_moltoimg() should honor drawOptions.prepareMolsBeforeDrawing #6792
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added 3 commits
October 8, 2023 12:25
… run PrepareMolForDrawing if requested not to
…l-if-requested-not-to
…awing and not call PrepareMolForDrawing if asked not to
greglandrum
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Oct 19, 2023
* fixes #6773 * removed unused captures * update release notes and cmakelists for beta (#6788) * Removed some code duplication between Depictor.cpp and common.h (#6368) * - 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> * Revert "Removed some code duplication between Depictor.cpp and common.h (#6368)" (#6797) This reverts commit ddfe708. * All 3d des (#6741) * add function to calc all 3D descriptors * fix indentation in CalcMolDescriptors3D * add error handling for 2D molecules * suggested changes * change exception type * add unit tests * add random seed to conf gen in unit tests * fix function call in unit tests * fix expected PMI1 value in tests --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * _moltoimg() should honor drawOptions.prepareMolsBeforeDrawing (#6792) * _moltoimg() should honor drawOptions.prepareMolsBeforeDrawing and not run PrepareMolForDrawing if requested not to * _moltoimg() and _moltoSVG() should honor drawOptions.prepareMolsForDrawing and not call PrepareMolForDrawing if asked not to --------- Co-authored-by: ptosco <paolo.tosco@novartis.com> * Bad lasso (#6751) * Better separation of lines. * Only put atoms in colour list once. * Test. * Hash codes. * Response to review. * First attempt at fixing stray line. * Tidier. * Squared distances. * tag release (#6801) * fixes #6773 * removed unused captures * - fixed comment - fixed bug found in checkIfRingsAreClosed() * - removed redundant NRing queries - added ring size queries to avoid incorrect matches with MCS results originated with MatchFusedRingsStrict * fixed doctests --------- Co-authored-by: ptosco <paolo.tosco@novartis.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com> Co-authored-by: John Mayfield <john@nextmovesoftware.com> Co-authored-by: Rachael Pirie <56546141+RPirie96@users.noreply.github.com> Co-authored-by: David Cosgrove <davidacosgroveaz@gmail.com>
greglandrum
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Nov 10, 2023
* fixes #6773 * removed unused captures * update release notes and cmakelists for beta (#6788) * Removed some code duplication between Depictor.cpp and common.h (#6368) * - 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> * Revert "Removed some code duplication between Depictor.cpp and common.h (#6368)" (#6797) This reverts commit ddfe708. * All 3d des (#6741) * add function to calc all 3D descriptors * fix indentation in CalcMolDescriptors3D * add error handling for 2D molecules * suggested changes * change exception type * add unit tests * add random seed to conf gen in unit tests * fix function call in unit tests * fix expected PMI1 value in tests --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * _moltoimg() should honor drawOptions.prepareMolsBeforeDrawing (#6792) * _moltoimg() should honor drawOptions.prepareMolsBeforeDrawing and not run PrepareMolForDrawing if requested not to * _moltoimg() and _moltoSVG() should honor drawOptions.prepareMolsForDrawing and not call PrepareMolForDrawing if asked not to --------- Co-authored-by: ptosco <paolo.tosco@novartis.com> * Bad lasso (#6751) * Better separation of lines. * Only put atoms in colour list once. * Test. * Hash codes. * Response to review. * First attempt at fixing stray line. * Tidier. * Squared distances. * tag release (#6801) * fixes #6773 * removed unused captures * - fixed comment - fixed bug found in checkIfRingsAreClosed() * - removed redundant NRing queries - added ring size queries to avoid incorrect matches with MCS results originated with MatchFusedRingsStrict * fixed doctests --------- Co-authored-by: ptosco <paolo.tosco@novartis.com> Co-authored-by: Greg Landrum <greg.landrum@gmail.com> Co-authored-by: John Mayfield <john@nextmovesoftware.com> Co-authored-by: Rachael Pirie <56546141+RPirie96@users.noreply.github.com> Co-authored-by: David Cosgrove <davidacosgroveaz@gmail.com>
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_moltoimg()should honordrawOptions.prepareMolsBeforeDrawingand not runPrepareMolForDrawingif requested not to.This is annoying when trying to visualize a molecule with original molblock wedging as, for example, chiral Hs were still being added even if one does not want to.