align

Aligns the attached atoms such that: anchors line segments a->b are in the same direction and have midpoints coincident at m. anchor wedges c<-m->d are rotated about the a-b axis so their center directions are parallel. Since the different anchors can have different lengths of the a-b line segments, and different dihedral angles c->a->b->d, this method is an approximate method for aligning the two coordinate systems that tries to keep the error from accumulating all in one linear or angular distance.