2020_09_3 (Q3 2020) Release

Release_2020.09.3

(Changes relative to Release_2020.09.2)

Acknowledgements

Ivan Chernyshov, David Cosgrove, James Gayvert, Mark Mackey, Philippe Schwaller,
Ricardo Rodriguez-Schmidt, Paolo Tosco, Piotr Wawrzyniak, James Gayvert

Bug Fixes:

• Error in ChemAxon SMILES "parsing"
  (github #3320 from IvanChernyshov)
• Error adding PNG metadata when kekulize=False
  (github #3543 from gayverjr)
• rdMolDraw2D, problems during generation of pictures from SMARTS, differences between Cairo and SVG
  (github #3572 from wopozka)
• Get MolDraw2DQt working again
  (github #3592 from greglandrum)
• Scientific notation in SDF V3000 files
  (github #3597 from mark-cresset)
• Fix: add missing python wrappers for MolDraw2DQt
  (github #3613 from greglandrum)
• V3K mol block parser not saving the chiral flag
  (github #3620 from greglandrum)
• Inconsistent metal disconnectors
  (github #3625 from pschwllr)
• Ring stereochemistry not properly removed from N atoms
  (github #3631 from greglandrum)
• moldraw2djs should not close all polygonal paths
  (github #3634 from greglandrum)

2020_09_2 (Q3 2020) Release

Release_2020.09.2

(Changes relative to Release_2020.09.1)

Acknowledgements

David Cosgrove, Steven Kearnes, Dan Nealschneider, Dan Skatov, Jaime
Rodríguez-Guerra, Ricardo Rodriguez-Schmidt, Paolo Tosco, Kazuya Ujihara,
Riccardo Vianello, Shuzhe Wang, 'amateurcat', 'GintasKam'

Bug Fixes:

• Problem with lifetime linkage of mols and conformers
  (github #3492 from amateurcat)
• Traceback when pickling ROMol after BCUT descriptors are calculated
  (github #3511 from d-b-w)
• Fix AUTOCORR2D descriptors
  (github #3512 from ricrogz)
• SDMolSupplier requires several attempts to load a SDF file in Python 3.6/3.7
  (github #3517 from jaimergp)
• Remove accidentally included boost header
  (github #3518 from ricrogz)
• legend_height_ should be preserved after drawing the molecule
  (github #3520 from greglandrum)
• remove the include directive for unused <access/tuptoaster.h> header
  (github #3525 from rvianello)
• C++ build fails when configured with RDKIT_USE_BOOST_SERIALIZATION=OFF
  (github #3529 from rvianello)
• Newest RDKIT version allowing chemically invalid smiles
  (github #3531 from GintasKam)
• Behaviour of generate_aligned_coords for erroneous inputs
  (github #3539 from dskatov)
• Drawing artifacts in draw_to_canvas_with_offset
  (github #3540 from dskatov)
• Add missing methods to remove SubstanceGroup attributes
  (github #3547 from greglandrum)
• Error writing SDF data containing UTF-8 to a StringIO object
  (github #3553 from greglandrum)
• correct handling of amide distances for macrocycles
  (github #3559 from hjuinj)
• Fix example of SmilesToMol
  (github #3575 from kazuyaujihara)
• atom/bond notes handle capital letters incorrectly
  (github #3577 from greglandrum)

2020_09_1 (Q3 2020) Release

Release_2020.09.1

(Changes relative to Release_2020.03.1)

Backwards incompatible changes

• We've added additional allowed valences for Cl (now 1, 3, 5), Br (now 1, 3,
  5), I (now 1, 3, 5), At (now 1, 3, 5), Xe (now 0, 2, 4, 6), and Po (now 2, 4,
  6). Molecules with atoms in the new valence states will no longer generate
  sanitization errors. Note that this has an impact on the chemistry of
  molecules containing 3-valent I and at least one implict H (present 24 times
  in ChEMBL 27): previously this was incorrectly assigned two implicit Hs, now
  it has no implicit Hs.
• Aromaticity perception of molecules like Cc1nnc2n1c1ccccc1n1c(C)nnc12 now
  correctly recognizes the full outer envelope, i.e. the bonds joining the rings
  are now also aromatic.
• FindMCS() may return single atom MCSs, whereas previously it returned an empty
  MCS unless there was at least one commond bond across the input structures.
  So the MCS between molecules CC and CO is now [#6] rather than being null.
• The fontSize()/setFontSize() (FontSize()/SetFontSize()) methods in MolDraw2D
  now work in units of pixels (more or less) instead of the molecule units.
• The Open3DAlign functionality is now in its own separate library - O3AAlign
  in cmake. If you are working in C++ and using O3A functionality, you'll need
  to link against this library as well now.
• Due to improvements in the tautomer enumeration code, the method
  TautomerEnumerator::enumerate now returns a TautomerEnumeratorResult
  object instead of a vector of molecules. Note that if you are iterating over
  the results of a call to enumerate() you shouldn't need to change your code.
  If you want to invoke the old (and deprecated, see below) form from C++, call
  TautomerNumerator::enumerate(mol, nullptr) or explicitly pass a
  boost::dynamic_bitset* to capture the modified atoms.
• The default precision setting for coordgen has been changed. The new default
  was selected to greatly reduce the number of molecules for which it takes a
  very long time to generate coordinates while still producing nice looking
  structures. We may continue to tweak this default value if/when problems
  with it are reported. If you would like to go back to the previous setting, set
  CoordgenParams.minimizerPrecision to CoordgenParams.sketcherStandardPrecision
  when you invoke rdCoordGen.AddCoords()
• Uncharger::uncharge() will now neutralize [Cl,Br,I][O-], [Cl,Br,I](=O)[O-], [Cl,Br,I](=O)(=O)[O-], [Cl,Br,I](=O)(=O)(=O)[O-], [O-]N=N[O-], [N,P](=O)[O-], [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O-])[O-], S(=O)([O-])[O-], S(=O)(=O)([O-])[O-], S(=O)(=O)([O-])OOS(=O)(=O)[O-].
  Previously not all of these inorganic acid counterions were consistently
  neutralized.
• The None value in the RGroupCoreAlignment enum was renamed to NoAlignment
  in both C++ and Python, in order to avoid issues when attempting to access it
  from Python.

