Mario Valle Web

STM4 – changes from STM3

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

Motivations for this effort are:

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

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

Atoms Numbering Now integrated in Draw Structure
Fill Unit CellIntegrated inside the modules that needs it
Crop Inside Unit CellWhy it was created in the first instance?
Crop AtomsNow integrated inside Crop Structure
Crop Unit CellCan be done using Crop Structure
Float 2 ByteNow integrated inside the Volume Render module
Add BondsSuperseded by Set Manual Bonds
Read Anim MoleculeThere will be a single reader
Read Gaussian CubeMerged inside Read Structure
Read CHGCARMerged inside Read Structure
Read Kino and CellMerged inside Read Structure
AnimDisplayAppMerged inside MolDisplayApp
ReadCHGCARAppMerged inside MolDisplayApp

Modules deeply changed

Write StructureThe various writers have been consolidated into this module using a plugin architecture
Read StructureThe various readers and the animated molecule readers have been consolidated into this module using a plugin architecture
Draw PolyhedraIt combine the various Find {Tetrahedra, Octahedra, Polyhedra}
Accumulate TracesRemoved options to accumulate and playback a trace (never used)
Scat2VolumeMethod changed, now it is a module, not an application

STM3 module correspondence in 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Add Bonds Superseded by Set Manual Bonds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
CHGCARDisplayApp MolDisplayApp
Color Legend Color Legend
Compute SE Surface Solvent Excluded Surface
Count Bonds Count Bonds
Count H Bonds Count H Bonds
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
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
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