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Regression in depiction of double bonds in aromatic rings #3744

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ptosco opened this issue Jan 18, 2021 · 0 comments
Closed

Regression in depiction of double bonds in aromatic rings #3744

ptosco opened this issue Jan 18, 2021 · 0 comments
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@ptosco
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ptosco commented Jan 18, 2021

Describe the bug
Using the current master branch, double bonds in aromatic rings are often drawn on the outer side rather than on the inner side.

To Reproduce
Build RDKit from the current master branch, then:

from rdkit import Chem

Chem.MolFromMolBlock("""
     RDKit          2D

 10 10  0  1  0  0  0  0  0  0999 V2000
   -1.7411    0.8920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4555    0.4795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4555   -0.3455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7411   -0.7580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0266   -0.3455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0266    0.4795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1003    1.6065    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3121    0.8920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1003    0.1775    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1371    0.8920    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  1  1  0
  6  8  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
M  END
""")

or

Chem.MolFromSmiles("c1cccn1C")

Expected behavior
Released RDKit yields respectively:
image
image

Screenshots
Master RDKit yield respectivelys:
image
image

Configuration (please complete the following information):

  • RDKit version: current master branch
  • OS: CentOS 7
  • Python version (if relevant): Python 3.6
  • Are you using conda? no
  • If you are using conda, which channel did you install the rdkit from?
  • If you are not using conda: how did you install the RDKit? Compiling from master
@ptosco ptosco added the bug label Jan 18, 2021
ptosco added a commit to ptosco/rdkit that referenced this issue Jan 18, 2021
@greglandrum greglandrum added this to the 2020_09_4 milestone Jan 20, 2021
greglandrum added a commit that referenced this issue Jan 21, 2021
* fixes #3744

* added a unit test

* fix by stopping with the unnecessary copies

Co-authored-by: greg landrum <greg.landrum@gmail.com>
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