Programs used in "Dextrosinistral Reading of SMILES Notation: Investigation into Origin of Non-Sense Code from String Manipulations"

Article Information

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This article has been submitted for publication.

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About this repository

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This repository provides python codes of ASCII Text Based Chemical Structure Tuner (ACST): String Reversal Mechanism for SMILES Notation. There are total twelve python script and a User_Manual.pdf.

• The User_Manual.pdf provides the following details:
  • Author and Date of Documentation
  • Audience
  • Content
  • Introduction to the ACST
  • Installation Instructions
  • Description of Home Page
  • Description of Panel 1: Chemical File Translator (CFT)
  • Description and User Instruction for Panel 2: Logical Processor (LP)
  • Examples
  • Troubleshoot Problems

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Installation

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Pre-installation Requirements

• Hardware Requirements
  • Processor : Core i3 and above
  • RAM : minimum 2GB
  • Hard Disk : 0.5 GB (for ACST only)
  • Display : 1366 X 768
• Software Requirments
  • System Software : Windows 10 and above
  • Python : Version 3.11 and above
  • Tkinter : Version 8.6 and above
• External Software Requirements
  • Molecule Structure Drawing Software : PerkinElmer's ChemDraw [1], ACD Labs ChemSketch [2], or Avogadro software [3].
  • File Translation Software : OpenBabel [4]
  • Text Editing Software : Notepad++ [5]

Installation Procedure

Download: The source code of the software device ACST is available on the GitHub link http://github.com/paulat0grant/ACST. The source code can be cloned via download ZIP format.

Installation: Unzip the GitHub cloned ZIP file of ACST source code. Then edit the following files:

DrawMolecule.py

Edit line 2 written as:

subprocess.Popen(‘path of the installation directory/Avogadro.exe')

to the installation path like

subprocess.Popen(‘I:/avogadro/Install/bin/Avogadro.exe')

FileTranslate.py

Edit the line 6 written as:

subprocess.Popen(‘path of the installation directory/obgui.exe')

to the installation path like

subprocess.Popen(‘I:/openbabel/install/obgui.exe.exe')

TextEditor.py

Edit line 2 written as:

subprocess.Popen(‘path of the installation directory/notepad++.exe')

to the installation path like

subprocess.Popen('I:/notepadpp/install/notepad++.exe')

Launch ACST:

Double-click setup.py of unzipped ACST source code.

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Author

Anup Paul paulat0grant@rediffmail.com

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References

[1] Elmer, P., ChemBioDraw Ultra Version (14.0). CambridgeSoft Waltham, MA, USA, 2014.

[2] Acd/Labs, Acd/chemsketch (freeware), version 12.01. 2009, Canada Advanced Chemistry Developement, Inc.: Canada Toronto.­

[3] Hanwell, M.D., et al., Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of cheminformatics, 2012. 4(1): p. 1-17, DOI: https://doi.org/10.1186/1758-2946-4-17.

[4] O'Boyle, N.M., et al., Open Babel: An open chemical toolbox. Journal of cheminformatics, 2011. 3(1): p. 1-14, DOI: https://doi.org/10.1186/1758-2946-3-33.

[5] Ho, D., Notepad++. Notepad Plus Plus,[Online]. Available: https://notepad-plus-plus. org/.[Accessed 7 8 2020], 2011.