Highlights

• There's been another big improvement in the quality of molecule drawings:
  character and font handling is greatly improved thanks to the use of the
  FreeType library
• A new feature has been added to efficiently allow tautomer-insensitive
  substructure search.
• A new, much more accurate, algorithm is available for calculating CIP labels
  on atoms and bonds.
• There's a new rdDeprotect module to allow automatically deprotecting molecules
  before putting them into reactions
• Molecule and reaction metadata can now be added to PNG files generated by
  MolDraw2DCairo

Acknowledgements

Shrey Aryan, Jinserk Baik, Francois Berenger, Cédric Bouysset, David Cosgrove,
Ivan Chernyshov, Guillaume Godin, Manan Goel, Jan H. Jensen, Gareth Jones, Maria
Kadukova, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Joos Kiener, Kenneth
Lum, Joshua Meyers, Rocco Moretti, Paul R Moses, Dan Nealschneider, Jin Pan,
Joann Prescott-Roy, Matthew Robinson, Jaime Rodríguez-Guerra, Ricardo
Rodriguez-Schmidt, Jeff van Santen, Roger Sayle Vincent F. Scalfani Eric Taw,
Ansgar Schuffenhauer, Paolo Tosco, Ivan Tubert-Brohman, Riccardo Vianello,
Rachel Walker, Maciej Wójcikowski, Christopher Zou, daverona, hjuinj,
intrigus-lgtm, autodataming, paconius, sailfish009

Bug Fixes:

