Assets 2

Release_2018.03.4

(Changes relative to Release_2018.03.3)

Acknowledgements:

Brian Kelley, Noel O'Boyle, Rim Shayakhmetov, Jon Sorenson

Bug Fixes:

  • Possibly incorrect aromatic SMILES generated for structure
    (github issue #1928 from baoilleach)
  • Update KNIME URLs in overview.md
    (github pull #1966 from greglandrum)
  • CXN extended SMILES labels are not applied to the correct atom in SMILES
    with explicit H
    (github issue #1928 from baoilleach)
  • MolFromSmarts MolToSmarts fails to roundtrip on patterns with chirality
    (github issue #1985 from bp-kelley)
  • RemoveHs not properly updating double bond stereoatoms
    (github issue #1990 from shayakhmetov)
  • Error while parsing empty atom list in Mol files.
    (github issue #2000 from drkeoni)

@greglandrum greglandrum released this Jul 18, 2018 · 8 commits to Release_2018_03 since this release

Assets 2

Release_2018.03.3

(Changes relative to Release_2018.03.2)

Acknowledgements:

Thomas Blaschke, Brian Kelley, Josh Meyers, Dan Nealschneider, Noel O'Boyle,
Jon Sorenson, Paulo Tosco, 'jaechanglim'

Bug Fixes:

  • R-group Decomposition: allow H replacements when matchOnlyAtRgroups is set
    (github pull #1871 from bp-kelley)
  • Fixes locale handling on Windows
    (github pull #1892 from ptosco)
  • get the pandas tests working with pandas 0.23
    (github pull #1896 from greglandrum)
  • Fix curl fallback for downloading files
    (github pull #1904 from d-b-w)
  • Bond stereo information not output to SMARTS
    (github issue #1906 from greglandrum)
  • Library .so names missing RDKit?
    (github issue #1913 from baoilleach)
  • Negated atom number queries in SMARTS should not set atomic number of query atom
    (github issue #1920 from greglandrum)
  • memory leak in Get3DDistanceMatrix
    (github issue #1924 from jaechanglim)
  • Atom with bond to itself is accepted by the SMILES parser.
    (github issue #1925 from tblaschke)
  • Using the coordgen library seems to cause a seg fault
    (github issue #1929 from JoshuaMeyers)
  • Aromaticity failure in 7-ring with charged radical carbon
    (github issue #1936 from bp-kelley)
  • Fix embarassing bug, check the counter each iteration
    (github pull #1939 from bp-kelley)
  • RuntimeError when importing rdkit.Chem.Descriptors with Python 3.7
    (github issue #1948 from drkeoni)
  • Query features in products of rxn files not properly handled
    (github issue #1950 from greglandrum)
  • ReactionToSmarts broken for multi-component templates
    (github issue #1955 from bp-kelley)

@greglandrum greglandrum released this Jun 4, 2018 · 25 commits to Release_2018_03 since this release

Assets 2

Release_2018.03.2

(Changes relative to Release_2018.03.1)

Acknowledgements:

Brian Kelley, Dan Nealschneider, Noel O'Boyle, Stephen Roughley, Roger Sayle,
Paulo Tosco

Bug Fixes:

  • Feature request: #defines to test RDKit version
    (github issue #1454 from baoilleach)
  • SMARTS parse failure for some queries involving Hs
    (github issue #1719 from greglandrum)
  • allow libs to not be installed
    (github pull #1832 from greglandrum)
  • RWMol::addAtom(Atom,bool) missing from Java wrappers
    (github issue #1837 from greglandrum)
  • RWMol::clear now calls ROMol::initMol
    (github pull #1844 from bp-kelley)
  • Allow types.h to be included in applications that use /D_USE_MATH_DEFINES
    (github pull #1846 from d-b-w)
  • Fixes failing Python tests on Windows
    (github pull #1855 from ptosco)
  • Allow building on cygwin using -std=c++11
    (github pull #1856 from greglandrum)
  • Stop using the cmake Boost:: targets
    (github pull #1858 from greglandrum)

@greglandrum greglandrum released this Apr 20, 2018 · 36 commits to Release_2018_03 since this release

Assets 2

Release_2018.03.1

(Changes relative to Release_2017.09.1)

C++11 notes

Starting with this release, the RDKit core C++ code is written in modern C++;
for this release that means C++11. This means that the compilers used to build
it cannot be completely ancient. Here are the minimum tested versions:

  • g++ v4.8: though note that the SLN parser code cannot be built with v4.8. It
    will automatically be disabled when this older compiler is used.
  • clang v3.9: it may be that older versions of the compiler also work, but we
    haven't tested them.
  • Visual Studio 2015: it may be that older versions of the compiler also work,
    but we haven't tested them.

Backwards incompatible changes

This release includes a set of changes to make the default arguments to common
functions less error prone (github #1679).

  • MolToSmiles() now generates isomeric SMILES by default.
  • The embedding code now uses the ETKDG method by default.
  • MolToMolBlock() will now by default generate a set of 2D coordinates for
    molecules when the includeStereo option is set to True. The changes are made
    to a copy of the molecule; the molecule itself will not be modified.
  • The Mol file (and SDF) parser now determines atomic stereochemisty based on
    the 3D coordinates provided (if 3D coordinates are provided).
  • The SMILES parser now supports CXSMILES by default (assuming that additional
    text that looks like CXSMILES extensions is there).

