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Dative bond and alkali and alkaline earth metals #5120

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marcostenta opened this issue Mar 22, 2022 · 1 comment
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Dative bond and alkali and alkaline earth metals #5120

marcostenta opened this issue Mar 22, 2022 · 1 comment
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@marcostenta
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Describe the bug
the dative bond with group 1 and 2 metals does not work as for other metals
reading smiles/mol files generates an error on valence

To Reproduce
a colab link: https://colab.research.google.com/drive/19OZtX8IqICZQ4B2jLpr02owkSLc0FeZ6?usp=sharing

Steps to reproduce the behavior, feel free to paste a bit of Python in here.
Chem.MolFromSmiles('O->[Fe+2]<-O') # works
Chem.MolFromSmiles('[O-]->[Fe+2]<-[O-]') # works

Chem.MolFromSmiles('O->[Mg+2]<-O') # it does not work
[Explicit valence for atom # 1 Mg, 4, is greater than permitted ]

Chem.MolFromSmiles('O->[K]<-O')
[Explicit valence for atom # 1 K, 2, is greater than permitted]

Expected behavior
I and II group metals to behave as other metals.
read in the molecule with sanitization=True leading to a functioning molecule
not splitting the molecule in fragments by breaking on the dative bond
work by reading in smiles, cxsmiles with dative bond arrows
work by reading in MDL sdfiles in V3000 format with dative as type=9 bond

Screenshots
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Configuration (please complete the following information):

  • RDKit version:
  • OS: windows
  • Python version (if relevant): 3.7
  • Are you using conda? yes
  • If you are using conda, which channel did you install the rdkit from? conda-forge
  • If you are not using conda: how did you install the RDKit?

Additional context
Add any other context about the problem here.

@greglandrum
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Closed in #6139

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