• Python tests fail when RDK_BUILD_COMPRESSED_SUPPLIERS is enabled
  (github issue #1888 from greglandrum)
• ResonanceMolSupplier potentially stuck in infinite loop
  (github issue #2597 from tawe141)
• ctest pythonTestDirChem failed
  (github issue #2757 from jinserk)
• Issue with inversion/retention of stereochemistry
  (github issue #2891 from mc-robinson)
• cannot parse reaction SMILES/SMARTS with dative bonds
  (github issue #2954 from greglandrum)
• ResonanceMolSupplier can fail with small maxStructs values
  (github issue #3041 from greglandrum)
• seg fault in ResonanceMolSupplier()
  (github issue #3048 from greglandrum)
• Bug in image rendering of dative bonds
  (github issue #3056 from IvanChernyshov)
• Coordinates from coordgen are not centered around the origin
  (github pull #3058 from DavidACosgrove)
• fix a typo in ScaffoldNetwork/CMakeLists.txt
  (github pull #3060 from greglandrum)
• Bad double bond placement in polycyclic aromatics
  (github issue #3061 from DavidACosgrove)
• SGroups with more than one attachment point are now properly parsed
  (github pull #3072 from greglandrum)
• Reactions should not use strict implicit valence calculations
  (github issue #3097 from mwojcikowski)
• partial reacting atom detection
  (github issue #3119 from thegodone)
• DrawMolecules does not center molecules
  (github issue #3126 from JoshuaMeyers)
• results from coordgen are sometimes not centered
  (github issue #3131 from greglandrum)
• GCC 10.0.1 compile error
  (github issue #3135 from rvianello)
• Memory leak when parsing bad SMILES
  (github issue #3139 from intrigus-lgtm)
• Error breaking StereoBonds in reactions
  (github issue #3147 from mc-robinson)
• MolOps::removeHs() removes hydrides
  (github issue #3150 from jhjensen2)
• Kekulization error from CreateScaffoldNetwork
  (github issue #3153 from greglandrum)
• Fix drawing of N plus
  (github pull #3165 from DavidACosgrove)
• RWMol::clear() does not explicitly clean up SubstanceGroups or StereoGroups
  (github issue #3167 from greglandrum)
• Modifying a molecule should not automatically clear SubstanceGroups
  (github issue #3168 from greglandrum)
• removeHs() should not remove atoms in SubstanceGroups
  (github issue #3169 from greglandrum)
• fix a memory problem detected in malformed SMILES
  (github pull #3171 from greglandrum)
• Python wrapper: SetQuery and ExpandQuery for bonds
  (github pull #3172 from i-tub)
• S-groups: PARENT field should reference index
  (github issue #3175 from greglandrum)
• rdScaffoldNetwork causes segmenation fault upon None molecule
  (github issue #3177 from AnsgarSchuffenhauer)
• fix a small inconsistency in the name of the inchi package
  (github pull #3182 from rvianello)
• Molecule constructed from CXSMILES cannot be translated to SMARTS
  (github issue #3197 from greglandrum)
• Formatting fix of CalcRMS
  (github pull #3203 from chmnk)
• fix the CompressedSDMolSupplier python iterator interface
  (github pull #3204 from rvianello)
• Queries generated from PreprocessReaction cannot be translated to SMARTS
  (github issue #3206 from greglandrum)
• Attachment point info not being read from V2000 mol blocks
  (github issue #3207 from greglandrum)
• Memory Sanitizer fails on molFromPickle on empty file
  (github issue #3211 from intrigus-lgtm)
• Throw exception when reading from stream fails.
  (github pull #3212 from intrigus-lgtm)
• fix molstogridimage on certain fragments/smarts patterns
  (github pull #3217 from bp-kelley)
• Lines in wedge bonds being drawn too closely together
  (github issue #3226 from paconius)
• EnumerateStereochemistry should clear CIP labels
  (github issue #3231 from greglandrum)
• lock CI cairo version to force an install from the rdkit repo
  (github pull #3240 from greglandrum)
• XBCORR and XBHEAD in Sgroups no longer cause parse failures
  (github pull #3242 from greglandrum)
• LINKNODEs are ignored by the CTAB parsers
  (github pull #3247 from greglandrum)
• add GetStringVectProp() to SubstanceGroup class
  (github pull #3251 from greglandrum)
• Envelope aromaticity not detected in complex fused system
  (github issue #3256 from greglandrum)
• Draw.MolsToGridImage repeating atom indices
  (github issue #3258 from greglandrum)
• Atom indices clash with atom symbols in small pictures.
  (github issue #3262 from DavidACosgrove)
• MinimalLib Dockerfile is broken at HEAD
  (github issue #3267 from skearnes)
• Fixes #2757
  (github pull #3268 from greglandrum)
• RGroupDecomposition restructuring
  (github pull #3270 from bp-kelley)
• Get PPC builds working
  (github pull #3285 from greglandrum)
• ScaffoldNetwork not in C# wrappers
  (github pull #3289 from jones-gareth)
• bonds with "either' stereo cannot be read from JSON
  (github pull #3290 from greglandrum)
• Small bug fixes and cleanups from fuzz testing
  (github pull #3299 from greglandrum)
• DrawOptions: bondLineWidth behaving differently since 2020 versions
  (github issue #3305 from kienerj)
• Not possible to copy SubstanceGroups in Python
  (github issue #3312 from greglandrum)
• Stereochemistry perception getting confused by a bad drawing.
  (github issue #3314 from greglandrum)
• SubstanceGroups should not be written with quotes around missing fields
  (github issue #3315 from greglandrum)
• SetDoubleBondNeighborDirections() not overwriting existing bond directions
  (github issue #3322 from greglandrum)
• AdjustQueryParameters.adjustSingleBondsBetweenAromaticAtoms does not modify ring bonds
  (githu...

2020_09_1b1 (Q3 2020) Release

Release_2020.09.1

(Changes relative to Release_2020.03.1)

Backwards incompatible changes

• FindMCS() may return single atom MCSs, whereas previously it returned an empty
  MCS unless there was at least one commond bond across the input structures.
  So the MCS between molecules CC and CO is now [#6] rather than being null.
• The fontSize()/setFontSize() (FontSize()/SetFontSize()) methods in MolDraw2D
  now work in units of pixels (more or less) instead of the molecule units.
• The Open3DAlign functionality is now in its own separate library - O3AAlign
  in cmake. If you are working in C++ and using O3A functionality, you'll need
  to link against this library as well now.
• Due to improvements in the tautomer enumeration code, the method
  TautomerEnumerator::enumerate now returns a TautomerEnumeratorResult
  object instead of a vector of molecules. Note that if you are iterating over
  the results of a call to enumerate() you shouldn't need to change your code.
  If you want to invoke the old (and deprecated, see below) form from C++, call
  TautomerNumerator::enumerate(mol, nullptr) or explicitly pass a
  boost::dynamic_bitset* to capture the modified atoms.
• The default precision setting for coordgen has been changed. The new default
  was selected to greatly reduce the number of molecules for which it takes a
  very long time to generate coordinates while still producing nice looking
  structures. We may continue to tweak this default value if/when problems
  with it are reported. If you would like to go back to the previous setting, set
  CoordgenParams.minimizerPrecision to CoordgenParams.sketcherStandardPrecision
  when you invoke rdCoordGen.AddCoords()
• Uncharger::uncharge() will now neutralize [Cl,Br,I][O-], [Cl,Br,I](=O)[O-], [Cl,Br,I](=O)(=O)[O-], [Cl,Br,I](=O)(=O)(=O)[O-], [O-]N=N[O-], [N,P](=O)[O-], [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O-])[O-], S(=O)([O-])[O-], S(=O)(=O)([O-])[O-], S(=O)(=O)([O-])OOS(=O)(=O)[O-].
  Previously not all of these inorganic acid counterions were consistently
  neutralized.
• We've added additional allowed valences for Cl (now 1, 3, 5), Br (now 1, 3,
  5), I (now 1, 3, 5), At (now 1, 3, 5), Xe (now 0, 2, 4, 6), and Po (now 2, 4,
  6). Molecules with atoms in the new valence states will no longer generate
  sanitization errors

