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
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
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See also
- Molecule Alignment chapter