In every case the old behavior can be obtained by providing an optional argument
to the function(s) mentioned.

Acknowledgements:

Boran Adas, José Emilio Sánchez Aparicio, Patrick Avery, Jason Biggs, Brian
Cole, Andrew Dalke, JW Feng, Peter Gedeck, Guillaume Godin, Richard Hall, Thomas
Heavy, Gareth Jones, Brian Kelley, Karl Leswing, Susan Leung, Chris Morris, Dan
Nealschneider, Noel O'Boyle, Axel Pahl, Pavel Polishchuk, Sereina Riniker, Jeff
van Santen, Roger Sayle, Martin Šícho, Matt Swain, Paolo Tosco, Sam Webb, Maciej
Wójcikowski, Nicola Zonta, 'clinntt', 'hjuinj', 'iwatobipen',

Highlights:

  • An initial version of an integration with Schrodinger's coordgen library is
    included. This produces much better 2D coordinates for complex molecules.
  • Thanks to the move to modern C++ the RDKit is now faster and uses less
    memory
  • A number of improvements were made to the PDB reader
  • v2 of the ETKDG torsions and potentials is now available

Contrib updates:

  • Implementation of Peter Ertl's IFG method for identifying functional groups
    from Guillaume Godin and Richard Hall
    (github pull #1813 from thegodone)

New Features and Enhancements:

  • Support InChi 1.05
    (github issue #1533 from greglandrum)
  • Update CPack to create .deb files correctly
    (github pull #1580 from psavery)
  • Initial commit of EnumerateHeterocycles
    (github pull #1588 from coleb)
  • Version 2 of ETKDG
    (github pull #1597 from sriniker)
  • GetMolFrags now optionally returns atom indices along with mols
    (github pull #1602 from ptosco)
  • NP Likeness with confidence value
    (github pull #1608 from apahl)
  • Adding an option to EnumerateStereoisomers to only return unique isomers
    (github pull #1612 from coleb)
  • Add function wedgeBond()
    (github issue #1615 from greglandrum)
  • Dev/substructlibrary docs
    (github pull #1620 from bp-kelley)
  • Turns off exception throwing for certain classes Rlabel sanitization.
    (github pull #1621 from bp-kelley)
  • Add an "MDL" aromaticity model
    (github issue #1622 from hjuinj)
  • Add support for %(NNN) notation for ring closures
    (github pull #1624 from baoilleach)
  • Enable windows build that uses cairo
    (github pull #1628 from greglandrum)
  • [MRG] Fix PDB reader + add argument to toggle proximity bonding
    (github pull #1629 from mwojcikowski)
  • Improve AddHs for molecules read from PDB
    (github pull #1647 from mwojcikowski)
  • Improved regression test for ETKDG version 2
    (github pull #1640 from sriniker)
  • RDKit interpretation of atom stereo SMILES is different from 4 other toolkits
    (github issue #1652 from coleb)
  • Treat bonds in PDB CONECT records explicitly, but make blacklisted ones zero-order.
    (github pull #1658 from mwojcikowski)
  • There is no need to enforce that (i, j) and (k, l) be bonded when setting a i, j, k, l dihedral
    (github pull #1673 from ptosco)
  • Make default arguments to common functions less error prone
    (github issue #1679 from greglandrum)
  • Add Fast cluster script
    (github pull #1683 from iwatobipen)
  • Update embedded InChI to v1.05
    (github pull #1684 from mcs07)
  • Add AllChem.MMFFGetMoleculeForceField().CalcGradient() to Python wrappers
    (github issue #1688 from theavey)
  • Play nice with naughty MOL blocks
    (github issue #1689 from jw-feng)
  • Make the defaults for some functions less error prone.
    (github pull #1690 from greglandrum)
  • implemented Python wrappers for computing PMI axes and moments
    (github pull #1700 from ptosco)
  • Enable range-based for loops for molecules
    (github pull #1701 from bp-kelley)
  • Support some cactvs extensions to SMARTS
    (github pull #1704 from greglandrum)
  • Integrate Coordgen
    (github pull #1708 from greglandrum)
  • Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
    (github pull #1713 from greglandrum)
  • Set atomic properties from SMARTS
    (github pull #1716 from greglandrum)
  • Allow installation of Python tests to facilitate testing installations
    (github pull #1724 from greglandrum)
  • setAromaticity() should work even if there are aromatic atoms present
    (github issue #1730 from greglandrum)
  • Use uint32 atom and bond indices
    (github pull #1742 from greglandrum)
  • Switch from boost::thread to std::thread
    (github pull #1745 from greglandrum)
  • switch to using std::regex in the SLN parser
    (github pull #1746 from greglandrum)
  • replace the usage of rdk_auto_ptr with std::unique_ptr
    (github pull #1752 from greglandrum)
  • getMolBoundsMatrix() should do triangle bound smoothing by default
    (github issue #1763 from greglandrum)
  • Added Morgan feature fingerprints to Java API
    (github pull #1764 from jones-gareth)
  • Reaction fingerprints not exposed in Java wrapper
    (github issue #1776 from webbres)
  • add Tversky index calculation for shapes
    (github pull #1777 from susanhleung)
  • Add MolToInchiKey function()
    (github pull #1784 from greglandrum)
  • speedup the NumBitsInCommon operation
    (github pull #1785 from greglandrum)
  • Stop putting brackets around * atoms in SMILES
    (github pull #1788 from greglandrum)
  • Support for a JSON-based molecule interchange format
    (github pull #1798 from greglandrum)

