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77 lines
3.3 KiB
Plaintext
Executable File
77 lines
3.3 KiB
Plaintext
Executable File
****** Release_April2007_1 *******
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(Changes relative to Release_Jan2007_1)
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Bug Fixes
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- handing of isotope information in SMILES has been fixed
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- "implicit" hydrogens are now added to charged atoms explicitly when
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writing SMILES. (issue 1670149)
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- the 2D->3D code no longer generates non-planar conjugated 4-rings
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(e.g. C1=CC=C1). (issue 1653802)
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- removing explicit hydrogens no longer produces incorrect smiles
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(issue 1694023)
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- bit indices and signature lengths in the AtomPairs code no longer
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being calculated incorrectly. *NOTE* this changes the bits that are
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set, so if you have existing signatures, they will need to be
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regenerated.
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- Fixed a bug causing MolSuppliers to generate incorrect length
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information when a combination of random access and iterator
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interfaces are used. (issue 1702647)
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- Fixed a bug leading to incorrect line numbers in error messages
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from the SDMolSuppler. (issue 1695221)
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New Features
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- chemical reactions are now supported
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- there is a new entry point into the 2D depictor code,
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compute2DCoordsMimicDistMat(), that attempts to generate 2D
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depictions that are similar to the structure described by the
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distance matrix. There's also a shorthand approach for calling this
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to mimic a 3D structure available as:
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AllChem.GenerateDepictionMatching3DStructure()
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- DiscreteValueVect and UniformGrid3D now support the binary
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operators |, &, +, and -.
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- a reader/writer for TPL files has been added.
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- support has been added for MolCatalogs: hierarchical catalogs that
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can store complete molecules.
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- the protrude distance metric for shapes has been added
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- pickle support added to classes: UniformGrid, DiscreteValueVect,
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Point
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- added the class DataStructs/SparseIntVect to improve performance
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and clarity of the AtomPairs code
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Other
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- the non-GUI code now supports python2.5; the GUI code may work with
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python2.5, but that has not been tested
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- the Mol and SD file parsers have been sped up quite a bit.
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- the "Crippen" descriptors are now calculated somewhat faster.
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- in-code documentation updates
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- new documentation for beginners in $RDBASE/Docs/Book
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****** Release_Jan2007_1 *******
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(Changes relative to Release_Oct2006_1)
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Bug Fixes
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- zero-atom molecules now trigger an exception
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- dummy atoms are no longer labelled 'Xe'
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- core leak in the mol file writer fixed
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- mol files with multiple charge lines are now correctly parsed
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- a workaround was installed to prevent crashes in the regression
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tests on Windows when using the newest VC++ v7 series compiler.
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(http://sourceforge.net/tracker/index.php?func=detail&aid=1607290&group_id=160139&atid=814650)
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- chirality perception (which requires partial sanitization) is no
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longer done by the MolFileParser when sanitization is switched
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off.
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- Two potential memory corruption problems were fixed (rev's 150 and
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151).
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New Features
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- optional use of chirality in substructure searches
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- MolWriters can now all take a stream as an argument
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- Chiral terms can now be included in the DistanceGeometry
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embedding.
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Other
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- $RDBASE/Code/Demos/RDKit/BinaryIO is a demonstration of using
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boost IOStreams and the ROMol pickling mechanism to generate
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highly compressed, random-access files of molecules.
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- the Point code has been refactored
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