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Merge pull request #32 from RuleWorld/rasilab-cleanup_output
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Rasilab cleanup output
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@ASinanSaglam
ASinanSaglam authored Jan 13, 2022
2 parents fb41f08 + 547a341 commit ccef9bf
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Showing 2 changed files with 59 additions and 50 deletions.
13 changes: 4 additions & 9 deletions src/NFinput/NFinput.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -2273,15 +2273,10 @@ bool NFinput::initReactionRules(
// Add the reactant and product templates to the reaction class
r->setAllReactantAndProductTemplates(reactants, products);
r->setTotalRateFlag(totalRateFlag);

// AS-7/1/2021
// TODO: Currently I'm tagging every reaction by default
// for connectivity calculations. This probably needs
// revisited down the line.
if (s->getConnectivityFlag()) {
r->tag();
s->turnOnTagRxnOutput();
}
// if (tagFlag) {
r->tag();
s->turnOnTagRxnOutput();
// }
// Use reaction connectivity flag
// Set to true if given on the command line
r->setConnectivityFlag(s->getConnectivityFlag());
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96 changes: 55 additions & 41 deletions src/NFsim.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -75,20 +75,24 @@
* -notf = disables On the Fly Observables, see manual
*
* -cb = turn on complex bookkeeping, see manual
*
*
* -connect - infer network connectivity before starting simulation. (default: no).
* Does not require any modification to BioNetGen or PySB.
* @author Arvind Rasi Subramaniam
*
* -printconnected - print connectivity of each reaction to an output file. (default: no).
*
* -rxnlog [filename] - write out firing time and participating molecules for all reactions to file
* Does not require any modification to BioNetGen or PySB.
* @author Arvind Rasi Subramaniam
*
* -trackconnected - write out the reactions whose rates change after firing of each reaction.
* Default: false
* this works only if -rxnlog switch is included
* @author: Arvind Rasi Subramaniam
*
* -printconnected - print connectivity of each reaction to an output file. (default: no).
* this works only if -rxnlog switch is included
* @author Arvind Rasi Subramaniam
*
* -trackrxnnum - track reaction number instead of name. this helps to keep the rxn log file small.
* Default: false
* this works only if -rxnlog switch is included
* @author: Arvind Rasi Subramaniam
*
* -maxcputime - maximum run time for simulation in seconds (default: 1000s).
Expand Down Expand Up @@ -533,45 +537,40 @@ System *initSystemFromFlags(map<string,string> argMap, bool verbose)
}
}

if (s->getAnyRxnTagged()) {
if (argMap.find("rxnlog") != argMap.end()) {
string rxnLogFileName = argMap.find("rxnlog")->second;
if (argMap.find("rxnlog") != argMap.end()) {
string rxnLogFileName = argMap.find("rxnlog")->second;
s->registerReactionFileLocation(rxnLogFileName);
// track the reactions whose rates change upon each each reaction
// firing. This is useful for debugging to make sure that all the
// right reactions are updated after each firing.
// Arvind Rasi Subramaniam Nov 21, 2018
if (argMap.find("trackconnected") != argMap.end()) {
s->registerConnectedRxnFileLocation(
rxnLogFileName.replace(
rxnLogFileName.end()-4,
rxnLogFileName.end(),
"_connected.tsv"));
s->setTrackConnected(true);
} else {
s->setTrackConnected(false);
}
if (argMap.find("printconnected") != argMap.end()) {
s->registerListOfConnectedRxnFileLocation(
rxnLogFileName.replace(
rxnLogFileName.end()-4,
rxnLogFileName.end(),
"_connectedlist.tsv"));
s->setPrintConnected(true);
} else {
s->setPrintConnected(false);
}
if (argMap.find("trackrxnnum") != argMap.end()) {
s->setRxnNumberTrack(true);
s->registerReactionFileLocation(rxnLogFileName);
// track the reactions whose rates change upon each each reaction
// firing. This is useful for debugging to make sure that all the
// right reactions are updated after each firing.
// Arvind Rasi Subramaniam Nov 21, 2018
if (argMap.find("trackconnected") != argMap.end()) {
s->registerConnectedRxnFileLocation(
rxnLogFileName.replace(
rxnLogFileName.end()-4,
rxnLogFileName.end(),
"_connected.tsv"));
s->setTrackConnected(true);
} else {
s->setTrackConnected(false);
}
if (argMap.find("printconnected") != argMap.end()) {
s->registerListOfConnectedRxnFileLocation(
rxnLogFileName.replace(
rxnLogFileName.end()-4,
rxnLogFileName.end(),
"_list.tsv"));
s->setPrintConnected(true);
} else {
s->setPrintConnected(false);
}
} else {
if (argMap.find("trackrxnnum") != argMap.end()) {
s->setRxnNumberTrack(true);
s->registerReactionFileLocation(
s->getName() + "_rxns.dat");
} else {
s->setRxnNumberTrack(false);
}
s->setRxnNumberTrack(false);
}
}
// }


//turn off on the fly calculation of observables
Expand Down Expand Up @@ -777,6 +776,21 @@ void printHelp(string version)
cout<<""<<endl;
cout<<" -logo prints out the ascii NFsim logo, for your viewing pleasure."<<endl;
cout<<""<<endl;
cout<<" -connect infer network connectivity before starting simulation. (default: no)."<<endl;
cout<<""<<endl;
cout<<" -rxnlog [filename] write out firing time and participating molecules for all reactions."<<endl;
cout<<""<<endl;
cout<<" -trackconnected write out the reactions whose rates change after firing of each reaction."<<endl;
cout<<" this works only if -rxnlog switch is included. Useful for debugging models."<<endl;
cout<<""<<endl;
cout<<" -printconnected print connectivity of each reaction to an output file."<<endl;
cout<<" this works only if -rxnlog switch is included. Useful for debugging models."<<endl;
cout<<""<<endl;
cout<<" -trackrxnnum track reaction number instead of name. this helps to keep the rxn log file small."<<endl;
cout<<" this works only if -rxnlog switch is included."<<endl;
cout<<""<<endl;
cout<<" -maxcputime maximum run time for simulation in seconds (default: 1000s)."<<endl;
cout<<""<<endl;
cout<<""<<endl;
}

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