subproptools.sub_reor

subreor Module to reorient a substituent to match a defined coordinate system First an atom is positioned at the origin. By convention, this is the atom of the group that is directly bonded to the rest of the molecule. The rest of the molecule is placed along the -x axis. The remaining axes are defined as follows: * if there is one lone pair(VSCC), that point lies on the +y * if there are two lone pairs, the average position of them lies on the +y * if there are no lone pairs, map the BCPs of the atom at the origin to a reference. Identify the closest match to the reference to determine a BCP to set as +y

Functions

output_to_gjf(old_file_name, reor_geom[, ...])	Given a rotated molecule, writes new geometry to single point Gaussian calculation
rotate_sheet(csv_file, esm, basis[, ...])	Given csv file and Gaussian calculation options, reorient files in csv_file and output gjf
rotate_substituent(sumFileNoExt, originAtom, ...)	Rotates a substituent to the defined coordinate system.
rotate_substituent_aiida(sum_file_folder, ...)	Rotates a substituent to the defined coordinate system.