kinetics/lookupVolumeFromMesh.h File Reference
Go to the source code of this file.
Functions | |
| double | lookupVolumeFromMesh (const Eref &e) |
| unsigned int | getReactantVols (const Eref &reac, const SrcFinfo *pools, vector< double > &vols) |
| double | convertConcToNumRateUsingMesh (const Eref &e, const SrcFinfo *pools, bool doPartialConversion) |
| double | convertConcToNumRateUsingVol (const Eref &e, const SrcFinfo *pools, double volume, double scale, bool doPartialConversion) |
| double | convertConcToNumRateInTwoCompts (double v1, unsigned int n1, double v2, unsigned int n2, double scale) |
| ObjId | getCompt (Id id) |
Variables | |
| const double | CONC_UNIT_CONV |
Function Documentation
| double convertConcToNumRateInTwoCompts | ( | double | v1, | |
| unsigned int | n1, | |||
| double | v2, | |||
| unsigned int | n2, | |||
| double | scale | |||
| ) |
Generates conversion factor for rates from concentration to mol# units. This variant is used when the reactants are in different compartments or mesh entries, and may therefore have different volumes. We already know the reactants and their affiliations. We use the first vol, v1, as the reference. The outcome of this calculation is: kf = Kf * convertConcToNumRate. The scale term is a conversion from the conc units to SI: The scale term is 1 if conc units are in SI, which is equal to moles per cubic metre, which is equal to millimolar. The scale term is 1e-3 for micromolar, uM.
Generates conversion factor for rates from concentration to mol# units. This variant is used when the reactants are in different compartments or mesh entries, and may therefore have different volumes. We already know the reactants and their affiliations.
References NA.
| double convertConcToNumRateUsingMesh | ( | const Eref & | e, | |
| const SrcFinfo * | pools, | |||
| bool | doPartialConversion | |||
| ) |
Generates conversion factor for rates from concentration to mol# units. Assumes that all reactant pools (substrate and product) are within the same mesh entry and therefore have the same volume. The outcome of this calculation is: kf = Kf * convertConcToNumRate. The Eref is an Enz or Reac. The SrcFinfo is a message to the pools. The meshIndex specifies the mesh voxel to use. The scale term is a conversion from the conc units to SI: The scale term is 1 if conc units are in SI, which is equal to moles per cubic metre, which is equal to millimolar. The scale term is 1e-3 for micromolar, uM. The doPartialConversion flag tells the function that there are other substrates not in the 'pools' list, and so it should compute the conversion for all pools, not n-1. This flag defaults to 0.
Returns conversion factor to convert rates from concentration to mol# units. Handles arbitrary combinations of volumes. Assumes that the reference volume for computing rates is the smallest volume. 26 Feb 2013: This is now changed to use the volume of the first entry. Should only be used for substrates. For products need to find the first substrate, separately, and use that to scale down the conv factor. Assumes all calculations are in SI: cubic metres and millimolar. 27 Feb 2013: This is changed to use the volume of a voxel of the the home compartment of the reac. Be warned: this can cause unexpected problems if the home compartment isn't according to convention. For example, if there is a single substrate and the home compartment is elsewhere, you will get very odd Kf:kf values. 9 Oct 2013: This is now changed to use the volume of the first substrate. Note that if the conversion is for products, then the routine has to look up the substrate list to get the first substrate. Reason is that the home compartment was often wrong in ReadKkit. Unfortunately this may yet cause problems with SBML. I don't know what conventions they use for cross-compartment reactions.
References Element::cinfo(), Eref::element(), Cinfo::findFinfo(), getReactantVols(), NA, and Finfo::name().
Referenced by ZombieEnz::vGetK1(), ZombieReac::vGetNumKb(), Reac::vGetNumKb(), ZombieReac::vGetNumKf(), Reac::vGetNumKf(), ZombieMMenz::vGetNumKm(), ZombieEnz::vGetNumKm(), MMenz::vGetNumKm(), Enz::vGetNumKm(), Reac::vReinit(), Reac::vRemesh(), MMenz::vRemesh(), Enz::vSetConcK1(), Reac::vSetConcKb(), Reac::vSetConcKf(), ZombieEnz::vSetK1(), Enz::vSetK1(), MMenz::vSetKm(), Enz::vSetKm(), ZombieReac::vSetNumKb(), Reac::vSetNumKb(), ZombieReac::vSetNumKf(), Reac::vSetNumKf(), ZombieMMenz::vSetNumKm(), ZombieEnz::vSetNumKm(), MMenz::vSetNumKm(), Enz::vSetNumKm(), and Enz::vSetRatio().
| double convertConcToNumRateUsingVol | ( | const Eref & | e, | |
| const SrcFinfo * | pools, | |||
| double | volume, | |||
| double | scale, | |||
| bool | doPartialConversion | |||
| ) |
Generates conversion factor for rates from concentration to mol# units. This variant already knows the volume, but has to figure out # of reactants. The scale term is a conversion from the conc units to SI: The scale term is 1 if conc units are in SI, which is equal to moles per cubic metre, which is equal to millimolar. The scale term is 1e-3 for micromolar, uM. The doPartialConversion flag tells the function that there are other substrates not in the 'pools' list, and so it should compute the conversion for all pools, not n-1. This flag defaults to 0.
Generates conversion factor for rates from concentration to mol# units. This variant already knows the volume, but has to figure out # of reactants.
References Eref::element(), SrcFinfo::getBindIndex(), Element::getMsgAndFunc(), and NA.
Returns the compartment in which the specified object is located. Traverses the tree toward the rood till it finds a compartment.
References Element::cinfo(), ObjId::element(), getCompt(), ObjId::id, Cinfo::isA(), and Neutral::parent().
Referenced by ReadKkit::assignPoolCompartments(), ReadKkit::assignReacCompartments(), findMeshOfEnz(), findParentComptOfReac(), getCompt(), and lookupVolumeFromMesh().
Utility function to get volumes for all reactants (substrates or products) of Reacs or Enzymes. Does NOT get volumes for the Enzyme itself.
| double lookupVolumeFromMesh | ( | const Eref & | e | ) |
Utility function for kinetics classes to find their volume from the attached mesh. Works for Pools and subclasses.
Utility function to find the size of a pool. We assume one-to-one match between pool indices and mesh indices: that is what they are for.
References Eref::dataIndex(), LookupField< L, A >::get(), getCompt(), and Eref::id().
Referenced by getReactantVols(), PoolBase::setNinit(), ZombiePool::vGetConc(), Pool::vGetConc(), ZombiePool::vGetVolume(), Pool::vGetVolume(), ZombiePool::vSetConc(), ZombieBufPool::vSetConc(), Pool::vSetConc(), BufPool::vSetConc(), ZombiePool::vSetConcInit(), and Pool::vSetConcInit().
Variable Documentation
| const double CONC_UNIT_CONV |
Used to provide the conversion factor from preferred units to SI.