Highlights

• There's been another big improvement in the quality of molecule drawings: character
  and font handling is greatly improved thanks to the use of the FreeType library
• A new feature has been added to efficiently allow tautomer-insensitive
  substructure search.
• A new, much more accurate, algorithm is available for calculating CIP labels on
  atoms and bonds.
• There's a new rdDeprotect module to allow automatically deprotecting molecules
  before putting them into reactions

Acknowledgements

Shrey Aryan, Jinserk Baik, Francois Berenger, Cédric Bouysset, David Cosgrove,
Ivan Chernyshov, Guillaume Godin, Manan Goel, Jan H. Jensen, Gareth Jones, Maria
Kadukova, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Joos Kiener, Kenneth
Lum, Joshua Meyers, Paul R Moses, Dan Nealschneider, Jin Pan, Joann
Prescott-Roy, Matthew Robinson, Jaime Rodríguez-Guerra, Ricardo
Rodriguez-Schmidt, Jeff van Santen, Roger Sayle Vincent F. Scalfani Eric Taw,
Ansgar Schuffenhauer, Paolo Tosco, Ivan Tubert-Brohman, Riccardo Vianello,
Rachel Walker, Maciej Wójcikowski, Christopher Zou, daverona, hjuinj,
intrigus-lgtm, autodataming, paconius

Bug Fixes:

• Python tests fail when RDK_BUILD_COMPRESSED_SUPPLIERS is enabled
  (github issue #1888 from greglandrum)
• ResonanceMolSupplier potentially stuck in infinite loop
  (github issue #2597 from tawe141)
• ctest pythonTestDirChem failed
  (github issue #2757 from jinserk)
• Issue with inversion/retention of stereochemistry
  (github issue #2891 from mc-robinson)
• cannot parse reaction SMILES/SMARTS with dative bonds
  (github issue #2954 from greglandrum)
• ResonanceMolSupplier can fail with small maxStructs values
  (github issue #3041 from greglandrum)
• seg fault in ResonanceMolSupplier()
  (github issue #3048 from greglandrum)
• Bug in image rendering of dative bonds
  (github issue #3056 from IvanChernyshov)
• Coordinates from coordgen are not centered around the origin
  (github pull #3058 from DavidACosgrove)
• fix a typo in ScaffoldNetwork/CMakeLists.txt
  (github pull #3060 from greglandrum)
• Bad double bond placement in polycyclic aromatics
  (github issue #3061 from DavidACosgrove)
• SGroups with more than one attachment point are now properly parsed
  (github pull #3072 from greglandrum)
• Reactions should not use strict implicit valence calculations
  (github issue #3097 from mwojcikowski)
• partial reacting atom detection
  (github issue #3119 from thegodone)
• DrawMolecules does not center molecules
  (github issue #3126 from JoshuaMeyers)
• results from coordgen are sometimes not centered
  (github issue #3131 from greglandrum)
• GCC 10.0.1 compile error
  (github issue #3135 from rvianello)
• Memory leak when parsing bad SMILES
  (github issue #3139 from intrigus-lgtm)
• Error breaking StereoBonds in reactions
  (github issue #3147 from mc-robinson)
• MolOps::removeHs() removes hydrides
  (github issue #3150 from jhjensen2)
• Kekulization error from CreateScaffoldNetwork
  (github issue #3153 from greglandrum)
• Fix drawing of N plus
  (github pull #3165 from DavidACosgrove)
• RWMol::clear() does not explicitly clean up SubstanceGroups or StereoGroups
  (github issue #3167 from greglandrum)
• Modifying a molecule should not automatically clear SubstanceGroups
  (github issue #3168 from greglandrum)
• removeHs() should not remove atoms in SubstanceGroups
  (github issue #3169 from greglandrum)
• fix a memory problem detected in malformed SMILES
  (github pull #3171 from greglandrum)
• Python wrapper: SetQuery and ExpandQuery for bonds
  (github pull #3172 from i-tub)
• S-groups: PARENT field should reference index
  (github issue #3175 from greglandrum)
• rdScaffoldNetwork causes segmenation fault upon None molecule
  (github issue #3177 from AnsgarSchuffenhauer)
• fix a small inconsistency in the name of the inchi package
  (github pull #3182 from rvianello)
• Molecule constructed from CXSMILES cannot be translated to SMARTS
  (github issue #3197 from greglandrum)
• Formatting fix of CalcRMS
  (github pull #3203 from chmnk)
• fix the CompressedSDMolSupplier python iterator interface
  (github pull #3204 from rvianello)
• Queries generated from PreprocessReaction cannot be translated to SMARTS
  (github issue #3206 from greglandrum)
• Attachment point info not being read from V2000 mol blocks
  (github issue #3207 from greglandrum)
• Memory Sanitizer fails on molFromPickle on empty file
  (github issue #3211 from intrigus-lgtm)
• Throw exception when reading from stream fails.
  (github pull #3212 from intrigus-lgtm)
• fix molstogridimage on certain fragments/smarts patterns
  (github pull #3217 from bp-kelley)
• Lines in wedge bonds being drawn too closely together
  (github issue #3226 from paconius)
• EnumerateStereochemistry should clear CIP labels
  (github issue #3231 from greglandrum)
• lock CI cairo version to force an install from the rdkit repo
  (github pull #3240 from greglandrum)
• XBCORR and XBHEAD in Sgroups no longer cause parse failures
  (github pull #3242 from greglandrum)
• LINKNODEs are ignored by the CTAB parsers
  (github pull #3247 from greglandrum)
• add GetStringVectProp() to SubstanceGroup class
  (github pull #3251 from greglandrum)
• Envelope aromaticity not detected in complex fused system
  (github issue #3256 from greglandrum)
• Draw.MolsToGridImage repeating atom indices
  (github issue #3258 from greglandrum)
• Atom indices clash with atom symbols in small pictures.
  (github issue #3262 from DavidACosgrove)
• MinimalLib Dockerfile is broken at HEAD
  (github issue #3267 from skearnes)
• Fixes #2757
  (github pull #3268 from greglandrum)
• RGroupDecomposition restructuring
  (github pull #3270 from bp-kelley)
• Get PPC builds working
  (github pull #3285 from greglandrum)
• ScaffoldNetwork not in C# wrappers
  (github pull #3289 from jones-gareth)
• bonds with "either' stereo cannot be read from JSON
  (github pull #3290 from greglandrum)
• Small bug fixes and cleanups from fuzz testing
  (github pull #3299 from greglandrum)
• DrawOptions: bondLineWidth behaving differently since 2020 versions
  (github issue #3305 from kienerj)
• Not possible to copy SubstanceGroups in Python
  (github issue #3312 from greglandrum)
• Stereochemistry perception getting confused by a bad drawing.
  (github issue #3314 from greglandrum)
• SubstanceGroups should not be written with quotes around missing fields
  (github issue #3315 from greglandrum)
• SetDoubleBondNeighborDirections() not overwriting existing bond directions
  (github issue #3322 from greglandrum)
• AdjustQueryParameters.adjustSingleBondsBetweenAromaticAtoms does not modify ring bonds
  (github issue #3325 from greglandrum)
• Fixes for aromatic bond fuzzy queries
  (github pull #3328 from jones-gareth)
• lock sphinx version in CI due to problem with v3.2.0
  (github pull #3332 from greglandrum)
• Remove deprecated Sphinx options
  (github pull #3335 from greglandrum)
• more bug fixes and cleanups from fuzz testing
  (github pull #3339 from greglandrum)
• unspecified branch bonds in SMARTS don't have aromaticity set
  (github issue #3342 from greglandrum)
• Incorrect resonance structures in presence of dative bonds
  (github issue #3349 from IvanChernyshov)
• Converting atoms with high radical counts to InChI generates incorrect results
  (github issue #3365 from greglandrum)
• Replace ...

