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ReleaseNotes.txt
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****** Release_2015.03.1 *******
(Changes relative to Release_2014.09.2)
!!!!!! IMPORTANT !!!!!!
Acknowledgements: David Cosgrove
Bug Fixes:
New Features:
New Database Cartridge Features:
New Java Wrapper Features:
Deprecated modules (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superseded by the new drawing code in $RDBASE/Code/GraphMol and will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.
- rdkit/Dbase/Pubmed
Removed modules:
Contrib updates:
Other:
****** 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