Bug Fixes:

  • Fixes Java wrapper build error with Boost 1.64
    (github pull #1613 from ptosco)
  • AssignStereochemistry cleanIt=True incorrectly removing new CIS/TRANS bond stereo
    (github issue #1614 from coleb)
  • switch to using a specific freesasa version
    (github pull #1619 from greglandrum)
  • Add support for %(NNN) notation for ring closures
    (github pull #1624 from baoilleach)
  • Draw._moltoSVG() raises an exception
    (github issue #1625 from greglandrum)
  • MolDrawCairo2D does not build on windows
    (github issue #1627 from greglandrum)
  • Enable windows build that uses cairo
    (github pull #1628 from greglandrum)
  • don't always download the FreeSASA source
    (github issue #1630 from greglandrum)
  • Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0
    (github pull #1635 from coleb)
  • from rdkit.Chem import AllChem has grown a six dependency
    (github issue #1637 from bp-kelley)
  • Fixing bug in IPythonConsole SVG rendering introduced in 1027d44
    (github pull #1641 from coleb)
  • changes required to allow replacing the obsolete conda_version in conda-rdkit
    (github pull #1644 from ptosco)
  • GetConformerRMSMatrix does not work if some conformers were removed
    (github issue #1650 from DrrDom)
  • EnumerateLibrary with initFromString called twice doesn't clear the reaction
    (github issue #1657 from bp-kelley)
  • Missed symmetrization in R-Group decomposition
    (github issue #1659 from greglandrum)
  • Use numpy not numeric for boost 1.65+ - fixes #1581
    (github pull #1664 from mcs07)
  • Support valence 7 for As, Sb, and Bi
    (github issue #1668 from greglandrum)
  • Fix: GetDonor2FeatVects heavy atoms confusion
    (github pull #1676 from josan82)
  • Acetylenic hydrogens not given appropriate 2D coordinates
    (github issue #1691 from jasondbiggs)
  • Warning on import of rgroup decomposition package
    (github issue #1695 from greglandrum)
  • AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required
    (github issue #1702 from baoilleach)
  • Dative bonds interfere with kekulization and the perception of aromaticity
    (github issue #1703 from greglandrum)
  • Fix/rgroup prefer matching nonhs over hs
    (github pull #1707 from bp-kelley)
  • bonds that are STEREOCIS or STEREOTRANS cannot be depickled
    (github issue #1710 from greglandrum)
  • Get queries from the new cactvs SMARTS extensions to pickle correctly
    (github pull #1712 from greglandrum)
  • fix an irritating cmake problem
    (github pull #1715 from greglandrum)
  • Added dependency from Boost headers to PgSQL CMakeLists.txt
    (github pull #1717 from ptosco)
  • Updates python test runner to always use sys.executable
    (github pull #1721 from bp-kelley)
    • make bond stereo detection in rings consistent
      (github pull #1727 from ptosco)
  • xlocale.h not needed to compile with clang
    (github issue #1728 from adalke)
  • BreakBRICSBonds() not preserving stereochemistry
    (github issue #1734 from greglandrum)
  • rdmolfiles.CanonicalRankAtoms segfaults on 0 atom molecules
    (github issue #1735 from lilleswing)
  • deprecated apply() function causes GetRDKFingerprint to fail in Python 3
    (github issue #1747 from clinntt)
  • Stop dereferencing end() iterators
    (github pull #1748 from greglandrum)
  • out of range fromAtom causes GetMorganFingerprintAsBitVect to segfault
    (github issue #1749 from adalke)
  • Generated SMARTS does not contain atomic chiral tags
    (github issue #1756 from greglandrum)
  • make the build work even if boost::serialization is disabled
    (github pull #1767 from greglandrum)
  • Fix typo in GetBoolProp documentation
    (github pull #1770 from jvansan)
  • Fingerprint segfaults with branchedPaths=False and useHs=False
    (github issue #1793 from chrishmorris)
  • Fix python linkage (primarily for conda builds)
    (github pull #1808 from greglandrum)
  • removeHs() should not remove H atoms that are contributing to the definition of a stereo bond
    (github pull #1810 from d-b-w)
  • global EmbedParameters objects should not be writeable in SWIG wrappers
    (github issue #1826 from greglandrum)
  • RDKit crashes when MolsToGridImage function is called with an empty iterable.
    (github issue #1829 from martin-sicho)
Apr 5, 2018
status of master before the modern_cxx merge

@greglandrum greglandrum released this Apr 5, 2018 · 121 commits to master since this release

Assets 2

Release_2018.03.1

(Changes relative to Release_2017.09.1)

C++11 notes

Starting with this release, the RDKit core C++ code is written in modern C++; for this release that means C++11.
This means that the compilers used to build it cannot be completely ancient. Here are the minimum tested versions:

  • g++ v4.8: though note that the SLN parser code cannot be built with v4.8. It will automatically be disabled when this older compiler is used.
  • clang v3.9: it may be that older versions of the compiler also work, but we haven't tested them.
  • Visual Studio 2015: it may be that older versions of the compiler also work, but we haven't tested them.

Backwards incompatible changes

This release includes a set of changes to make the default arguments to common functions less error prone (github #1679).