2020_03_6 (Q1 2020) Release

Release_2020.03.6

(Changes relative to Release_2020.03.5)

Acknowledgements:

Brian Kelley, Kenneth Lum, Paolo Tosco

Bug Fixes:

• unspecified branch bonds in SMARTS don't have aromaticity set
  (github #3342 from greglandrum)
• Converting atoms with high radical counts to InChI generates incorrect results
  (github #3365 from greglandrum)
• Replace fill-opacity= with fill-opacity: in MolDraw2DSVG and tests
  (github #3368 from lummyk)
• Fixes a bug in AddHs() involving sp2 centers with degree 1
  (github #3383 from ptosco)
• Information about charges and isotopes lost when calling AdjustQueryProperties
  (github #3388 from greglandrum)
• prepareMolForDrawing() incorrectly adds chiral Hs if no ring info is present
  (github #3392 from greglandrum)
• CXSMILES parser should not set atom maps for attachment points
  (github #3393 from greglandrum)
• Doing a match of a recursive smarts leaves traces of the previous match
  (github #3403 from bp-kelley)
• Recursive smarts cannot be used in the core for rgroup decomposition
  (github #3404 from bp-kelley)
• V3K mol blocks with no atoms fail to parse
  (github #3413 from greglandrum)
• Problem parsing SGroup data containing ""
  (github #3415 from greglandrum)

2020_03_5 (Q1 2020) Release

Release_2020.03.5

(Changes relative to Release_2020.03.5)

Acknowledgements:

Jinserk Baik, Gareth Jones, Steven Kearnes, Jaime Rodriguez-Guerra

Bug Fixes:

• ctest pythonTestDirChem failed
  (github #2757 from jinserk)
• MinimalLib Dockerfile is broken at HEAD
  (github #3267 from skearnes)
• Get PPC builds working
  (github #3285 from greglandrum)
• ScaffoldNetwork not in C# wrappers
  (github #3289 from jones-gareth)
• bonds with "either' stereo cannot be read from JSON
  (github #3290 from greglandrum)
• Not possible to copy SubstanceGroups in Python
  (github #3312 from greglandrum)
• Stereochemistry perception getting confused by a bad drawing.
  (github #3314 from greglandrum)
• SubstanceGroups should not be written with quotes around missing fields
  (github #3315 from greglandrum)

