Add model's vibration — m_vibrate • r3dmol

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.

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()