.
|
|
|
|
## Contrib updates:
|
|
|
|
## Other:
|
|
- Python 2.6 support is deprecated. Starting with the next RDKit
|
|
release, we will only support python 2.7 and python 3.4 and
|
|
higher. Python 2.6 has not been supported since October 2013. If you
|
|
believe that you are stuck with python 2.6 because of the version of
|
|
RHEL you are running, please read this post to learn about your
|
|
options:
|
|
http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html
|
|
- The RDKit molecule objects (ROMol and RWMol) now require about 15%
|
|
less memory to store
|
|
|
|
|
|
# Release_2014.09.2
|
|
(Changes relative to Release_2014.09.1)
|
|
|
|
## Acknowledgements:
|
|
Sereina Riniker, Nadine Schneider, Paolo Tosco
|
|
|
|
## Bug Fixes:
|
|
- SMILES parser doing the wrong thing for odd dot-disconnected construct
|
|
(github issue #378)
|
|
- O3A code generating incorrect results for multiconformer molecules
|
|
(github issue #385)
|
|
- Suppliers probably not safe to read really large files
|
|
(github issue #392)
|
|
- Torsion constraints not worrking properly for negative torsions
|
|
(github issue #393)
|
|
- Core leak in reactions
|
|
(github issue #396)
|
|
|
|
|
|
# Release_2014.09.1
|
|
(Changes relative to Release_2014.03.1)
|
|
|
|
## Acknowledgements:
|
|
Andrew Dalke, James Davidson, Jan Domanski, Patrick Fuller, Seiji
|
|
Matsuoka, Noel O'Boyle, Sereina Riniker, Alexander Savelyev, Roger
|
|
Sayle, Nadine Schneider, Matt Swain, Paolo Tosco, Riccardo Vianello,
|
|
Richard West
|
|
|
|
## Bug Fixes:
|
|
- Bond query information not written to CTAB
|
|
(github issue #266)
|
|
- Bond topology queries not written to CTABs
|
|
(github issue #268)
|
|
- Combined bond query + topology query not correctly parsed from CTAB
|
|
(github issue #269)
|
|
- SWIG wrapped suppliers leak memory on .next()
|
|
(github issue #270)
|
|
- SWIG wrappers don't build with SWIG 3.0.x
|
|
(github issue #277)
|
|
- core leak from DataStructs.ConvertToNumpyArray
|
|
(github issue #281)
|
|
- MolTransforms not exposed to Java wrapper
|
|
(github issue #285)
|
|
- Seg fault in ReactionFromRxnBlock
|
|
(github issue #290)
|
|
- BitInfo from GetHashedMorganFingerprint() has non-folded values
|
|
(github issue #295)
|
|
- bad inchi for chiral S when the molecule is sanitized
|
|
(github issue #296)
|
|
- Cannot generate smiles for ChEBI 50252
|
|
(github issue #298)
|
|
- Either molecule-molecule substruct matching is wrong *OR* the docs for Atom::Match incorrect
|
|
(github issue #304)
|
|
- fluorine F-F gives segmentation fault with MMFF forcefield
|
|
(github issue #308)
|
|
- cartridge: MACCS similarity wrong when using the builtin popcount and the index
|
|
(github issue #311)
|
|
- Substructure Search via SMARTS implicit hydrogens
|
|
(github issue #313)
|
|
- SMARTS output for [x] is wrong
|
|
(github issue #314)
|
|
- Bonds not being set up properly in renumberAtoms
|
|
(github issue #317)
|
|
- Python 2 code in python 3 branch
|
|
(github issue #326)
|
|
- Linking error with ICC 15.0 on Linux
|
|
(github issue #327)
|
|
- Using explicit hydrogens in the SMILES lead to the same AP FP for two different molecules
|
|
(github issue #334)
|
|
- memory leaks when smiles/smarts parsers fail
|
|
(github issue #335)
|
|
- No double bond stereo perception from CTABs when sanitization is turned off
|
|
(github issue #337)
|
|
- missing MACCS key 44 might be found
|
|
(github issue #352)
|
|
- Hydrogens in mol blocks have a valence value set
|
|
(github issue #357)
|
|
- Computed props on non-sanitized molecule interfering with substructure matching
|
|
(github issue #360)
|
|
- Fixed a weakness in the angular restraint code
|
|
(github pull #261 from ptosco)
|
|
- A few fixes to improve MMFF/UFF robustness
|
|
(github pull #274 from ptosco)
|
|
- Static webGL rendering fix
|
|
(github pull #287 from patrickfuller)
|
|
- Revert #include ordering in SmilesMolSupplier.cpp
|
|
(github pull #297 from mcs07)
|
|
- Add missing include for RDDepict::compute2DCoords
|
|
(github pull #301 from baoilleach)
|
|
- Herschbach-Laurie fallback implemented to fix GitHub 308
|
|
(github pull #312 from ptosco)
|
|
- Issue #320 Making GetBestRMS more idiot-proof
|
|
(github pull #322 from jandom)
|
|
- Update URLs to InChI API after inchi-trust.org website redesign.
|
|
(github pull #341 from rwest)
|
|
|
|
## New Features:
|
|
- Should be able to do intramolecular bond breaking in reactions.
|
|
(github issue #58)
|
|
- Support reactions in cartridge
|
|
(github issue #223)
|
|
- Documentation of Inchi methods
|
|
(github issue #240)
|
|
- add DescribeQuery() to Bond python wrapper
|
|
(github issue #267)
|
|
- support avalon fingerprint in cartridge
|
|
(github issue #286)
|
|
- support partial fragmentation with fragmentOnSomeBonds
|
|
(github issue #288)
|
|
- Add calcNumHeterocycles() descriptor
|
|
(github issue #351)
|
|
- C++ implementation of FMCS algorithm
|
|
- Reordering feature for Butina clustering
|
|
(github pull #302 from sriniker)
|
|
- Changes and new functions for the calculation of RMS values between conformers of a molecule
|
|
(github pull #306 from sriniker)
|
|
- Extended chemical reaction functionality and add chemical reactions to cartridge
|
|
(github pull #315 from NadineSchneider)
|
|
- Custom color to highlight atoms in Mol2Image
|
|
(github pull #316 from jandom)
|
|
- Several different fingerprint algorithms for chemical reactions are now available
|
|
- add Chem.Draw.MolToQPixmap
|
|
(github pull #355 from mojaie)
|
|
|
|
|
|
## New Database Cartridge Features:
|
|
- *NOTE:* the configuration variable rdkit.ss_fp_size has been renamed to rdkit.sss_fp_size
|
|
- Chemical reactions and several operations on them are now supported
|
|
- Avalon fingerprints now supported (when support has been compiled in)
|
|
|
|
|
|
## New Java Wrapper Features:
|
|
- FMCS implementation exposed
|
|
- Fingerprints for chemical reactions
|
|
- Possible core leak in some of the MolSuppliers was fixed
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
- Projects/SDView4
|
|
- rdkit/utils/
|
|
- GUIDs.py
|
|
- GenLicense.py
|
|
- Licensing.py
|
|
- PiddleTools.py
|
|
- PilTools.py
|
|
- REFile.py
|
|
- SliceTools.py
|
|
- rdkit/Logger
|
|
|
|
Removed modules:
|
|
|
|
## Contrib updates:
|
|
|
|
## Other:
|
|
- The RDKit now supports both python3 and python2.
|
|
- There is now conda integration for the RDKit.
|
|
- SMILES generation is substantially faster
|
|
|
|
|
|
# Release_2014.03.1
|
|
(Changes relative to Release_2013.09.2)
|
|
|
|
## IMPORTANT
|
|
- Due to a bug fix in the rotatable bonds definition, the default
|
|
rotatable bond calculation returns different values than before.
|
|
This also affects MQN descriptor #18.
|
|
|
|
## Acknowledgements:
|
|
Paul Czodrowski, James Davidson, Markus Elfring, Nikolas Fechner, Jan Holst Jensen, Christos Kannas, Sereina Riniker, Roger Sayle, Paolo Tosco, Samo Turk, Riccardo Vianello, Maciej Wójcikowski, Toby Wright
|
|
|
|
## Bug Fixes:
|
|
- Dict::DataType declaration causing problems with C++11 std::lib
|
|
(github issue 144)
|
|
- Pre-condition Violation in AllChem.Compute2DCoords
|
|
(github issue 146)
|
|
- GetSimilarityMapForFingerprint() fails when similarity is zero
|
|
(github issue 148)
|
|
- PatternFingerprint failure for substructure matching
|
|
(github issue 151)
|
|
- query atoms don't match ring queries
|
|
(github issue 153)
|
|
- Incorrect SMILES generated after calling MMFF parameterization
|
|
(github issue 162)
|
|
- Problems with Xe from SDF
|
|
(github issue 164)
|
|
- Radicals not being used in atom--atom matches
|
|
(github issue 165)
|
|
- Cannot skip sanitization while reading PDB
|
|
(github issue 166)
|
|
- Distance Geometry embedding not thread safe
|
|
(github issue 167)
|
|
- O3A::align() and O3A::trans() now return "true" RMSD value
|
|
(github pull 173)
|
|
- RangeError when pre-incrementing or decrementing AtomIterators
|
|
(github issue 180)
|
|
- ctabs do not contain wedged bonds for chiral s
|
|
(github issue 186)
|
|
- ctabs do not contain "A" when appropriate
|
|
(github issue 187)
|
|
- Problems round-tripping Al2Cl6 via CTAB
|
|
(github issue 189)
|
|
- Don't merge Hs onto dummies
|
|
(github issue 190)
|
|
- Wavy bonds to Hs in CTABs should affect the stereochemistry of attached double bonds
|
|
(github issue 191)
|
|
- Rendering binary compounds as ClH, FH, BrH or IH rather than putting H first.
|
|
(github issue 199)
|
|
- Fixed data race condition in Code/GraphMol/MolAlign/testMolAlign.cpp
|
|
(github pull 202)
|
|
- Re-prepared SDF/SMILES files of the MMFF validation suite + a fix
|
|
(github pull 205)
|
|
- Problems round-tripping P with non-default valence.
|
|
(github issue 206)
|
|
- Added a stricter definition of rotatable bonds as a new function in the ...
|
|
(github pull 211)
|
|
- Code/GraphMol/AddHs patch proposal
|
|
(github pull 212)
|
|
- Fix: Changed getNumReactantTemplates to GetNumReactantTemplates.
|
|
(github pull 219)
|
|
- aromatic B ("b") causes errors from SMARTS parser
|
|
(github issue 220)
|
|
- Segmentation fault for MMFF optimization with dummy atoms
|
|
(github issue 224)
|
|
- isMoleculeReactantOfReaction() and isMoleculeProductOfReaction() not useable from SWIG wrappers
|
|
(github issue 228)
|
|
- cartridge: mol_from_ctab() ignores argument about keeping conformers
|
|
(github issue 229)
|
|
- Reaction not correctly preserving chirality on unmapped atoms.
|
|
(github issue 233)
|
|
- AllChem.AssignBondOrdersFromTemplate() fails with nitro groups
|
|
(github issue 235)
|
|
- Fix molecule dataframe rendering in pandas 0.13.x
|
|
(github pull 236)
|
|
- Dummy labels copied improperly into products
|
|
(github issue 243)
|
|
- Two bugfixes in MMFF code
|
|
(github pull 248)
|
|
- seg fault when trying to construct pharmacophore with no conformation
|
|
(github issue 252)
|
|
- EmbedMolecule() should not create a conformer for molecules that have zero atoms
|
|
(github issue 256)
|
|
- cartridge: dice similarity calculation does not use USE_BUILTIN_POPCOUNT flag
|
|
(github issue 259)
|
|
- cartridge: similarity calculations wrong for maccs fps when USE_BUILTIN_POPCOUNT flag is set
|
|
(github issue 260)
|
|
|
|
## New Features:
|
|
- Expose gasteiger charge calculation to SWIG
|
|
(github issue 152)
|
|
- Added additional functionality to PandasTools
|
|
(github pull 155)
|
|
- Add MMFFHasAllMoleculeParams() to SWIG interface
|
|
(github issue 157)
|
|
- O3A code should throw an exception if the parameterization is not complete.
|
|
(github issue 158)
|
|
- Support zero order bonds
|
|
(github issue 168)
|
|
- Add attachmentPoint argument to ReplaceSubstructs
|
|
(github issue 171)
|
|
- Forcefield constraints (distances, angles, torsions, positions)
|
|
(github pull 172)
|
|
- Add kekulize flag to SDWriter
|
|
(github issue 174)
|
|
- Support operator= for RWMol
|
|
(github issue 175)
|
|
- Get GetAromaticAtoms() and GetQueryAtoms() working from python
|
|
(github issue 181)
|
|
- Support richer QueryAtom options in Python
|
|
(github issue 183)
|
|
- Support writing V3000 mol blocks
|
|
(github issue 184)
|
|
- Allow disabling the building of tests
|
|
(github issue 185)
|
|
- Expand DbCLI to allow updating databases
|
|
(github issue 197)
|
|
- Code refactoring and enhancement to allow for O3A alignment according to atom-based Crippen logP contribs
|
|
(github pull 201)
|
|
- call MolOps::assignStereochemistry() with flagPossibleStereoCenters true from within the molecule parsers.
|
|
(github issue 210)
|
|
- Support passing of file-like PandasTools.LoadSDF
|
|
(github pull 221)
|
|
- Reaction SMARTS parser should support agents
|
|
(github issue 222)
|
|
- Add function to MolOps to allow a molecule to be split into fragments based on a query function
|
|
This is useable from python as Chem.SplitMolByPDBResidues() and Chem.SplitMolByPDBChainId()
|
|
(github issue 234)
|
|
- Adding option useCounts for Morgan fingerprints
|
|
(github pull 238)
|
|
- support SimpleEnum functionality for adding recursive queries to reactions
|
|
(github issue 242)
|
|
- Additional functions for bit vectors
|
|
(github pull 244)
|
|
- Support of RDK fingerprints added to SimilarityMaps
|
|
(github pull 246)
|
|
- add get3DDistance
|
|
- support 3D distances in the atom pair fingerprints
|
|
(github issue 251)
|
|
- added MolOps::get3DDistanceMat() (Chem.Get3DDistanceMatrix() from python)
|
|
|
|
|
|
## New Database Cartridge Features:
|
|
- Support configuration of fingerprint sizes in cartridge.
|
|
(github issue 216)
|
|
- Add mol_to_ctab(mol, bool default true) to Postgres cartridge.
|
|
(github pull 230)
|
|
- Adds sum formula function to PG cartridge.
