zoom zoom by a factor. example: zoom(1.2); showProgress show progress in percent (0-100). example: showProgress(50); clear clear all text. example: clear(); write print text. example: write("hello world") writeFile print text contents of a file. example: write("myfile.txt") errorReport print error report. example: errorReport("error here") createInputWindow create an input window for running another library. example: createInputWindow(("model","type","time","dt"),(0,0,100,0.1),"dlls/mydll","main","My Program"); addInputWindowOptions create an input window for running another library. example: addInputWindowOptions("My Program",0,0,("all","selected"); openNewWindow open a new window or tab. example: openNewWindow(); outputOn turn on all outputs from Python to console. example: outputOn() outputOff turn off all outputs from Python to console. example: outputOff() errorOn turn on all error messages from Python to console. example: errorOn() errorOff turn off all error messages from Python to console. example: errorOff() getString display a dialog and get a string from the user. example: getString("please enter text"); getFilename display a dialog and get a file name from the user. example: s = getFilename(); getNumber display a dialog and get a number from the user. example: getNumber("please enter number"); getNumbers display a dialog and get a set of numbers from the user. example: l = getNumbers(('A','B','C')); getFromList display a dialog and ask the user to make a selection. example: i = getFromList("please select one:",["option 1","option 1","option 1"]); askQuestion display a dialog that asks the user a question. example: p = askQuestion('are you sure?'); messageDialog display a message dialog. example: messageDialog('the model has been updated'); allItems get addresses for all items. example: Array = allItems(); selectedItems get addresses for selected items. example: Array = selectedItems(); itemsOfFamily get addresses of all items belonging to a family. example: Array = itemsOfFamily("Protein"); find get the address of an item using its full name. example: A = find("A") or B = find("Cell1.A"); selectItem select an item. example: A = find("A"); selectItem(A); removeItem remove the given item. example: A = find("A"); removeItem(A); deselect deselect all selected items. example: deselectItems(); getName get the name of an item. example: Array = selectedItems(); s = getName(Array[0]); rename set the name of an item. example: Array = selectedItems(); rename(Array[0],"S"); getNames get the names of given items. example: Array = selectedItems(); names = getNames(Array[0]); family get the family of an item. example: A = find("A"); s = getFamily(A); isA checks whether the given item belongs in the given family. example: Array = find("A"); i = isA(A,"Receptor"); getX get the X coordinate of an item. example: A = find("A"); x = getX(A); getY get the Y coordinate of an item. example: A = find("A"); y = getY(A); getPos get the X and Y coordinates of a set of items. example: A = (find("A"),find("B")); xy = getPos(A); print xy; setPos set and X and Y coordinate of a given item. example: A = find("A"); setPos(A,100,200); setPosMulti set and X and Y coordinate of severak items. example: A = (find("A"),find("B")); setPosMulti(A, ((100,200),(150,500))); moveSelected move all selected items by the given amount in the x and y direction. example: moveSelected(100,200); isWindows returns 1 is this is a Windows operating system. example: i = isWindows(); isMac returns 1 is this is a Mac operating system. example: i = isMac(); isLinux returns 1 is this is a Linux operating system. example: i = isLinux(); appDir returns the application directory. example: s = appDir() annotation get the annotation for an item, e.g. author, etc.. example: A = find("A"); print annotation(A); setAnnotation set the annotation for an item, e.g. author, etc.. example: A = find("A"); setAnnotation(A,("Mickey Mouse","Apr. 27, 2009","my device","more about my device","www.tinkercell.com","ref#12345")); getNumericalDataNames get the names of all the numerical data for an item. example: A = find("A"); t = getNumericalDataNames(A); getTextDataNames get the names of all the text data for an