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SMARTS parser fails on high-numbered ring closures in branches #2909

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greglandrum opened this issue Jan 26, 2020 · 0 comments · Fixed by #2912
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SMARTS parser fails on high-numbered ring closures in branches #2909

greglandrum opened this issue Jan 26, 2020 · 0 comments · Fixed by #2912
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bug
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2020_03_1

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@greglandrum
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  • RDKit Version: master
  • Operating system: all

Here's the demo:

In [9]: Chem.MolFromSmarts('C%(5000)CCCC%(5000)')                               
Out[9]: <rdkit.Chem.rdchem.Mol at 0x7f8f98da6490>

In [10]: Chem.MolFromSmarts('C%(5000)CCC(C%(5000))')                            
[16:52:20] SMARTS Parse Error: unclosed ring for input: 'C%(5000)CCC(C%(5000))'

In [11]: Chem.MolFromSmarts('C%(5000)CCC.C%(5000)')                             
Out[11]: <rdkit.Chem.rdchem.Mol at 0x7f8f98dbb170>
@greglandrum greglandrum modified the milestones: 2019_09_4, 2020_03_1 Jan 26, 2020
greglandrum added a commit to greglandrum/rdkit that referenced this issue Jan 27, 2020
@greglandrum
Fixes rdkit#2909
58d131a
@greglandrum greglandrum mentioned this issue Jan 27, 2020
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greglandrum added a commit that referenced this issue Jan 29, 2020
@greglandrum
cleanup of the SMILES/SMARTS parsing and writing code (#2912)
9991c52 
* first cleanup

* next round of changes. all tests pass

* Fixes #2909

* Fixes #2910

* further cleanup

* some cleanup/refactoring of the Dict class

* remove now extraneous calls to hasProp() before clearProp()

* minor refactoring of RDProps.h

* Switch from using our own version of round() to std::round()

* replace some boost::math stuff with the equivalents from std::

* cleanups in SmartsWrite

* refactor out a bunch of duplicated code

* fix an instance of undefined behavior

* changes in response to review
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cleanup of the SMILES/SMARTS parsing and writing code greglandrum/rdkit
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@greglandrum