smina is a very good tool for docking and minimization, thank you for your work! I'm good at using Python in my project and the code of smina is written in c++, it's too hard for me to read and modify c++ code. Is there a python wrapper to import libsmina in python scripts? I want to use smina to minimize protein-ligand complexes in python with openbabel or rdkit mol object, could you help me?
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A python interface is an interesting idea and I'd certainly accept a pull request with that functionality, but ultimately I don't think it would end up being meaningfully more efficient than calling the program directly through subprocess so it isn't a priority for me to implement.
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I'm developing a program like pharmit, the program will search for a lot of ligands from the database. Ligands is written out to the disk and then minimized by smina is time-consuming. Do you have any suggestions to minimize complexes without writing out the file by smina.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
smina is a very good tool for docking and minimization, thank you for your work! I'm good at using Python in my project and the code of smina is written in c++, it's too hard for me to read and modify c++ code. Is there a python wrapper to import libsmina in python scripts? I want to use smina to minimize protein-ligand complexes in python with openbabel or rdkit mol object, could you help me?
A python interface is an interesting idea and I'd certainly accept a pull request with that functionality, but ultimately I don't think it would end up being meaningfully more efficient than calling the program directly through subprocess so it isn't a priority for me to implement.
I'm developing a program like pharmit, the program will search for a lot of ligands from the database. Ligands is written out to the disk and then minimized by smina is time-consuming. Do you have any suggestions to minimize complexes without writing out the file by smina.
You can launch the smina server as a separate process. An example python client script can be found here:
https://sourceforge.net/p/smina/code/ci/master/tree/src/server/client.py
Ligands must be in smina binary format (as generated by the tosmina binary).