def atomsToVec(atoms): a1 = hf.atomCoord(atoms[1]) a2 = hf.atomCoord(atoms[2]) a3 = hf.atomCoord(atoms[3]) centroid = hf.avgCoord(atoms) pvector = hf.calcPlane(a1, a2, a3) v1 = hf.vector(centroid, a1) v2 = hf.vector(centroid, a2) normal1 = hf.normalize(cross(v1 ,v2)) normal2 = hf.normalize(cross(v2 ,v1)) centroid_norm1 = hf.normalize(hf.vector(centroid, normal1)) centroid_norm2 = hf.normalize(hf.vector(centroid, normal2)) return {"centroid":centroid,"plane":hf.normalize(pvector),"normal":[normal1, normal2],\ 'cnormal' : [centroid_norm1, centroid_norm2]}