2020_03_4 (Q1 2020) Release

Release_2020.03.4

(Changes relative to Release_2020.03.3)

Acknowledgements:

David Cosgrove, Brian Kelley, Ricardo Rodriguez Schmidt, 'paconius'

Bug Fixes:

• Attachment point info not being read from V2000 mol blocks
  (github #3207 from greglandrum)
• Lines in wedge bonds being drawn too closely together
  (github #3226 from paconius)
• EnumerateStereochemistry should clear CIP labels
  (github #3231 from greglandrum)
• lock CI cairo version to force an install from the rdkit repo
  (github #3240 from greglandrum)
• XBCORR and XBHEAD in Sgroups no longer cause parse failures
  (github #3242 from greglandrum)
• LINKNODEs are ignored by the CTAB parsers
  (github #3247 from greglandrum)
• add GetStringVectProp() to SubstanceGroup class
  (github #3251 from greglandrum)
• Draw.MolsToGridImage repeating atom indices
  (github #3258 from greglandrum)

2020_03_3 (Q1 2020) Release

Release_2020.03.3

(Changes relative to Release_2020.03.2)

Acknowledgements:

David Cosgrove, Manan Goel, Jan H. Jensen, Brian Kelley, Matthew Robinson,
Roger Sayle, Ansgar Schuffenhauer, Ivan Tubert-Brohman, Riccardo Vianello,

Bug Fixes:

• Python tests fail when RDK_BUILD_COMPRESSED_SUPPLIERS is enabled
  (github #1888 from greglandrum)
• SGroups with more than one attachment point are now properly parsed
  (github #3072 from greglandrum)
• GCC 10.0.1 compile error
  (github #3135 from rvianello)
• Error breaking StereoBonds in reactions
  (github #3147 from mc-robinson)
• MolOps::removeHs() removes hydrides
  (github #3150 from jhjensen2)
• Kekulization error from CreateScaffoldNetwork
  (github #3153 from greglandrum)
• Fix drawing of N plus
  (github #3165 from DavidACosgrove)
• RWMol::clear() does not explicitly clean up SubstanceGroups or StereoGroups
  (github #3167 from greglandrum)
• Modifying a molecule should not automatically clear SubstanceGroups
  (github #3168 from greglandrum)
• removeHs() should not remove atoms in SubstanceGroups
  (github #3169 from greglandrum)
• fix a memory problem detected in malformed SMILES
  (github #3171 from greglandrum)
• Python wrapper: SetQuery and ExpandQuery for bonds
  (github #3172 from i-tub)
• S-groups: PARENT field should reference index
  (github #3175 from greglandrum)
• rdScaffoldNetwork causes segmenation fault upon None molecule
  (github #3177 from AnsgarSchuffenhauer)
• fix a small inconsistency in the name of the inchi package
  (github #3182 from rvianello)
• Molecule constructed from CXSMILES cannot be translated to SMARTS
  (github #3197 from greglandrum)
• Queries generated from PreprocessReaction cannot be translated to SMARTS
  (github #3206 from greglandrum)

2020_03_2 (Q1 2020) Release

Release_2020.03.2
(Changes relative to Release_2020.03.1)

Acknowledgements:

Ivan Chernyshov, David Cosgrove, Guillaume Godin, Eisuke Kawashima, Brian
Kelley, Joshua Meyers, Paolo Tosco, Maciej Wójcikowski, intrigus-lgtm

Bug Fixes:

• cannot parse reaction SMILES/SMARTS with dative bonds
  (github #2954 from greglandrum)
• ResonanceMolSupplier can fail with small maxStructs values
  (github #3041 from greglandrum)
• seg fault in ResonanceMolSupplier()
  (github #3048 from greglandrum)
• Bug in image rendering of dative bonds
  (github #3056 from IvanChernyshov)
• Coordinates from coordgen are not centered around the origin
  (github #3058 from DavidACosgrove)
• fix a typo in ScaffoldNetwork/CMakeLists.txt
  (github #3060 from greglandrum)
• Bad double bond placement in polycyclic aromatics
  (github #3061 from DavidACosgrove)
• Remove unnecessary files
  (github #3065 from e-kwsm)
• SGroups with more than one attachment point are now properly parsed
  (github #3072 from greglandrum)
• Reactions should not use strict implicit valence calculations
  (github #3097 from mwojcikowski)
• partial reacting atom detection
  (github #3119 from thegodone)
• DrawMolecules does not center molecules
  (github #3126 from JoshuaMeyers)
• results from coordgen are sometimes not centered
  (github #3131 from greglandrum)
• Memory leak when parsing bad SMILES
  (github #3139 from intrigus-lgtm)

2020_03_1 (Q1 2020) Release

Release_2020.03.1

(Changes relative to Release_2019.09.1)

