Type: Package
Title: Perform Analysis and Create Visualizations of Proteins
Version: 0.0.1
Author: Simon Liles
Maintainer: Simon Liles <simon@quantknot.com>
Description: Read Protein Data Bank (PDB) files, performs its analysis, and presents the result using different visualization types including 3D. The package also has additional capability for handling Virus Report data from the National Center for Biotechnology Information (NCBI) database. Nature Structural Biology 10, 980 (2003) <doi:10.1038/nsb1203-980>. US National Library of Medicine (2021) https://www.ncbi.nlm.nih.gov/datasets/docs/reference-docs/data-reports/virus/.
Depends: R (≥ 3.1.2)
Imports: pryr, lattice, methods, magick, dplyr, grid, gridExtra, ggplot2, rjson, rlang, shiny
License: CC0
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-08-13 15:36:41 UTC; simon
Repository: CRAN
Date/Publication: 2021-08-16 08:30:07 UTC

Protein Class Definitions

Description

Protein Class used to Define Protein Objects of S3 and S4 Types. Currently still in development, Integrity checks still need to be added.

Format

Breakdown of a Protein Object's structure:

plot3DInteractive

Description

Opens a viewer for exploratory and interactive analysis of a protein structure.

Usage

Protein3D(protein)

Arguments

protein

Protein object to use in plotting

Value

Does not return a value.

fromJSONL

Description

Decode a JSON List into an R List Object.

Usage

fromJSONL(filepath, maxLines = -1)

Arguments

filepath

A character string indicating the filepath from the working directory to the desired file.

maxLines

An integer representing the max number of lines to read. Negative values indicate that one should read up to the end of input on the connection.

Value

a large list, each element containg the contents of a JSON file after being converted.

getAtomicRecord

Description

Retrieve the Atomic Record from a Protein Object

Usage

getAtomicRecord(protein)

Arguments

protein

input for a a protein object

Format

Dataframe with 16 columns:

  1. record_type:Type of record in this section. Generally ATOM or HETATM

  2. serial_num: The serial number for the position of the atom in the sequence

  3. atom_name: A name to identify the atom in a structure

  4. alt_location_id:

  5. residue_name: 3 character identifier for a residue

  6. chain_id:

  7. residue_seq_num: Number representing where in the sequence a residue is.

  8. insert_residue_code:

  9. x_ortho_coord: X coordinate in Ångstroms on an orthogonal plane

  10. y_ortho_coord: Y coordinate in Ångstroms on an orthogonal plane

  11. z_ortho_coord: Z coordinate in Ångstroms on an orthogonal plane

  12. occupancy:

  13. temp_factor: The amount of overall error in the measurement of an atom.

  14. segment_id:

  15. element_symbol: Periodic symbol representing an atom.

  16. charge: Charge of the given atom. Can be +, -, or none at all

Details

This is an accessor function for retrieving the Atomic Record from a Protein object.

Value

Returns a dataframe containing the atomic record. There are 16 variables in this data frame.

getTitleSection

Description

Retrieve the title section from a Protein Object

Usage

getTitleSection(protein)

Arguments

protein

input for a a protein object

Details

This is an accessor function for retrieving the title section from a Protein object.

Value

Returns a list containing elements from the title section.

P53 Tetramerization Domain Crystal Structure

Description

Formal class protein representing data from a PDB, code 1AIE, p53 tetramerization Domain Crystal Structure. This is a small and simple R object of example data for users to play with and is used in example vignettes.

Usage

p53_tetramerization

Format

A Protein S4 object. List comprised of several sublists and dataframes

plot3D

Description

plot the protein structure in 3D

Usage

plot3D(
  protein,
  animated = FALSE,
  type = "p",
  groups = NULL,
  screen = list(x = -60, z = 0, y = 0),
  image_width = 480,
  image_height = 480
)

Arguments

protein

Protein object to be plotted. Can be either of S3 or S4 Protien object type.

animated

logical indicating whether the object is to be animated in the viewer. Will spin the plot on the Z axis.