|
|
(github pull 232)
|
|
|
|
## New Java Wrapper Features:
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
|
|
Removed modules:
|
|
- The CMIM integration (previously available to python in the rdkit.ML.FeatureSelect package)
|
|
has been removed due to license incompatibility.
|
|
|
|
## Contrib updates:
|
|
- Added Contribution to train ChEMBL-based models
|
|
(github pull 213)
|
|
- ConformerParser functionality
|
|
(github pull 245)
|
|
|
|
## Other:
|
|
- The Open3DAlign code is considerably faster.
|
|
- The SMILES parsing code is faster.
|
|
- Fix Bison 3.x incompabtility
|
|
(github pull 226)
|
|
- Add Travis support
|
|
(github pull 227)
|
|
- port of rdkit.ML bindings from Python/C API to boost::python
|
|
(github pull 237)
|
|
- The code now builds more easily using the Anaconda python distribution's
|
|
conda package manager
|
|
(github pull 247)
|
|
|
|
# Release_2013.09.2
|
|
(Changes relative to Release_2013.09.1)
|
|
|
|
## Acknowledgements:
|
|
Andrew Dalke, JP Ebejer, Daniel Moser, Sereina Riniker, Roger Sayle, Manuel Schwarze, Julia Weber
|
|
|
|
## Bug Fixes:
|
|
- cannot pickle unsanitized molecules
|
|
(github issue 149)
|
|
- Problems reading PDB files when locale is DE
|
|
(github issue 170)
|
|
- calling RWMol::clear() leaves property dict empty
|
|
(github issue 176)
|
|
- zero atom molecule generates exception in MolToSmiles when
|
|
rootedAtAtom is provided
|
|
(github issue 182)
|
|
- bond orders not being set when PDB files are read
|
|
(github issue 194)
|
|
- GenMACCSKeys() raises an exception with an empty molecule
|
|
(github issue 195)
|
|
- left-justified SDF bond topology of "0" raises an unexpected
|
|
exception
|
|
(github issue 196)
|
|
|
|
# Release_2013.09.1
|
|
(Changes relative to Release_2013.06.1)
|
|
|
|
## Acknowledgements:
|
|
James Davidson, JP Ebejer, Nikolas Fechner, Grégori Gerebtzoff, Michal Nowotka, Sereina Riniker, Roger
|
|
Sayle, Gianluca Sforna, Matthew Szymkiewicz, Paolo Tosco, Dan Warner,
|
|
|
|
## IMPORTANT
|
|
- Due to a bug fix in the parameter set, the MolLogP and MolMR
|
|
descriptor calculators now return different values for molecules
|
|
with pyrrole (or pyrrole-like) Ns.
|
|
|
|
## Bug Fixes:
|
|
- The pymol ShowMol method can now handle molecules with more than
|
|
999 atoms (they are sent via PDB)
|
|
- Various stability improvements to the Pandas integration.
|
|
(github issues 129 and 51)
|
|
- Some RDKit methods require python lists and don't allow passing
|
|
numpy arrays or pandas series directly
|
|
(github issue 119)
|
|
- mol2 parser not setting E/Z flags on double bonds
|
|
(github issue 114)
|
|
- Incorrect angle terms in UFF
|
|
(github issue 105)
|
|
- Problems with stereochemistry flags and PathToSubmol()
|
|
(github issue 103)
|
|
- Bad Crippen atom type for pyrrole H
|
|
(github issue 92)
|
|
- PandasTools tests fail with Pandas v0.12
|
|
(github issue 91)
|
|
- Isotope information not affecting chirality
|
|
(github issue 90)
|
|
- properties are not read from SDF files with V3000 mol blocks.
|
|
(github issue 88)
|
|
- assignStereochemistry does not remove bond wedging that shouldn't be there.
|
|
(github issue 87)
|
|
- Drawing code modifies wedge bonds in reactions
|
|
(github issue 86)
|
|
- Stereochemistry not perceived when parsing CTABs unless sanitization is done.
|
|
(github issue 82)
|
|
- 2D rendering issue for epoxide ( CAS 70951-83-6)
|
|
(github issue 78)
|
|
- PandasTools doctests should be failing, but are not
|
|
(github issue 75)
|
|
- Better handling of radicals to/from mol files
|
|
(github issue 73)
|
|
- Benzothiazolium structure can be parsed from ctab, but the SMILES generated cannot be processed.
|
|
(github issue 72)
|
|
- Chem.MolFromInch hangs on CID 23691477 and CID 23691480
|
|
(github issue 68)
|
|
- Chem.MolFromInchi on CHEMBL104337 leads to segmentation fault
|
|
(github issue 67)
|
|
- "Could not embed molecule." (The Anthony Conundrum)
|
|
(github issue 55)
|
|
|
|
## New Features:
|
|
- Add fragmentOnBonds() to python wrapper
|
|
(github issue 142)
|
|
- Allow renumbering atoms in a molecule.
|
|
(github issue 140)
|
|
- MMFF94 and MMFF94S support
|
|
- implementation of the Open3DAlign rigid alignment algorithm
|
|
- Support for reading and writing PDB files
|
|
- The python function AllChem.AssignBondOrdersFromTemplate() can be
|
|
used to assign bond orders from a reference molecule to the bonds
|
|
in another molecule. This is helpful for getting bond orders
|
|
correct for PDB ligands.
|
|
(github issue 135)
|
|
- Bond lengths, angles, and torsions can now be queries and adjusted.
|
|
(github issue 132)
|
|
- Implementation of similarity maps
|
|
(github issue 94)
|
|
- Python implementation of the Fraggle similarity algorithm.
|
|
See Jameed Hussain's presentation from the 2013 UGM for details:
|
|
https://github.com/rdkit/UGM_2013/blob/master/Presentations/Hussain.Fraggle.pdf?raw=true
|
|
- SparseIntVects now support -=, +=, /=, and *= with ints from C++
|
|
and Python
|
|
- support \\ in SMILES
|
|
(github issue 136)
|
|
- Support a similarity threshold in DbCLI
|
|
(github issue 134)
|
|
- Support construction molecules from other molecules in the python wrapper
|
|
(github issue 133)
|
|
- support tversky similarity in DbCLI
|
|
(github issue 130)
|
|
- support tversky similarity in cartridge
|
|
(github issue 121)
|
|
- support reading and writing reactionComponentType and reactionComponentNumber from ctabs
|
|
(github issue 118)
|
|
- Add in-place forms of addHs(), removeHs(), and mergeQueryHs()
|
|
(github issue 117)
|
|
- modify MolOps::cleanUp() to support this azide formulation: C-N=N#N
|
|
(github issue 116)
|
|
- Dihedral rotation exposed in python
|
|
(github issue 113)
|
|
- Support for cairocffi (cairo drop-in replacement that plays nicely with virtualenv)
|
|
(github issue 80)
|
|
- Grey color for Hydrogens
|
|
(github issue 97)
|
|
- Improvements to the Dict interface in C++
|
|
(github issue 74)
|
|
- customizable drawing options
|
|
(github issue 71)
|
|
- Add method for setting the chiral flag in mol blocks
|
|
(github issue 64)
|
|
- New descriptors added (Python only for now):
|
|
MaxPartialCharge(),MinPartialCharge(),MaxAbsPartialCharge(),MinAbsPartialCharge(),
|
|
MaxEStateIndex(),MinEStateIndex(),MaxAbsEStateIndex(),MinAbsEStateIndex()
|
|
|
|
## New Database Cartridge Features:
|
|
|
|
## New Java Wrapper Features:
|
|
- MMFF support
|
|
- PDB reading and writing
|
|
- Open3DAlign support
|
|
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
|
|
Removed modules:
|
|
|
|
## Contrib updates:
|
|
- The MMPA implementation has been updated
|
|
See Jameed Hussain's tutorial from the 2013 UGM for details:
|
|
https://github.com/rdkit/UGM_2013/tree/master/Tutorials/mmpa_tutorial
|
|
[Jameed Hussain]
|
|
- An implementation of Ertl and Schuffenhauer's Synthetic
|
|
Accessibility score is available in Contrib/SA_Score
|
|
[Peter Ertl, Greg Landrum]
|
|
- Command line scripts for the Fraggle similarity algorithm
|
|
See Jameed Hussain's presentation from the 2013 UGM for details:
|
|
https://github.com/rdkit/UGM_2013/blob/master/Presentations/Hussain.Fraggle.pdf?raw=true
|
|
[Jameed Hussain]
|
|
|
|
## Other:
|
|
- Some of the changes to UFF deviate from the published force
|
|
field. Specifics of the changes, and the reasoning behind them, are
|
|
in Paolo Tosco's 2013 RDKit UGM presentation:
|
|
https://github.com/rdkit/UGM_2013/blob/master/Presentations/Tosco.RDKit_UGM2013.pdf?raw=true
|
|
- Reaction drawing has been improved. Support for reaction drawing
|
|
has been added to the IPython notebook.
|
|
|
|
|
|
# Release_2013.06.1
|
|
(Changes relative to Release_2013.03.2)
|
|
|
|
Administrivia note:
|
|
In the course of this release cycle, development was moved over
|
|
entirely to github. The sourceforge svn repository no longer contains
|
|
an up-to-date version of the code.
|
|
|
|
## Acknowledgements:
|
|
Andrew Dalke, JP Ebejer, Nikolas Fechner, Roger Sayle, Riccardo Vianello,
|
|
Yingfeng Wang, Dan Warner
|
|
|
|
## Bug Fixes:
|
|
- The docs for Descriptors.MolWt are now correct (GitHub #38)
|
|
- Molecules coming from InChi now have the correct molecular
|
|
weight. (GitHub #40)
|
|
- RemoveAtoms() no longer leads to problems in canonical SMILES
|
|
generation when chiral ring atoms are present. (GitHub #42)
|
|
- Atom invariants higher than the number of atoms in the molecule can
|
|
now be provided to the atom pairs and topological torsions
|
|
fingerprinters. (GitHub #43)
|
|
- A typo with the handling of log levels was fixed in the python
|
|
wrapper code for InChI generation. (GitHub #44)
|
|
- Stereochemistry no longer affects canonical SMILES generation if
|
|
non-stereo SMILES is being generated. (GitHub #45)
|
|
- The ExactMolWt of [H+] is no longer zero. (GitHub #56)
|
|
- The MPL canvas now has an addCanvasDashedWedge() method. (GitHub
|
|
#57)
|
|
- RWMol::insertMol() now copies atom coordinates (if
|
|
present). (GitHub #59)
|
|
- The "h" primitive in SMARTS strings now uses the method
|
|
getTotalNumHs(false) instead of getImplicitValence().
|
|
(GitHub #60)
|
|
- bzip2 files now work better with the SDWriter class. (GitHub #63)
|
|
- a crashing bug in InChI generation was fixed. (GitHub #67)
|
|
|
|
## New Features:
|
|
- Sanitization can now be disabled when calling GetMolFrags() from
|
|
Python (GitHub #39)
|
|
- Bond.GetBondTypeAsDouble() has been added to the python
|
|
wrapper. (GitHub #48)
|
|
- The fmcs code now includes a threshold argument allowing the MCS
|
|
that hits a certain fraction of the input molecules (instead of all
|
|
of them) to be found. The code has also been synced with the most
|
|
recent version of Andrew Dalke's version.
|
|
- Atoms now have a getTotalValence() (GetTotalValence() from Python)
|
|
method. (GitHub #61)
|
|
- R labels from Mol files now can go from 0-99
|
|
- chiral flags in CTABs are now handled on both reading and writing.
|
|
The property "_MolFileChiralFlag" is used.
|
|
|
|
|
|
## New Database Cartridge Features:
|
|
|
|
## New Java Wrapper Features:
|
|
- {Get,Set}Prop() methods are now available for both Atoms and
|
|
Bonds. (GitHub #32)
|
|
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
|
|
Removed modules:
|
|
- rdkit.utils.pydoc_local
|
|
|
|
## Other:
|
|
- the handling of flex/bison output files as dependencies has been
|
|
improved (GitHub #33)
|
|
- the molecule drawing code should now also work with pillow (a fork of
|
|
PIL)
|
|
- the PANDAS integration has been improved.
|
|
|
|
|
|
# Release_2013.03.2
|
|
(Changes relative to Release_2013.03.1)
|
|
|
|
## Acknowledgements:
|
|
Manuel Schwarze
|
|
|
|
## Bug Fixes:
|
|
- The hashed topological torsion fingerprints generated are now the
|
|
same as in previous rdkit versions. (GitHub issue 25)
|
|
|
|
|
|
# Release_2013.03.1
|
|
(Changes relative to Release_2012.12.1)
|
|
|
|
## IMPORTANT
|
|
|
|
- The algorithm for hashing subgraphs used in the RDKit fingerprinter
|
|
has changed. The new default behavior will return different
|
|
fingerprints than previous RDKit versions. This affects usage from
|
|
c++, python, and within the postgresql cartridge. See the "## Other"
|
|
section below for more details.
|
|
|
|
## Acknowledgements:
|
|
Paul Czodrowski, Andrew Dalke, Jan Domanski, Jean-Paul Ebejer, Nikolas
|
|
Fechner, Jameed Hussain, Stephan Reiling, Sereina Riniker, Roger
|
|
Sayle, Riccardo Vianello
|
|
|
|
## Bug Fixes:
|
|
- removeBond now updates bond indices (sf.net issue 284)
|
|
- dummy labels are no longer lost when atoms are copied (sf.net issue
|
|
285)
|
|
- more specific BRICS queries now match before less specific ones
|
|
(sf.net issue 287, github issue 1)
|
|
- molAtomMapNumber can now be set from Python (sf.net issue 288)
|
|
- the legend centering for molecular image grids has been improved
|
|
(sf.net issue 289)
|
|
- make install now includes all headers (github issue 2)
|
|
- InChIs generaged after clearing computed properties are now correct
|
|
(github issue 3)
|
|
- Reacting atoms that don't change connectivity no longer lose
|
|
stereochemistry (github issue 4)
|
|
- Aromatic Si is now accepted (github issue 5)
|
|
- removeAtom (and deleteSubstructs) now correctly updates stereoAtoms
|
|
(github issue 8)
|
|
- [cartridge] pg_dump no longer fails when molecules cannot be
|
|
converted to SMILES (github issue 9)
|
|
- a canonicalization bug in MolFragmentToSmiles was fixed (github issue 12)
|
|
- atom labels at the edge of the drawing are no longer cut off (github issue 13)
|
|
- a bug in query-atom -- query-atom matching was fixed (github issue 15)
|
|
- calling ChemicalReaction.RunReactants from Python with None
|
|
molecules no longer leads to a seg fault. (github issue 16)
|
|
- AllChem.ReactionFromSmarts now generates an error message when called
|
|
with an empty string.
