STM4 – changes from STM3

STM4 is an effort to refactor and clean the current STM3 implementation.

Motivations for this effort are:

The list of modules has been defined incrementally answering requests and solving real user problems. That means interesting problems, but also: disorder, things learned on the job, discontinuous development and not every case covered (e.g. multi-component PDB).
Besides some basic design, STM3 grow organically, sometimes with duplication of efforts and code.
The algorithms are tightly linked with AVS/Express API, so it is difficult to replace them or to reuse them inside other tools.

From a concrete point of view, I’m developing:

A more complete MolecularDataType
An interface library between this data type and the modules code
Cleaning and unifying GUI elements and common routines
Upgrading modules to take advantage of those common elements (plus the accumulated knowledge about them)

I presented the STM4 design and development process during the Swiss AVS User Meeting on December 6, 2006.

Here below you find:

Modules not ported
Modules deeply changed
STM3 module correspondence in STM4

Modules not ported

Module	Reason
Atoms Numbering	Now integrated in Draw Structure
Fill Unit Cell	Integrated inside the modules that needs it
Crop Inside Unit Cell	Why it was created in the first instance?
Crop Atoms	Now integrated inside Crop Structure
Crop Unit Cell	Can be done using Crop Structure
Float 2 Byte	Now integrated inside the Volume Render module
Add Bonds	Superseded by Set Manual Bonds
Read Anim Molecule	There will be a single reader
Read Gaussian Cube	Merged inside Read Structure
Read CHGCAR	Merged inside Read Structure
Read Kino and Cell	Merged inside Read Structure
AnimDisplayApp	Merged inside MolDisplayApp
ReadCHGCARApp	Merged inside MolDisplayApp

Modules deeply changed

Module	Reason
Write Structure	The various writers have been consolidated into this module using a plugin architecture
Read Structure	The various readers and the animated molecule readers have been consolidated into this module using a plugin architecture
Draw Polyhedra	It combine the various Find {Tetrahedra, Octahedra, Polyhedra}
Accumulate Traces	Removed options to accumulate and playback a trace (never used)
Scat2Volume	Method changed, now it is a module, not an application

STM3 module correspondence in STM4

STM3	STM4
Accumulate Traces	Accumulate Traces
Add Bonds	Superseded by Set Manual Bonds
AnimDisplayApp	MolDisplayApp
Apply Symmetries	Apply Symmetries
Atoms Numbering	Now an option of Display Structure
Axis Glyph	Axis Glyph
Bicolor Surface	Bicolor Surface
Bonds by Atom	Compute Selected Bonds
BondsByAtomApp
CHGCARDisplayApp	MolDisplayApp
Color Legend	Color Legend
Compute SE Surface	Solvent Excluded Surface
Count Bonds	Count Bonds
Count H Bonds	Count H Bonds
CountHBondsApp
Crop Atoms	Now integrated inside Crop Structure
Crop Cluster	Crop Structure
Crop Inside Unit Cell	Not ported
Crop Unit Cell	Not ported. Can be done using Crop Structure
CrystalDisplayApp	CrystalDisplayApp
Cube on Surface	Cube on Surface
Cut Surface	Cut Surface
Display Molecule	Draw Structure
Display Molecule Sw	Draw Sw Structure
Display Unit Cell	Display Unit Cell
Error Tube	Error Tube
Fill Unit Cell	Integrated inside the modules that needs it
Find Octahedra	Draw Polyhedra
Find Polyhedra	Draw Polyhedra
Find Tetrahedra	Draw Polyhedra
Float 2 Byte	Now integrated inside the Volume Render module
Generate Crystal	Not ported
Interpolate Sequence	Interpolate Sequence
Isosurface	Isosurface
Logo	Logo
make movie	Make Movie
Measure Closer Atoms	Measure Closer Atoms
Measure Molecule	Measure Structure
MeasureCloserAtomApp
Merge Charges	Merge Values
Miller Plane	Miller Plane
MolDisplayApp	MolDisplayApp
NCAC Tube	Backbone
Occupancy Histogram	Not ported
Orthoslice	Orthoslice
output image	Output Image
Particle Density	Particle Density
ParticleDensityApp
Pick Unit Cell	Pick Unit Cell
PickMoleculeApp	PickDisplayApp
PickUnitCellApp	PickUnitCellApp
Read Anim Molecule	Read Structure
Read CHGCAR	Read Structure
Read Gaussian Cube	Read Structure
Read Kino And Cell	Read Structure
Read Molecule	Read Structure
Recompute Bonds	Compute Bonds
Replicate Lattice	Replicate Lattice
Scat2VolumeApp	Now it is the module Atoms Values Trasp
Select Atoms	Select Atoms
Select Residues	Select Fragments
Set Manual Bonds	Set Manual Bonds
Shift Unit Cell	Shift Unit Cell
Smooth Tube	Smooth Tube
Threshold Charge	Threshold Data
Time Legend	Time Legend
TracesDisplayApp	TracesDisplayApp
Velocity Mean	Velocity Mean
Write Kino	Write Structure
Write PDB	Write Structure
Write POV Ray	Write POV Ray
Write VASP Poscar	Write Structure
X Ray Structure Factor	X Ray Structure Factor
XRayStructureFactorsApp