Configuration

The custom Geant4 commands available in the molecularDNA application are listed here. These commands are implemented in the messenger classes of molecularDNA.

Table of contents

analysisDNA
cell
chromosome
damage
dnageom
dnatests
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)
analysisDNA/strandDir	Directory to save DNA damage fragments	DNA fragments (str, Default: Not Set, Omittable: False)
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)
analysisDNA/diagnosticChain	Save the position of hits histones only on one chain	Chain Index (int, Default: Not Set, Omittable: True)
analysisDNA/dsbDistance	Max separation of DSBs. Must be less than 31.	Max. DSB distance. (int, Default: Not Set, Omittable: False)
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)

chromosome

command	description	parameters (example for cyl)
chromosome/add	Add a chromosomal region for analysis of damage. Format: shape name geometry-commands shape is: sphere or cyl or rod or ellipse geometry-commands are: - for sphere: radius x y z unit [rx ry rz] - for cyl: radius height x y z unit [rx ry rz] - for rod: radius height x y z unit [rx ry rz] - for ellipse: x-half-axis y-half-axis z-half-axis x y z unit [rx ry rz] Rotations are optional and in degrees. For example, for an ellipsoid chromosomal region corresponding to a cell nucleus, one can use the following command (as in the macro human_cell.mac): /chromosome/add cell ellipse 7100 2500 7100 0 0 0 nm 0 0 0	radius (double, Default: Not Set, Omittable: False) height (double, Default: Not Set, Omittable: False) x (double, Default: Not Set, Omittable: False) y (double, Default: Not Set, Omittable: False) z (double, Default: Not Set, Omittable: False) Unit (str, Default: Not Set, Omittable: False) [xrotation (double, Default: Not Set, Omittable: False) yrotation (double, Default: Not Set, Omittable: False) zrotation] (double, Default: Not Set, Omittable: False)
chromosome/plotData	Save plot data to specified file	name (str, Default: Not Set, Omittable: False)

damage

command	description	parameters
dnadamage/directDamageLower	Minimum Energy required for an SSB. Chance grows linearly until it reaches the upper value.	energy value (double, Default: Not Set, Omittable: False) Unit (str, Default: Not Set, Omittable: False)
dnadamage/directDamageUpper	Energy required for an SSB to definitely occur	energy value (double, Default: Not Set, Omittable: False) Unit (str, Default: Not Set, Omittable: False)
dnadamage/indirectOHBaseChance	Chance [0,1] of a OH damaging a base	chance (double, Default: Not Set, Omittable: False)
dnadamage/indirectOHStrandChance	Chance [0,1] of a OH damaging sugar-phosphate	chance (double, Default: Not Set, Omittable: False)
dnadamage/inductionOHChance	Chance [0,1] of a Base + OH -> strand break	chance (double, Default: Not Set, Omittable: False)
dnadamage/indirectHBaseChance	Chance [0,1] of a H damaging a base	chance (double, Default: Not Set, Omittable: False)
dnadamage/indirectHStrandChance	Chance [0,1] of a H damaging sugar-phosphate	chance (double, Default: Not Set, Omittable: False)
dnadamage/inductionHChance	Chance [0,1] of a Base + H -> strand break	chance (double, Default: Not Set, Omittable: False)
dnadamage/indirectEaqBaseChance	Chance [0,1] of a Eaq damaging a base	chance (double, Default: Not Set, Omittable: False)
dnadamage/indirectEaqStrandChance	Chance [0,1] of a Eaq damaging sugar-phosphate	chance (double, Default: Not Set, Omittable: False)
dnadamage/inductionEaqChance	Chance [0,1] of a Base + Eaq -> strand break	chance (double, 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)
dnageom/verbose	Verbosity for DNA geometry	int verbose level (int, Default: Not Set, Omittable: False)
dnageom/setSmartVoxels	Optimisation value (int) for smart voxels The G4 default is 2	Optimisation value (int, Default: Not Set, Omittable: False)
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)
dnageom/drawCellVolumes	Draw cell/chromosome volumes rather than DNA (makes DNA invisible)	true/false draw cell volumes (bool, Default: Not Set, Omittable: False)
dnageom/setVoxelPlacementAnglesAsMultiplesOfPi	Take the angles in the voxel placement file as multiples of pi. E.g. set to true if the angle 0.5 should mean 90 degrees.	true/false (bool, Default: Not Set, Omittable: False)
dnageom/useCustomMoleculeSizes	Enable custom molecule sizes. These can be set via /dnageom/moleculeSize.	true/false (bool, Default: Not Set, Omittable: False)
dnageom/moleculeSize	Set a molecule size in angstrom. format: molecule_name x y z. E.g.: PHOSPHATE 3 4 5. Note: molecule names are case insensitive.	name (str, Default: Not Set, Omittable: False) xlength (double, Default: Not Set, Omittable: False) ylength (double, Default: Not Set, Omittable: False) zlength (double, Default: Not Set, Omittable: False)

dnatests

command	description	parameters
dnatests/basepairs	Test chromosome placement classes	None
dnatests/chromosome	Test base pair indices are correct	None
dnatests/uniqueid	Test unique ID algorithm	None

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)