sliding_comparison: Sliding Comparison

In BradyAJohnston/mdfret: Processing and Plotting of MD Data

Sliding Comparison

Description

Takes an AA region of size segment_size, and compares between structures entirety of AA sequence. Moves segment by segment_slide each time.

Usage

sliding_comparison(
  segment_size,
  segment_slide,
  bound_pdb,
  apo_pdb,
  frames_model,
  ncore = 6,
  fit = T
)

Arguments

segment_size	Size of AA sequence in the comparison segment.
segment_slide	Change in segment comparison, per comparison.
bound_pdb	The bound_pdb reference structure.
apo_pdb	The apo_pdb reference structure.
frames_model	The bio3d model that contains the frames to be analysed.
ncore	Number of cores to parallelise the workload (defaults to 6). Requires package parallel.
fit	Whether or not to fit the structures prior to calculating the RMSD values.

Details

Returns a dataframe with corresponding frames, rmsds and regions.

BradyAJohnston/mdfret documentation built on April 16, 2022, 8:32 a.m.