maestro2charmmgui 0.1.6

PDB Format transformation from Maestro to CHARMM-GUI. This can make the CHARMM-GUI recognise the original orientation of the hydrogen atoms generated by Maestro.

Maestro2CharmmGUI

PDB Format transformation from Maestro to CHARMM-GUI. This can make the CHARMM-GUI recognise the original orientation of the hydrogen atoms generated by Maestro.

Get started

# install by pypi
pip install maestro2charmmgui

# install by poetry
poetry add maestro2charmmgui

from maestro2charmmgui.rename import transform_with_resname

# rename the atoms by using a residue-based corresponding dictionary with a single function
input = "path/to/pdbfile.pdb"
output = "path/to/pdbfile_charmm.pdb"

transform_with_resname(input, output)

For further usage, see the jupyter notebook for renaming the hydrogens defined in Maestro into CHARMM's definition.

Change log

0.1.6

• fix bugs in rename.py: transform_self_defined_dict. Use resname to find the key for self defined dictionary.

0.1.5

• addional hydrogen at terminal nitrogen renaming (H -> HT3)
• change the order of the conditions of universal modifications of the hydrogen and the termini atoms' modification

Developer note

Check whether it works:

poetry run pytest

# 2 passed, 1 warnining