Closed kkanekal closed 4 years ago
I have fixed the problem. Please re-run your tests. If everything works out, please close this issue.
Hi Andrew,
I found another mismatch with the smiles string 'CCOC(C)C'. For some reason, the dev version is mapping this molecule to a single bead while the refactor branch is mapping it to a dimer. I checked the constants used in the mapping optimizations and they are the same for both versions, so I am unsure why this is happening.
refactor result:
; GENERATED WITH auto_martini.py ; None ; Tristan Bereau (2014)
[moleculetype] ; molname nrexcl MOL 2
[atoms] ; id type resnr residue atom cgnr charge smiles 1 P1 1 MOL P01 1 0 ; CCO 2 C3 1 MOL C01 2 0 ; CCC
[bonds] ; i j funct length force.c. 1 2 1 0.24 1250
dev result:
; GENERATED WITH auto_Martini v0.0.2 for MOL ; Developed by: Kiran Kanekal, Tristan Bereau, and Andrew Abi-Mansour
[moleculetype] ; molname nrexcl MOL 2
[atoms] ; id type resnr residue atom cgnr charge smiles 1 C5 1 MOL C01 1 0 ; CCOC(C)C
Thanks,
Kiran
I get the same output (single bead) with both branches using rdkit v2018.09.3 and python v2.7.15 and v3.7.3. Plz specify which rdkit version you're using.
; GENERATED WITH auto_martini.py ; INPUT SMILES: [H]C([H])([H])C([H])([H])OC([H])(C([H])([H])[H])C([H])([H])[H] ; Tristan Bereau (2014)
[moleculetype] ; molname nrexcl MOL 2
[atoms] ; id type resnr residue atom cgnr charge smiles 1 C5 1 MOL C01 1 0 ; CCOC(C)C
Hi Andrew,
I checked the rdkit version that I was using for the refactor branch and it was indeed different. Using version 2017.09.3 gives a 2-bead mapping but after updating, my results are in agreement with yours. I wonder what specifically changed in the updated version causing the change in the mapping result? In any case, I will rerun my tests and hopefully close this issue soon.
Thanks,
Kiran
The issue is closed. The rdkit version discrepancy was the last problem when running my tests.
Hi Andrew,
I'm not sure if I should have opened this issue here or in your forked repo. I have continued doing my test comparing results from the refactor and the dev branch and have found another smiles string for which there are different results. Using the refactor branch:
python auto_martini.py --smi "CC(O)C=NO" --mol MOL [refactor] ; GENERATED WITH auto_martini.py ; None ; Tristan Bereau (2014)
[moleculetype] ; molname nrexcl MOL 2
[atoms] ; id type resnr residue atom cgnr charge smiles 1 P1 1 MOL P01 1 0 ; CCO 2 P1 1 MOL P02 2 0 ; C=NO
[bonds] ; i j funct length force.c. 1 2 1 0.25 1250
using the dev branch:
python -m auto_martini --smi "CC(O)C=NO" --mol MOL --top testmol.itp *[dev] ALOGPS can't predict fragment: NO
It seems there is a hang up in the smi2alogps function?
Thanks, Kiran