In JerrieFeng/pdbSelectOcclude: Select occluding structures in a 3D molecular visualization environment
library(knitr)
opts_chunk$set(fig.align = "center",
out.width = "90%",
fig.width = 6, fig.height = 5.5,
dev.args=list(pointsize=10),
par = TRUE, # needed for setting hook
collapse = TRUE, # collapse input & ouput code in chunks
warning = FALSE)
knit_hooks$set(par = function(before, options, envir)
{ if(before && options$fig.show != "none")
par(family = "sans", mar=c(4.1,4.1,1.1,1.1), mgp=c(3,1,0), tcl=-0.5)
})
set.seed(1) # for exact reproducibility
Introduction
pdbSelectOcclude is an R package for visualizing relationships between protein
structural and non-spatial data, and for selecting occluding structures in a 3D
molecular visualization environment.
To download pdbSelectOcclude, use the following commands:
require("devtools")
devtools::install_github("JerrieFeng/pdbSelectOcclude", build_vignettes = TRUE)
library("pdbSelectOcclude")
To list all sample functions available in the package:
ls("package:pdbSelectOcclude")
To list all sample datasets available in the package:
data(package = "pdbSelectOcclude")
Components
## Set up
There are 5 functions in `pdbSelectOcclude`. All which require *bio3d*, *r3dmol*, and *dplyr*. Shiny will also need to be installed in order to interact with the 3D protein models.
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## Functions
* The **showInfoPDB** A function that takes a PDB file as input, and then returns the AA (amino acid) and chain information of the chosen protein.
Example:
wzxhzdk:5
* The **selAA** A function that allow users to select an AA (may or may not be occluded) to view and interact with. The output will display the protein with only the selected AA visible, while the rest is translucent.
Example:
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* The **selAASlider** A function that allow users to interact with any AA with a slider. Use the slider to select which AA to view on Shiny app.
Example:
wzxhzdk:7
* The **selChain** A function that allow users to select a chain (may or may not occluded)
to view and interact with. The output will display the protein with only the selected chain visible,
while the rest is translucent.
Example:
wzxhzdk:8
* The **selChainSlider** A function that allow users to interact with any chain with a slider. It opens
the slider and 3D model on Shiny app.
Example:
wzxhzdk:9
## Package References
[Feng, J. (2021) pdbSelectOcclude: R Package for selecting occluding structures in a 3D molecular visualization environment. Unpublished.](https://github.com/JerrieFeng/pdbSelectOcclude)
## Other References
Chang, W, et al. (2017). Using sliders. Shiny from Rstudio. https://shiny.rstudio.com/articles/sliders.html.
Chang, W, et al. (2021). shiny: Web Application Framework for R. R package version 1.7.1. https://CRAN.R-project.org/package=shiny.
Skjaerven, L., Yao X.Q., Grant B.J. (2006). Getting started with Bio3D. Grant Lab: ComputationalBiophysics & Bioinformatics. http://thegrantlab.org/bio3d/articles/online/intro_vignette/Bio3D_introduction.html#references-1.
Skjaerven, L., Yao X.Q., Grant B.J. (2020). chain.pdb: Find Possible PDB Chain Breaks.
bio3D. https://rdrr.io/cran/bio3d/man/chain.pdb.html.
Su, W., Johnston, B. (2021). r3dmol: Create Interactive 3D Visualizations of Molecular Data. Github.https://github.com/swsoyee/r3dmol.
Su, W., Johnston, B. (2021). r3dmol-shiny: Shiny bindings for r3dmol. https://rdrr.io/cran/r3dmol/man/r3dmol-shiny.html.
----
wzxhzdk:10
JerrieFeng/pdbSelectOcclude documentation built on May 12, 2022, 8:07 a.m.
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library(knitr) opts_chunk$set(fig.align = "center", out.width = "90%", fig.width = 6, fig.height = 5.5, dev.args=list(pointsize=10), par = TRUE, # needed for setting hook collapse = TRUE, # collapse input & ouput code in chunks warning = FALSE) knit_hooks$set(par = function(before, options, envir) { if(before && options$fig.show != "none") par(family = "sans", mar=c(4.1,4.1,1.1,1.1), mgp=c(3,1,0), tcl=-0.5) }) set.seed(1) # for exact reproducibility
Introduction
pdbSelectOcclude is an R package for visualizing relationships between protein
structural and non-spatial data, and for selecting occluding structures in a 3D
molecular visualization environment.
To download pdbSelectOcclude, use the following commands:
require("devtools") devtools::install_github("JerrieFeng/pdbSelectOcclude", build_vignettes = TRUE) library("pdbSelectOcclude")
To list all sample functions available in the package:
ls("package:pdbSelectOcclude")
To list all sample datasets available in the package:
data(package = "pdbSelectOcclude")
Components
## Set up
There are 5 functions in `pdbSelectOcclude`. All which require *bio3d*, *r3dmol*, and *dplyr*. Shiny will also need to be installed in order to interact with the 3D protein models.
wzxhzdk:4
## Functions
* The **showInfoPDB** A function that takes a PDB file as input, and then returns the AA (amino acid) and chain information of the chosen protein.
Example:
wzxhzdk:5
* The **selAA** A function that allow users to select an AA (may or may not be occluded) to view and interact with. The output will display the protein with only the selected AA visible, while the rest is translucent.
Example:
wzxhzdk:6
* The **selAASlider** A function that allow users to interact with any AA with a slider. Use the slider to select which AA to view on Shiny app.
Example:
wzxhzdk:7
* The **selChain** A function that allow users to select a chain (may or may not occluded)
to view and interact with. The output will display the protein with only the selected chain visible,
while the rest is translucent.
Example:
wzxhzdk:8
* The **selChainSlider** A function that allow users to interact with any chain with a slider. It opens
the slider and 3D model on Shiny app.
Example:
wzxhzdk:9
## Package References [Feng, J. (2021) pdbSelectOcclude: R Package for selecting occluding structures in a 3D molecular visualization environment. Unpublished.](https://github.com/JerrieFeng/pdbSelectOcclude)
## Other References Chang, W, et al. (2017). Using sliders. Shiny from Rstudio. https://shiny.rstudio.com/articles/sliders.html. Chang, W, et al. (2021). shiny: Web Application Framework for R. R package version 1.7.1. https://CRAN.R-project.org/package=shiny. Skjaerven, L., Yao X.Q., Grant B.J. (2006). Getting started with Bio3D. Grant Lab: ComputationalBiophysics & Bioinformatics. http://thegrantlab.org/bio3d/articles/online/intro_vignette/Bio3D_introduction.html#references-1. Skjaerven, L., Yao X.Q., Grant B.J. (2020). chain.pdb: Find Possible PDB Chain Breaks. bio3D. https://rdrr.io/cran/bio3d/man/chain.pdb.html. Su, W., Johnston, B. (2021). r3dmol: Create Interactive 3D Visualizations of Molecular Data. Github.https://github.com/swsoyee/r3dmol. Su, W., Johnston, B. (2021). r3dmol-shiny: Shiny bindings for r3dmol. https://rdrr.io/cran/r3dmol/man/r3dmol-shiny.html. ---- wzxhzdk:10
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.