List of Command Line Scripts

These are the command line scripts included in AaronTools. For convenience, they are grouped by function. If appropriate, a script may be listed in multiple sections (e.g., bond.py, which can measure and change bond lengths).

The page for each command line script shows the usage info and possibly further explanation.

Structure Editing

• 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
  • Examples
• removeFragment.py
• rmsdAlign.py
• rotate.py
• substitute.py
• symmetrize.py
• translate.py

Structure Analysis

• averageBuriedVolume.py
• averageSterimol.py
• bond.py
• coneAngle.py
• findAtoms.py
• ligandSterimol.py
• percentVolumeBuried.py
• pointGroup.py
• rmsdAlign.py
• solidAngle.py
• stericMap.py
  • Gallery
• stericMapDifference.py
• substituentSterimol.py
• unique.py

Structures from Scratch

• fetchMolecule.py
• getCoordinationComplexes.py

Job Prepraration

• jobSubmit.py
• makeCrestInput.py
• makeInput.py

Output Processing

• condensedFukui.py
• grabStatus.py
• grabThermo.py
• plotIR.py
  • Gallery
• plotAverageIR.py
• plotUVVis.py
• plotAverageUVVis.py
• plotNMR.py
• plotAverageNMR.py
• printAtomInfo.py
• printAtomPairInfo.py
• printCube.py
• printFreq.py
• printFreqBild.py
• printInfo.py
• printXYZ.py

AaronTools Utilities and Miscellaneous

• getCitations.py
• libaddLigand.py
• libaddRing.py
• libaddSubstituent.py
• listChanges.py
• parsePDF.py