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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
If applicable, add screenshots to help explain your problem.
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.
The text was updated successfully, but these errors were encountered:
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
If applicable, add screenshots to help explain your problem.
Configuration (please complete the following information):
Additional context
Add any other context about the problem here.
The text was updated successfully, but these errors were encountered: