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AaronTools 1.1 documentation
AaronTools 1.1 documentation

Pages:

  • Installation Guide
  • Tutorials
    • Intro to Command Line Scripts
    • Example BASH Scripts for Common Tasks
    • Adding Structures to your AaronTools Library
    • Coding with Geometry Objects
    • Coding with Theory Objects
    • Coding with FileReader objects
    • Example Python Scripts for Common Tasks
    • Converting Z-Matrices to Cartesian Coordinates
    • Working with AaronTools in Jupyter Notebooks
    • AaronTools and Psi4
    • AaronTools and Matplotlib
  • List of Command Line Scripts
    • angle.py
    • bond.py
    • changeChirality.py
    • changeElement.py
    • closeRing.py
    • dihedral.py
    • follow.py
    • getMonomers.py
    • combineMonomers.py
    • interpolate.py
    • makeConf.py
    • mapLigand.py
    • mirror.py
    • multiSubstitute.py
    • removeFragment.py
    • rmsdAlign.py
    • rotate.py
    • substitute.py
    • symmetrize.py
    • translate.py
    • averageBuriedVolume.py
    • averageSterimol.py
    • bond.py
    • coneAngle.py
    • findAtoms.py
    • ligandSterimol.py
    • percentVolumeBuried.py
    • pointGroup.py
    • rmsdAlign.py
    • solidAngle.py
    • stericMap.py
    • stericMapDifference.py
    • substituentSterimol.py
    • unique.py
    • fetchMolecule.py
    • getCoordinationComplexes.py
    • jobSubmit.py
    • makeCrestInput.py
    • makeInput.py
    • condensedFukui.py
    • grabStatus.py
    • grabThermo.py
    • plotIR.py
    • plotAverageIR.py
    • plotUVVis.py
    • plotAverageUVVis.py
    • plotNMR.py
    • plotAverageNMR.py
    • printAtomInfo.py
    • printAtomPairInfo.py
    • printCube.py
    • printFreq.py
    • printFreqBild.py
    • printInfo.py
    • printXYZ.py
    • getCitations.py
    • libaddLigand.py
    • libaddRing.py
    • libaddSubstituent.py
    • listChanges.py
    • parsePDF.py
  • Customization
    • Job Submission Templates
    • AaronTools Libraries
    • INI Files
  • Python API Documentation
    • Geometry class
    • Reading and Writing Files
      • FileReader class
      • FileWriter class
    • Finders
    • theory module
      • Theory class
      • Theory parameters
      • JobType classes
      • Basis Set classes
      • Method classes
      • EmpiricalDispersion class
      • ImplicitSolvent class
      • IntegrationGrid class
    • Atom class
    • Component class
    • Substituent class
    • Ring class
    • Spectra
    • CompOutput class
    • Orbital class
    • SubmitProcess class
    • JSON Caching
    • PointGroup class
    • Utilities
  • Advanced Topics
    • Structure Analysis and Descriptor Implementation
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Pages:

  • Job Submission Templates
    • Examples
  • AaronTools Libraries
    • Substituents
    • Ligands
    • Rings
  • INI Files
    • INI configuration format overview
    • Configuration sections and their options
    • Using functions
    • Software Specific Theory Options
    • Basis Options
    • Atom Types
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parsePDF.py
Copyright © 2023, V. M. Ingman, A. J. Schaefer, L. R. Andreola, and S. E. Wheeler
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