  • MolToSmiles() now generates isomeric SMILES by default.
  • The embedding code now uses the ETKDG method by default.
  • MolToMolBlock() will now by default generate a set of 2D coordinates for molecules when the includeStereo option is set to True. The changes are made to a copy of the molecule; the molecule itself will not be modified.
  • The Mol file (and SDF) parser now determines atomic stereochemisty based on the 3D coordinates provided (if 3D coordinates are provided).
  • The SMILES parser now supports CXSMILES by default (assuming that additional text that looks like CXSMILES extensions is there).

In every case the old behavior can be obtained by providing an optional argument to the function(s) mentioned.

Acknowledgements:

Boran Adas, José Emilio Sánchez Aparicio, Patrick Avery, Jason Biggs, Brian Cole, Andrew Dalke, JW Feng, Peter Gedeck, Thomas Heavy, Gareth Jones, Brian Kelley, Karl Leswing, Susan Leung, Chris Morris, Noel O'Boyle, Axel Pahl, Pavel Polishchuk, Sereina Riniker, Jeff van Santen, Roger Sayle, Matt Swain, Palo Tosco, Sam Webb, Maciej Wójcikowski, Nicola Zonta, 'clinntt', 'hjuinj', 'iwatobipen',

Highlights:

  • A number of improvements were made to the PDB reader
  • Thanks to the move to modern C++ the RDKit is now faster and uses less memory

New Features and Enhancements:

  • Support InChi 1.05
    (github issue #1533 from greglandrum)
  • Update CPack to create .deb files correctly
    (github pull #1580 from psavery)
  • Initial commit of EnumerateHeterocycles
    (github pull #1588 from coleb)
  • Version 2 of ETKDG
    (github pull #1597 from sriniker)
  • GetMolFrags now optionally returns atom indices along with mols
    (github pull #1602 from ptosco)
  • NP Likeness with confidence value
    (github pull #1608 from apahl)
  • Adding an option to EnumerateStereoisomers to only return unique isomers
    (github pull #1612 from coleb)
  • Add function wedgeBond()
    (github issue #1615 from greglandrum)
  • Dev/substructlibrary docs
    (github pull #1620 from bp-kelley)
  • Turns off exception throwing for certain classes Rlabel sanitization.…
    (github pull #1621 from bp-kelley)
  • Add an "MDL" aromaticity model
    (github issue #1622 from hjuinj)
  • Add support for %(NNN) notation for ring closures
    (github pull #1624 from baoilleach)
  • Enable windows build that uses cairo
    (github pull #1628 from greglandrum)
  • [MRG] Fix PDB reader + add argument to toggle proximity bonding
    (github pull #1629 from mwojcikowski)
  • Improve AddHs for molecules read from PDB
    (github pull #1647 from mwojcikowski)
  • Improved regression test for ETKDG version 2
    (github pull #1640 from sriniker)
  • RDKit interpretation of atom stereo SMILES is different from 4 other toolkits
    (github issue #1652 from coleb)
  • Treat bonds in PDB CONECT records explicitly, but make blacklisted ones zero-order.
    (github pull #1658 from mwojcikowski)
  • There is no need to enforce that (i, j) and (k, l) be bonded when setting a i, j, k, l dihedral
    (github pull #1673 from ptosco)
  • Make default arguments to common functions less error prone
    (github issue #1679 from greglandrum)
  • Add Fast cluster script
    (github pull #1683 from iwatobipen)
  • Update embedded InChI to v1.05
    (github pull #1684 from mcs07)
  • Add AllChem.MMFFGetMoleculeForceField().CalcGradient() to Python wrappers
    (github issue #1688 from theavey)
  • Play nice with naughty MOL blocks
    (github issue #1689 from jw-feng)
  • Make the defaults for some functions less error prone.
    (github pull #1690 from greglandrum)
  • implemented Python wrappers for computing PMI axes and moments
    (github pull #1700 from ptosco)
  • Enable range-based for loops for molecules
    (github pull #1701 from bp-kelley)
  • Support some cactvs extensions to SMARTS
    (github pull #1704 from greglandrum)
  • Integrate Coordgen
    (github pull #1708 from greglandrum)
  • Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
    (github pull #1713 from greglandrum)
  • Set atomic properties from SMARTS
    (github pull #1716 from greglandrum)
  • Allow installation of Python tests to facilitate testing installations
    (github pull #1724 from greglandrum)
  • setAromaticity() should work even if there are aromatic atoms present
    (github issue #1730 from greglandrum)
  • Use uint32 atom and bond indices
    (github pull #1742 from greglandrum)
  • Switch from boost::thread to std::thread
    (github pull #1745 from greglandrum)
  • switch to using std::regex in the SLN parser
    (github pull #1746 from greglandrum)
  • replace the usage of rdk_auto_ptr with std::unique_ptr
    (github pull #1752 from greglandrum)
  • getMolBoundsMatrix() should do triangle bound smoothing by default
    (github issue #1763 from greglandrum)
  • Added Morgan feature fingerprints to Java API
    (github pull #1764 from jones-gareth)
  • Reaction fingerprints not exposed in Java wrapper
    (github issue #1776 from webbres)
  • add Tversky index calculation for shapes
    (github pull #1777 from susanhleung)
  • Add MolToInchiKey function()
    (github pull #1784 from greglandrum)
  • speedup the NumBitsInCommon operation
    (github pull #1785 from greglandrum)
  • Stop putting brackets around * atoms in SMILES
    (github pull #1788 from greglandrum)
  • Support for a JSON-based molecule interchange format
    (github pull #1798 from greglandrum)

Bug Fixes:

  • Fixes Java wrapper build error with Boost 1.64
    (github pull #1613 from ptosco)
  • AssignStereochemistry cleanIt=True incorrectly removing new CIS/TRANS bond stereo
    (github issue #1614 from coleb)
  • switch to using a specific freesasa version
    (github pull #1619 from greglandrum)
  • Add support for %(NNN) notation for ring closures
    (github pull #1624 from baoilleach)
  • Draw._moltoSVG() raises an exception
    (github issue #1625 from greglandrum)
  • MolDrawCairo2D does not build on windows
    (github issue #1627 from greglandrum)
  • Enable windows build that uses cairo
    (github pull #1628 from greglandrum)
  • don't always download the FreeSASA source
    (github issue #1630 from greglandrum)
  • Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0
    (github pull #1635 from coleb)
  • from rdkit.Chem import AllChem has grown a six dependency
    (github issue #1637 from bp-kelley)
  • Fixing bug in IPythonConsole SVG rendering introduced in 1027d44
    (github pull #1641 from coleb)
  • changes required to allow replacing the obsolete conda_version in conda-rdkit
    (github pull #1644 from ptosco)
  • GetConformerRMSMatrix does not work if some conformers were removed
    (github issue #1650 from DrrDom)
  • EnumerateLibrary with initFromString called twice doesn't clear the reaction
    (github issue #1657 from bp-kelley)
  • Missed symmetrization in R-Group decomposition
    (github issue #1659 from greglandrum)
  • Use numpy not numeric for boost 1.65+ - fixes #1581
    (github pull #1664 from mcs07)
  • Support valence 7 for As, Sb, and Bi
    (github issue #1668 from greglandrum)
  • Fix: GetDonor2FeatVects heavy atoms confusion
    (github pull #1676 from josan82)
  • Acetylenic hydrogens not given appropriate 2D coordinates
    (github issue #1691 from jasondbiggs)
  • Warning on import of rgroup decomposition package
    (github issue #1695 from greglandrum)
  • AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required
    (github issue #1702 from baoilleach)
  • Dative bonds interfere with kekulization and the perception of aromaticity
    (github issue #1703 from greglandrum)
  • Fix/rgroup prefer matching nonhs over hs
    (github pull #1707 from bp-kelley)
  • bonds that are STEREOCIS or STEREOTRANS cannot be depickled
    (github issue #1710 from greglandrum)
  • Get queries from the new cactvs SMARTS extensions to pickle correctly
    (github pull #1712 from greglandrum)
  • fix an irritating cmake problem
    (github pull #1715 from greglandrum)
  • Added dependency from Boost headers to PgSQL CMakeLists.txt
    (github pull #1717 from ptosco)
  • Updates python test runner to always use sys.executable
    (github pull #1721 from bp-kelley)
    • make bond stereo detection in rings consistent
      (github pull #1727 from ptosco)
  • xlocale.h not needed to compile with clang
    (github issue #1728 from adalke)
  • BreakBRICSBonds() not preserving stereochemistry
    (github issue #1734 from greglandrum)
  • rdmolfiles.CanonicalRankAtoms segfaults on 0 atom molecules
    (github issue #1735 from lilleswing)
  • deprecated apply() function causes GetRDKFingerprint to fail in Python 3
    (github issue #1747 from clinntt)
  • Stop dereferencing end() iterators
    (github pull #1748 from greglandrum)
  • out of range fromAtom causes GetMorganFingerprintAsBitVect to segfault
    (github issue #1749 from adalke)
  • Generated SMARTS does not contain atomic chiral tags
    (github issue #1756 from greglandrum)
  • make the build work even if boost::serialization is disabled
    (github pull #1767 from greglandrum)
  • Fix typo in GetBoolProp documentation
    (github pull #1770 from jvansan)
  • Fingerprint segfaults with branchedPaths=False and useHs=False
    (github issue #1793 from chrishmorris)
  • Fix python linkage (primarily for conda builds)
    (github pull #1808 from greglandrum)
Assets 2

Release_2017.09.3

(Changes relative to Release_2017.09.2)

Acknowledgements:

Jason Biggs, Brian Kelley, Noel O'Boyle, Paolo Tosco

Bug Fixes:

  • Missed symmetrization in R-Group decomposition
    (github issue #1659 from bp-kelley)
  • Acetylenic hydrogens not given appropriate 2D coordinates
    (github issue #1691 from jasondbiggs)
  • Warning on import of rgroup decomposition package
    (github issue #1695 from greglandrum)
  • AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required
    (github issue #1702 from baoilleach)
  • Dative bonds interfere with kekulization and the perception of aromaticity
    (github issue #1703 from greglandrum)
  • bonds that are STEREOCIS or STEREOTRANS cannot be depickled
    (github issue #1710 from greglandrum)
  • Added dependency from Boost headers to PgSQL CMakeLists.txt
    (github pull #1717 from ptosco)

@greglandrum greglandrum released this Dec 3, 2017 · 12 commits to Release_2017_09 since this release

Assets 2

Release_2017.09.2

(Changes relative to Release_2017.09.1)

Acknowledgements:

Brian Cole, Brian Kelley, Noel O'Boyle, Pavel Polishchuk, Matt Swain,
Paolo Tosco, Hsiao Yi

Bug Fixes:

  • switch to using a specific freesasa version
    (github pull #1619 from greglandrum)
  • Add support for %(NNN) notation for ring closures
    (github pull #1624 from baoilleach)
  • Draw._moltoSVG() raises an exception
    (github issue #1625 from greglandrum)
  • MolDrawCairo2D does not build on windows
    (github issue #1627 from greglandrum)
  • Enable windows build that uses cairo
    (github pull #1628 from greglandrum)
  • Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0
    (github pull #1635 from coleb)
  • Fixing bug in IPythonConsole SVG rendering introduced in 1027d44
    (github pull #1641 from coleb)
  • changes required to allow replacing the obsolete conda_version in conda-rdkit
    (github pull #1644 from ptosco)
  • GetConformerRMSMatrix does not work if some conformers were removed
    (github issue #1650 from DrrDom)
  • EnumerateLibrary with initFromString called twice doesn't clear the reaction
    (github issue #1657 from bp-kelley)
  • Add 2017 UGM into README.md
    (github pull #1660 from hsiaoyi0504)
  • Use numpy not numeric for boost 1.65+ - fixes #1581
    (github pull #1664 from mcs07)
  • Support valence 7 for As, Sb, and Bi
    (github issue #1668 from greglandrum)

@greglandrum greglandrum released this Oct 7, 2017 · 28 commits to Release_2017_09 since this release

Assets 2

Release_2017.09.1

(Changes relative to Release_2017.03.1)

Important

  • The fix for bug #1567 changes the way fragment SMILES are canonicalized.
    MolFragmentToSmiles() and canonicalizeFragment() will now often return
    different results
  • The fix for bug #1604 changes the behavior of QueryAtom::setQuery(), which
    now deletes the current query before setting the new value. If you are using
    QueryAtom::setQuery() from C++ (or possibly Java), be sure that you are not
    also deleting that memory.

Acknowledgements:

Brian Cole, Peter Gedeck, Guillaume Godin, Jan Halborg Jensen, Malitha Kabir,
Tuomo Kalliokoski, Brian Kelley, Noel O'Boyle, Matthew O'Meara, Pavel
Polishchuk, Cameron Pye, Christian Ribeaud, Stephen Roughley, Patrick Savery,
Roger Sayle, Nadine Schneider, Gregor Simm, Matt Swain, Paolo Tosco, Alain
Vaucher, Sam Webb, 'phenethyl', 'xiaotaw'

Highlights:

  • The new R-Group decomposition code provides a flexible and powerful tool for
    building R-group tables or datasets look in $RDBASE/Docs/Notebooks for
    example notebooks showing how to use this.
  • Drawing of chemical reactions has been greatly improved and is now done using
    the C++ rendering code.
  • The MaxMinPicker is dramatically faster.
  • New descriptors: the QED descriptor has been added as have a large collection
    of new 3D descriptors and implementations of the USR and USRCAT fingerprints.

New Features and Enhancements:

  • Bring back USR and USRCAT descriptors
    (github pull #1417 from greglandrum)
  • Generate a warning for conflicting bond directions
    (github issue #1423 from greglandrum)
  • expose and test GetDrawCoords()
    (github pull #1427 from greglandrum)
  • Improvement suggestions for SaltRemover
    (github issue #1431 from ribeaud)
  • Remove obsolete scripts from Scripts dir
    (github pull #1440 from greglandrum)
  • Support drawing reactions from C++
    (github pull #1444 from greglandrum)
  • QED code with unit test file
    (github pull #1445 from gedeck)
  • Add support for other datatypes to ConvertToNumpyArray
    (github issue #1447 from pyeguy)
  • updated FindCairo.cmake
    (github pull #1455 from ptosco)
  • fixes PgSQL CMakeLists.txt to enable conda build on Windows
    (github pull #1457 from ptosco)
  • Some cleanups to make Travis builds faster
    (github pull #1464 from greglandrum)
  • ExplainPairScore does not support includeChirality=True
    (github issue #1466 from xiaotaw)
  • Add a collection of new 3D descriptors
    (github pull #1467 from greglandrum)
  • Update cartridge documentation to use ChEMBL 23
    (github issue #1491 from greglandrum)
  • First entry of the SubstructLibrary module
    (github pull #1493 from bp-kelley)
  • assorted fixes to get the current master branch to build on Windows
    (github pull #1495 from ptosco)
  • Support assignment of stereochemistry tags to bonds from 3D structure
    (github issue #1497 from gncs)
  • Support black and white molecule drawing
    (github issue #1510 from greglandrum)
  • Missing def_readwrite for backgroundColour in rdMolDraw2D.cpp
    (github issue #1519 from goraj)
  • Adds canonicalization of atom maps
    (github pull #1521 from bp-kelley)
  • Implement stereoisomer enumeration
    (github pull #1531 from greglandrum)
  • Add a MolBundle class
    (github pull #1537 from greglandrum)
  • Provide support for color palettes in MolDraw2D
    (github pull #1546 from greglandrum)
  • A few reaction drawing tweaks
    (github pull #1549 from greglandrum)
  • R group improvements
    (github pull #1552 from greglandrum)
  • Add a canned Atom query for heavy atom degree
    (github issue #1563 from greglandrum)
  • Adds FreeSASA adapter
    (github pull #1565 from bp-kelley)
  • Added C++ version of getBestRMS()
    (github pull #1568 from psavery)
  • SMILES lexer optimization/enhancement
    (github pull #1575 from greglandrum)
  • Update IPythonConsole and PandasTools to use new drawing code
    (github pull #1577 from greglandrum)
  • Squashes warnings on cygwin
    (github pull #1578 from bp-kelley)
  • Support continuous highlighting in drawMolecules().
    (github pull #1579 from greglandrum)
  • Enhanced Similarity Maps depiction
    (github pull #1594 from gerebtzoff)