Backwards incompatible changes

• Searches for equal molecules (i.e. mol1 @= mol2) in the PostgreSQL cartridge
  now use the do_chiral_sss option. So if do_chiral_sss is false (the
  default), the molecules CC(F)Cl and C[C@H](F)Cl will be considered to be equal.
  Previously these molecules were always considered to be different.
• Attempting to create a MolSupplier from a filename pointing to an empty file,
  a file that does not exist or sometihing that is not a standard file (i.e.
  something like a directory) now generates an exception.
• The cmake option RDK_OPTIMIZE_NATIVE has been renamed to RDK_OPTIMIZE_POPCNT

Highlights:

• The drawings generated by the MolDraw2D objects are now significantly improved
  and can include simple atom and bond annotations (#2931 and #3010)
• An initial implementation of a modified scaffold network algorithm is now
  available (#2911)
• A few new descriptor/fingerprint types are available - BCUTs (#2957), Morse
  atom fingerprints (#1773), Coulomb matrices (#2993), and MHFP and SECFP
  fingerprints (#2643)
• There is a new, and greatly improved, version of the RDKit Cookbook (#2884)
• There is a new version (v3) of the ETKDG conformer generator along with
  optional new terms for handling small rings and macrocyles (http://doi.org/dqnh) (#2999)

Acknowledgements:

Marcel Baltruschat, Jason Biggs, Eliane Briand, Ben Cornett, David Cosgrove,
Andrew Dalke, Tim Dudgeon, Zhenting Gao, Guillaume Godin, Manan Goel, Gareth
Jones, Zachary Kaplan, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Maxim
Koltsov, Franziska Kruger, Mieszko Manijak, Dan Nealschneider, Daniil
Polykovskiy, Daniel Probst, Sereina Riniker, Matthew Robinson, Steve Roughley,
Kevin Ryan, Vincent F. Scalfani, Ricardo Rodriguez Schmidt, Rim Shayakhmetov,
Aryan Shrey, Nik Stiefl, Matt Swain, Paolo Tosco, Wiep van der Toorn, Riccardo
Vianello, Shuzhe Wang, Piotr Wawrzyniak, Hsiao Yi, 'jasad1',
'luancarvalhomartins'

Bug Fixes:

• Mol rendering within DataFrames in a Jupyter Notebook is broken with Pandas 0.25.1
  (github issue #2673 from mrcblt)
• Removed RDKIT_SIMDIVPICKERS_EXPORT
  (github pull #2740 from ptosco)
• • enable building RDKitRingDecomposerLib.dll under Windows
    (github pull #2742 from ptosco)
• Do a windows DLL build as part of the Azure DevOps setup
  (github pull #2743 from greglandrum)
• Fix data race in sascorer.py
  (github pull #2744 from skearnes)
• Uncharger not properly setting explicit/implicit H count
  (github issue #2749 from greglandrum)
• MSVC compile error: MolHash scoped enum cannot be redeclared as unscoped
  (github issue #2752 from mcs07)
• Molecules whose Y size is very small won't display as SVG
  (github issue #2762 from ptosco)
• Make the cartridge tests work with PostgreSQL 12
  (github pull #2767 from greglandrum)
• Salt stripper should consider bond matches as well as atom matches
  (github pull #2768 from greglandrum)
• Bismuth should count as an early element
  (github issue #2775 from greglandrum)
• addHs() fails on atoms with "bad" valences
  (github issue #2782 from greglandrum)
• Element symbol lookup for some transuranics returns incorrect results
  (github issue #2784 from LeanAndMean)
• [cartridge] molecular equality should use do_chiral_sss setting
  (github issue #2790 from greglandrum)
• uncharger removes Hs from carbocations instead of adding them
  (github issue #2792 from greglandrum)
• Fix build without boost serialization library
  (github pull #2796 from maksbotan)
• Using SetBoundsMat significantly slows down conformer generation process.
  (github issue #2800 from hjuinj)
• rdkit.Ched.rdFMCS.FindMCS generates invalid smarts
  (github issue #2801 from luancarvalhomartins)
• Remove confId from *FFOptimizeMoleculeConfs Python docs
  (github issue #2805 from ptosco)
• Hybridization queries on dummy atoms not written properly to SMARTS
  (github issue #2814 from greglandrum)
• Charge range queries not properly written to SMARTS
  (github issue #2815 from greglandrum)
• RDKit segfaults in MMFFOptimizeMoleculeConfs()
  (github issue #2820 from ptosco)
• Trusted Smiles holder doesn't handle ring queries
  (github issue #2830 from bp-kelley)
• Fix windows substructure crash
  (github pull #2836 from greglandrum)
• Fix YAeHMOP build
  (github pull #2838 from ptosco)
• testGithub2245 in testPickers.cpp occasionally fails
  (github issue #2839 from ptosco)
• add define for RDK_USE_BOOST_SERIALIZATION
  (github pull #2859 from greglandrum)
• fix start/end atoms when wedging bonds
  (github pull #2861 from greglandrum)
• Fixes the size of the reduced charge matrix from eHT calculations
  (github pull #2864 from greglandrum)
• Dev/pvs studio cleanups2
  (github pull #2877 from greglandrum)
• segfault in MaeMolSupplier
  (github issue #2881 from greglandrum)
• update maven url in build system
  (github pull #2889 from greglandrum)
• EnumerateStereoisomers cannot handle STEREOANY bonds
  (github issue #2890 from ricrogz)
• Update one of the cartridge tests that got missed
  (github pull #2894 from greglandrum)
• acepentalene aromaticity perception
  (github issue #2895 from adalke)
• New Similarity Maps drawing code Java Wrappers non-functional
  (github issue #2896 from sroughley)
• Fix to allow multistructure images in Java/C# and use MCS for c# wrapper
  (github pull #2898 from jones-gareth)
• Remove bogus URFLib library
  (github pull #2900 from greglandrum)
• java wrapper build cleanups
  (github pull #2901 from greglandrum)
• SMARTS parser fails on high-numbered ring closures in branches
  (github issue #2909 from greglandrum)
• patch to make PandasTools tests pass with pandas v0.22
  (github pull #2913 from greglandrum)
• fix doctest problem with Pandas v1.0
  (github pull #2918 from greglandrum)
• Build with -D RDK_BUILD_COORDGEN_SUPPORT=OFF includes a test case that depends on MaeMolSupplier
  (github issue #2929 from rvianello)
• MinimalLib: get_stereo_tags() should also return unspecified centers
  (github issue #2936 from greglandrum)
• Fix regression introduced by e245349
  (github pull #2945 from cornett)
• Avoid data race warning in SmilesParse.cpp
  (github pull #2946 from skearnes)
• Empty molecule has non-zero LabuteASA
  (github issue #2948 from jasondbiggs)
• Fix a problem with aromatic heteroatom tautomer enumeration
  (github pull #2952 from greglandrum)
• Molecule properties not retained with MolStandardize.rdMolStandardize.Cleanup()
  (github issue #2965 from ZacharyKaplan)
• Fix build without boost serialization.
  (github pull #2972 from ricrogz)
• RDKFuncs.chargeParent() core dumps when standardization is skipped
  (bithub issue #2970 from tdudgeon)
• fix a typo in the scaffold network wrappers and add some tests
  (github pull #2982 from greglandrum)
• Tautomer enumeration should remove stereo in all tautomers
  (github issue #2990 from greglandrum)
• Segmentation fault on EmbedMolecule
  (github issue #3019 from shayakhmetov)
• Removed dllexport from a function that lives in the anonymous namespace
  (github pull #3027 from ptosco)

