* Tweak the scoring function to penalize non h matches considerably. Only full H rgroups get a one. Might need to tweak int the future
* Scale the hydrogens as 1/# mols unless they are a full group
* Make sure EmbedMultipleConfs is deterministic for very large seeds and a seed of 0.
Fixing two distinct bugs:
- A randomSeed of 0 didn't use '0' as the seed even though the
documentation said that it should.
- Very large seeds could overflow the 'int' representation during
calculation of a new internal seed. This would make
EmbedMultipleConfs non-deterministic even though the user provided a
valid seed.
* Adding a C++ test for case pull request #1635.
* add cairo to moldraw2d wrappers link (for windows)
* add ChemReactions to moldraw2d wrappers link (for windows)
* add SmilesParse to moldraw2d wrappers link (for windows)
* add threshold argument
* expose the new options to python
not yet tested, but it at least compiles
* support threshold on the python side;
fix a bug with the way the threshold is returned
* initial submission; needs review
* minor
* line endings
* remove cache functionality since it's now redundant
* add test data
* add a test
* changes from review
* handle the heavy-atom degree queries differently
* Fixes#1563
* add a test for the heavy atom degree option
* Support (and test) adjustHeavyDegree in the cartridge too.
* test results
* Adds RGroupDecomp free function and python wrapper
* Fixes subtle bug, adds new RGroupDecomp API
* Updates results for the subtle bug fix. Verified results were correct.
* Removes smilesCaching.
* Changes RGroupDecompose ordering, adds docstrings and more tests
* Fixes atom documentation
* Fixes#1461
This is a complicated one. Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0. The standard operations is
to check
URANGE(num, size-1)
Which (for unsigned integers) obviously rolls over.
This fixes all usage cases to be
URANGE(num+1, size)
And fixes the bugs found. (addBond and the mmff tests)
* Fixes#1461 - Updates URANGE_CHECK to be 0<=x<hi
* very basics
* add the version to get all matches
* better exceptions, including tests
* documentation and actually add the test code
* responses to review
* move detectBondStereoChemistry() into MolOps
* switch more code over to using the new function
* add an addStereoChemistryFrom3D() function. Needs testing still.
* add some tests
* cleanups and rename
This actually just causes the molecule processing to fail in a reasonable amount of time; it is not an actual fix to the underlying ring-finding problem
* Fixes#1550
* might as well update properties on the r groups too
* add option to remove Hs from sidechains;
expose a few more parameters to python;
expose ctor with parameter object to python
* first steps towards flexible colour palettes
* add B&W palette and a test for it
* add python support;
this is, once again, not the best API due to the inability to auto-translate boost::tuples at this point
* more palette control from python
* rename some of the swig-wrapped types to make them more consistent
* handle palettes that do not have a default value
* Fixes blanking of non-query atom data when QueryAtomData was being pickled
* Adds old version pickle test for properties
* Makes pickle py2 and py3 compatible
* switch from using `[D0]` to `[*]` to ensure single atom fragments are correctly handled in the pattern fingerprint;
Fixes#1496
* update expected reaction similarity results
