Danny Diaz

icon indicating a website link https://danny305.github.io icon indicating an email [email protected]

icon company Institute for Foundations of Machine Learning icon location Austin, TX icon location Organic Chemist who put down the chemicals. Software Engineer/Data Scientist at UT Austin.

Results 37 comments of Danny Diaz

How to handle charge and radii in mmCIF

Ready to start contributing. I'm guessing it's the nathan/cif branch?

How to handle charge and radii in mmCIF

Why don't we just use Gemmi to convert between the two?

Fixed parsing bugs for input cif and added cif write functionality.

Let me know what else I need to do!

mmCIF based PQR format

Has this feature been implemented yet?

mmCIF based PQR format

We use the partial charge and Hydrogen atoms added by pdb2pqr to engineer a data structure to train CNN models. However, we are trying to switch our data engineering infrastructure...

mmCIF based PQR format

Nathan, I totally understand! How long do you believe this cloud migration will take? Danny

mmCIF based PQR format

We would like to run your software where we feed in either a pub-redo file or a mmCIF/cif file of a protein and receive back a mmCIF/cif file that has...

mmCIF based PQR format

Will you guys extend the pqr functionality to non-protein atoms (water, ligands, sugars, chemical modifications, etc)? Or should we prioritize obtaining partial charge for non-protein atoms else where? I am...

mmCIF based PQR format

Has this been approved/resolved? Danny

No hydrogens (neither implicit nor explicit) are added to mol2 file

RDKit version 2021.03.2 I just copied the codes from ^^ and I do not get any atoms added. Is this going to get resolved??