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Toolkits-2018.Feb.1-python
  • Docs »
  • OEDepict Toolkit 2.4.0 »
  • OEDepict Examples »
  • Aligning Molecules Based on Substructure Search

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 -ref ref.ism -fit fit.ism -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
../_images/smartsalign2D-out-1.png ../_images/smartsalign2D-out-2.png ../_images/smartsalign2D-out-3.png

See also

  • Molecule Alignment chapter
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© Copyright 2018, OpenEye Scientific Software, Inc. Last updated on Feb 27, 2018.