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> java MCSAlign2D --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.java and MCSAlign2D.txt interface file

See also

• Molecule Alignment chapter

• OEIs2DFormat function

• OEPrepareDepiction function

• OEMCSSearch class

• OEPrepareAlignedDepiction function

Example

prompt> java MCSAlign2D -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

See also

• Molecule Alignment chapter