Function reference • moleculaR

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.