|
|
- Writing CTABs now includes information about atom aliases.
|
|
- An error in the example fdef file
|
|
$RDBASE/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef
|
|
has been fixed. (github issue 17)
|
|
- Quantize.FindVarMultQuantBounds() no longer generates a seg fault
|
|
when called with bad arguments. (github issue 18)
|
|
- The length of SDMolSuppliers constructed from empty files is no
|
|
longer reported as 1. (github issue 19)
|
|
- Partial charge calculations now work for B, Si, Be, Mg, and Al.
|
|
(github issue 20)
|
|
- Two logging problems were fixed (github issues 21 and 24)
|
|
- Molecules that have had kappa descriptors generated can now be
|
|
written to SD files (github issue 23)
|
|
|
|
## New Features:
|
|
- The handling of chirality in reactions has been reworked and
|
|
improved. Please see the RDKit Book for an explanation.
|
|
- Atom-pair and topological-torsion fingerprints now support the
|
|
inclusion of chirality in the atom invariants.
|
|
- A number of new compositional descriptors have been added:
|
|
calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
|
|
calcNum{Aromatic,Aliphatic,Saturated}Heterocycles,
|
|
calcNum{Aromatic,Aliphatic,Saturated}Carbocycles
|
|
- An implementation of the molecular quantum number (MQN) descriptors
|
|
has been added.
|
|
- RDKFingerprintMol now takes an optional atomBits argument which is
|
|
used to return information about which bits atoms are involved in.
|
|
- LayeredFingerprintMol no longer takes the arguments tgtDensity and
|
|
minSize. They were not being used.
|
|
- LayeredFingerprintMol2 has been renamed to PatternFingerprintMol
|
|
- The substructure matcher can now properly take stereochemistry into
|
|
account if the useChirality flag is provided.
|
|
- The module rdkit.Chem.Draw.mplCanvas has been added back to svn.
|
|
- A new module integrating the RDKit with Pandas (rdkit.Chem.PandasTools)
|
|
has been added.
|
|
|
|
## New Database Cartridge Features:
|
|
- The new compositional descriptors are available:
|
|
calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
|
|
calcNum{Aromatic,Aliphatic,Saturated}Heterocycles,
|
|
calcNum{Aromatic,Aliphatic,Saturated}Carbocycles
|
|
- MACCS fingerprints are available
|
|
- the substruct_count function is now available
|
|
- substructure indexing has improved. NOTE: indexes on molecule
|
|
columns will need to be rebuilt.
|
|
|
|
## New Java Wrapper Features:
|
|
- The new compositional descriptors are available:
|
|
calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
|
|
calcNum{Aromatic,Aliphatic,Saturated}Heterocycles,
|
|
calcNum{Aromatic,Aliphatic,Saturated}Carbocycles
|
|
- The molecular quantum number (MQN) descriptors are available
|
|
- MACCS fingerprints are available
|
|
- BRICS decomposition is available.
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
|
|
Removed modules:
|
|
|
|
## Other:
|
|
- RDKit fingerprint generation is now faster. The hashing algorithm
|
|
used in the RDKit fingerprinter has changed.
|
|
- Force-field calculations are substantially faster (sf.net issue 290)
|
|
- The core of the BRICS implementation has been moved into C++.
|
|
- The MACCS fingerprint implementation has been moved into
|
|
C++. (contribution from Roger Sayle)
|
|
- New documentation has been added: Cartridge.rst, Overview.rst,
|
|
Install.rst
|
|
|
|
# Release_2012.12.1
|
|
(Changes relative to Release_2012.09.1)
|
|
|
|
## IMPORTANT
|
|
|
|
## Acknowledgements:
|
|
Andrew Dalke, James Davidson, Robert Feinstein, Nikolas Fechner,
|
|
Nicholas Firth, Markus Hartenfeller, Jameed Hussain, Thorsten Meinl,
|
|
Sereina Riniker, Roger Sayle, Gianluca Sforna, Pat Walters, Bernd
|
|
Wiswedel
|
|
|
|
## Bug Fixes:
|
|
- Using parentheses for zero-level grouping now works in reaction
|
|
SMARTS. This allows intramolecular reactions to be expressed.
|
|
- SMILES generated for molecules with ring stereochemistry
|
|
(e.g. N[C@H]1CC[C@H](CC1)C(O)=O) are now canonical. (issue 40)
|
|
- SKP lines in a CTAB property block are now properly handled. (issue
|
|
255)
|
|
- The molecular drawing code now shows dotted lines for Any bonds.
|
|
(issue 260)
|
|
- ROMol::debugMol() (ROMol.DebugMol() in Python) now reports isotope
|
|
information. (issue 261)
|
|
- The molecular drawing code now correctly highlights wedged bonds.
|
|
(issue 262)
|
|
- RWMol::addAtom() now adds atoms to conformers.
|
|
(issue 264)
|
|
- TDT files with atomic coordinates now have those coordinates in the
|
|
correct order. (issue 265)
|
|
- A ring-finding error/crash has been fixed. (issue 266)
|
|
- Dummy atoms now have a default valence of 0 and no maximim
|
|
valence. (issue 267)
|
|
- The Python code no longer throws string exceptions. (issue 268)
|
|
- Invalid/unrecognized atom symbols in CTABs are no longer
|
|
accepted. (issue 269)
|
|
- Chem.RDKFingerprint now accepts atom invariants with values larger
|
|
than the number of atoms. (issue 270)
|
|
- The code should now all work when the locale (LANG) is set to
|
|
values other than "C" or one of the English locales. (issue 271)
|
|
- Two-coordinate Hs are no longer removed by
|
|
MolOps::removeHs(). (issue 272)
|
|
- R groups read from CTABs are now marked using setIsotope() instead
|
|
of setMass(). (issue 273)
|
|
- Hs present in the molecule graph no longer incorrectly impact
|
|
substructure matches. (issue 274)
|
|
- Murcko decomposition of molecules with chiral ring atoms now
|
|
works. (issue 275)
|
|
- Methane now shows up in molecular drawings. (issue 276)
|
|
- '&' in SLN properties is now correctly handled. (issue 277)
|
|
- Molecules with string-valued molAtomMapNumber atomic properties can
|
|
now be serialized. (issue 280)
|
|
- SMARTS strings containing a dot in a recursive piece are now
|
|
properly parsed. (issue 281)
|
|
- The SMILES and SLN parsers no longer leak memory when sanitization
|
|
of the result molecule fails. (issue 282)
|
|
- The cairo canvas drawing code now works with PIL v1.1.6 as well as
|
|
more recent versions.
|
|
|
|
## New Features:
|
|
- RDKit ExplicitBitVects and DiscreteValueVects can now be directly
|
|
converted into numpy arrays.
|
|
- Rogot-Goldberg similarity has been added.
|
|
- C++: BitVects and SparseIntVects now support a size() method.
|
|
- C++: DiscreteValueVects now support operator[].
|
|
- An initial version of a SWIG wrapper for C# has been added.
|
|
- Support for easily adding recursive queries to molecules and
|
|
reactions has been added. More documentation is required for this
|
|
feature.
|
|
- To allow more control over the reaction, it is possible to flag reactant
|
|
atoms as being protected by setting the "_protected" property on those
|
|
atoms. Flagged atoms will not be altered in the reaction.
|
|
- Atoms and Bonds now support a ClearProp() method from python.
|
|
- The new Python module rdkit.ML.Scoring.Scoring includes a number of
|
|
standard tools for evaluating virtual screening experiments: ROC
|
|
curve generation, AUC, RIE, BEDROC, and Enrichment.
|
|
- The function RDKit::Descriptors::getCrippenAtomContribs()
|
|
(rdkit.Chem.rdMolDescriptors._CalcCrippenContribs() from Python)
|
|
can now optionally return atom-type information as ints or text.
|
|
|
|
|
|
## New Database Cartridge Features:
|
|
- The Chi and Kappa descriptors are now available
|
|
|
|
## New Java Wrapper Features:
|
|
- The Chi and Kappa descriptors are now available
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
|
|
Removed modules:
|
|
- The old SWIG wrapper code in $RDBASE/Code/Demos/SWIG has been
|
|
removed. The SWIG wrappers are now in $RDBASE/Code/JavaWrappers
|
|
|
|
## Other:
|
|
- The C++ code for drawing molecules previously found in
|
|
$RDBASE/Code/Demos/RDKit/Draw has been moved to
|
|
$RDBASE/Code/GraphMol/MolDrawing
|
|
- Calculation of the Chi and Kappa descriptors has been moved into
|
|
C++.
|
|
- To make builds easier, the thread-safety of the recursive-smarts
|
|
matcher has been made optional. The build option is
|
|
RDK_BUILD_THREADSAFE_SSS.
|
|
- There are two new entries in the Contrib directory:
|
|
* Contrib/PBF : An implementation of the Plane of Best Fit
|
|
contributed by Nicholas Firth.
|
|
* Contrib/mmpa : An implementation of GSK's matched molecular pairs
|
|
algorithm contributed by Jameed Hussain
|
|
- A new "Cookbook" has been added to the documentation to provide
|
|
a collection of recipes for how to do useful tasks.
|
|
|
|
|
|
# Release_2012.09.1
|
|
(Changes relative to Release_2012.06.1)
|
|
|
|
## IMPORTANT
|
|
- Some of the bug fixes affect the generation of SMILES. Canonical
|
|
SMILES generated with this version of the RDKit will be different
|
|
from previous versions.
|
|
- The fix to Issue 252 (see below) will lead to changes in calculated
|
|
logP and MR values for some compounds.
|
|
- The fix to Issue 254 (see below) will lead to changes in some
|
|
descriptors and geometries for sulfur-containing compounds.
|
|
- The fix to Issue 256 (see below) has changed the name of the
|
|
optional argument to mol.GetNumAtoms from onlyHeavy to
|
|
onlyExplicit. For compatibility reasons, Python code that uses
|
|
explicitly uses onlyHeavy will still work, but it will generate
|
|
warnings. This compatibility will be removed in a future release.
|
|
|
|
## Acknowledgements:
|
|
Gianpaolo Bravi, David Cosgrove, Andrew Dalke, Fabian Dey, James
|
|
Davidson, JP Ebejer, Gabriele Menna, Stephan Reiling, Roger Sayle,
|
|
James Swetnam
|
|
|
|
## Bug Fixes:
|
|
- The molecules that come from mergeQueryHs() now reset the RingInfo
|
|
structure. (issue 245)
|
|
- The output from MurckoScaffold.MakeScaffoldGeneric no longer
|
|
includes stereochemistry or explicit Hs. (issue 246)
|
|
- D and T atoms in CTABs now have their isotope information
|
|
set. (issue 247)
|
|
- Some problems with ring finding in large, complex molecules have
|
|
been fixed. (issue 249)
|
|
- The "rootedAtAtom" argument for FindAllSubgraphsOfLengthN is now
|
|
handled properly. (issue 250)
|
|
- Bonds now have a SetProp() method available in Python. (issue 251)
|
|
- A number of problems with the Crippen atom parameters have been
|
|
fixed. (issue 252)
|
|
- Ring closure digits are no longer repeated on the same atom in
|
|
SMILES generated by the RDKit. (issue 253)
|
|
- Non-ring sulfur atoms adjacent to aromatic atoms are no longer set
|
|
to be SP2 hybridized. This allows them to be stereogenic. (issue
|
|
254)
|
|
- The combineMols() function now clears computed properties on the
|
|
result molecule.
|
|
- A couple of problems with the pickling functions on big endian
|
|
hardware were fixed.
|
|
- The molecule drawing code now uses isotope information
|
|
- Superscript/Subscript handling in the agg canvas has been improved.
|
|
- SKP lines in CTABS are now propertly handled. (Issue 255)
|
|
- The name of the optional argument to mol.GetNumAtoms has been
|
|
changed from onlyHeavy to onlyExplicit. The method counts the number
|
|
of atoms in the molecular graph, not the number of heavy
|
|
atoms. These numbers happen to usually be the same (which is why
|
|
this has taken so long to show up), but there are exceptions if Hs
|
|
or dummy atoms are in the graph. (Issue 256)
|
|
- Unknown bonds in SMILES are now output using '~' instead of '?'. The
|
|
SMILES parser now recognizes '~' as an "any bond" query. (Issue 257)
|
|
- Lines containing only white space in SDF property blocks are no
|
|
longer treated as field separators.
|
|
- Transition metals and lanthanides no longer have default valences
|
|
assigned.
|
|
|
|
## New Features:
|
|
- The RDKit now has a maximum common substructure (MCS) implementation
|
|
contributed by Andrew Dalke. This is currently implemented in Python
|
|
and is available as: from rdkit.Chem import MCS Documentation is
|
|
available as a docstring for the function MCS.FindMCS and in the
|
|
GettingStarted document.
|
|
- A few new functions have been added to rdkit.Chem.Draw:
|
|
MolsToImage(), MolsToGridImage(), ReactionToImage()
|
|
- CalcMolFormula() now provides the option to include isotope
|
|
information.
|
|
- The RDKit and Layered fingerprinters both now accept "fromAtoms"
|
|
arguments that can be used to limit which atoms contribute to the
|
|
fingerprint.
|
|
- Version information is now available in the Java wrapper.
|
|
- The descriptor NumRadicalElectrons is now available.
|
|
- The PyMol interface now supports a GetPNG() method which returns the
|
|
current contents of the viewer window as an PIL Image object.
|
|
- Molecules (ROMol in C++, rdkit.Chem.Mol in Python) now have a
|
|
getNumHeavyAtoms() method.
|
|
- Component-level grouping (parens) can be used in reaction SMARTS.
|
|
|
|
|
|
## New Database Cartridge Features:
|
|
- support for molecule <-> pickle conversion via the functions
|
|
mol_to_pkl, mol_from_pkl, and is_valid_mol_pkl.
|
|
- support for bit vector <-> binary text conversion via the functions
|
|
bfp_to_binary_text, bfp_from_binary_text
|
|
|
|
## New Java Wrapper Features:
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
|
|
Removed modules:
|
|
|
|
## Other:
|
|
- During this release cycle, the sourceforge project was updated to
|
|
their new hosting system. This explains the change in bug/issue
|
|
ids.
|
|
- the SMILES parser is now substantially faster.
|
|
- The molecular drawings generated by Code/Demo/RDKit/Draw/MolDrawing.h
|
|
have been improved.
|
|
- There is now demo code availble for using the C++ drawing code
|
|
within Qt applications. (contributed by David Cosgrove)
|
|
- The directory $RDBASE/Regress now contains sample data and
|
|
scripts for benchmarking the database cartridge.
|
|
- Fused-ring aromaticity is now only considered in rings of up to size
|
|
24.
|
|
- It is no longer necessary to have flex and bison installed in order
|
|
to build the RDKit.
|
|
|
|
|
|
# Release_2012.06.1
|
|
(Changes relative to Release_2012.03.1)
|
|
|
|
## IMPORTANT
|
|
- Some of the bug fixes affect the generation of SMILES. Canonical
|
|
SMILES generated with this version of the RDKit will be different
|
|
from previous versions.
|
|
|
|
## Acknowledgements:
|
|
Andrew Dalke, JP Ebejer, Igor Filippov, Peter Gedeck, Jan Holst
|
|
Jensen, Adrian Jasiński, George Papadatos, Andrey Paramonov, Adrian
|
|
Schreyer, James Swetnam
|
|
|
|
## Bug Fixes:
|
|
- Radicals are now indicated in molecular depictions. (Issue 3516995)
|
|
- Calling .next() on an SDMolSupplier at eof no longer results in an
|
|
infinite loop. (Issue 3524949)
|
|
- Chirality perception no longer fails in large molecules.
|
|
(Issue 3524984)
|
|
- problem creating molblock for atom with four chiral nbrs
|
|
(Issue 3525000)
|
|
- A second sanitization leads to a different molecule.
|
|
(Issue 3525076)
|
|
- can't parse Rf atom in SMILES
|
|
(Issue 3525668)
|
|
- generates [HH2-] but can't parse it
|
|
(Issue 3525669)
|
|
- improper (re)perception of 1H-phosphole
|
|
(Issue 3525671)
|
|
- ForwardSDMolSupplier not skipping forward on some errors
|
|
(Issue 3525673)
|
|
- SMILES/SMARTS parsers don't recognize 0 atom maps
|
|
(Issue 3525776)
|
|
- R group handling in SMILES
|
|
(Issue 3525799)
|
|
- Canonical smiles failure in symmetric heterocycles
|
|
(Issue 3526810)
|
|
- Canonical smiles failure with "extreme" isotopes
|
|
(Issue 3526814)
|
|
- Canonical smiles failure with many symmetric fragments
|
|
(Issue 3526815)
|
|
- Canonical smiles failure with dependent double bonds
|
|
(Issue 3526831)
|
|
- Build Fails Due to Missing include in Code/RDBoost/Wrap.h
|
|
(Issue 3527061)
|
|
- Incorrect template parameter use in std::make_pair
|
|
(Issue 3528136)
|
|
- Canonicalization failure in cycle
|
|
(Issue 3528556)
|
|
- incorrect values reported in ML analysis
|
|
(Issue 3528817)
|
|
- Cartridge does not work on 32bit ubuntu 12.04
|
|
(Issue 3531232)
|
|
- Murcko Decomposition generates unuseable molecule.
|
|
(Issue 3537675)
|
|
- A few memory leaks were fixed in the Java Wrappers
|
|
- The exact mass of molecules with non-standard isotopes is now
|
|
calculated correctly.
|
|
- The default (Euclidean) distance metric should now work with Butina
|
|
clustering.
|
|
- Some bugs in the depictor were fixed.
|
|
- AvalonTools bug with coordinate generation for mols with no
|
|
conformers fixed.
|
|
|
|
## New Features:
|
|
- ChemicalFeatures now support an optional id
|
|
- Isotope handling has been greatly improved. Atoms now have a
|
|
getIsotope() (GetIsotope() in Python) method that returns zero if
|
|
no isotope has been set, the isotope number otherwise.
|
|
- The function MolFragmentToSmiles can be used to generate canonical
|
|
SMILES for pieces of molecules.
|
|
- The function getHashedMorganFingerprint (GetHashedMorganFingerprint
|
|
in Python) has been added.
|
|
|
|
## New Database Cartridge Features:
|
|
- The functions mol_from_smiles(), mol_from_smarts(), and
|
|
mol_from_ctab() now return a null value instead of generating an
|
|
error when the molecule processing fails. This allows molecule
|
|
tables to be constructed faster.
|
|
- The functions mol_to_smiles() and mol_to_smarts() have been added.
|
|
- Creating gist indices on bit-vector fingerprint columns is faster.
|
|
- The indexing fingerprint for molecular substructures has been changed.
|
|
The new fingerprint is a bit slower to generate, but is
|
|
considerably better at screening. More information here:
|
|
http://code.google.com/p/rdkit/wiki/ImprovingTheSubstructureFingerprint
|
|
|
|
## New Java Wrapper Features:
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
- Support for older (pre9.1) postgresql versions.
|
|
|
|
Removed modules:
|
|
- rdkit.Excel
|
|
- the code in $RDBASE/Code/PgSQL/RDLib
|
|
- rdkit.Chem.AvailDescriptors : the same functionality is now available
|
|
in a more useable manner from rdkit.Chem.Descriptors
|
|
|
|
## Other:
|
|
- Similarity calculations on ExplicitBitVectors should now be much faster
|
|
- Use of [Xa], [Xb], etc. for dummy atoms in SMILES is no longer
|
|
possible. Use the "*" notation and either isotopes (i.e. [1*],
|
|
[2*]) or atom maps (i.e. [*:1], [*:2]) instead.
|
|
- Initial work was done towards make the RDKit work on big endian
|
|
hardware (mainly changes to the way pickles are handled)
|
|
- Canonical SMILES generation is now substantially faster.
|
|
|
|
# Release_2012.03.1
|
|
(Changes relative to Release_2011.12.1)
|
|
|
|
## IMPORTANT
|
|
- The atom-atom match behavior for non-query atoms has been changed.
|
|
This affects the results of doing substructure matches using
|
|
query molecules that are not constructed from SMARTS.
|
|
|
|
## Acknowledgements:
|
|
JP Ebejer, Paul Emsley, Roger Sayle, Adrian Schreyer, Gianluca Sforna,
|
|
Riccardo Vianello
|
|
|
|
## Bug Fixes:
|
|
- the older form of group evaluations in Mol blocks is now correctly
|
|
parsed. (Issue 3477283)
|
|
- some problems with handling aromatic boron were fixed. (Issue 3480481)
|
|
- the SD writer no longer adds an extra $$$$ when molecule parsing
|
|
fails (Issue 3480790)
|
|
- molecules in SD files that don't contain atoms are now parsed
|
|
without warnings and their properties are read in. (Issue 3482695)
|
|
- it's now possible to embed molecules despite failures in the triangle
|
|
bounds checking (Issue 3483968)
|
|
- Isotope information in Mol blocks is now written to M ISO lines
|
|
instead of going in the atom block. (Issue 3494552)
|
|
- Better 2D coordinates are now generated for neighbors of atoms with
|
|
unspecified hybridization. (Issue 3487469)
|
|
- Dummy atoms and query atoms are now assigned UNSPECIFIED hybridization
|
|
instead of SP. (Issue 3487473)
|
|
- Error reporting for SMARTS involving recursion has been improved.
|
|
(Issue 3495296)
|
|
- Some problems of queries and generating SMARTS for queries were resolved.
|
|
(Issues 3496759, 3496799, 3496800)
|
|
- It's now possible to do database queries with SMARTS that use the index.
|
|
(Issue 3493156).
|
|
- A series of problems related to thread safety were fixed.
|
|
- Tracking the lifetime of owning molecules across the C++/Python
|
|
border is now being handled better (Issue 3510149)
|
|
- A bug with ring-finding in some complex fused ring systems was fixed.
|
|
(Issue 3514824)
|
|
- The AllChem module now imports successfully even if the SLN parser
|
|
hasn't been built.
|
|
|
|
## New Features:
|
|
- The molecular sanitization is now configurable using an optional
|
|
command-line argument.
|
|
- It's now possible to get information from the sanitization routine
|
|
about which operation failed.
|
|
- Suppliers support GetLastItemText()
|
|
- ComputeDihedralAngle() and ComputeSignedDihedralAngle() were added
|
|
to the rdkit.Geometry module.
|
|
- computeSignedDihedralAngle() was added to the C++ API
|
|
- ChemicalReactions now support a GetReactingAtoms() method
|
|
- the Mol file and Mol block parsers, as well as the SD suppliers,
|
|
now support an optional "strictParsing" argument.
|
|
When this is set to False, problems in the structure of the
|
|
input file are ignored when possible
|
|
- EditableMols return the index of the atom/bond added by AddAtom/AddBond
|
|
- rdkit.Chem.Draw.MolToImage() now supports an optional "legend" argument
|
|
- The MolToSmiles function now supports an optional "allBondsExplicit" argument.
|
|
|
|
## New Database Cartridge Features:
|
|
- the functions mol_from_smiles() and mol_from_smarts() were added
|
|
|
|
## New Java Wrapper Features:
|
|
- the diversity picker now supports an optional random-number seed
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
- rdkit.Excel
|
|
|
|
Removed modules:
|
|
- rdkit.ML.Descriptors.DescriptorsCOM
|
|
- rdkit.ML.Composite.CompositeCOM
|
|
|
|
## Other:
|
|
- Assigning/cleaning up stereochemistry is now considerably
|
|
faster. This makes standard molecule construction faster.
|
|
|
|
|
|
# Release_2011.12.1
|
|
(Changes relative to Release_2011.09.1)
|
|
|
|
## IMPORTANT
|
|
- The functions for creating bit vector fingerprints using atom pairs
|
|
and topological torsions have been changed. The new default
|
|
behavior will return different fingerprints than previous RDKit
|
|
versions. This affects usage from c++, python, and within the
|
|
postgresql cartridge. See the "## Other" section below for more
|
|
details.
|
|
- Due to a bug fix in the parameter set, the MolLogP and MolMR
|
|
descriptor calculators now return different values for some
|
|
molecules. See the "## Bug Fixes" section below for more details.
|
|
- To make storage more efficient, the size of the fingerprint
|
|
used to store morgan fingerprints in the database cartridge
|
|
has been changed from 1024 bits to 512 bits. If you update
|
|
the cartridge version all morgan and featmorgan fingerprints
|
|
and indices will need to be re-generated.
|
|
|
|
## Acknowledgements:
|
|
Andrew Dalke, JP Ebejer, Roger Sayle, Adrian Schreyer, Gianluca
|
|
Sforna, Riccardo Vianello, Toby Wright
|
|
|
|
## Bug Fixes:
|
|
- molecules with polymeric S group information are now rejected by the
|
|
Mol file parser. (Issue 3432136)
|
|
- A bad atom type definition and a bad smarts definition were fixed in
|
|
$RDBASE/Data/Crippen.txt. This affects the values returned by the
|
|
logp and MR calculators. (Issue 3433771)
|
|
- Unused atom-map numbers in reaction products now produce warnings
|
|
instead of errors. (Issue 3434271)
|
|
- rdMolDescriptors.GetHashedAtomPairFingerprint() now works. (Issue
|
|
3441641)
|
|
- ReplaceSubstructs() now copies input molecule conformations to the
|
|
output molecule. (Issue 3453144)
|
|
- three-coordinate S and Se are now stereogenic (i.e. the
|
|
stereochemistry of O=[S@](C)F is no longer ignored). (Issue 3453172)
|
|
|
|
## New Features:
|
|
- Integration with the new IPython graphical canvas has been
|
|
added. For details see this wiki page:
|
|
http://code.google.com/p/rdkit/wiki/IPythonIntegration
|
|
- Input and output from Andrew Dalke's FPS format
|
|
(http://code.google.com/p/chem-fingerprints/wiki/FPS) for
|
|
fingerprints.
|
|
- The descriptor CalcNumAmideBonds() was added.
|
|
|
|
## New Database Cartridge Features:
|
|
- Support for PostgreSQL v9.1
|
|
- Integration with PostgreSQL's KNN-GIST functionality. (Thanks to
|
|
Adrian Schreyer)
|
|
- the functions all_values_gt(sfp,N) and all_values_lt(sfp,N) were
|
|
added.
|
|
|
|
## New Java Wrapper Features:
|
|
- A function for doing diversity picking using fingerprint similarity.
|
|
- support for the Avalon Toolkit (see below)
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
- rdkit.Excel
|
|
- rdkit.ML.Descriptors.DescriptorsCOM
|
|
- rdkit.ML.Composite.CompositeCOM
|
|
|
|
Removed modules:
|
|
- rdkit.WebUtils
|
|
- rdkit.Reports
|
|
- rdkit.mixins
|
|
|
|
## Other:
|
|
- Improvements to the SMARTS parser (Roger Sayle)
|
|
- The atom-pair and topological-torsion fingerprinting functions that
|
|
return bit vectors now simulate counts by setting multiple bits in
|
|
the fingerprint per atom-pair/torsion. The number of bits used is
|
|
controlled by the nBitsPerEntry argument, which now defaults to 4.
|
|
The new default behavior does a much better job of reproducing the
|
|
similarities calculated using count-based fingerprints: 95% of
|
|
calculated similarities are within 0.09 of the count-based value
|
|
compared with 0.22 or 0.17 for torsions and atom-pairs previously.
|
|
To get the old behavior, set nBitsPerEntry to 1.
|
|
- Optional support has been added for the Avalon Toolkit
|
|
(https://sourceforge.net/projects/avalontoolkit/) to provide an
|
|
alternate smiles canonicalization, fingerprint, and 2D coordination
|
|
generation algorithm.
|
|
- The SLN support can now be switched off using the cmake variable
|
|
RDK_BUILD_SLN_SUPPORT.
|
|
- There are now instructions for building the RDKit and the SWIG
|
|
wrappers in 64bit mode on windows.
|
|
|
|
# Release_2011.09.1
|
|
(Changes relative to Release_2011.06.1)
|
|
|
|
## IMPORTANT
|
|
- A bug in the definition of the Lipinski HBD descriptor was fixed in
|
|
this release. The descriptor Lipinski.NHOHCount will return
|
|
different values for molecules containing Ns or Os with more than
|
|
one attached H.
|
|
|
|
## Acknowledgements:
|
|
Eddie Cao, Richard Cooper, Paul Czodrowski, James Davidson, George
|
|
Papadatos, Riccardo Vianello
|
|
|
|
## Bug Fixes:
|
|
- A problem with interpretation of stereochemistry from mol files was
|
|
fixed (Issue 3374639)
|
|
- Sterochemistry information for exocyclic double bonds in mol blocks
|
|
is no longer lost. (Issue 3375647)
|
|
- linear double bonds from mol files now have their stereochemistry
|
|
set correctly(Issue 3375684)
|
|
- Chirality for phosphates and sulfates is not longer automatically
|
|
removed. (Issue 3376319)
|
|
- A bug with the reading of query information from mol files was
|
|
fixed. (Issue 3392107)
|
|
- Sterochemistry is now cleaned up after processing mol2
|
|
files. (Issue 3399798)
|
|
- mergeQueryHs now correctly handles atoms with multiple Hs (Issue
|
|
3415204)
|
|
- mergeQueryHs now correctly handles atoms without initial query
|
|
information (Issue 3415206)
|
|
- the calcLipinskiHBD() (equivalent to Lipinski.NHOHCount) descriptor
|
|
now correctly handles Ns or Os with multiple Hs. (Issue 3415534)
|
|
- Morgan fingerprints generated using the fromAtoms argument now have
|
|
all bits from those atoms set.(Issue 3415636)
|
|
- A problem with the way MolSuppliers handle the EOF condition when
|
|
built with the most recent versions of g++ was fixed.
|
|
- Translation of RDKit stereochemistry information into InChI
|
|
stereochemistry information is improved.
|
|
|
|
## New Features:
|
|
|
|
## New Database Cartridge Features:
|
|
- molecules can now be built from mol blocks using the function
|
|
mol_from_ctab(). The corresponding is_valid_ctab() function was
|
|
also added.
|
|
- the radius argument is now optional for the functions morganbv_fp,
|
|
morgan_fp, featmorganbv_fp, and featmorgan_fp. The default radius
|
|
for all four functions is 2.
