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Main Functions

Command Line Functionalities for Interactive Usgae

extRactoR

Extract Information from Gaussian log files

extRactoR()
Extract and compress all needed information from Gaussian log files.

unwRapper

Utilize compressed .feather files

unwRapper()
Unwrapper for feather files

moleculaR

Extract and Compute Complete Data Sets

moleculaR()
User interface for the extraction of all possible features
moleculaR.input()
User function for the extraction of all possible features based on a ready input file

User Functions - Features

Command Line Functionalities for Interactive Usgae

dip.gaussian.multi()
Pulls and manipulates dipole moment vector. Allows for use of several substructures.
mol.angles.multi()
Compute several angles and dihedrals in a set of molecules
npa.dipole.subunit.multi()
Compute NBO based DM for several substructures
ring.vib.multi()
Get a ring's characteristic vibrations frequencies
steRimol.multi()
Verloop's sterimol values from moleculaR's csv files
steRimol.xyz.multi()
Verloop's sterimol values from xyz files
atoms.distance.df()
Compute atom distances of a set of molecules
bend.vib.df()
Get bending vibrations frequencies for a set of molecules
dip.gaussian.df()
Pulls and manipulates dipole moment vector.
nbo.df()
Pull NBO charges for specific atoms
polar.df()
Pull polarizability info for a set of molecules
ring.vib.df()
Get a ring's characteristic vibrations frequencies, for a set of molecules
steRimol.cube.df()
Compute cube based sterimol parameters
steRimol.df()
Verloop's sterimol values from moleculaR's csv files
steRimol.xyz.df()
Verloop's sterimol values from xyz files
stretch.vib.df()
Get a bond's stretching frequency for a set of molecules
steRimol.cube()
Compute cube based sterimol parameters
xyz.from.cube()
Extract xyz file from Gausssian cube file
plot_molecule()
Generate a 3D plot of an xyz file, including atom indices

User Functions - modeling

Command Line Functionalities for Modeling

model.cv()
Cross validate (k-fold) a single model
model.plot()
ggplot2 plot of a linear model for QSAR
model.report()
Generate models and a plot
model.report.log.ordinal()
Generate a model report - ordinal logistic regression
model.report.logistic()
Generate a model report - logistic regression
model.subset()
Brute force model search with a min and max number of features.
model.subset.log.ordinal()
Get ordinal logistic models of all feature subsets within a scope
model.subset.logistic()
Get logistic models of all feature subsets within a scope
mod.info.log.ordinal()
Model summary - ordinal model
mod.info.logistic()
Model summary - logistic model
ct.plot()
Create a nice classification table (confusion matrix)
prob.heatmap()
Create a nice probabilities of predictions table
simi.sampler()
a similarity based sampling algorithm

User Functions - Utilities

Command Line Functionalities for File Manipulation

coor.trans.file()
Transform coordinate system for a file of choice
extract.connectivity()
Create a bonding data frame
name_changer()
Change names of files in a directory, based on a matched pattern.