item. example: A = find("A"); t = getTextDataNames(A); getNumericalData get a numerical data. example: A = find("A"); t = getNumericalData(A,"Stoichiometry","J0","A"); getTextData get a text data. example: A = find("A"); t = getTextData(A,"Assignments","f","function"); setNumericalData set a numerical data. example: A = find("A"); setNumericalData(A,"Stoichiometry","J0","A",-4); setTextData set a text data. example: A = find("A"); t = setTextData(A,"Assignments","f","function","sin(time)"); getChildren get child items. example: A = find("A"); children = getChildren(A);"); getParent get child items. example: A = find("A"); p = getParent(A);"); getNumericalDataRowNames get the row names of a numerical data matrix. example: A = find("J0"); getNumericalDataRowNames(A,"Stoichiometry"); getNumericalDataColNames get the column names of a numerical data matrix. example: A = find("J0"); getNumericalDataColNames(A,"Stoichiometry"); getTextDataRowNames get the row names of a text data matrix. example: A = find("J0"); getTextDataRowNames(A,"Rates"); getTextDataColNames get the column names of a text data matrix. example: A = find("J0"); getTextDataColNames(A,"Rates"); getNumericalDataMatrix get an enitre numerical data matrix. Use 0 as the first argument for global matrices. example: A = find("J0"); getNumericalDataMatrix(A,"Stoichiometry"); setNumericalDataMatrix set an enitre numerical data matrix. Use 0 as the first argument for global matrices example: A = find("J0"); setNumericalDataMatrix("My Data",("col1","col2"),("row1","row2","row3"),((1,2,3),(4,5,6)),A); print getNumericalDataMatrix(A,"My Data"); getTextDataRow get the values in a particular row of a text data matrix. example: A = find("J0"); getTextDataRow(A,"Stoichiometry","A"); getTextDataCol get the values in a particular column of a text data matrix. example: A = find("J0"); getTextDataCol(A,"Stoichiometry","J0"); insertNode insert a new node with the given name and family. example: insertNode("A") or insertNode("A","Receptor"); insertConnection insert a connection that connects one set of items to another and has the given name and family. example: Array1 = [find("A"), find("B")]; Array2 = [find("C")]; insertConnection(Array1,Array2,"name","Reaction"); getConnectedNodes get all the parts in the given connections. example: J = find("J0"); Array = getConnectedParts(J); getConnectedNodesIn get all the parts in the given connections that are in-nodes, such as reactants. example: J = find("J0"); Array = getConnectedPartsIn(J); getConnectedNodessOut get all the parts in the given connections that are out-nodes, such as products. example: J = find("J0"); Array = getConnectedPartsOut(J); getConnectedNodesOther get all the parts in the given connections that are not in- or out-nodes. example: J = find("J0"); Array = getConnectedPartsOther(J); getConnections get all the connections for the given part. example: A = find("A"); Array = getConnections(A); getConnectionsIn get all the connections for the given part where the part is an in-node. example: A = find("A"); Array = getConnectionsIn(A); getConnectionsOut get all the connections for the given part where the part is an out-node. example: A = find("A"); Array = getConnectionsOut(A); getConnectionsOther get all the connections for the given part where the part is not an in- or out-node. example: A = find("A"); Array = getConnectionsOther(A); allParameters get all the parameters [ [name1,name2..], [value1,value2..] ]for the given items, whether or not they are used in the model. example: items = allItems(); Array = allParameters(items); write(Array[0][0] + " = " + str(Array[1][0])); parameters get all the parameters [ [name1,name2..], [value1,value2..] ] for the given items that are in use. example: items = allItems(); Array = parameters(items); write(Array[0][0] + " = " + str(Array[1][0])); initialValues get initial values for floating variables [ [name1,name2..], [value1,value2..] ] for the given items. example: items = allItems(); Array = initialValues(items); write(Array[0][0] + " = " + str(Array[1][0])); setInitialValues set initial values for floating variables [ [name1,name2..], [value1,value2..] ] in the given items. example: items = find(("A","B")); setInitialValues(items,[0.1, 0.2]); parametersAndFixedVariables get all the parameters and fixed variables [ [name1,name2..], [value1,value2..] ] in the given items. example: items = allItems(); Array = getParametersAndFixedVariables(items); write(Array[0][0] + " = " + str(Array[1][0])); fixedVariables get all the fixed variables [ [name1,name2..], [value1,value2..] ] for the given items. example: items = allItems(); Array = fixedVariables(items); write(Array[0] [0]+ " = " + str(Array[1][0])); getParameter get a specific parameter for the given items. example: A = find("A"); getParameter(A,"concentration"); getTextAttribute get a specific text attribute for the given items. example: A = find("A"); getTextAttribute(A,"sequence"); getParametersNamed get the specified parameters for the given items. example: items = allItems(); Array = getParametersNamed(items,["concentration","copy"]); write(Array[0][0] + " = " + str(Array[1][0])); getParametersExcept get all parameters EXCEPT the ones specified for the given items. example: items = allItems(); Array = getParametersExcept(items,["concentration","copy"]); write(Array[0][0] + " = " + str(Array[1][0])); getAllTextNamed get the specified text attributes for the given items. example: items = allItems(); Array = getAllTextNamed(items,["concentration","copy"]); write(Array[0]); setParameter set a parameter value for the given items. example: A = find("A"); setParameter(A,"Ka",1.2E5); setTextAttribute set a text attribute for the given items. example: A = find("A"); setTextAttribute(A,"sequence","AACGCTGAG"); getControlPointX get the X co-ordinate of a control point in a connection. example: J = find("J0"); Array = getConnectedParts(J); A = Array[0]; x = getControlPointX(J,A,1); getControlPointY get the Y co-ordinate of a control point in a connection. example: J = find("J0"); Array = getConnectedParts(J); A = Array[0]; y = getControlPointY(J,A,1); setControlPoint set the x,y co-ordinate of a control point in a connection. example: J = find("J0"); Array = getConnectedParts(J); A = Array[0]; y = setControlPoint(J,A,1,100,100); setCenterPoint set the x,y co-ordinate of the center point of a connection. example: J = find("J0"); setCenterPoint(J,100,100); getCenterPointX get the X co-ordinate of the center point of a connection. example: J = find("J0"); x = getCenterPointX(J); getCenterPointY get the Y co-ordinate of the center point of a connection. example: J = find("J0"); y = getCenterPointY(J); compileAndRun compile and execute a C program. example: compileAndRun("mycode.c -lm","arg1 arg2"); #will make the executable for mycode.c and run it using arg1 and arg2 compileBuildLoad build a C program as a dynamic library and load into TinkerCell. example: compileBuildLoad("mycode.c -lm","main"); #will call the main function in mycode.c callFunction execute a program that is listed in the functions menu. example: callFunction("Deterministic simulation"); loadLibrary load a dynamic C library. example: loadLibrary("mycode.dll"); getColorR get the Red value of the color of the given object. example: A = find("A"); r = getColorR(A); getColorG get the Green value of the color of the given object. example: A = find("A"); r = getColorG(A); getColorB get the Blue value of the color of the given object. example: A = find("A"); r = getColorB(A); setColor set the Red,Green,Blue values for the color of the given object. The last argument indicated whether the color is permanent or termporary. example: A = find("A"); setColor(A,250,100,100,1); setStraight toggle between straight of curved lines for drawing a connector. example: J = find("J"); setStraight(J,1); setAllStraight toggle between straight of curved lines for drawing all connectors. example: setAllStraight(1); setLineWidth set the line width of a connector. The last argument indicated whether the change is permanent or termporary. example: J = find("J0"); setLineWidth(J,5.0,1); changeNodeImage change the image for a node by specifying the arrowhead graphics file. example: A = find("A"); changeNodeImage(A, "NodeItems/Molecule.xml"); changeArrowHead change the arrowhead for a connection by specifying the arrowhead graphics file. example: J = find("J0"); changeArrowHead(J, "ArrowItems/Binding.xml"); plot