C1CNc2ccccc2N1 | Alignment starts by defining the substructure which each structure has in common. This is done by reading a SMARTS string supplied by the user. |
The first structure is read and the coordinates of the first three atoms matching the SMARTS are retained for later reference. Call these coordinates A_{1}, B_{1} and C_{1}. The structure is output unchanged. | |
As each subsequent structure is read, the coordinates of the first two atoms (A_{n} and B_{n}) matching the SMARTS are used to compute the angle between the lines(bonds) A_{1}B_{1} and A_{n}B_{n}. | |
All atoms of structure #n are rotated around the z-axis by the negative of that angle. All atoms of structure #n are translated in x and y so that B_{1} superimposes with B_{n}. The coordinates C_{1} are compared to the rotated coordinates C_{n}. If necessary, the coordinates of all atoms of structure #n are rotated/flipped by 180 degrees around A_{n}B_{n}. |
The following other options are also available: