sodium acetate
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SODIUM 1.5.1
SODIUM it arranges ions around biological macromolecules. more>>
This program places the required number of sodium ions around a system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex).
The ions are placed in the nodes of a cubic grid, in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy:
Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i|
All the constants are dropped out from this formula, resulting in some weird energy units; that doesnt matter for the purpose of energy comparison. To speed the program up, the atoms of the macromolecule are re-located to the grid nodes, closest to their original locations.
The resulting error is believed to be minor, compared to that resulting from the one-by-one ions placement, or from using the simplified energy function. The coordinates of the placed ions are printed out in the PDB format for further usage.
It is recommended that the placed ions are equilibrated in a separate Monte Carlo or Molecular Dynamics simulation. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.
<<lessThe ions are placed in the nodes of a cubic grid, in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy:
Energy(R) = Sum(i_atoms,ions) Q_i / |R-R_i|
All the constants are dropped out from this formula, resulting in some weird energy units; that doesnt matter for the purpose of energy comparison. To speed the program up, the atoms of the macromolecule are re-located to the grid nodes, closest to their original locations.
The resulting error is believed to be minor, compared to that resulting from the one-by-one ions placement, or from using the simplified energy function. The coordinates of the placed ions are printed out in the PDB format for further usage.
It is recommended that the placed ions are equilibrated in a separate Monte Carlo or Molecular Dynamics simulation. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.
Download (0.40MB)
Added: 2005-04-01 License: Free To Use But Restricted Price:
1699 downloads
E-Gantt 0.5.2
E-Gantt is an open source gantt chart library in Java / Swing which is intended for usage in logistics and scheduling app. more>>
E-Gantt is an open source gantt chart library in Java and Swing which is intended for usage in logistics and scheduling applications.
E-Gantt has been in-active for over a year, but has recently seen a lot of work done which includes a simplified interface and documentation in the form or tutorials to make the project easier to use.
Despite this E-Gantt has been succesfully implemented in many large open source projects and commercial projects with-in the following industries.
- Scheduling Research
- Medical Research
- US Military Defense Projects
- Network Administration tools
How E-Gantt works
Rather than develop a brand-new table component for Swing or extend the table component making it propreitry and difficult to work with. E-Gantt heavily utlilizes the existing JTable framework with modifying it, which serves to allow companies using E-Gantt the ability to use there own JTable extensions with E-Gantt with no futher work.
E-Gantt does this by mapping the DefaultCellRender, DefaultCellEditor of the table for its own column class. The Gantt chart will be rendered with-in each column of the table.
The value returned by the getValueAt of the table model is required to be of a DrawingState which is the value for each column.
Drawing State
The DrawingState is a value which is used for the rendering the gantt drawing which is returned by the methd call tableModel.getValueAt(row, column).
The DrawingState contains a lot of information about the actual drawing including:
- Location of the Top and Bottom of the Entry
- A reference key to indicate how the Entry should be drawn
- A reference key to indicate how the Entry should be coloured
For getting started this has been made easier by a helper class GanttEntryHelper. GanttEntryHelper can be called with as little information as a start time and a finish time this can be done as static data or called dynamically with-in the actual table model.
Enhancements:
- The drawing tool was fixed to determine the width of an entry.
- The GlassPane / Acetate layer for tools was introduced.
- A new demo for modifiying drawing context was included.
- A new example of text on diagrams (a layering example) was added.
- A new example of multi-entry was added to the examples.
<<lessE-Gantt has been in-active for over a year, but has recently seen a lot of work done which includes a simplified interface and documentation in the form or tutorials to make the project easier to use.
Despite this E-Gantt has been succesfully implemented in many large open source projects and commercial projects with-in the following industries.
- Scheduling Research
- Medical Research
- US Military Defense Projects
- Network Administration tools
How E-Gantt works
Rather than develop a brand-new table component for Swing or extend the table component making it propreitry and difficult to work with. E-Gantt heavily utlilizes the existing JTable framework with modifying it, which serves to allow companies using E-Gantt the ability to use there own JTable extensions with E-Gantt with no futher work.
E-Gantt does this by mapping the DefaultCellRender, DefaultCellEditor of the table for its own column class. The Gantt chart will be rendered with-in each column of the table.
The value returned by the getValueAt of the table model is required to be of a DrawingState which is the value for each column.
Drawing State
The DrawingState is a value which is used for the rendering the gantt drawing which is returned by the methd call tableModel.getValueAt(row, column).
The DrawingState contains a lot of information about the actual drawing including:
- Location of the Top and Bottom of the Entry
- A reference key to indicate how the Entry should be drawn
- A reference key to indicate how the Entry should be coloured
For getting started this has been made easier by a helper class GanttEntryHelper. GanttEntryHelper can be called with as little information as a start time and a finish time this can be done as static data or called dynamically with-in the actual table model.
Enhancements:
- The drawing tool was fixed to determine the width of an entry.
- The GlassPane / Acetate layer for tools was introduced.
- A new demo for modifiying drawing context was included.
- A new example of text on diagrams (a layering example) was added.
- A new example of multi-entry was added to the examples.
Download (3.9MB)
Added: 2006-03-26 License: QPL (QT Public License) Price:
1310 downloads
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