Bug Fixes:

  • RDKit gets stuck on PubChem CID 102128817
    (github issue #1281 from TuomoKalliokoski)
  • MMP code not including molecules with no cuts
    (github issue #1406 from greglandrum)
  • Fixes PandasTools to also work with pandas 0.20
    (github pull #1410 from bp-kelley)
  • csharp input files out of date
    (github issue #1413 from greglandrum)
  • Fix cxsmiles parse on VS2008
    (github pull #1415 from mcs07)
  • MaxMinPicker picking non-existent element
    (github issue #1421 from greglandrum)
  • _isCallable clashes with Celery
    (github issue #1434 from momeara)
  • Impossible to build the RDKit from source without Python installed
    (github issue #1435 from greglandrum)
  • RemoveHs() removes H atom attached to dummy if it came from AddHs()
    (github issue #1439 from DrrDom)
  • fix a couple failing windows tests related to temp file removal
    (github pull #1446 from greglandrum)
  • SanitizeRxn fails with a runtime exception when unused Rlabels are in product
    (github issue #1448 from bp-kelley)
  • String module conversion bug
    (github pull #1452 from coleb)
  • GetConformerRMS() documentation is misleading
    (github pull #1459 from greglandrum)
  • URANGE_CHECK not doing its job in RWMol::addBond
    (github issue #1461 from baoilleach)
  • ExplainPairScore does not support includeChirality=True
    (github issue #1466 from xiaotaw)
  • MolToSmarts does not include atom-map or isotope info for molecules built from SMILES
    (github issue #1472 from greglandrum)
  • AdjustQueryProperties() removing properties from dummy atoms
    (github issue #1474 from greglandrum)
  • Fixes lookup for HELM Monomer 'D'
    (github pull #1477 from bp-kelley)
  • Aromatic rings composed solely of dummy atoms should not be kekulized
    (github issue #1478 from bp-kelley)
  • Directly specify rotor model used in QED.
    (github pull #1483 from bp-kelley)
  • Unicode problem with pidPS tests on Mac
    (github issue #1490 from greglandrum)
  • Pattern fingerprint setting bad bits with degree zero atoms
    (github issue #1496 from greglandrum)
  • Remove xlocale header
    (github pull #1501 from greglandrum)
  • Fixes atom documentation
    (github pull #1505 from bp-kelley)
  • TypeError from PandasTools.SaveXlsxFromFrame
    (github issue #1507 from pyeguy)
  • Removes trailing spaces after \ to fix windows compilation errors
    (github pull #1516 from bp-kelley)
  • prepareMolForDrawing() not in SWIG wrappers
    (github issue #1522 from greglandrum)
  • Bond is missing IsInRing methods in Java wrapper
    (github issue #1535 from sroughley)
  • Fixes blanking of non-query atom data when QueryAtomData was being pi…
    (github pull #1541 from bp-kelley)
  • ChemicalReaction code not calling setNoImplicit() when H counts are set.
    (github issue #1544 from greglandrum)
  • Fixes failing build with MSVC
    (github pull #1547 from ptosco)
  • Kekulization error with cores from R-Group Decomposition
    (github issue #1550 from greglandrum)
  • Fixes double free for Dict::update
    (github pull #1571 from bp-kelley)
  • QueryAtom::setQuery() should delete the old query first
    (github pull #1604 from greglandrum)

@greglandrum greglandrum released this Sep 29, 2017 · 380 commits to master since this release

Assets 2

Release_2017.09.1

(Changes relative to Release_2017.03.1)

Important

  • The fix for bug #1567 changes the way fragment SMILES are canonicalized.
    MolFragmentToSmiles() and canonicalizeFragment() will now often return
    different results

Acknowledgements:

Brian Cole, Peter Gedeck, Guillaume Godin, Malitha Kabir, Tuomo Kalliokoski,
Brian Kelley, Noel O'Boyle, Matthew O'Meara, Pavel Polishchuk, Cameron Pye,
Christian Ribeaud, Stephen Roughley, Patrick Savery, Roger Sayle,
Nadine Schneider, Matt Swain, Paolo Tosco, Alain Vaucher, Sam Webb,
'phenethyl', 'xiaotaw'

Highlights:

  • The new R-Group decomposition code provides a flexible and powerful tool for
    building R-group tables or datasets look in $RDBASE/Docs/Notebooks for
    example notebooks showing how to use this.
  • Drawing of chemical reactions has been greatly improved and is now done using
    the C++ rendering code.
  • The MaxMinPicker is dramatically faster.
  • New descriptors: the QED descriptor has been added as have a large collection
    of new 3D descriptors and implementations of the USR and USRCAT fingerprints.