New Features and Enhancements:

• Morse atom fingerprint
  (github pull #1773 from thegodone)
• Allow serializing coordinates as doubles
  (github issue #2510 from danpol)
• Rework MaeMolSupplier, fix #2617
  (github pull #2620 from ricrogz)
• Implementation of MHFP and SECFP Fingerprints
  (github pull #2643 from daenuprobst)
• MatchFusedRings does not imply CompleteRingsOnly anymore
  (github pull #2748 from ptosco)
• Improvements to JS wrappers
  (github pull #2751 from greglandrum)
• Fix installed header directory structure
  (github pull #2754 from ricrogz)
• Add doRandom to the header docs
  (github pull #2756 from bp-kelley)
• Add queryMol data member to MCSResult
  (github pull #2759 from ptosco)
• Add functions to enable/disable the substructure matching monkey patching in IPythonConsole.py
  (github issue #2786 from greglandrum)
• Add a function to assign chiral tags from sss atom parity
  (github issue #2823 from ptosco)
• Support MRV_IMPLICIT_H S groups when reading Mol blocks
  (github issue #2829 from greglandrum)
• Unset executable flag
  (github pull #2833 from e-kwsm)
• Remove O(N) behavior of getNumBonds
  (github pull #2847 from bp-kelley)
• Feature proposal: add remove_stereochemistry=False flag for RemoveHs()
  (github issue #2848 from shayakhmetov)
• Expose SubstructLibrary serialization stream
  (github pull #2853 from bp-kelley)
• Fix typo
  (github pull #2862 from e-kwsm)
• Rename RDK_OPTIMIZE_NATIVE to RDK_OPTIMIZE_POPCNT
  (github pull #2865 from ElianeBriand)
• Update Draw.MolToImage() and Draw.MolToFile() to use the new drawing code
  (github pull #2866 from greglandrum)
• Improve PostgreSQL cartridge install documentation
  (github pull #2870 from yellowBirdy)
• Fixes #2858
  (github pull #2871 from greglandrum)
• Add a cartridge test to the azure devops config
  (github pull #2873 from greglandrum)
• Add a new Cookbook v2 to the RDKit docs
  (github pull #2884 from vfscalfani)
• Add MolVS tautomer canonicalization
  (github pull #2886 from greglandrum)
• add a convenience function for RGD--Pandas integration
  (github pull #2887 from greglandrum)
• run clang-tidy with readability-braces-around-statements
  (github pull #2899 from greglandrum)
• Allow RDProps::clearProp to succeed even if the prop doesn't exist
  (github issue #2910 from greglandrum)
• Add a scaffold network implementation
  (github pull #2911 from greglandrum)
• cleanup of the SMILES/SMARTS parsing and writing code
  (github pull #2912 from greglandrum)
• Add _ctab, _mol2, _pdb to allow direct mol construction from strings
  (github issue...