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3 votes
1 answer

Parsing pre-2007 SMILES string

How would one parse the SMILES string BrC[2]:C[3]:C(:CH:CH:CH:@2):CH:CH:CH:CH:@3 I rely on tools like rdkit and ...
Ryan Park's user avatar
2 votes
1 answer

Is it possible to correct bond order and conectivity problems in an sdf file according to mol2 files?

I was doing a Virtual Screening Search using Pharmer software. The .sdf output file contains a column in mol format and another column with Root Mean Square Deviations. I can see some bond order and ...
Laura Castro's user avatar
1 vote
1 answer

How to convert a SDF molecular structure file to a pandas dataframe with Python?

What is the best python tool to convert a SDF file to a structured data frame (pandas.DataFrame). Similar to Molconvert from ChemAxon? SDF can have different datafields for each compound which I would ...
Soerendip's user avatar
  • 1,295
1 vote
1 answer

DNA, molecular descriptors

Are there any programs (preferably command line tools) for calculating molecular descriptors of DNA? I am looking for something like Chemopy or RDKit but specifically for DNA. Thanks in advance!
Balint Biro's user avatar
1 vote
0 answers

From SMILE get Amber force in Python

I have a list of SMILES of small molecules and I want to be able to simulate these molecules with an Amber force field in Python. Currently, I use RDkit to convert the smile into a PDB file: ...
Anton B's user avatar
  • 11