Configuration
The custom Geant4 commands available in the molecularDNA application are listed here.
Table of contents
- analysisDNA
- cell
- dnageom
- world
analysisDNA
| command | description | parameters |
|---|
| analysisDNA/saveStrands | Bool to set whether strands ought be saved use /analysisDNA/strandDir to set location | - (bool, Default: Not Set, Omittable: False)
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| analysisDNA/strandDir | Directory to save DNA damage fragments | - DNA fragments (str, Default: Not Set, Omittable: False)
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| analysisDNA/fragmentGap | Gap between DNA fragments in base pairs. Set to zero to score placement volumes independently | - Base Pair gap (int, Default: Not Set, Omittable: False)
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| analysisDNA/diagnosticChain | Save the position of hits histones only on one chain | - Chain Index (int, Default: Not Set, Omittable: True)
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| analysisDNA/dsbDistance | Max separation of DSBs. Must be less than 31. | - Max. DSB distance. (int, Default: Not Set, Omittable: False)
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| analysisDNA/testClassifier | Run unit test for break classification | |
| analysisDNA/fileName | ROOT output file name | - ROOT output file name (str, Default: Not Set, Omittable: False)
|
cell
| command | description | parameters |
|---|
| cell/radiusSize | Set semi-major axes for cell (x, y, z) - unset, whole world is water | - xradius (double, Default: Not Set, Omittable: False)
- yradius (double, Default: Not Set, Omittable: False)
- zradius (double, Default: Not Set, Omittable: False)
- Unit (str, Default: Not Set, Omittable: False)
|
dnageom
| command | description | parameters |
|---|
| dnageom/placementVolume | Set a placement volume format: name path | - name path (str, Default: Not Set, Omittable: False)
|
| dnageom/definitionFile | Path to file that defines placement locations | - path (str, Default: Not Set, Omittable: False)
|
| dnageom/placementSize | Side length for each placement (x, y, z) | - xlength (double, Default: Not Set, Omittable: False)
- ylength (double, Default: Not Set, Omittable: False)
- zlength (double, Default: Not Set, Omittable: False)
- Unit (str, Default: Not Set, Omittable: False)
|
| dnageom/fractalScaling | Scaling of XYZ in fractal definition file | - xlength (double, Default: Not Set, Omittable: False)
- ylength (double, Default: Not Set, Omittable: False)
- zlength (double, Default: Not Set, Omittable: False)
- Unit (str, Default: Not Set, Omittable: False)
|
| dnageom/checkOverlaps | Check overlaps in DNA geometry region | - true/false check overlaps (bool, Default: Not Set, Omittable: False)
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| dnageom/verbose | Verbosity for DNA geometry | - int verbose level (int, Default: Not Set, Omittable: False)
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| dnageom/setSmartVoxels | Optimisation value (int) for smart voxels The G4 default is 2 | - Optimasation value (int, Default: Not Set, Omittable: False)
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| dnageom/interactionDirectRange | Critical range to start recording SSBs from direct effects | - Range (double, Default: Not Set, Omittable: False)
- Unit (str, Default: Not Set, Omittable: False)
|
| dnageom/radicalKillDistance | Distance from base pairs at which to kill radicals | - Range (double, Default: Not Set, Omittable: False)
- Unit (str, Default: Not Set, Omittable: False)
|
| dnageom/activateHistoneScavenging | Activate Histone scavenging function | - true/false Histone function (bool, Default: Not Set, Omittable: False)
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| dnageom/drawCellVolumes | Draw cell/chromosome volumes rather than DNA (makes DNA invisible) | - true/false draw cell volumes (bool, Default: Not Set, Omittable: False)
|
world
| command | description | parameters |
|---|
| world/worldSize | Side length for the world | - Side length (double, Default: Not Set, Omittable: False)
- Unit (str, Default: Not Set, Omittable: False)
|