MolVS

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Only one molecule from the input SMILES file is processed...

7

Hello, ``` molvs standardize -i smi input.smi -o smi -O output.smi ``` The input file has several molecules, the output a single one. Is this the expected behavior?

UnixJunkie

RDKit Integration

6

Hello, I am wondering if the documentation of this project should reflect the fact that much of this API has been integrated into newer version of the RDKit?

jvansan

Unable to standardize some PubChem molecules

1

Hello, I was using molvs standardizer on PubChem molecules and found out several molecules that cannot be standardized: 1. SMILES: CC(S(=O)CC1=CC=C(C=C1)C(S(=O)CC2=CC=C(C=C2)C(S(=O)CC3=CC=C(C=C3)C(S(=O)C4=CC=C(C=C4)Br)S(=O)C5=CC=C(C=C5)Br)S(=O)CC6=CC=C(C=C6)C(S(=O)C7=CC=C(C=C7)Br)S(=O)C8=CC=C(C=C8)Br)S(=O)CC9=CC=C(C=C9)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br Link: [https://pubchem.ncbi.nlm.nih.gov/compound/59827358](https://pubchem.ncbi.nlm.nih.gov/compound/59827358) 2. SMILES: CC1=CC=C(C=C1)C(S(=O)CC2=CC=C(C=C2)C(S(=O)CC3=CC=C(C=C3)C(S(=O)CC4=CC=C(C=C4)C(S(=O)C5=CC=C(C=C5)Br)S(=O)C6=CC=C(C=C6)Br)S(=O)CC7=CC=C(C=C7)C(S(=O)C8=CC=C(C=C8)Br)S(=O)C9=CC=C(C=C9)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br)S(=O)CC1=CC=C(C=C1)C(S(=O)C1=CC=C(C=C1)Br)S(=O)C1=CC=C(C=C1)Br Link: [https://pubchem.ncbi.nlm.nih.gov/compound/59827349]( https://pubchem.ncbi.nlm.nih.gov/compound/59827349) Code...

VladislavChernykh

tautomer.TautomerEnumerator() function

6

Hi, I am trying to enumerate tautomers using the tautomer.TautomerEnumerator() function. I am wondering if the returned list is sorted by scores so that the best-scoring tautomer in the list...

mmagithub

During compound standardization/registration, it can be helpful to preserve molecule identifiers for mapping synonyms or related molecules. This function mirrors the `super_parent` function, but captures InChI identifiers at each sanitization...

gjgetzinger

Updates SMARTS definitions for phosphinic acids. Requires 3 explicit (X3) and 3 total (D3) connections for tautomerizing phosphinic acids. New behavior properly handles compounds with 4 connections (e.g., phosphates, phosphonic...

gjgetzinger

or at least, there should be an option to trigger it

UnixJunkie

support several molecules in input file (for .smi and .sdf)

2

also, keep molecule names I don't write Python these days, feel free to rewrite as you wish. I tested on multi molecules smi and sdf input files.

UnixJunkie

Hi, I have noticed some erratic behaviour in the tautomer canonicalization procedure. In this specific example, double bonds jump from one ring to the next, erasing stereocenters as they go....

driesvr

test_tautomer.py extended results in C++ implementation

1

Hi, I implemented a part of MolVS in C++. Close to everything is working fine (against the examples in the test units). Just the tautomer enumeration are getting different (extended)...

doctorx84