form.grid: Form 3D grid for pdb file
In ShaoxunLiu/proteinStructureBoost: Generate Boosting Model for Structured Protein

This function generates a 3D grid for a given pdb structure or pdb file directory, with each atom shown as the designated atom.value.

form.grid(
  pdb = NA,
  pdb.name = "pdb0",
  pdb.file = NA,
  combine.chains = TRUE,
  size = 32,
  units = 16,
  center.median = TRUE,
  center = NA,
  show.grid = TRUE
)

`pdb`	pdb structure from bio3d::read.pdb. (if entered, should not enter pdb.file).
`pdb.name`	Name of the pdb structure entered. Only enter when pdb argument is used, and pdb.file is not.
`pdb.file`	Directory to the pdb file. (if entered, should not enter pdb).
`combine.chains`	If true, assign all chains in the pdb file in one grid. If false, generates a separate grid for each chain.
`size`	The length of the recognition cube in Angstroms
`units`	The number of blocks in each axis.
`center.median`	If true, centers each chain (or all chains depending on combine.chains) to the median of their xyz.
`center`	Designated center for all chains in pdb. Only enter value when center.median = FALSE.
`show.grid`	If true, outputs an .html file that contains the 3D representation of the grid. Directory to output 3D representation .html file is the same as the .pdb file.

A list of 3d arrays containing the 3D grids of each chain (or all chains as a whole when combine.chains = TRUE) of the pdb file with attributes of input parameters.

ShaoxunLiu/proteinStructureBoost documentation built on Dec. 18, 2021, 1:05 p.m.