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cd74dc2207
* very basics: actually parsing the new atom stereochem features * add some input verification for the chiral permutations * fix a typo add quadruple bond SMILES/SMARTS extension * add forgotten files * patch from Roger * add Roger's parsing examples * typo * new tests * adjusted version of next PR from Roger: - add SP2D hybridization for square planar (this may change) - some modernizationof Chirality.cpp - stop using < HybridizationType in Chirality.cpp (should probably do this elsewhere too) - improved handling of hybridization assignment for new stereochem - handle new stereo/hybridization in UFF - tests for the above * perception of non-tetrahedral stereo from 3D (from Roger S) Basic testing of SP and TB based on opensmiles docs * potential fixes for octahedral assignment more tests * docs update need way more! * map the TH tags directly to @ tags * very basics of SMILES writing this does not work with anything that changes the permutation order like canonicalization or writing things in rings. * start to support the getChiralAcross API * more testing * consistency * add hasNonTetrahedralStereo() and getIdealAngleBetweenLigands() * assignStereochemistry should only remove non-tetrahedral stereo * re-simplify those tests * cleanup matrix stream output * initial pass at supporting nontet stereo in distgeom * backup * start on the reference docs * TBP reference * first pass at Oh finished * update SP section * more doc updates * fix a typo * add param to not remove Hs connected to non-tetrahedral atoms * VERY basic coord generation for square planar * TBP basics * basic OH depiction * start testing missing ligands allow non-tet stereo in rings (ugly, but correct) * add new TBP functions from Roger * update depiction code for new API * backup, the new tests work so far * Finish the TB tests * OH tests pass too * cleanup * first pass at getting correct SMILES with reordering need way more testing than this * ensure permutation 0 is correctly preserved * some progress towards adding non-tetrahedral stereo to StereoInfo * doc update * add non-tet chiral classes to python wrappers * make sure removeAllHs also gets neighbors of non-tetrahedral centers more testing * a bit of depictor cleanup * make the assignment from 3D more tolerant more testing * improve the bulk testing * cleanup * remove a bit of redundant code * ensure we don't write bogus permutation values to SMILES * fix some rebase problems * allow assignStereochemistryFrom3D() to be called without sanitization * allow disabling the non-tetrahedral stereo when it's not explicit * get that working on windows too