STM4 module list

This is the list of STM4 modules in the 20110421 version.

The standard AVS/Express documentation provides instead reference for the standard modules used or modified inside STM4.

The modules are grouped by function:

Readers Writers	Readers and writer for various, static and dynamic, chemical file formats plus movies and images production.
Bonds	Bonds computation, editing and management.
Modules	Modules that compute derived structures.
Selection	Selector modules to extract a subset of the atoms.
Trajectories	Modules related to dynamic data.
Crystallography	Unit cells, periodic lattices and symmetries support.
Volume	Rendering of volumetric data like Gaussian cubes.
Display	Rendering of chemical structures and other graphical objects.
Probe and Measure	Interact with the structures: measure and editing.
Full Apps	Ready to run applications (plus display of the STM4 version).
Experimental	Modules not intended for general usage.
Crystal Fingerprints	Modules for analyzing USPEX output.
Align Structures	Modules to align structures given two sets of corresponding atoms.
Dataypes	Definition of data types used by the STM4 library.

To start using STM4 drag one of the Full Applications modules (MolDisplayApp for example) to the Network Editor area.

Readers Writers

Read Structure	Read structural and volumetric chemical data.
Read Structure No Bonds	Read a structure from file without computing bonds.
Read Scalar	Read a set of scalar values from a file.
Read Vector	Read a set of 3D vector values from a file.
Make Movie	Capture a sequence of frames, one for each different viewer content, and assemble them in a movie (AVI or MPEG).
Output Image	Save a snapshot of the content of the current viewer.
Write Structure	Write a single structure or a trajectory to a chemistry data file in the selected format.
Write POV Ray	Write the current view as a POV-Ray raytracer scene.
Read Fermi Surface	Read a file in EIGENVAL format and output a volume that, using Isosurface or Isosurface nest, display the Fermi surfaces at a given energy level.
Read Fermi Bands	Read a file in EIGENVAL format and output for all bands their energy along a given polyline.
Write Summary	Write a summary of the series of structures given as input.

Bonds

Compute Bonds	Compute atomic bonds.
Count Bonds	Add as atom data the atom's number of bonds.
Count H Bonds	Count the number of H Bonds present in the input structure. The count is added to the structure global data.
Compute Selected Bonds	Adds bonds to specific atoms using a distance criteria.
Set Manual Bonds	Manually add bonds between atoms.

Modules

Solvent Excluded Surface	Compute the molecule Solvent Excluded Surface.
Backbone	Compute a protein backbone.
General Backbone	Display a tube through user selected atoms.
Vector Glyph	Display with arrows the vector data associated with a given structure.
Merge Values	Add a new scalar or vector data to atoms, bonds or globally to the given structure.
Atoms Values Trasp	Atoms are rendered with transparency dependent on the associated scalar value
Particle Density	Compute the average particle mass density using uniform binning.
Interpolating Plane	Build the least square plane interpolating a set of picked atoms (n ≥ 3).

Selection

Select Atoms	Select specific atoms.
Select Fragments	Select specific structure fragments (i.e. residues).
Threshold Data	Select atoms whose associated scalar value meets various criteria.
Delete Atoms	Interactively delete atoms.

Trajectories

Accumulate Traces	Accumulate traces (accumulated positions) for specific atoms in a sequence of time steps.
Accumulate Global Data	Accumulate a global scalar data in a form suitable for charting.
Interpolate Sequence	Linearly interpolate a given number of positions between each pair of timesteps.
Velocity Mean	Compute the average particle velocity using uniform binning.
Enthalpy Transitions	Search a range of pressure values to find where the structure with the minimum enthalphy changes.

Crystallography

Replicate Lattice	Replicate the structure unit cell along the three base vectors.
Apply Symmetries	Compute new atoms positions from the space group of the input molecule.
Shift Unit Cell	Shift the unit cell to re-center periodic phenomena that are split between the opposite sides of the cell.
Enlarge Unit Cell	Add atoms outside the unit cell by different criteria.
Move Structure	Translate and rotate a given structure modifying all the atoms coordinates.
Crop Structure	Crop a structure and the optional volume data inside a given geometry.
Crop From Plane	Remove atoms that dist more than a given value from a plane.
Miller Plane	Crop the atoms using the plane identified by given Miller indices.
Draw Polyhedra	Display a convex polyhedron around selected atoms.
Draw Simple Polyhedra	Display a convex polyhedron around selected atoms using a different setup.
X Ray Structure Factor	Compute and display simplified X-Ray structure factors.
Remove Border Atoms	Remove atoms that bonds with atoms outside the unit cell.
Merge Unit Cell	Apply the unit cell of one structure to another one.
Find Symmetries	Find symmetries in the input structure and simplify it.

Volume

Isosurface	Create an isosurface for a given scalar volumetric value.
Orthoslice	Create an orthoslice for a given scalar volumetric value.
Volume Render	Volumetric render of a scalar valued volume.
Cube on Surface	Assign to a surface the values of the volume in which the surface is immersed in the positions occupied by the surface itself.
Cut Surface	Cut a surface (eg. a Solvent Excluded Surface) with a plane.
Bicolor Surface	Color a surface on one side with a user specified color leaving the other one with its original coloring.
Interpolate Volume	Interpolate a given scalar volume adding points between original grid points.

Display

Draw Structure	Transform the molecule structure data into graphic objects for display.
Draw Sw Structure	Transform the molecule structure data into graphic objects for display using a software render method.
Info Sets Editor	Manage, edit, create and destroy Info Sets.
Display Unit Cell	Displays the borders of the unit cell.
Set Rendering Mode	Set the rendering mode on an atom by atom base.
Axis Glyph	Display three arrows to mark the origin and the XYZ axis directions, or the unit cell abc vectors. The glyph could also be offset from the origin.
Background Fade	Provide a colored backdrop for which you can set the four corners colors.
Logo	Create a logo image to be added to a viewer. The image is locked in the viewer and is not transformed by standard mouse actions.
Enclosing Ellipsoid	Compute an ellipsoid that encloses the given set of atoms.
Time Legend	Display a progress bar to show the current timestep / current time for an animated molecule trajectory.
Color Legend	Display a legend for the structure representation colors.
Discrete Legend	Color legend for integer values in an user specified range.
Smooth Tube	Create a tube that connect all the given points.
Error Tube	Create a tube with a radius proportional to the values associated to the connected points.
Structure Info	Show count of the number of atoms present in the input structure.

Probe and Measure

Measure Structure	Access information about and measure a displayed structure.
Measure Closer Atoms	Measure intra-atomic distances between a given atom and the surrounding ones in a given range.
Pick Unit Cell	Redefines the unit cell for the displayed structure by picking on four atoms.

Full Apps

MolDisplayApp	Read and display a molecule.
CrystalDisplayApp	Read and display structures with symmetries and unit cell replication.
VolumeDisplayApp	Read and display a structure that has volumetric data associated.
PickDisplayApp	Read and display a structure and enable picking to measure it.
TracesDisplayApp	Read and display atom traces during a trajectory visualization.
TracesDisplaySwApp	Read and display atom traces during a trajectory visualization (using sw rendering).
PickUnitCellApp	Redefine the molecule unit cell by corner picking and crops the structure inside the new unit cell.
FermiSurfacesApp	This is a full application ready for use to display Fermi surfaces computed at a given Fermi energy.
FermiBandsApp	This is a full application ready for use to display energy for Fermi along a given polyline.

Datatype Definitions

MoleculeType	Datatype used by the modules that operate on molecular data.
DisplayParamsType	Datatype that carries information on how the molecules are rendered on screen.