Aligning Molecules Based on Substructure Search

A program that aligns the molecules based on a substructure search initialized with the given SMARTS pattern.

Command Line Interface

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

prompt> python smartsalign2D.py --help

Will generate the following output:

Simple parameter list
input/output options :
   -in : Filename of input molecules
   -out : Output filename
   -smarts : SMARTS for alignment match

Code

Download code

smartsalign2D.py

See also

• Molecule Alignment chapter

• OESubSearch class

• OEGenerate2DCoordinates function

• OEIs2DFormat function

• OEPrepareSearch function

• OEPrepareAlignedDepiction function

• OEPrepareDepiction function

Examples

prompt> python smartsalign2D.py -in test.sdf -out aligned.sdf -smarts "c1cc[c,n]c2c1ncc2" -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 molecule

Example of using the program to align molecules

See also

• Molecule Alignment chapter