Aligning Molecule Based on MCS

A program that aligns molecules based on their maximum common substructure.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> python mcsalign2D.py --help

will generate the following output:

Simple parameter list
 input/output options :
   -fit : Align filename
   -out : Output filename
   -ref : Ref filename

Code

Download code

mcsalign2D.py

See also

Example

prompt> python mcsalign2D.py -ref ace1.ism -fit ace2.ism -out out.mol

taking the output coordinates and generating the images with the mol2img program will produce the images shown in Table: Example of using the program to align two molecules based on MCS.

Example of using the program to align two molecules based on MCS
reference molecule aligned molecule
../_images/mcsalign2D-out-ref.png ../_images/mcsalign2D-out-fit.png

See also