R_for_ORCA

R code to visualise spectra from the ORCA output file.

Written by Anthony Nash PhD (inception: 21/07/200).

This is very much a personal-use pursuit but if you make use of these R functions please reference this page along with myself.

Introduction

These R functions were just a little bit of fun to tie my experience of using R with an attempt at forever improving my understanding of theoretical biophysics and computational chemistry.

A list of useful frequency scaling factors can be found here: https://cccbdb.nist.gov/vibscalejust.asp

Language dependencies

The code was written using R 4.0.1 (on a Windows 10 64 bit).

The following packages are required:

• ggplot2 (developed using v. 3.3.2)
• ggrepel (developed using v. 0.8.2)

A quick example

The R functions will look for the single instance of "IR SPECTRUM" and "RAMAN SPECTRUM" in the ORCA output file. If these are not present the user is informed. The code work flow is quite basic:

1. Read in the raw Raman or IR data: getRamanData() or getIRData().
2. Build the ggplot2 visuals and process the raw data: buildPlotSpectra().
3. Visualise the spectra: plotSpectra().

Consider the example of compraing the spectra of two IR and two Raman calculations:

#===============================================================================
source("IR_spectra_code.R")

#Compare two raman spectra
ramanFileDataONEDF <- getRamanData("M06_6-31G(d).OUT")
ramanFileDataTWODF <- getRamanData("M06_6-311G++(d,p).OUT") 
spectraNames <- c("M06_6-31G(d)","M06_6-311G++(d,p)")
ramanSpectraObject <- buildPlotSpectra(ramanFileDataONEDF, ramanFileDataTWODF,
                                        spectraNames=spectraNames, mode="RAMAN", 
                                        minLabelY=100, scalingFactor=c(0.947,0.950))
plotSpectra(ramanSpectraObject)

#===============================================================================
#Compare two IR spectra
irFileDataONEDF <- getIRData("M06_6-31G(d).OUT")
irFileDataTWODF <- getIRData("M06_6-311G++(d,p).OUT") 
spectraNames <- c("M06_6-31G(d)","M06_6-311G++(d,p)")
irSpectraObject <- buildPlotSpectra(irFileDataONEDF, irFileDataTWODF,
                                     spectraNames=spectraNames, mode="IR", 
                                     minLabelY=100, scalingFactor=c(1,1))
plotSpectra(ramanSpectraObject)
#===============================================================================

The peak value labels are assigned when a peak is greater than minLabelY. Labels can be turned off using minLabelY=0. Users can make unique adjustments to the ggplot2 object by retrieving the ggplot2 object found in the first element of the irSpectraObject data structure or by potting the raw spectrum data found in the second element.

Plotting the IR data will produce:

##To do list

1. Gaussian smoothing over groups of peaks. I've yet to find a means of pulling this off in ggplot2.
2. Option to change colours on the graph.
3. A hand save function to a 300 DPI image (publication ready images).