Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

RDKit segfaults in MMFFOptimizeMoleculeConfs() #2820

Closed
ptosco opened this issue Dec 3, 2019 · 0 comments
Closed

RDKit segfaults in MMFFOptimizeMoleculeConfs() #2820

ptosco opened this issue Dec 3, 2019 · 0 comments
Assignees
@ptosco
Labels
bug
Milestone
2019_09_3

Comments

@ptosco
Copy link
Contributor

ptosco commented Dec 3, 2019

How to reproduce:

from rdkit import Chem
from rdkit.Chem import AllChem

glycine = Chem.MolFromSmiles('NCC(=O)O')
glycine = Chem.AddHs(glycine)
glycineRW = Chem.RWMol(glycine)
Na = glycineRW.AddAtom((Chem.Atom(11)))
glycineRW.AddBond(3, Na, Chem.BondType.SINGLE)
glycineRW.GetAtomWithIdx(3).SetFormalCharge(1)
Chem.SanitizeMol(glycineRW)

potential = AllChem.ETKDG()
AllChem.EmbedMolecule(glycineRW, potential)
ids = AllChem.EmbedMultipleConfs(glycineRW, 50, enforceChirality=True)
_=AllChem.MMFFOptimizeMoleculeConfs(glycineRW)
@ptosco ptosco added the bug label Dec 3, 2019
@ptosco ptosco self-assigned this Dec 3, 2019
ptosco added a commit to ptosco/rdkit that referenced this issue Dec 3, 2019
@ptosco
- fixes GitHub rdkit#2820
ab1a2a1
@greglandrum greglandrum added this to the 2019_09_3 milestone Dec 4, 2019
greglandrum pushed a commit that referenced this issue Dec 4, 2019
@ptosco @greglandrum
Fixes GitHub #2820 (#2821)
7e27719 
* - fixes GitHub #2820

* - response to PR review
@greglandrum greglandrum mentioned this issue Dec 4, 2019
Merged
greglandrum pushed a commit that referenced this issue Jan 9, 2020
@ptosco @greglandrum
Fixes GitHub #2820 (#2821)
96938e6 
* - fixes GitHub #2820

* - response to PR review
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@ptosco ptosco

Labels
bug
Projects
None yet
Milestone
2019_09_3
Development

No branches or pull requests
2 participants
@greglandrum @ptosco