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
|
|
Removed modules:
|
|
|
|
## Other:
|
|
- The documentation in $RDBASE/Docs/Book has been migrated to use
|
|
Sphinx instead of OpenOffice.
|
|
- The optional InChI support can now be built using a system
|
|
installation of the InChI library.
|
|
|
|
|
|
|
|
# Release_2011.06.1
|
|
(Changes relative to Release_2011.03.2)
|
|
|
|
## Acknowledgements:
|
|
- Eddie Cao, Andrew Dalke, James Davidson, JP Ebejer, Gianluca
|
|
Sforna, Riccardo Vianello, Bernd Wiswedel
|
|
|
|
## Bug Fixes:
|
|
- A problem with similarity values between SparseIntVects that
|
|
contain negative values was fixed. (Issue 3295215)
|
|
- An edge case in SmilesMolSupplier.GetItemText() was fixed. (Issue
|
|
3299878)
|
|
- The drawing code now uses dashed lines for aromatic bonds without
|
|
kekulization. (Issue 3304375)
|
|
- AllChem.ConstrainedEmbed works again. (Issue 3305420)
|
|
- atomic RGP values from mol files are accessible from python (Issue
|
|
3313539)
|
|
- M RGP blocks are now written to mol files. (Issue 3313540)
|
|
- Atom.GetSymbol() for R atoms read from mol files is now
|
|
correct. (Issue 3316600)
|
|
- The handling of isotope specifications is more robust.
|
|
- A thread-safety problem in SmilesWrite::GetAtomSmiles() was fixed.
|
|
- some of the MACCS keys definitions have been corrected
|
|
- Atoms with radical counts > 2 are no longer always written to CTABs
|
|
with a RAD value of 3. (Issue 3359739)
|
|
|
|
## New Features:
|
|
- The smiles, smarts, and reaction smarts parsers all now take an additional
|
|
argument, "replacements", that carries out string substitutions pre-parsing.
|
|
- There is now optional support for generating InChI codes and keys
|
|
for molecules.
|
|
- the atom pair and topological torsion fingerprint generators now
|
|
take an optional "ignoreAtoms" argument
|
|
- a function to calculate exact molecular weight was added.
|
|
- new java wrappers are now available in $RDBASE/Code/JavaWrappers
|
|
- the methods getMostCommonIsotope() and getMostCommonIsotopeMass()
|
|
have been added to the PeriodicTable class.
|
|
|
|
## New Database Cartridge Features:
|
|
- Support for generating InChIs and InChI keys
|
|
(if the RDKit InChI support is enabled).
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
- The original SWIG wrappers in $RDBASE/Code/Demos/SWIG are deprecated
|
|
|
|
Removed modules:
|
|
|
|
## Other:
|
|
- The quality of the drawings produced by both the python molecule drawing
|
|
code and $RDBASE/Code/Demos/RDKit/Draw is better.
|
|
- the python molecule drawing code will now use superscripts and
|
|
subscripts appropriately when using the aggdraw or cairo canvases
|
|
(cairo canvas requires pango for this to work).
|
|
- $RDBASE/Code/Demos/RDKit/Draw now includes an example using cairo
|
|
- A lot of compiler warnings were cleaned up.
|
|
- The error reporting in the SMILES, SMARTS, and SLN parsers was improved.
|
|
- the code for calculating molecular formula is now in C++
|
|
(Descriptors::calcMolFormula())
|
|
|
|
|
|
# Release_2011.03.2
|
|
(Changes relative to Release_2011.03.1)
|
|
|
|
## Bug Fixes:
|
|
- A problem in the refactored drawing code that caused the
|
|
rdkit.Chem.Draw functionality to not work at all was fixed.
|
|
|
|
|
|
# Release_2011.03.1
|
|
(Changes relative to Release_2010.12.1)
|
|
|
|
## Acknowledgements:
|
|
- Eddie Cao, James Davidson, Kirk DeLisle, Peter Gedeck, George
|
|
Magoon, TJ O'Donnell, Gianluca Sforna, Nik Stiefl, Bernd Wiswedel
|
|
|
|
## Bug Fixes:
|
|
- The performance of SSSR finding for molecules with multiple highly-fused
|
|
ring systems has been improved. (Issue 3185548)
|
|
- Isotope information is now correctly saved when molecules are
|
|
serialized (pickled). (Issue 3205280)
|
|
- Generating SMILES for a molecule no longer changes the
|
|
molecule. This fixes a round-trip bug with certain highly symmetric
|
|
molecules read from SD files. (Issue 3228150)
|
|
- Another bounds-matrix generation bug for highly (con)strained
|
|
systems was fixed. (Issue 3238580)
|
|
- Conformation information is now better handled by deleteSubstructs(),
|
|
replaceSubstructs(), and replaceCore().
|
|
|
|
## New Features:
|
|
- the rdkit.Chem.Draw package has been significantly refactored.
|
|
- Code for doing Murcko decomposition of molecules has been
|
|
added. From Python this is in the module:
|
|
rdkit.Chem.Scaffolds.MurckoScaffold
|
|
It's available in C++ in the GraphMol/ChemTransforms area.
|
|
- rdkit.Chem.AllChem.TransformMol() now takes optional arguments
|
|
allowing the conformation to be transformed to be specified and
|
|
other existing conformations to be preserved.
|
|
- Calculations for most of the descriptors in rdkit.Chem.Lipinski and
|
|
rdkit.Chem.MolSurf have been moved into C++. The python API is the
|
|
same, but the calculations should be somewhat faster.
|
|
- Extensive feature additions to the SWIG-based java wrapper.
|
|
- The Chem.ReplaceCore() function is now better suited for use
|
|
in R-group decomposition.
|
|
- The Morgan fingerprinting code can now return information about
|
|
which atoms set particular bits.
|
|
- The function pathToSubmol() now copies coordinate information
|
|
from conformations (if present). The function is also now available
|
|
from Python
|
|
- The path and subgraph finding code now takes an optional
|
|
rootedAtAtom argument to allow only paths/subgraphs that start at a
|
|
particular atom to be generated.
|
|
- The function findAtomEnvironmentOfRadiusN has been added to allow
|
|
circular atom environments to be located in molecules.
|
|
- MolOps::assignStereochemistry now can also flag potential
|
|
stereocenters that are not specified.
|
|
|
|
## New Database Cartridge Features:
|
|
- the descriptor-calculation functions mol_numrotatablebonds(),
|
|
mol_numheteroatoms(), mol_numrings(), and mol_tpsa() have been
|
|
added.
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
|
|
Removed modules:
|
|
|
|
## Other:
|
|
- In C++, the functions CalcCrippenDescriptors and CalcAMW have been
|
|
renamed calcCrippenDescriptors and calcAMW to make them consistent
|
|
with the other descriptor calculators.
|
|
- The molecule serialization (pickling) format has been changed. The
|
|
new format is more compact.
|
|
|
|
|
|
|
|
# Release_2010.12.1
|
|
(Changes relative to Release_2010.09.1)
|
|
|
|
## IMPORTANT
|
|
- Due to changes made to the fingerprinting code, RDKit and layered
|
|
fingerprints generated with this release are not compatible with
|
|
those from previous releases. For users of the database cartridge:
|
|
you will need to re-generate RDKit fingerprint columns and any
|
|
indices on molecule tables.
|
|
|
|
## Acknowledgements:
|
|
- Eddie Cao, Andrew Dalke, James Davidson, Kirk DeLisle, Peter Gedeck,
|
|
TJ O'Donnell, Gianluca Sforna, Nik Stiefl, Riccardo Vianello
|
|
|
|
## Bug Fixes:
|
|
- The depiction code no longer crashes with single-atom templates
|
|
(issue 3122141)
|
|
- Aromatic bonds in the beginning of a SMILES branch are now
|
|
correctly parsed (issue 3127883)
|
|
- A crash when generating 2d constrained coordinates was fixed (issue
|
|
3135833)
|
|
- Stereochemistry no longer removed from double bonds in large
|
|
rings. (issue 3139534)
|
|
- Atom mapping information no longer in reaction products (issue
|
|
3140490)
|
|
- Smiles parse failure with repeated ring labels and dot disconnects
|
|
fixed (issue 3145697)
|
|
- a bug causing the molecule drawing code to not use the cairo canvas
|
|
when it's installed was fixed
|
|
- the SMILES generated for charged, aromatic Se or Te has been fixed
|
|
(issue 3152751)
|
|
- PropertyMols constructed from pickles and then written to SD files
|
|
will now include the properties in the SD file.
|
|
- SMILES can now be generated correctly for very large molecules
|
|
where more than 50 rings are open at once. (issue 3154028)
|
|
|
|
## New Features:
|
|
- All molecular descriptor calculators are now pulled in by the
|
|
rdkit.Chem.Descriptors module. So you can do things like:
|
|
Descriptors.MolLogP(mol) or Descriptors.fr_amide(mol)
|
|
- Atom-map numbers in SMILES are now supported. They can be accessed
|
|
as the atomic "molAtomMapNumber" property. (issue 3140494)
|
|
- It's now possible to tell the RDKit to generate non-canonical
|
|
SMILES via an optional argument to MolToSmiles. This is faster than
|
|
generating canonical SMILES, but is primarity intended for
|
|
debugging/testing. (issue 3140495)
|
|
- The function GenerateDepictionMatching2DStructure() has been added
|
|
to the rdkit.Chem.AllChem module to make generating
|
|
template-aligned depictions easier.
|
|
- Generating FCFP-like fingerprints is now more straightforward via
|
|
the useFeatures optional argument to GetMorganFingerprint()
|
|
- Extensive changes were made to the layered fingerprinting code to
|
|
allow better coverage of queries.
|
|
- Functionality for stripping common salts from molecules has been
|
|
added in rdkit.Chem.SaltRemover. The salts themselves are defined
|
|
in $RDBASE/Data/Salts.txt
|
|
- Functionality for recognizing common functional groups has been
|
|
added in rdkit.Chem.FunctionalGroups. The functional groups
|
|
themselves are defined in
|
|
$RDBASE/Data/Functional_Group_Hierarchy.txt
|
|
|
|
## New Database Cartridge Features:
|
|
- The cartridge now supports SMARTS queries.
|
|
- The functions is_valid_{smiles,smarts}() are now available
|
|
(issue 3097359).
|
|
- The operator @= is now supported for testing molecule equality.
|
|
(issue 3120707)
|
|
- The functions featmorgan_fp() and featmorganbv_fp() are now
|
|
available for generating FCFP-like fingerprints.
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
- rdkit.Chem.AvailDescriptors : the same functionality is now available
|
|
in a more useable manner from rdkit.Chem.Descriptors (see above).
|
|
|
|
Removed modules:
|
|
|
|
## Other:
|
|
- RDKit support has been added to the Knime data mining and reporting
|
|
tool. More information is available from the knime.org community
|
|
site: http://tech.knime.org/community/rdkit
|
|
Thanks to Thorsten, Bernd, Michael, and the rest of the crew at
|
|
knime.com for making this possible.
|
|
- RPMs to allow easy installation of the RDKit on Fedora/CentOS/RHEL
|
|
and similar systems are now available. Thanks to Gianluca Sforna
|
|
for doing this work.
|
|
- The database cartridge now statically links the RDKit libraries.
|
|
This should make installation easier.
|
|
- The RDKit fingerprinter now by default sets 2 bits per hashed
|
|
subgraph instead of 4. The old behavior can be regained by setting
|
|
nBitsPerHash to 4.
|
|
|
|
# Release_2010.09.1
|
|
(Changes relative to Release_Q22010_1)
|
|
|
|
## IMPORTANT
|
|
- Due to changes made to the layered fingerprinting code,
|
|
fingerprints generated with this release are not compatible with
|
|
fingerprints from earlier releases.
|
|
- The default arguments to the Morgan fingerprinting code will yield
|
|
fingerprints that are not backwards compatible.
|
|
|
|
## Acknowledgements:
|
|
- Andrew Dalke, James Davidson, Paul Emsley, Peter Gedeck,
|
|
Uwe Hoffmann, Christian Kramer, Markus Kossner, TJ O'Donnell,
|
|
Gianluca Sforna, Nik Stiefl, Riccardo Vianello
|
|
|
|
## Bug Fixes:
|
|
- A typo in the parameters for the Crippen clogp calculator was
|
|
fixed. (issue 3057201)
|
|
- some problems in the layered fingerprinting code were fixed. (issue
|
|
3030388)
|
|
- a bug in the ring-finding code that could lead to incorrect results
|
|
or crashes in large molecules was fixed.
|
|
- the Murtagh clustering code should now execute correctly on recent
|
|
versions of the MacOS.
|
|
- some problems with the cairo canvas were fixed
|
|
- a problem with matching non-default isotope SSS queries for molecules
|
|
read in from CTABs was fixed (issue 3073163).
|
|
- a problem with calculating AMW for molecules with non-default isotopes
|
|
was fixed.
|
|
|
|
## New Features:
|
|
- a PostgreSQL cartridge for similarity and substructure searching
|
|
has been added to the RDKit distribution.
