Changelog for librdkit1-2018_03_4-3.1.x86_64.rpm :
Fri Sep 14 14:00:00 2018 aeszterAATTgwdg.de
- update to rdkit 2018_03_4

Mon Mar 13 13:00:00 2017 dhallAATTwustl.edu
- update to rdkit 2016_09_4

Thu Dec 1 13:00:00 2016 dhallAATTwustl.edu
- update to rdkit 2016_09_2

Tue Jul 26 14:00:00 2016 dhallAATTwustl.edu
- update to rdkit 2016_03_3

Tue Jul 12 14:00:00 2016 dhallAATTwustl.edu
- update to rdkit 2016_03_2

Tue Apr 19 14:00:00 2016 dhallAATTwustl.edu
- add 64-bit extension for ppc64le and aarch64

Tue Apr 19 14:00:00 2016 dhallAATTwustl.edu
- turn off native optimization

Tue Apr 19 14:00:00 2016 dhallAATTwustl.edu
- update to rdkit 2016_03_1

Thu Nov 5 13:00:00 2015 dhallAATTwustl.edu
- update to rdkit 2015_09_1beta1

Mon Jan 5 13:00:00 2015 dhallAATTwustl.edu
- update to rdkit_2014_09_2

*
*
*
*
*
* 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)

Thu Oct 30 13:00:00 2014 dhallAATTwustl.edu
- update to rdkit_2014_09_1

*
*
*
*
*
* 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`

Wed Jun 25 14:00:00 2014 dhallAATTwustl.edu
- update to rdkit_2014_03_1

Tue Apr 1 14:00:00 2014 dhallAATTwustl.edu
- update to rdkit_2013_09_2

Sat Aug 3 14:00:00 2013 dhallAATTwustl.edu
- update to rdkit_2013_06_01

*
*
*
*
*
* 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:
drhallAATTtui:~/myosc/home:cowsandmilk/rdkit ☭ head -n 200 rdkit-2013_06_1/ReleaseNotes.txt

*
*
*
*
*
* 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

Sun Jan 13 13:00:00 2013 dhallAATTwustl.edu
- update to rdkit_2012_12_1
Acknowledgements:
Andrew Dalke, James Davidson, Robert Feinstein, Nikolas Fechner,
Nicholas Firth, Markus Hartenfeller, Jameed Hussain, Thorsten Meinl,
Sereina Riniker, Roger Sayle, 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[CAATTH]1CC[CAATTH](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)
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,
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.

Sat Sep 29 14:00:00 2012 drhallAATTbu.edu
- test rdkit_2012_09_1beta1

Wed Jul 11 14:00:00 2012 dhallAATTwustl.edu
- updated to rdkit_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.
- Due to changes in the cartridge indexes on molecule and bitvector
fingerprint columns will need to be rebuilt.
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.

Fri Apr 13 14:00:00 2012 dhallAATTwustl.edu
- updated to rdkit_2012_03_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)
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
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

Tue Jan 17 13:00:00 2012 dhallAATTwustl.edu
- updated to rdkit_2011_12_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=[SAATT](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.

Mon Oct 10 14:00:00 2011 dhallAATTwustl.edu
- build in support for inchi
- build in support for compressed files

Sun Oct 9 14:00:00 2011 dhallAATTwustl.edu
- updated to rdkit 2011_09_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.
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

Sun Oct 9 14:00:00 2011 dhallAATTwustl.edu
- modify spec file to build for i586

Fri Aug 19 14:00:00 2011 dhallAATTwustl.edu
- Updated to rdkit 2011_06_1
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())

Fri Apr 29 14:00:00 2011 dhallAATTwustl.edu
- Updated to version 2011_03_2

Tue Mar 29 14:00:00 2011 dhallAATTwustl.edu
-initial checkin