ReadKkit Class Reference
#include <ReadKkit.h>
Public Types | |
| enum | ParseMode { DATA, INIT, COMMENT, LINE_CONTINUE } |
Public Member Functions | |
| ReadKkit () | |
| double | getMaxTime () const |
| double | getPlotDt () const |
| double | getDefaultVol () const |
| string | getBasePath () const |
| unsigned int | getVersion () const |
| bool | getMoveOntoCompartment () const |
| void | setMoveOntoCompartment (bool v) |
| void | innerRead (ifstream &fin) |
| ParseMode | readInit (const string &line) |
| Id | read (const string &filename, const string &cellname, Id parent, const string &solverClass="Stoich") |
| void | readData (const string &line) |
| void | undump (const vector< string > &args) |
| void | run () |
| void | dumpPlots (const string &filename) |
| Id | buildCompartment (const vector< string > &args) |
| Id | buildPool (const vector< string > &args) |
| Id | buildReac (const vector< string > &args) |
| Id | buildEnz (const vector< string > &args) |
| Id | buildPlot (const vector< string > &args) |
| Id | buildTable (const vector< string > &args) |
| unsigned int | loadTab (const vector< string > &args) |
| Id | buildGroup (const vector< string > &args) |
| Id | buildText (const vector< string > &args) |
| Id | buildGraph (const vector< string > &args) |
| Id | buildGeometry (const vector< string > &args) |
| Id | buildStim (const vector< string > &args) |
| Id | buildChan (const vector< string > &args) |
| Id | buildInfo (Id parent, map< string, int > &m, const vector< string > &args) |
| void | buildSumTotal (const string &src, const string &dest) |
| Id | findSumTotSrc (const string &src) |
| void | addmsg (const vector< string > &args) |
| void | setupSlaveMsg (const string &src, const string &dest) |
| void | innerAddMsg (const string &src, const map< string, Id > &m1, const string &srcMsg, const string &dest, const map< string, Id > &m2, const string &destMsg, bool isBackward=0) |
| void | call (const vector< string > &args) |
| void | objdump (const vector< string > &args) |
| void | textload (const vector< string > &args) |
| void | separateVols (Id pool, double vol) |
| void | assignPoolCompartments () |
| void | assignReacCompartments () |
| void | assignEnzCompartments () |
| void | assignMMenzCompartments () |
| void | convertParametersToConcUnits () |
| void | convertPoolAmountToConcUnits () |
| Convert pool amounts. Initially given in n, but scaling issue. | |
| void | convertReacRatesToConcUnits () |
| Convert Reac rates, initially in n units. | |
| void | convertMMenzRatesToConcUnits () |
| void | convertEnzRatesToConcUnits () |
| string | pathTail (const string &path, string &head) const |
| string | cleanPath (const string &path) const |
Detailed Description
Loads in a kkit.g model. It makes a separate compartment for each distinct volume it finds in the system. The largest volume gets set to /model/kinetics. The next volume is in /model/compartment_1. The next volume is in /model/compartment_2. And so on. Has two options for handling compartments and solvers. By default, it puts the entire reaction system on /kinetics and makes just one solver. If the moveOntoCompartments_ flag is set it will put each model entity onto the appropriate compartment. It will create separate solvers for each compartment.
Member Enumeration Documentation
| enum ReadKkit::ParseMode |
Constructor & Destructor Documentation
| ReadKkit::ReadKkit | ( | ) |
Member Function Documentation
| void ReadKkit::addmsg | ( | const vector< string > & | args | ) |
| void ReadKkit::assignEnzCompartments | ( | ) |
Goes through all Enzs and connects them up to each of the compartments in which one or more of their reactants resides. Thus, if any of these compartments changes volume, the Enz will be informed.
| void ReadKkit::assignMMenzCompartments | ( | ) |
Goes through all MMenzs and connects them up to each of the compartments in which one or more of their reactants resides. Thus, if any of these compartments changes volume, the MMenz will be informed.
| void ReadKkit::assignPoolCompartments | ( | ) |
References Neutral::child(), Shell::doCreate(), Shell::doMove(), Id::eref(), findVolOrder(), getCompt(), and ObjId::id.
| void ReadKkit::assignReacCompartments | ( | ) |
Goes through all Reacs and connects them up to each of the compartments in which one or more of their reactants resides. Thus, if any of these compartments changes volume, the Reac will be informed.