|
|
- The Morgan fingerprinting code accepts additional arguments that
|
|
control whether or not bond order and chirality are taken into
|
|
account. By default chirality is ignored and the bond order is
|
|
used. Another change with the MorganFPs is that ring information is
|
|
now included by default.
|
|
- 2D coordinates can now be generated for chemical reactions.
|
|
- The functions IsMoleculeReactantOfReaction and
|
|
IsMoleculeProductOfReaction have been added to the C++
|
|
interface. From python these are methods of the ChemicalReaction
|
|
class:
|
|
rxn.IsMoleculeReactant and rxn.IsMoleculeProduct
|
|
- The default bond length for depiction can now be changed.
|
|
- FCFP-like fingerprints can now be generated with the Morgan
|
|
fingerprinting code by starting with feature invariants.
|
|
- The close() method has been added to MolWriters.
|
|
- Morgan, atom-pair, and topological-torsion fingerprints can now
|
|
also be calculated as bit vectors.
|
|
- RDKit and layered fingerprints can now be generated using only
|
|
linear paths.
|
|
- the function findAllPathsOfLengthMtoN() was added
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
|
|
Removed modules:
|
|
- rdkit/qtGui
|
|
- rdkit/RDToDo
|
|
- Projects/SDView
|
|
|
|
## Other:
|
|
- As of this release a new version numbering scheme is being used:
|
|
YYYY.MM.minor. An example, this release was done in Sept. of 2010
|
|
so it's v2010.09.1.
|
|
- the RDBASE environment variable is no longer required. It will be
|
|
used if set, but the code should work without it
|
|
- The directory Contrib/M_Kossner contains two new contributions from
|
|
Markus Kossner.
|
|
- A change was made to the subgraph matching code that speeds up
|
|
substructure searches involving repeated recursive queries.
|
|
- the deprecated registerQuery argument has been removed from the
|
|
substructure matching functions.
|
|
- the empty header files AtomProps.h and BondProps.h have been
|
|
removed.
|
|
- in order to simplify the build process the test databases are now
|
|
in svn
|
|
- some python functions to calculate descriptors (i.e. pyMolWt,
|
|
pyMolLogP, etc.) that have C++ equivalents have been removed to
|
|
clean up the interface
|
|
- the PIL canvas should no longer generate warnings
|
|
- Thanks to the help of Gianluca Sforna and Riccardo Vianello, it is
|
|
now much easier to package and distribute the RDKit.
|
|
- the bjam-based build system has been removed.
|
|
|
|
# Release_Q22010_1
|
|
(Changes relative to Release_Q12010_1)
|
|
|
|
## IMPORTANT
|
|
- There are a couple of refactoring changes that affect people using
|
|
the RDKit from C++. Please look in the ## Other section below for a list.
|
|
- If you are building the RDKit yourself, changes made in this
|
|
release require that you use a reasonably up-to-date version of
|
|
flex to build it. Please look in the ## Other section below for more
|
|
information.
|
|
|
|
## Acknowledgements:
|
|
- Andrew Dalke, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
|
|
Greg Magoon, Noel O'Boyle, Nik Stiefl,
|
|
|
|
## Bug Fixes:
|
|
- The depictor no longer generates NaNs for some molecules on
|
|
windows (issue 2995724)
|
|
- [X] query features work correctly with chiral atoms. (issue
|
|
3000399)
|
|
- mols will no longer be deleted by python when atoms/bonds returned
|
|
from mol.Get{Atom,Bond}WithIdx() are still active. (issue 3007178)
|
|
- a problem with force-field construction for five-coordinate atoms
|
|
was fixed. (issue 3009337)
|
|
- double bonds to terminal atoms are no longer marked as "any" bonds
|
|
when writing mol blocks. (issue 3009756)
|
|
- a problem with stereochemistry of double bonds linking rings was
|
|
fixed. (issue 3009836)
|
|
- a problem with R/S assignment was fixed. (issue 3009911)
|
|
- error and warning messages are now properly displayed when cmake
|
|
builds are used on windows.
|
|
- a canonicalization problem with double bonds incident onto aromatic
|
|
rings was fixed. (issue 3018558)
|
|
- a problem with embedding fused small ring systems was fixed.
|
|
(issue 3019283)
|
|
|
|
## New Features:
|
|
- RXN files can now be written. (issue 3011399)
|
|
- reaction smarts can now be written.
|
|
- v3000 RXN files can now be read. (issue 3009807)
|
|
- better support for query information in mol blocks is present.
|
|
(issue 2942501)
|
|
- Depictions of reactions can now be generated.
|
|
- Morgan fingerprints can now be calculated as bit vectors (as
|
|
opposed to count vectors.
|
|
- the method GetFeatureDefs() has been added to
|
|
MolChemicalFeatureFactory
|
|
- repeated recursive SMARTS queries in a single SMARTS will now be
|
|
recognized and matched much faster.
|
|
- the SMILES and SMARTS parsers can now be run safely in
|
|
multi-threaded code.
|
|
|
|
Deprecated modules (to be removed in next release):
|
|
- rdkit/qtGui
|
|
- Projects/SDView
|
|
|
|
Removed modules:
|
|
- SVD code: External/svdlibc External/svdpackc rdkit/PySVD
|
|
- rdkit/Chem/CDXMLWriter.py
|
|
|
|
## Other:
|
|
- The large scale changes in the handling of stereochemistry were
|
|
made for this release. These should make the code more robust.
|
|
- If you are building the RDKit yourself, changes made in this
|
|
release require that you use a reasonably up-to-date version of
|
|
flex to build it. This is likely to be a problem on Redhat, and
|
|
redhat-derived systems. Specifically: if your version of flex is
|
|
something like 2.5.4 (as opposed to something like 2.5.33, 2.5.34,
|
|
etc.), you will need to get a newer version from
|
|
http://flex.sourceforge.net in order to build the RDKit.
|
|
|
|
- Changes only affecting C++ programmers:
|
|
- The code for calculating topological-torsion and atom-pair
|
|
fingerprints has been moved from $RDBASE/Code/GraphMol/Descriptors
|
|
to $RDBASE/Code/GraphMol/Fingerprints.
|
|
- The naming convention for methods of ExplicitBitVect and
|
|
SparseBitVect have been changed to make it more consistent with
|
|
the rest of the RDKit.
|
|
- the bjam-based build system should be considered
|
|
deprecated. This is the last release it will be actively
|
|
maintained.
|
|
|
|
|
|
# Release_Q12010_1
|
|
(Changes relative to Release_Q42009_1)
|
|
|
|
## Acknowledgements:
|
|
- Andrew Dalke, Jean-Marc Nuzillard, Noel O'Boyle, Gianluca Sforna,
|
|
Nik Stiefl, Anna Vulpetti
|
|
|
|
## Bug Fixes
|
|
- Substantial improvements were made to the SLN parser
|
|
- A bad depiction case was fixed. (issue 2948402)
|
|
- Hs added to planar carbons are no longer in the same plane as the
|
|
other atoms. (issue 2951221)
|
|
- Elements early in the periodic table (e.g. Mg, Na, etc.) no longer
|
|
have their radical counts incorrectly assigned. (issue 2952255)
|
|
- Some improvements were made to the v3k mol file parser. (issue
|
|
2952272)
|
|
- Double bonds with unspecified stereochemistry are now correctly
|
|
flagged when output to mol files. (issue 2963522)
|
|
- A segmentation fault that occured when kekulizing modified
|
|
molecules has been fixed. (issue 2983794)
|
|
|
|
## New Features
|
|
- The MaxMin diversity picker can now be given a seed for the random
|
|
number generator to ensure reproducible results.
|
|
|
|
## Other
|
|
- the vflib source, which is no longer used, was removed from the
|
|
External source tree. It's still available in svn at rev1323 or via
|
|
this tarball:
|
|
http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/External/vflib-2.0.tar.gz?view=tar&pathrev=1323
|
|
- the directory Contrib has been added to the RDKit distribution to
|
|
house contributions that don't necessarily fit anywhere else. The
|
|
first contribution here is a collection of scripts required to
|
|
implement local-environment fingerprints contributed by Anna
|
|
Vulpetti.
|
|
- Some optimization work was done on the molecule initialization code:
|
|
reading in molecules is now somewhat faster.
|
|
- Some optimization work was done on the RDK and Layered fingerprinting code.
|
|
|
|
# Release_Q42009_1
|
|
(Changes relative to Release_Q32009_1)
|
|
|
|
## IMPORTANT
|
|
- A bug fix in the SMARTS parser has changed the way atom-map
|
|
numbers in Reaction SMARTS are parsed.
|
|
Earlier versions of the RDKit required that atom maps be
|
|
specified at the beginning of a complex atom query:
|
|
[CH3:1,NH2]>>[*:1]O
|
|
The corrected version only accepts this form:
|
|
[CH3,NH2:1]>>[*:1]O
|
|
This change may break existing SMARTS patterns.
|
|
- A switch to using cmake as the build system instead of bjam has
|
|
made the RDKit much easier to build.
|
|
|
|
## Acknowledgements
|
|
- Andrew Dalke, Kirk DeLisle, David Hall, Markus Kossner, Adrian
|
|
Schreyer, Nikolaus Stiefl, Jeremy Yang
|
|
|
|
## Bug Fixes
|
|
- the SMARTS parser now correctly requires tha atom-map numbers be
|
|
at the end of a complex atom query.
|
|
(issue 1804420)
|
|
- a bug in the way SMARTS matches are uniquified has been fixed
|
|
(issue 2884178)
|
|
|
|
## New Features
|
|
- The new SMARTS atomic query feature "x" (number of ring bonds) is
|
|
now supported.
|
|
- The proof-of-concept for a SWIG-based wrapper around the RDKit has
|
|
been expanded a bit in functionality. Samples are now included for
|
|
Java, C#, and Python.
|
|
- Information about the current RDKit and boost versions is now
|
|
available from C++ (file RDGeneral/versions.h) and Python
|
|
(rdBase.rdkitVersion and rdBase.boostVersion)
|
|
- The KNN code now supports weighted nearest-neighbors calculations
|
|
with a radius cutoff.
|
|
|
|
## Other
|
|
- The lapack dependency has been completely removed from the RDKit.
|
|
- The supported build system for the RDKit is now cmake
|
|
(http://www.cmake.org) instead of bjam. See the file INSTALL for
|
|
the new installation instructions. Files for bjam are still
|
|
included in the distribution but are deprecated and will be
|
|
removed in a future version.
|
|
|
|
|
|
# Release_Q32009_1
|
|
(Changes relative to Release_Q22009_1)
|
|
|
|
## IMPORTANT
|
|
- Due to bug fixes in the boost random-number generator, RDK
|
|
fingerprints generated with boost 1.40 are not backwards
|
|
compatible with those from earlier versions.
|
|
|
|
## Acknowledgements
|
|
- Uwe Hoffmann, Nik Stiefl, Greg Magoon, Ari Gold-Parker,
|
|
Akihiro Yokota, Kei Taneishi, Riccardo Vianello, Markus Kossner
|
|
|
|
## Bug Fixes
|
|
- the canonOrient argument to the depiction code now works
|
|
(issue 2821647)
|
|
- typo in the depictor 2D embedding code fixed
|
|
(issue 2822883)
|
|
- single aromatic atoms in chains now (correctly) fail sanitization
|
|
(issue 2830244)
|
|
- problem with embedding and fused rings fixed
|
|
(issue 2835784)
|
|
- crash when reading some large molecules fixed
|
|
(issue 2840217)
|
|
- trailing newline in TemplateExpand.py fixed
|
|
(issue 2867325)
|
|
- fingerprint incompatibility on 64bit machines fixed
|
|
(issue 2875658)
|
|
- PropertyMol properties are now written to SD files
|
|
(issue 2880943)
|
|
|
|
## New Features
|
|
- to the extent possible, reactions now transfer coordinates from
|
|
reactant molecules to product molecules (issue 2832951)
|
|
## Other
|
|
- the function DaylightFingerprintMol() has been removed
|
|
- the outdated support for Interbase has been removed
|
|
- the Compute2DCoords() function in Python now canonicalizes the
|
|
orientation of the molecule by default.
|
|
- the distance-geometry code should now generate less bad amide
|
|
conformations. (issue 2819563)
|
|
- the quality of distance-geometry embeddings for substituted- and
|
|
fused-ring systems should be better.
|
|
|
|
# Release_Q22009_1
|
|
(Changes relative to Release_Q12009_2)
|
|
|
|
## Acknowledgements
|
|
- Uwe Hoffmann, Marshall Levesque, Armin Widmer
|
|
|
|
## Bug Fixes
|
|
- handling of crossed bonds in mol files fixed (issue 2804599)
|
|
- serialization bug fixed (issue 2788233)
|
|
- pi systems with 2 electrons now flagged as aromatic (issue 2787221)
|
|
- Chirality swap on AddHs (issue 2762917)
|
|
- core leak in UFFOptimizeMolecule fixed (issue 2757824)
|
|
|
|
## New Features
|
|
- cairo support in the mol drawing code (from Uwe Hoffmann) (issue 2720611)
|
|
- Tversky and Tanimoto similarities now supported for SparseIntVects
|
|
- AllProbeBitsMatch supported for BitVect-BitVect comparisons
|
|
- ChemicalReactions support serialization (pickling) (issue 2799770)
|
|
- GetAtomPairFingerprint() supports minLength and maxLength arguments
|
|
- GetHashedTopologicalTorsionFingerprint() added
|
|
- preliminary support added for v3K mol files
|
|
- ForwardSDMolSupplier added
|
|
- CompressedSDMolSupplier added (not supported on windows)
|
|
- UFFHasAllMoleculeParams() added
|
|
- substructure searching code now uses an RDKit implementation of
|
|
the vf2 algorithm. It's much faster.
|
|
- Atom.GetPropNames() and Bond.GetPropNames() now available from
|
|
python
|
|
- BRICS code now supports FindBRICSBonds() and BreakBRICSBonds()
|
|
- atom labels Q, A, and * in CTABs are more correctly supported
|
|
(issue 2797708)
|
|
- rdkit.Chem.PropertyMol added (issue 2742959)
|
|
- support has been added for enabling and disabling logs
|
|
(issue 2738020)
|
|
|
|
## Other
|
|
- A demo has been added for using the MPI with the RDKit
|
|
($RDBASE/Code/Demos/RDKit/MPI).
|
|
- Embedding code is now better at handling chiral structures and
|
|
should produce results for molecules with atoms that don't have
|
|
UFF parameters.
