Always rotate the N-terminal

Pranavkhade / PACKMAN

PACKMAN: PACKing and Motion ANalysis

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Always rotate the N-terminal #48

Closed Pranavkhade closed 1 year ago

Pranavkhade commented 1 year ago

https://github.com/Pranavkhade/PACKMAN/blob/52001f3e59607c263950beaafa329436e741868a/packman/molecule/model.py#L490-L491

When we rotate the C or N terminal based on the size, we do achieve good computational efficiency but the axis of rotation ($\vec{e_a}$) changes and the calculations are not right if the angles calculated are from N to C terminal.
The rotational component should depend on the first neighbor (neighbor of first atoms parsed as an argument for the bond) being on the rotating side.

Pranavkhade commented 1 year ago

Suggested code:

# Whatever component neighbour 1 is in, rotate that. This keeps $\vec{e_a}$ condition satisfied
        if( self.__AllAtoms_inverse[neighbor1] in changed_components[0] ):
            to_rotate = list(changed_components[0])
        elif( self.__AllAtoms_inverse[neighbor1] in changed_components[1] ):
            to_rotate = list(changed_components[1])
        else:
            logging.warning('Atom :'+str(neighbor1.get_id())+' is not in connected to the components')