mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
ddfe708b37
* - implemented alignOnly mode into RDDepict::generateDepictionMatching2DStructure() - the allowRGroups option now also supports potentially missing R groups (i.e., R groups that do not match any atom, such as those connected to generic aromatic atoms) - added the adjustMolBlockWedging parameter (which defaults to true) to invert/clear molblock wedging information as appropriate - added unit tests for the above new features - added RDDepict::generateDepictionMatching2DStructure() overloads taking RDDepict::ConstrainedDepictionParams parameter for convenience - removed some redundant RDDepict:: namespace specifications * Fix chirality handling when the chiral atom is the first one in a SMARTS (#6730) * Set _SmilesStart when parsing SMARTS. * SmartsWriter should also invert first atoms, like SMILES. * Update test cases now these SMILES match themselves as SMARTS. * rerun bison * cleanup a possible repeated define * When an atom moves from the first to second position winding should flip in SMARTS (i.e. same as SMILES). --------- Co-authored-by: greg landrum <greg.landrum@gmail.com> * Some small cleanups from the UGM Hackathon (#6744) * move definition of a couple global constants from a .h to a .cpp * careful removal of some redundant atom PRECONDITIONS * careful remove of some redundant ROMol PRECONDITIONS a bit of additional cleanup * optimization masquerading as modernization * some more tidying * a bit more atom cleanup * change in response to review * Fixes #6756 (#6780) * update release notes and cmakelists for beta (#6788) * move problematic functions to Chirality namespace * - implemented alignOnly mode into RDDepict::generateDepictionMatching2DStructure() - the allowRGroups option now also supports potentially missing R groups (i.e., R groups that do not match any atom, such as those connected to generic aromatic atoms) - added the adjustMolBlockWedging parameter (which defaults to true) to invert/clear molblock wedging information as appropriate - added unit tests for the above new features - added RDDepict::generateDepictionMatching2DStructure() overloads taking RDDepict::ConstrainedDepictionParams parameter for convenience - removed some redundant RDDepict:: namespace specifications * move problematic functions to Chirality namespace * added missing dependency * let's check what is going wrong * CoordGen tests should not run if CoordGen support is not available in the build --------- Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com> Co-authored-by: John Mayfield <john@nextmovesoftware.com> Co-authored-by: greg landrum <greg.landrum@gmail.com>