|
|
- the UFF code is more robust w.r.t. missing parameters
|
|
- GetHashedAtomPairFingerprint() returns SparseIntVect instead of
|
|
ExplicitBitVect
|
|
- the CTAB parser (used for mol files and SD files) is faster
|
|
- extensive changes to the layered fingerprinting code;
|
|
fingerprinting queries is now possible
|
|
- molecule discriminator code moved into $RDBASE/Code/GraphMol/Subgraphs
|
|
- the SDView4 prototype has been expanded
|
|
- $RDBASE/Regress has been added to contain regression and
|
|
benchmarking data and scripts.
|
|
- support for sqlalchemy has been added to $RDBASE/rdkit/Chem/MolDb
|
|
- $RDBASE/Projects/DbCLI/SDSearch.py has been removed; use the
|
|
CreateDb.py and SearchDb.py scripts in the same directory instead.
|
|
- the BRICS code has been refactored
|
|
|
|
# Release_Q12009_2
|
|
(Changes relative to Release_Q42008_1)
|
|
|
|
## IMPORTANT
|
|
|
|
- The directory structure of the distribution has been changed in
|
|
order to make installation of the RDKit python modules more
|
|
straightforward. Specifically the directory $RDBASE/Python has been
|
|
renamed to $RDBASE/rdkit and the Python code now expects that
|
|
$RDBASE is in your PYTHONPATH. When importing RDKit Python modules,
|
|
one should now do: "from rdkit import Chem" instead of "import
|
|
Chem". Old code will continue to work if you also add $RDBASE/rdkit
|
|
to your PYTHONPATH, but it is strongly suggested that you update
|
|
your scripts to reflect the new organization.
|
|
- For C++ programmers: There is a non-backwards compatible change in
|
|
the way atoms and bonds are stored on molecules. See the *## Other*
|
|
section for details.
|
|
|
|
## Acknowledgements
|
|
- Kirk DeLisle, Noel O'Boyle, Andrew Dalke, Peter Gedeck, Armin Widmer
|
|
|
|
## Bug Fixes
|
|
- Incorrect coordinates from mol2 files (issue 2727976)
|
|
- Incorrect handling of 0s as ring closure digits (issues 2525792,
|
|
and 2690982)
|
|
- Incorrect handling of atoms with explicit Hs in reactions (issue 2540021)
|
|
- SmilesMolSupplier.GetItemText() crashes (issue 2632960)
|
|
- Incorrect handling of dot separations in reaction SMARTS (issue 2690530)
|
|
- Bad charge lines in mol blocks for large molecules (issue 2692246)
|
|
- Order dependence in AssignAtomChiralTagsFromStructure (issue 2705543)
|
|
- Order dependence in the 2D pharmacophore code
|
|
- the LayeredFingerprints now handle non-aromatic single ring bonds
|
|
between aromatic atoms correctly.
|
|
|
|
|
|
## New Features
|
|
- BRICS implementation
|
|
- Morgan/circular fingerprints implementation
|
|
- The 2D pharmacophore code now uses standard RDKit fdef files.
|
|
- Atom parity information in CTABs now written and read. If present
|
|
on reading, atom parity flags are stored in the atomic property
|
|
"molParity".
|
|
- An optional "fromAtoms" argument has been added to the atom pairs
|
|
and topological torsion fingerprints. If this is provided, only atom
|
|
pairs including the specified atoms, or torsions that either start
|
|
or end at the specified atoms, will be included in the fingerprint.
|
|
- Kekulization is now optional when generating CTABs. Since the MDL
|
|
spec suggests that aromatic bonds not be used, this is primarily
|
|
intended for debugging purposes.
|
|
- the removeStereochemistry() (RemoveStereoChemistry() from Python)
|
|
function has been added to remove all stereochemical information
|
|
from a molecule.
|
|
|
|
## Other
|
|
- The Qt3-based GUI functionality in $RDBASE/rdkit/qtGui and
|
|
$RDBASE/Projects/SDView is deprecated. It should still work, but it
|
|
will be removed in a future release. Please do not build anything
|
|
new on this (very old and creaky) framework.
|
|
- The function DaylightFingerprintMol() is now deprecated, use
|
|
RDKFingerprintMol() instead.
|
|
- For C++ programmers: The ROMol methods getAtomPMap() and
|
|
getBondPMap() have been removed. The molecules themselves now support
|
|
an operator[]() method that can be used to convert graph iterators
|
|
(e.g. ROMol:edge_iterator, ROMol::vertex_iterator,
|
|
ROMol::adjacency_iterator) to the corresponding Atoms and Bonds.
|
|
New API for looping over an atom's bonds:
|
|
... molPtr is a const ROMol * ...
|
|
... atomPtr is a const Atom * ...
|
|
ROMol::OEDGE_ITER beg,end;
|
|
boost::tie(beg,end) = molPtr->getAtomBonds(atomPtr);
|
|
while(beg!=end){
|
|
const BOND_SPTR bond=(*molPtr)[*beg];
|
|
... do something with the Bond ...
|
|
++beg;
|
|
}
|
|
New API for looping over a molecule's atoms:
|
|
... mol is an ROMol ...
|
|
ROMol::VERTEX_ITER atBegin,atEnd;
|
|
boost::tie(atBegin,atEnd) = mol.getVertices();
|
|
while(atBegin!=atEnd){
|
|
ATOM_SPTR at2=mol[*atBegin];
|
|
... do something with the Atom ...
|
|
++atBegin;
|
|
}
|
|
|
|
# Release_Q42008_1
|
|
(Changes relative to Release_Q32008_1)
|
|
|
|
## IMPORTANT
|
|
- A fix in the handling of stereochemistry in rings means that the
|
|
SMILES generated with this release are different from those in
|
|
previous releases. Note that the canonicalization algorithm does
|
|
not work in cases of pure ring stereochemistry : the SMILES should
|
|
be correct, but it is not canonical. Rings containing chiral
|
|
centers should be fine.
|
|
|
|
## Acknowledgements:
|
|
- Kirk DeLisle, Markus Kossner, Greg Magoon, Nik Stiefl
|
|
|
|
## Bug Fixes
|
|
- core leaks in learning code (issue 2152622)
|
|
- H-bond acceptor definitions (issue 2183240)
|
|
- handling of aromatic dummies (issue 2196817)
|
|
- errors in variable quantization (issue 2202974)
|
|
- errors in information theory functions on 64 bit machines (issue 2202977)
|
|
- kekulization problems (issue 2202977)
|
|
- infinite loop in getShortestPaths() for disconnected structures (issue 2219400)
|
|
- error in depictor for double bonds with stereochemistry connected
|
|
to rings (issue 2303566)
|
|
- aromaticity flags not copied to null atoms in reaction products
|
|
(issue 2308128)
|
|
- aromaticity perception in large molecule hangs (issue 2313979)
|
|
- invariant error in canonicalization (issue 2316677)
|
|
- mol file parser handling of bogus bond orders (issue 2337369)
|
|
- UFF optimization not terminating when atoms are on top of each
|
|
other (issue 2378119)
|
|
- incorrect valence errors with 4 coordinate B- (issue 2381580)
|
|
- incorrect parsing of atom-list queries with high-numbered atoms
|
|
(issue 2413431)
|
|
- MolOps::mergeQueryHs() crashing with non-query molecules. (issue
|
|
2414779)
|
|
|
|
## New Features
|
|
- SLN parser (request 2136703).
|
|
- Mol2 parser : Corina atom types (request 2136705).
|
|
- Building under mingw (request 2292153).
|
|
- Null bonds in reaction products are replaced with the corresponding
|
|
bond from the reactants (request 2308123).
|
|
|
|
## Other
|
|
- a bunch of deprecation warnings from numpy have been cleaned up
|
|
(issue 2318431)
|
|
- updated documentation
|
|
- some optimization work on the fingerprinter
|
|
|
|
# Release_Q32008_1
|
|
(Changes relative to Release_May2008_1)
|
|
|
|
## Acknowledgements:
|
|
- Noel O'Boyle, Igor Filippov, Evgueni Kolossov, Greg Magoon
|
|
|
|
## Bug Fixes
|
|
- A memory leak in the ToBase64 and FromBase64 wrapper functions was
|
|
fixed.
|
|
- The UFF atom typer has been made more permissive: it now will pick
|
|
"close" atom types for things it does not recognize. (issue
|
|
2094445)
|
|
- The handling of molecules containing radicals has been greatly
|
|
improved (issues 2091839, 2091890, 2093420)
|
|
- Iterative (or secondary, or dependent) chirality is now supported,
|
|
see this page for more information:
|
|
http://code.google.com/p/rdkit/wiki/IterativeChirality
|
|
(issue 1931470)
|
|
- Isotope handling has been changed, this allows correct matching of
|
|
SMARTS with specified isotopes. (issue 1968930)
|
|
- Some problems with the MACCS key definitions have been
|
|
fixed. (issue 2027446)
|
|
- Molecules with multiple fragments can now be correctly
|
|
embedded. (issue 1989539)
|
|
- Adding multiple bonds between the same atoms in a molecule now
|
|
produces an error. (issue 1993296)
|
|
- The chemical reaction code now handles chiral atoms correctly in
|
|
when applying reactions with no stereochem information
|
|
provided. (issue 2050085)
|
|
- A problem with single-atom cores in TemplateExpand.py has been
|
|
fixed. (issue 2091304)
|
|
- A problem causing bicyclobutane containing molecules to not be
|
|
embeddable has been fixed. (issue 2091864)
|
|
- The default parameters for embedding are now molecule-size
|
|
dependent. This should help with the embedding of large, and
|
|
crowded molecules. (issue 2091974)
|
|
- The codebase can now be built with boost 1.36. (issue 2071168)
|
|
- A problem with serialization of bond directions was fixed.
|
|
(issue 2113433)
|
|
|
|
## New Features
|
|
- The RDKit can now be built under Darwin (Mac OS/X).
|
|
- Tversky similarity can now be calculated. (request 2015633)
|
|
- Many of the core datastructures now support equality comparison
|
|
(operator==). (request 1997439)
|
|
- Chirality information can now be assigned based on the 3D
|
|
coordinates of a molecule using
|
|
MolOps::assignChiralTypesFrom3D(). (request 1973062)
|
|
- MolOps::getMolFrags() can now return a list of split molecules
|
|
instead of just a list of atom ids. (request 1992648)
|
|
- ROMol::getPropNames() now supports the includePrivate and
|
|
includeComputed options. (request 2047386)
|
|
|
|
|
|
## Other
|
|
- the pointers returned from Base64Encode/Decode are now allocated
|
|
using new instead of malloc or calloc. the memory should be
|
|
released with delete[].
|
|
- the generation of invariants for chirality testing is now quite a
|
|
bit faster; this results in faster parsing of molecules.
|
|
- The use of C include files instead of their C++ replacements has
|
|
been dramatically reduced.
|
|
- The new (as of May2008) hashing algorithm for fingerprints is now
|
|
the default in the python fingerprinting code
|
|
(Chem.Fingerprints.FingerprintMols).
|
|
- The functions MolOps::assignAtomChiralCodes() and
|
|
MolOps::assignBondStereoCodes() are deprecated. Use
|
|
MolOps::assignStereochemistry() instead.
|
|
- The RDKit no longer uses the old numeric python library. It now
|
|
uses numpy, which is actively supported.
|
|
- By default Lapack++ is no longer used. The replacement is the boost
|
|
numeric bindings: http://mathema.tician.de/software/boost-bindings.
|
|
|
|
|
|
# Release_May2008_1
|
|
(Changes relative to Release_Jan2008_1)
|
|
|
|
## IMPORTANT
|
|
- A fix to the values of the parameters for the Crippen LogP
|
|
calculator means that the values calculated with this version are
|
|
not backwards compatible. Old values should be recalculated.
|
|
- topological fingerprints generated with this version *may* not be
|
|
compatible with those from earlier versions. Please read the note
|
|
below in the "## Other" section.
|
|
- Please read the point about dummy atoms in the "## New Features"
|
|
section. It explains a change that affects backwards compatibility
|
|
when dealing with dummy atoms.
|
|
|
|
|
|
## Acknowledgements:
|
|
- Some of the bugs fixed in this release were found and reported by
|
|
Adrian Schreyer, Noel O'Boyle, and Markus Kossner.
|
|
|
|
## Bug Fixes
|
|
- A core leak in MolAlign::getAlignmentTransform was fixed (issue
|
|
1899787)
|
|
- Mol suppliers now reset the EOF flag on their stream after they run
|
|
off the end (issue 1904170)
|
|
- A problem causing the string "Sc" to not parse correctly in
|
|
recursive SMARTS was fixed (issue 1912895)
|
|
- Combined recursive smarts queries are now output correctly.
|
|
(issue 1914154)
|
|
- A bug in the handling of chirality in reactions was fixed (issue
|
|
1920627)
|
|
- Looping directly over a supplier no longer causes a crash (issue
|
|
1928819)
|
|
- a core leak in the smiles parser was fixed (issue 1929199)
|
|
- Se and Te are now potential aromatic atoms (per the proposed
|
|
OpenSmiles standard). (issue 1932365)
|
|
- isotope information (and other atomic modifiers) are now correctly
|
|
propagated by chemical reactions (issue 1934052)
|
|
- triple bonds no longer contribute 2 electrons to the count for
|
|
aromaticity (issue 1940646)
|
|
- Two bugs connected with square brackets in SMILES were fixed
|
|
(issues 1942220 and 1942657)
|
|
- atoms with coordination numbers higher than 4 now have tetrahedral
|
|
stereochemistry removed (issue 1942656)
|
|
- Bond.SetStereo() is no longer exposed to Python (issue 1944575)
|
|
- A few typos in the parameter data for the Crippen logp calculator
|
|
were fixed. Values calculated with this version should be assumed
|
|
to not be backwards compatible with older versions (issue 1950302)
|
|
- Isotope queries are now added correctly (if perhaps not optimally)
|
|
to SMARTS.
|
|
- some drawing-related bugs have been cleared up.
|
|
- A bug in Chem.WedgeMolBonds (used in the drawing code) that was
|
|
causing incorrect stereochemistry in drawn structures was
|
|
fixed. (issue 1965035)
|
|
- A bug causing errors or crashes on Windows with [r<n>] queries was
|
|
fixed. (issue 1968930)
|
|
- A bug in the calculation of TPSA values in molecules that have Hs
|
|
in the graph was fixed. (issue 1969745)
|
|
|
|
## New Features
|
|
- Support for supplying dummy atoms as "[Du]", "[X]", "[Xa]", etc. is
|
|
now considered deprecated. In this release a warning will be
|
|
generated for these forms and in the next release the old form will
|
|
generate errors. Note that the output of dummy atoms has also
|
|
changed: the default output format is now "*", this means that the
|
|
canonical SMILES for molecules containing dummies are no longer
|
|
compatible with the canonical SMILES from previous releases.
