newanalysis.helpers.centerOrientBox

newanalysis.helpers.centerOrientBox(com, xyz, boxlength, isolute, atoms_per_residue, residue_first_atom, coorA, coorB)

Centers the box to the center of mass of a given molecule and rotates the box so that two sets of coordinates are as identical as possible.

Parameters:

• box (boxlength .. edge length of the cubic) –

• atoms (xyz .. coordinates of all) –

• box –

• molecule (isolute .. index of the solute / center) –

• contains (atoms_per_residue .. array showing how many atoms each residue) –

• residue (residue_first_atom .. index of the first atom of each) –

• coordinates (coorA .. template) –

• frame (coorB .. corresponding coordinates of the current) –