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Charge range queries not properly written to SMARTS #2815

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greglandrum opened this issue Nov 29, 2019 · 0 comments
Closed

Charge range queries not properly written to SMARTS #2815

greglandrum opened this issue Nov 29, 2019 · 0 comments
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2019_09_2

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Configuration:

  • RDKit Version: 2019.09.1
  • Operating system: all
  • Python version (if relevant): n/a
  • Are you using conda? yes
  • If you are using conda, which channel did you install the rdkit from? rdkit

Description:
here's the demo

In [12]: Chem.MolToSmarts(Chem.MolFromSmarts('[+{0-3}]'))                                                                                 
Out[12]: '[+0{0-3}]'

In [13]: Chem.MolToSmarts(Chem.MolFromSmarts('[-{0-3}]'))                                                                                 
Out[13]: '[-0{0-3}]'
@greglandrum greglandrum added this to the 2019_09_2 milestone Nov 29, 2019
@greglandrum greglandrum self-assigned this Nov 29, 2019
greglandrum added a commit to greglandrum/rdkit that referenced this issue Dec 2, 2019
@greglandrum
Fixes rdkit#2815
db15cec
@greglandrum greglandrum mentioned this issue Dec 2, 2019
Merged
greglandrum added a commit that referenced this issue Dec 3, 2019
@greglandrum
Fix a couple of smarts bugs (#2816)
b681988 
* turn back on some tests that shouldn't have been disabled

* improve SMARTS testing

make sure we can generate SMARTS from all the examples and then parse that again.

* Fixes #2814

* Fixes #2815
greglandrum added a commit to greglandrum/rdkit that referenced this issue Dec 16, 2019
@greglandrum
Fixes rdkit#2815
e0a60ae
@greglandrum greglandrum mentioned this issue Dec 16, 2019
Merged
bp-kelley pushed a commit that referenced this issue Jan 9, 2020
@greglandrum @bp-kelley
Cleanups and additional tests to improve test coverage (#2852)
a75018f 
* disable builds of the StructChecker code by default

* operator"" _smarts() doesn't need to catch sanitization errors

* remove unused function

* turn back on some tests that shouldn't have been disabled

* Remove unused code from SMARTS parser and simplify a bit

SmilesParseOps::AddFragToMol is now used only from the SMARTS parser, so we can simplify the API

* Removes obsolete special case code for SMARTS

This was relevant when organic atoms in SMARTS queries were stored as two-part queries.

* improve SMARTS testing

make sure we can generate SMARTS from all the examples and then parse that again.

* Fixes #2814

* Fixes #2815

* some additional smarts tests to improve coverage

* test copy ctor and getPos

* remove obsolete test_list files

* include tests for the morgan invariant generators

* more cleanups and coverage improvements

* remove files that were mistakenly added
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