|
|
(feature request 186217)
|
|
- Atom and bond query information is now serializable; i.e. query
|
|
molecules can now be pickled and not lose the query
|
|
information. (feature request 1756596)
|
|
- Query features from mol files are now fully supported. (feature
|
|
request 1756962)
|
|
- Conformations now support a dimensionality flag. Dimensionality
|
|
information is now read from mol blocks and TDT files. (feature request
|
|
1906758)
|
|
- Bulk Dice similarity functions have been added for IntSparseIntVect
|
|
and LongSparseIntVect (feature request 1936450)
|
|
- Exceptions are no longer thrown during molecule parsing. Failure in
|
|
molecule parsing is indicated by returning None. Failure to *open* a
|
|
file when reading a molecule throws BadFileExceptions (feature
|
|
requests 1932875 and 1938303)
|
|
- The various similarity functions for BitVects and SparseIntVects
|
|
now take an optional returnDistance argument. If this is provided,
|
|
the functions return the corresponding distance instead of
|
|
similarity.
|
|
- Some additional query information from Mol files is now translated
|
|
when generating SMARTS. Additional queries now translated:
|
|
- number of ring bonds
|
|
- unsaturation queries
|
|
- atom lists are handled better as well
|
|
(feature request 1902466)
|
|
- A new algorithm for generating the bits for topological
|
|
fingerprints has been added. The new approach is a bit quicker and
|
|
more robust than the old, but is not backwards compatible.
|
|
Similarity trends are more or less conserved.
|
|
- The molecule drawing code in Chem.Draw.MolDrawing has been modified
|
|
so that it creates better drawings. A new option for drawing that
|
|
uses the aggdraw graphics library has been added.
|
|
- The RingInfo class supports two new methods: AtomRings() and
|
|
BondRings() that return tuples of tuples with indices of the atoms
|
|
or bonds that make up the molecule's rings.
|
|
|
|
## Other
|
|
- Changes in the underlying boost random-number generator in version
|
|
1.35 of the boost library may have broken backwards compatibility
|
|
of 2D fingerprints generated using the old fingerprinter. It is
|
|
strongly suggested that you regenerate any stored fingerprints (and
|
|
switch to the new fingerprinter if possible). There is an explicit
|
|
test for this in $RDBASE/Code/GraphMol/Fingerprints/test1.cpp
|
|
- The unofficial and very obsolete version of John Torjo's v1
|
|
boost::logging library that was included with the RDKit
|
|
distribution is no longer used. The logging library has been
|
|
replaced with the much less powerful and flexible approach of just
|
|
sending things to stdout or stderr. If and when the logging library
|
|
is accepted into Boost, it will be integrated.
|
|
- The DbCLI tools (in $RDBASE/Projects/DbCLI) generate topological
|
|
fingerprints using both the old and new algorithms (unless the
|
|
--noOldFingerprints option is provided). The default search
|
|
uses the newer fingerprint.
|
|
- The directory $RDBASE/Data/SmartsLib contains a library of sample
|
|
SMARTS contributed by Richard Lewis.
|
|
|
|
|
|
# Release_Jan2008_1
|
|
(Changes relative to Release_Aug2007_1)
|
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## IMPORTANT
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- Bug fixes in the canonicalization algorithm have made it so that
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the canonical SMILES from this version are not compatible with
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those from older versions of the RDKit.
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- Please read the point about dummy atoms in the "## New Features"
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section. It explains a forthcoming change that will affect
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backwards compatibility when dealing with dummy atoms.
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- The build system has been completely changed. Makefiles and Visual
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Studio project files have been removed. See the "## Other" section for
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more info.
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## Acknowledgements:
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- Adrian Schreyer uncovered and reported a number of the bugs fixed
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in this release.
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## Bug Fixes
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- the Recap code no longer generates illegal fragments for
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highly-branched atoms. (issue 1801871)
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- the Recap code no longer breaks cyclic bonds to N
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(issue 1804418)
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- A bug in the kekulization of aromatic nitrogens has been fixed
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(issue 1811276)
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- Bugs in the Atom Type definitions for polar carbons and positive
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nitrogens in BaseFeatures.fdef have been fixed. (issue 1836242)
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- A crash in the sanitization of molecules that only have degree 4
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atoms has been fixed; it now generates an exception. The underlying
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problem with ring-finding in these systems is still present. (issue
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1836576)
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- Mol files for molecules that have more than 99 atoms or bonds are
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no longer incorrectly generated. (issue 1836615)
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- Problems with the sping PIL and PDF canvases have been cleared
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up. The PIL canvas still generates a lot of warnings, but the
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output is correct.
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- The query "rN" is now properly interpreted to be "atom whose
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smallest ring is of size N" in SMARTS queries. It was previously
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interpreted as "atom is in a ring of size N". (issue 1811276)
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This change required that the default feature definitions for
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aromaticity and lumped hydrophobes be updated.
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- The MolSuppliers (SDMolSupplier, TDTMolSupplier, SmilesMolSupplier)
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no longer fail when reading the last element. (issue 1874882)
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- A memory leak in the constructor of RWMols was fixed.
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- A problem causing rapid memory growth with Recap analysis was fixed.
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(issue 1880161)
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- The Recap reactions are no longer applied to charged Ns or Os
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(issue 1881803)
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- Charges, H counts, and isotope information can now be set in
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reactions. (issue 1882749)
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- The stereo codes from double bonds (used for tracking cis/trans)
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are now corrected when MolOps::removeHs is called. (issue 1894348)
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- Various small code cleanups and edge case fixes were done as a
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result of things discovered while getting the VC8 build working.
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## New Features
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- The SparseIntVect class (used by the atom pairs and topological
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torsions) is now implemented in C++.
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- The package $RDKit/Python/Chem/MolDb has been added to help deal
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with molecular databases. (this was intended for the August release
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and overlooked)
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- The module $RDKit/Python/Chem/FastSDMolSupplier has been added to
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provide a fast (at the expense of memory consumption) class for
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working with SD files. (this was intended for the August release
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and overlooked)
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- A new directory $RDKit/Projects has been created to hold things
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that don't really fit in the existing directory structure.
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- The new project $RDKit/Projects/DbCLI has been added. This contains
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command-line scripts for populating molecular database and
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searching them using substructure or similarity.
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- The code for calculating some descriptors has been moved into C++
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in the new module Chem.rdMolDescriptors. The C++ implementation is
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considerably faster than the Python one and should be 100%
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backwards compatible.
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- The MaxMinPicker (in Code/SimDivPickers) supports two new options:
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1) the user can provide a set of initial picks and the algorithm
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will pick new items that are diverse w.r.t. to those
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2) the user can provide a function to calculate the distance matrix
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instead of calculating it in advance. This saves the N^2 step of
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calculating the distance matrix.
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- A new piece of code demo'ing the use of the RDKit to add chemical
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functionality to SQLite is in Code/Demos/sqlite. This will
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eventually move from Demos into Code/sqlite once some more
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functionality has been added and more testing is done.
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- The distance geometry embedding code now supports using random
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initial coordinates for atoms instead of using the eigenvalues of
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the distance matrix. The default behavior is still to use the
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eigenvalues of the distance matrix.
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- The function Recap.RecapDecompose now takes an optional argument
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where the user can specify the minimum size (in number of atoms)
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of a legal fragment. (feature request 180196)
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- Dummy atoms can be expressed using asterixes, per the Daylight spec.
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Dummy atoms are also now legal members of aromatic systems (e.g.
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c1cccc*1 is a legal molecule). Support for supplying dummy atoms
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as "[Du]", "[X]", "[Xa]", etc. is now considered deprecated. In
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the next release a warning will be generated for these forms and
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in the release after that the old form will generate errors. Note
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that the output of dummy atoms will also change: in the next release
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the default output format will be "*".
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(feature request 186217)
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- A proof of concept for doing a SWIG wrapper of RDKit functionality
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has been added in: $RDBASE/Code/Demos/SWIG/java_example. This isn't
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even remotely production-quality; it's intended to demonstrate that
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the wrapping works and isn't overly difficult.
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## Other
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- The full set of tests is now easier to setup and run on new
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machines. (issue 1757265)
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- A new build system, using Boost.Build, has been put into place on
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both the windows and linux sides. The new system does much better
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dependency checking and handles machine-specific stuff a lot
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better. The new system has been tested using Visual Studio 2003,
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Visual Studio Express 2005, Ubuntu 7.10, and RHEL5.
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- The "Getting Started in Python" document has been expanded.
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- There's now an epydoc config file for building the python
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documentation ($RDBASE/Python/epydoc.config).
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# Release_Aug2007_1
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(Changes relative to Release_April2007_1)
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## Bug Fixes
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- operators and SparseIntVects. (issue 1716736)
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- the Mol file parser now calculates cis/trans labels for double
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bonds where the two ends had the same substituents. (issue 1718794)
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- iterator interface to DiscreteValueVects and UniformGrid3D. (issue
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1719831)
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- improper removal of stereochemistry from ring atoms (issue
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1719053)
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- stereochemistry specifications and ring bonds. (issue 1725068)
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- handling of aromatic bonds in template molecules for chemical
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reactions. (issue 1748846)
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- handling of unrecognized atom types in the descriptor calculation
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code. (issue 1749494)
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- ChemicalReactionException now exposed to Python. (issue 1749513)
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- some small problems in topological torsions and atom pairs
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## New Features
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- The Atom Pairs and Topological Torsions code can now provide
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"explanations" of the codes. See $RDBASE/Python/Chem/AtomPairs for
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details.
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- The PointND class has been exposed to Python
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- The "Butina" clustering algorithm [JCICS 39:747-50 (1999)] is now
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available in $RDBase/Python/Ml/Cluster/Butina.py
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- A preliminary implementation of the subshape alignment algorithm is
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available.
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- The free version of MS Visual C++ is now supported.
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- There is better support for queries in MDL mol files. (issue 1756962)
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Specifically: ring and chain bond queries; the not modifier for
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atom lists; R group labels.
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- An EditableMol class is now exposed to Python to allow molecules to
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be easily edited. (issue 1764162)
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- The RingInfo class is now exposed to Python.
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- The replaceSidechains and and replaceCore functions have been added
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in the ChemTransforms library and are exposed to Python as
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Chem.ReplaceSidechains and Chem.ReplaceCore.
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- pickle support added to classes: PointND
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- atoms and bonds now support the HasQuery() and GetSmarts() methods
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from Python.
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## Other
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- Similarity scores can now be calculated from Python in bulk
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(i.e. calculating the similarity between one vector and a list of
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others). This can be substantially faster than calling the
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individual routines multiple times. The relevant functions are
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BulkTanimotoSimilarity, BulkDiceSimilarity, etc.
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- The calculation of AtomPairs and TopologicalTorsions fingerprints
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is now a lot more efficient.
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- Optimization of the Dice metric implementation for SparseIntVects
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- The Visual Studio build files have been moved to the directories
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$RDBASE/Code/Build.VC71 and $RDBASE/Code/Build.VC80. This allows
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simultaneous support of both versions of the system and cleans up
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the source trees a bit.
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- Boost version 1.34 is now supported (testing has been done on 1.34 and 1.34.1).
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- Updates to the "Getting Started" documentation.
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# Release_April2007_1
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(Changes relative to Release_Jan2007_1)
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## Bug Fixes
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- handing of isotope information in SMILES has been fixed
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- "implicit" hydrogens are now added to charged atoms explicitly when
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writing SMILES. (issue 1670149)
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- the 2D->3D code no longer generates non-planar conjugated 4-rings
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(e.g. C1=CC=C1). (issue 1653802)
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- removing explicit hydrogens no longer produces incorrect smiles
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(issue 1694023)
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- bit indices and signature lengths in the AtomPairs code no longer
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being calculated incorrectly. *NOTE* this changes the bits that are
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set, so if you have existing signatures, they will need to be
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regenerated.
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- Fixed a bug causing MolSuppliers to generate incorrect length
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information when a combination of random access and iterator
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interfaces are used. (issue 1702647)
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- Fixed a bug leading to incorrect line numbers in error messages
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from the SDMolSuppler. (issue 1695221)
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## New Features
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- chemical reactions are now supported
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- there is a new entry point into the 2D depictor code,
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compute2DCoordsMimicDistMat(), that attempts to generate 2D
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depictions that are similar to the structure described by the
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distance matrix. There's also a shorthand approach for calling this
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to mimic a 3D structure available as:
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AllChem.GenerateDepictionMatching3DStructure()
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- DiscreteValueVect and UniformGrid3D now support the binary
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operators |, &, +, and -.
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- a reader/writer for TPL files has been added.
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- support has been added for MolCatalogs: hierarchical catalogs that
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can store complete molecules.
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- the protrude distance metric for shapes has been added
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- pickle support added to classes: UniformGrid, DiscreteValueVect,
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Point
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- added the class DataStructs/SparseIntVect to improve performance
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and clarity of the AtomPairs code
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## Other
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- the non-GUI code now supports python2.5; the GUI code may work with
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python2.5, but that has not been tested
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- the Mol and SD file parsers have been sped up quite a bit.
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- the "Crippen" descriptors are now calculated somewhat faster.
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- in-code documentation updates
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- new documentation for beginners in $RDBASE/Docs/Book
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# Release_Jan2007_1
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(Changes relative to Release_Oct2006_1)
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## Bug Fixes
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- zero-atom molecules now trigger an exception
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- dummy atoms are no longer labelled 'Xe'
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- core leak in the mol file writer fixed
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- mol files with multiple charge lines are now correctly parsed
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- a workaround was installed to prevent crashes in the regression
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tests on Windows when using the newest VC++ v7 series compiler.
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(http://sourceforge.net/tracker/index.php?func=detail&aid=1607290&group_id=160139&atid=814650)
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- chirality perception (which requires partial sanitization) is no
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longer done by the MolFileParser when sanitization is switched
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off.
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- Two potential memory corruption problems were fixed (rev's 150 and
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151).
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## New Features
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- optional use of chirality in substructure searches
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- MolWriters can now all take a stream as an argument
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- Chiral terms can now be included in the DistanceGeometry
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embedding.
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## Other
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- $RDBASE/Code/Demos/RDKit/BinaryIO is a demonstration of using
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boost IOStreams and the ROMol pickling mechanism to generate
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highly compressed, random-access files of molecules.
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- the Point code has been refactored
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