References Shell::doMove(), findParentComptOfReac(), getCompt(), and ObjId::id.
| Id ReadKkit::buildChan | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildCompartment | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildEnz | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildGeometry | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildGraph | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildGroup | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildPlot | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildPool | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildReac | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildStim | ( | const vector< string > & | args | ) |
| void ReadKkit::buildSumTotal | ( | const string & | src, | |
| const string & | dest | |||
| ) |
| Id ReadKkit::buildTable | ( | const vector< string > & | args | ) |
| Id ReadKkit::buildText | ( | const vector< string > & | args | ) |
| void ReadKkit::call | ( | const vector< string > & | args | ) |
| string ReadKkit::cleanPath | ( | const string & | path | ) | const |
Utility function. Cleans up path strings. In most cases, it replaces things with underscores. Replaces square braces with underscores. Replaces '*' with 'p' as it is usually there to indicate phosphorylation Replaces '-' with underscore Replaces '@' with underscore Replaces ' ' with underscore
| void ReadKkit::convertEnzRatesToConcUnits | ( | ) |
Convert regular Enz rates. Binding step k1 has similar issues as reac rates. k2 and k3 are both in units of 1/time, so OK.
References NA.
Referenced by convertParametersToConcUnits().
| void ReadKkit::convertMMenzRatesToConcUnits | ( | ) |
Convert MMEnz rates. Km should be in conc units. Actually rates stored as k1, k2, k3 in num units, so this has to be computed and then converted.
References NA.
Referenced by convertParametersToConcUnits().
| void ReadKkit::convertParametersToConcUnits | ( | ) |
We have a slight problem because MOOSE has a more precise value for NA than does kkit. Also, at the time the model is loaded, the volume relationships are unknown. So we need to fix up conc units of all pools reacs post-facto. Here we assume that the conc units from Kkit are meant to be OK, so they override the #/cell (lower case k) units. So we convert all the Kfs and Kbs in the entire system after the model has been created, once we know the order of each reac.
References convertEnzRatesToConcUnits(), convertMMenzRatesToConcUnits(), convertPoolAmountToConcUnits(), and convertReacRatesToConcUnits().
| void ReadKkit::convertPoolAmountToConcUnits | ( | ) |
Convert pool amounts. Initially given in n, but scaling issue.
References NA.
Referenced by convertParametersToConcUnits().
| void ReadKkit::convertReacRatesToConcUnits | ( | ) |
Convert Reac rates, initially in n units.
References NA.
Referenced by convertParametersToConcUnits().
| void ReadKkit::dumpPlots | ( | const string & | filename | ) |
Referenced by testReadKkit().
| Id ReadKkit::findSumTotSrc | ( | const string & | src | ) |
Finds the source pool for a SumTot. It also deals with cases where the source is an enz-substrate complex
| string ReadKkit::getBasePath | ( | ) | const |
| double ReadKkit::getDefaultVol | ( | ) | const |
| double ReadKkit::getMaxTime | ( | ) | const |
| bool ReadKkit::getMoveOntoCompartment | ( | ) | const |
| double ReadKkit::getPlotDt | ( | ) | const |
| unsigned int ReadKkit::getVersion | ( | ) | const |
| void ReadKkit::innerAddMsg | ( | const string & | src, | |
| const map< string, Id > & | m1, | |||
| const string & | srcMsg, | |||
| const string & | dest, | |||
| const map< string, Id > & | m2, | |||
| const string & | destMsg, | |||
| bool | isBackward = 0 | |||
| ) |
| void ReadKkit::innerRead | ( | ifstream & | fin | ) |
| unsigned int ReadKkit::loadTab | ( | const vector< string > & | args | ) |
| void ReadKkit::objdump | ( | const vector< string > & | args | ) |
| string ReadKkit::pathTail | ( | const string & | path, | |
| string & | head | |||
| ) | const |
Splits up kkit path into head and tail portions, tail is returned. Note that this prepends the basePath to the head.
| Id ReadKkit::read | ( | const string & | filename, | |
| const string & | cellname, | |||
| Id | parent, | |||
| const string & | solverClass = "Stoich" | |||
| ) |
Referenced by testReadKkit().
| void ReadKkit::readData | ( | const string & | line | ) |
| ParseMode ReadKkit::readInit | ( | const string & | line | ) |
| void ReadKkit::run | ( | ) |
This function sets up the kkit model for a run using the GSL, which means numerical integration using the GSL, all the plots specified by the kkit file, and the timestep for plots as specified by the kkit file.
References Shell::doReinit(), Shell::doSetClock(), and Shell::doStart().
Referenced by testReadKkit().
| void ReadKkit::separateVols | ( | Id | pool, | |
| double | vol | |||
| ) |
| void ReadKkit::setMoveOntoCompartment | ( | bool | v | ) |
| void ReadKkit::setupSlaveMsg | ( | const string & | src, | |
| const string & | dest | |||
| ) |
| void ReadKkit::textload | ( | const vector< string > & | args | ) |
| void ReadKkit::undump | ( | const vector< string > & | args | ) |
The documentation for this class was generated from the following files:
- kinetics/ReadKkit.h
- kinetics/ReadKkit.cpp
