Make pseudo AFM images from a structure file.

All the configurations are written in .toml file. No command-line option is available.

$ afmize example.toml

It uses toml format as a config file format. For more information about the format, see the spec of toml-v0.5.0.

file.input           = "example.pdb"
file.output.basename = "output"
file.output.formats  = ["csv", "json", "ppm", "svg"]
probe.size           = {radius = "1.0nm", angle = 10.0}
resolution.x         = "1.0nm"
resolution.y         = "1.0nm"
resolution.z         = "0.64angstrom"
range.x              = ["0.0nm", "100.0nm"]
range.y              = ["0.0nm", "100.0nm"]
scale_bar.length     = "5.0nm"
stage.align          = true

Length unit is angstrom by default. You can explicitly specify "nm", "pm", and "angstrom".

• file.input: String
  • An input structure. .pdb or .xyz are available.
  • note that it may fail reading pdb files that does not conform wwPDB 3.3.
• file.output.basename: String
  • An output filename. An extension will be added.
• file.output.formats: Array of Strings
  • An output format. One or more formats can be selected from ["csv", "json", "ppm", "svg"].

• method: String, "rigid" or "smooth".
  • By default, "rigid".
  • "rigid" is a collision-detection based method.
  • "smooth" is a method introduced in the paper

In the "rigid" method, the AFM cantilever tip will be modeled as a hemisphere on top of truncated cone. If you specify "smooth" method, the value will be ignored.

• probe.size.radius: String or Floating
  • The radius of the probe.
• probe.size.angle: Floating
  • The angle of the cone. The unit is degree, not radian.

• resolution.x: String or Floating
  • The resolution in x direction. The same as the pixel width.
• resolution.y: String or Floating
  • The resolution in y direction. The same as the pixel height.
• resolution.z: String or Floating
  • The resolution in z direction. The output height will be rounded using this.

• range.x: Array of Strings or Floatings
  • The minimum and maximum coordinate of scanning range in x direction.
  • Atoms that exceed this boundary will not be scanned.
• range.y: Array of Strings or Floatings
  • The minimum and maximum coordinate of scanning range in y direction.
  • Atoms that exceed this boundary will not be scanned.

• stage.position: String or Floating
  • The stage position in Z direction.
  • By default, 0.
• stage.align: Boolean
  • If true, the position in Z axis of the structure will be aligned to 0.
  • Otherwise, the position will be kept intact.
  • By default, true.

You can change the atom radius in this table. By defualt, only a few number of atoms are supported. If you got some error like unknown atom, specify its radius in this table.

• radii.atom.[name-of-atom]: String or Floating
  • Replace [name-of-atom] by your atom name.
  • The atom [name-of-atom] will have the radius you specified here.
• radii.residue.[name-of-residue]: String or Floating
  • Replace [name-of-residue] by your residue name.
  • All the atoms in the residue [name-of-residue] will have the same radius you specified here.

Scale bar option is only available with .svg output format. If you specify other format, the value will be ignored.

• length: String or Floating
  • The length of the scale bar.

Parameters sigma and gamma that are used in the "smooth" method. If you specify "rigid" method, the value will be ignored.

• sigma: String or Floating
  • The value of sigma in the formula described in the paper.
• gamma: String or Floating
  • The value of gamma in the formula described in the paper.

Use your favorite package managers (e.g. apt) to install them.

• CMake (> 3.2)
  • to generate Makefile.
• git
  • to download submodules.
• C++14 compliant compiler. tested with ...
  • g++-7 or later
  • clang++-6 or later
  • or others that fully support C++14 ISO standard.

All other dependencies are managed by CMake script and git submodule.

$ git submodule update --init
$ mkdir build
$ cd build
$ cmake ..
$ make
$ make test # optional

After this, you will find the executable at bin/ directory.

Please cite the following.

• Toru Niina, Sotaro Fuchigami, & Shoji Takada (2020, January 7). Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations. JCTC. doi:10.1021/acs.jctc.9b00991
• Toru Niina, & Suguru Kato. (2019, August 7). ToruNiina/afmize: version 1.1.0 (Version v1.1.0). Zenodo. doi:10.5281/zenodo.2556444

If you have any question, please feel free to make an issue to this repository.

Issues are public. Everyone can share information about problems and save time.

If you want to share a sensitive data with the repository owner to solve the problem, you can e-mail to me.

This product is licensed under the terms of the MIT License.

• Copyright (c) 2018-2020 Toru Niina

All rights reserved.