type

character vector indicating the type of cloud plot. Can include one or more of "p", "l", "h", or "b". "p" and "l" mean points and lines respectively, and "b" means both. "h" stands for histogram and draws lines from each point to the XY plane, either lower or upper bounding box face, whichever is closer.

groups

the name of a column from the Atomic Record of the protein. Causes the points to be colored by the different values in that group.

screen

A list determining the sequence of rotations to be applied to the data before plotting. Each componenet of the list should be one of "x", "y" or "z", repetitions are allowed with values indicating amount of rotation in degrees.

image_width

width of the resulting image in pixels. Currently only applies when 'animated = TRUE'. Defaults to 480 pixels.

image_height

hieght of the resulting image in pixels. Currently only applies when 'animated = TRUE'. Defaults to 480 pixels.

Details

This function uses lattice and magick to create the 3D plot and animate it.

Currently this function is incomplete and will change dramatically as new features and documentation are added.

Value

An object to be plotted. If not assigned to a variable, it will plot directly in the viewer.

plotModels

Description

plot models of the protein structure using ggplot.

Usage

plotModels(protein, separate = FALSE)

Arguments

protein

Protein object to be plotted

separate

indicate wether to plot each plane separately or as one visual.

Details

Create a plot of each plane and model the shape of the protein.

This function uses ggplot and grid to create 3 plots, one for each plane, of the protein model, and then create a smoothing model.

Currently this function is incomplete and will change dramatically as new features and documentation are added.

Value

An object to be plotted. If not assigned to a variable, it will plot directly in the viewer.

read.pdb

Description

Read in a Protein Data Bank file

Usage

read.pdb(fileName, createAsS4 = TRUE)

Arguments

fileName

character string for location and name of file to be read.

createAsS4

Logical indicating whether to create the new protein object as S4 or not. Defaults to TRUE if not specified. This argument is optional.

Format

A Protein object. List comprised of several sublists and dataframes

Details

Reads a Protein Data Bank file (PDB) from the given location. The function then parses the file and creates a new object of the Protein class. This object can be either defined as an S3 or S4 object if different capabilities are required.

Value

A new protein object as either an S3 or S4 object.

In general terms, the new object will be a list of two, a data frame containing the atomic record, and a list of header elements.

report_as_dataframe

Description

Function to transform a list of NCBI Virus Report metadata into a table.

Usage

report_as_dataframe(report, records = c(1:length(report)))

Arguments

report

a list derived a vaccine report from NCBI Datasets.

records

a vector of indices to pull from the report.

Value

A large dataframe with 23 variables containig metadata from NCBI Virus report.

summary.Protein

Description

summary.Protein

Usage

## S4 method for signature 'Protein'
summary(object)

## S4 method for signature 'Protein,ANY'
summary(object,...)

Arguments

object

A Protein object of either S3 or S4 type.

...

other objects passed to 'summary()'. Currently not supported.

Details

Prints a description of the protein object to the console. The lines of out put are as follows.

  1. Prints if it is S3 or S4 object type.

  2. ID Code of the PDB and the Data it was deposited in the Data Bank.

  3. The Classification of the protein.

  4. The title of the PDB.

  5. The number of rows in the Atomic Record.

Value

Does not return a value.

summary.Protein

Description

summary.Protein

Usage

## S3 method for class 'Protein'
summary(object, ...)

Arguments

object

A Protein object of either S3 or S4 type.

...

other objects passed to 'summary()'. Currently not supported.

Details

Prints a description of the protein object to the console. The lines of out put are as follows.

  1. Prints if it is S3 or S4 object type.

  2. ID Code of the PDB and the Data it was deposited in the Data Bank.

  3. The Classification of the protein.

  4. The title of the PDB.

  5. The number of rows in the Atomic Record.

Value

Does not return a value.

write_viz

Description

Wrapper function for writing images to the disk. This function comes from the magick package under the same name.

Usage

write_viz(image, path = "my_image", format = "png")

Arguments

image

magick image object or trellis object.

path

a file path starting from the working directory

format

file type to save the image as. Can be "png", "jpeg", "gif", "rgb", or "rgba".

Value

Does not return a value.