Plot the given set of values (2D array) with the given headers and x-axis. example: data = [[0,0] , [1,1] , [2,4] , [3,9] , [4,16] ]; where each pair is a row. plot(["x","y"],data,0,"my plot"); scatterplot Plot the given set of values (2-column array) with the given headers. example: data = [[0,0] , [1,1] , [2,4] , [3,9] , [4,16] ]; where each pair is a row. scatterplot(["x","y"],data,"my plot"); surface Plot 3D surface, given a matrix with 3 columns (x,y,z). example: data = [ [0,1,2,3,4] , [1,2,3,4,5] , [2,3,4,5,6] ]; surface(["x","y","z"],data,"my plot"); getPlotData Get the values and headers of the data that is displayed in the plot window. example: data = plotData(); print data; histogram plot a histogram of each column in the data. example: p = plotData(); histogram(p[0],p[1]); multiplot setup plot layout for multiple plot. example: multiplot(2,2); writeModel Write the differential equations and propentity functions to a file (do not include .py suffix). example: writeModel("ode",selectedItems()); or writeModel("ode2"); defaults to all items stoichiometry get the column names and the linearized stoichiometry matrix for given item(s). example: items = selectedItems(); N = stoichiometry(items); N1 = stoichiometry(items[0]); rates get the rates for multiple items. example: items = selectedItems(); v = rates(items); getRate get the rate for a given item. example: item = find('J0'); v = getRate(item); setRates set the rates for multiple items. example: items = ( find('J0'), find('J1') ); setRates(items,('rate1','rate2')); setRates(items[0],'rate1'); setRate set the rate for a given item. example: item = find('J0'); setRate(item,'rate1'); eventTriggers get all the event triggers. example: print eventTriggers(); eventResponses get all the event responses corresponding to triggers. example: print eventResponses(); addEvent set an event defined by a trigger and a response. example: addEvent("time > 10","a = 0"); forcingFunctionNames get all forcing function name for given items. example: A = allItems(); forcingFunctionNames(A); forcingFunctionAssignments get all forcing function assignment rules for given items. example: A = allItems(); forcingFunctionAssignments(A); setForcingFunction add or modify a function for the given item. example: a = find("A"); setForcingFunction(a,"func","sin(time)*a"); highlight display a circle around the given item temporarily. example: a = find("A"); highlight(a); or highlight(a,255,0,0); for color displayText display the given text on top of the given item. example: a = find("A"); displayText(a,"Hello World"); displayNumber display the given number on top of the given item. example: a = find("A"); displayNumber(a,3.14159); merge Merge a list of items. example: a = find("A"); a = find("B"); merge((a,b)); separate Separate an item. example: a = find("A"); separate(a); partsIn get all the DNA parts inside a Module or Compartment. example: a = find("A"); A = partsIn(a); prints getNames(A); partsUpstream get all the DNA parts upstream of this part. example: a = find("A"); A = partsUpstream(a); prints getNames(A); partsDownstream get all the DNA parts downstream of this part. example: a = find("A"); A = partsDownstream(a); prints getNames(A); loadSBMLString load SBML model using the XML string as input. example: loadSBMLString(sbml_text) loadAntimonyString load Antimony model using the model string as input. example: loadAntimonyString(sbml_text) loadSBMLFile load SBML model using the file name as input. example: loadSBMLString("myfile.sbml") loadAntimonyFile load Antimony model using the file name as input. example: loadAntimonyFile("myfile.txt"); getSBMLString get SBML as a string from either a subset of items or all items. example: A = selectedItems(); s1 = getSBMLString(A); s2 = getSBMLString(); getAntimonyString get Antimony model string from either a subset of items or all items. example: A = selectedItems(); s1 = getAntimonyString(A); s2 = getAntimonyString(); writeSBMLFile write the SBML to an xml file. example: writeSBMLFile("myfile.sbml") writeAntimonyFile write the Antimony model to a text file. example: writeAntimonyFile("myfile.txt") |
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