m_vibrate: Add model's vibration

In r3dmol: Create Interactive 3D Visualizations of Molecular Data

Description

If atoms have dx, dy, dz properties (in some xyz files), vibrate populates each model's frame property based on parameters. Models can then be animated.

Usage

m_vibrate(id, numFrames, amplitude, bothWays, arrowSpec)

Arguments

id	R3dmol id or a r3dmol object (the output from r3dmol())
numFrames	Number of frames to be created, default to 10
amplitude	Amplitude of distortion, default to 1 (full)
bothWays	If true, extend both in positive and negative directions by numFrames
arrowSpec	Specification for drawing animated arrows. If color isn't specified, atom color (sphere, stick, line preference) is used.

Value

R3dmol id or a r3dmol object (the output from r3dmol())

Examples

library(r3dmol)

xyz <- "4
* (null), Energy   -1000.0000000
N     0.000005    0.019779   -0.000003   -0.157114    0.000052   -0.012746
H     0.931955   -0.364989    0.000003    1.507100   -0.601158   -0.004108
H    -0.465975   -0.364992    0.807088    0.283368    0.257996   -0.583024
H    -0.465979   -0.364991   -0.807088    0.392764    0.342436    0.764260
"

r3dmol() %>%
  m_add_model(data = xyz, format = "xyz") %>%
  m_set_style(style = m_style_stick()) %>%
  m_vibrate(numFrames = 10, amplitude = 1) %>%
  m_animate(options = list(loop = "backAndForth", reps = 0)) %>%
  m_zoom_to()

r3dmol documentation built on March 14, 2021, 5:08 p.m.