merge: Compile all functions into Shiny

In JerrieFeng/pdbSelectOcclude: Select occluding structures in a 3D molecular visualization environment

Compile all functions into Shiny

Description

Function that takes a PDB file and visualizes it as a 3D model.

Usage

merge(
  pdbFile,
  name,
  styleSel,
  codes = NULL,
  polarity = NULL,
  letter = "ALL",
  values = NULL
)

Arguments

pdbFile	A PDB file, could be downloaded from PDB online
name	the 4-letter PDB codes/identifiers of the PDB file to be visualized.
index	Valid index that refers to a chain found in the protein. Run 'showInfoPDB' to get all possible chains in chain_info

Value

Returns output-text stating the chain, and it displays the 3D model of the protein with the selected chain visible.

References

Yao, X., G. Scarabelli, L. Skjaerven, and B. Grant (2020). Protein Structure Networks with Bio3D. bio3D. http://thegrantlab.org/bio3d/articles/online/cna_vignette/cna_vignette.spin.html#references-1.

Yao, X., G. Scarabelli, L. Skjaerven, and B. Grant (2020). chain.pdb: Find Possible PDB Chain Breaks. bio3D. https://rdrr.io/cran/bio3d/man/chain.pdb.html.

Su, W. (2021). Introduction to r3dmol. r3dmol. https://cran.r-project.org/web/packages/r3dmol/vignettes/r3dmol.html.

Examples

# merge(pdb2, "1SI4", "m_style_stick", "VAL", NULL, "ALL", "Metal")
# runModel(pdb2, "1SI4")

JerrieFeng/pdbSelectOcclude documentation built on May 12, 2022, 8:07 a.m.