New Features and Enhancements:

  • Bring back USR and USRCAT descriptors
    (github pull #1417 from greglandrum)
  • Generate a warning for conflicting bond directions
    (github issue #1423 from greglandrum)
  • expose and test GetDrawCoords()
    (github pull #1427 from greglandrum)
  • Improvement suggestions for SaltRemover
    (github issue #1431 from ribeaud)
  • Remove obsolete scripts from Scripts dir
    (github pull #1440 from greglandrum)
  • Support drawing reactions from C++
    (github pull #1444 from greglandrum)
  • QED code with unit test file
    (github pull #1445 from gedeck)
  • Add support for other datatypes to ConvertToNumpyArray
    (github issue #1447 from pyeguy)
    • updated FindCairo.cmake
      (github pull #1455 from ptosco)
    • fixes PgSQL CMakeLists.txt to enable conda build on Windows
      (github pull #1457 from ptosco)
  • Some cleanups to make Travis builds faster
    (github pull #1464 from greglandrum)
  • ExplainPairScore does not support includeChirality=True
    (github issue #1466 from xiaotaw)
  • Add a collection of new 3D descriptors
    (github pull #1467 from greglandrum)
  • Update cartridge documentation to use ChEMBL 23
    (github issue #1491 from greglandrum)
  • First entry of the SubstructLibrary module
    (github pull #1493 from bp-kelley)
  • assorted fixes to get the current master branch to build on Windows
    (github pull #1495 from ptosco)
  • Support black and white molecule drawing
    (github issue #1510 from greglandrum)
  • Missing def_readwrite for backgroundColour in rdMolDraw2D.cpp
    (github issue #1519 from goraj)
  • Adds canonicalization of atom maps
    (github pull #1521 from bp-kelley)
  • Implement stereoisomer enumeration
    (github pull #1531 from greglandrum)
  • Add a MolBundle class
    (github pull #1537 from greglandrum)
  • Provide support for color palettes in MolDraw2D
    (github pull #1546 from greglandrum)
  • A few reaction drawing tweaks
    (github pull #1549 from greglandrum)
  • R group improvements
    (github pull #1552 from greglandrum)
  • Add a canned Atom query for heavy atom degree
    (github issue #1563 from greglandrum)
  • Adds FreeSASA adapter
    (github pull #1565 from bp-kelley)
  • Added C++ version of getBestRMS()
    (github pull #1568 from psavery)
  • SMILES lexer optimization/enhancement
    (github pull #1575 from greglandrum)
  • Update IPythonConsole and PandasTools to use new drawing code
    (github pull #1577 from greglandrum)
  • Squashes warnings on cygwin
    (github pull #1578 from bp-kelley)
  • Support continuous highlighting in drawMolecules().
    (github pull #1579 from greglandrum)
  • Enhanced Similarity Maps depiction
    (github pull #1594 from gerebtzoff)

Bug Fixes:

  • RDKit gets stuck on PubChem CID 102128817
    (github issue #1281 from TuomoKalliokoski)
  • MMP code not including molecules with no cuts
    (github issue #1406 from greglandrum)
  • Fixes PandasTools to also work with pandas 0.20
    (github pull #1410 from bp-kelley)
  • csharp input files out of date
    (github issue #1413 from greglandrum)
  • Fix cxsmiles parse on VS2008
    (github pull #1415 from mcs07)
  • MaxMinPicker picking non-existent element
    (github issue #1421 from greglandrum)
  • _isCallable clashes with Celery
    (github issue #1434 from momeara)
  • Impossible to build the RDKit from source without Python installed
    (github issue #1435 from greglandrum)
  • RemoveHs() removes H atom attached to dummy if it came from AddHs()
    (github issue #1439 from DrrDom)
  • fix a couple failing windows tests related to temp file removal
    (github pull #1446 from greglandrum)
  • SanitizeRxn fails with a runtime exception when unused Rlabels are in product
    (github issue #1448 from bp-kelley)
  • String module conversion bug
    (github pull #1452 from coleb)
  • GetConformerRMS() documentation is misleading
    (github pull #1459 from greglandrum)
  • URANGE_CHECK not doing its job in RWMol::addBond
    (github issue #1461 from baoilleach)
  • ExplainPairScore does not support includeChirality=True
    (github issue #1466 from xiaotaw)
  • MolToSmarts does not include atom-map or isotope info for molecules built from SMILES
    (github issue #1472 from greglandrum)
  • AdjustQueryProperties() removing properties from dummy atoms
    (github issue #1474 from greglandrum)
  • Fixes lookup for HELM Monomer 'D'
    (github pull #1477 from bp-kelley)
  • Aromatic rings composed solely of dummy atoms should not be kekulized
    (github issue #1478 from bp-kelley)
  • Directly specify rotor model used in QED.
    (github pull #1483 from bp-kelley)
  • Unicode problem with pidPS tests on Mac
    (github issue #1490 from greglandrum)
  • Pattern fingerprint setting bad bits with degree zero atoms
    (github issue #1496 from greglandrum)
  • Remove xlocale header
    (github pull #1501 from greglandrum)
  • Fixes atom documentation
    (github pull #1505 from bp-kelley)
  • TypeError from PandasTools.SaveXlsxFromFrame
    (github issue #1507 from pyeguy)
  • Removes trailing spaces after \ to fix windows compilation errors
    (github pull #1516 from bp-kelley)
  • prepareMolForDrawing() not in SWIG wrappers
    (github issue #1522 from greglandrum)
  • Bond is missing IsInRing methods in Java wrapper
    (github issue #1535 from sroughley)
  • Fixes blanking of non-query atom data when QueryAtomData was being pi…
    (github pull #1541 from bp-kelley)
    • Fixes failing build with MSVC
      (github pull #1547 from ptosco)
  • Kekulization error with cores from R-Group Decomposition
    (github issue #1550 from greglandrum)
  • Fixes double free for Dict::update
    (github pull #1571 from bp-kelley)