Man pages for DanielKneipp/DNAr
Simulates chemical reaction networks constructed with DNA

add_gate_binding_on_neuron_hjeAdd a gate binding into a neuron
analyze_behaviorThis function returns the concentration derivative of each...
arg_listGet the arguments of the current function
check_crnCheck if a CRN is respecting the limitations of the function...
check_fix_reactionCheck and fix a reaction
check_neuron_circuit_hjeChecks the circuit structure
check_neuron_gate_binding_hjeCheck the gate binding structure
check_neuron_gate_hjeChecks the gate specification
check_reaction_4domainCheck if the reaction is compatible with the ones supported...
combine_crnsCombine CRNs into one single larger CRN
combine_reaction_partsCombines two reaction parts to form a reaction
compare_behaviors_nrmseCompare the behavior of two reactions
define_neuron_gate_binding_hjeGet the binding between two neuron gates
dsd_4d_make_module_strGet a DSD 4domain module string
dsd_4d_modulesGet the available 4-domain modules for DSD script
dsd_4d_module_strReturns a string with the 4-domain dsd module
eval_derivativeEvaluate a derivative returned by 'analyze_behavior()'
eval_derivative_partEvaluate subexpressions of a derivative returned by...
expand_speciesFunction to expand species according to their stoichiometry
fte_theme'ggplot2' theme developed by Max Woolf.
get_buff_modulesGet buffer modules
get_circuit_from_neuron_gates_hjeGet a circuit from a list of gates
get_crn_from_neuron_circuit_hjeGet a CRN from a circuit
get_crn_from_neuron_gate_hjeGet a CRN given a gate
get_dsd_0eApBpC_strInstantiate a '0 -> A + B + C' module in the DSD script
get_dsd_0eApB_strInstantiate a '0 -> A + B' module in the DSD script
get_dsd_0eA_strInstantiate a '0 -> A' module in the DSD script
get_dsd_4domain_modules_strGet the 4-domain modules for the DSD script.
get_dsd_Ae0_strInstantiate a 'A -> 0' module in the DSD script
get_dsd_AeBpCpD_strInstantiate a 'A -> B + C + D' module in the DSD script
get_dsd_AeBpC_strInstantiate a 'A -> B + C' module in the DSD script
get_dsd_AeB_strInstantiate a 'A -> B' module in the DSD script
get_dsd_ApBe0_strInstantiate a 'A + B -> 0' module in the DSD script
get_dsd_ApBeCpDpE_strInstantiate a 'A + B -> C + D + E' module in the DSD script
get_dsd_ApBeCpD_strInstantiate a 'A + B -> C + D' module in the DSD script
get_dsd_ApBeC_strInstantiate a 'A + B -> C' module in the DSD script
get_dsd_buff_strInstantiate a buffer module in the DSD script
get_dsd_def_strGet a definition string for the DSD script
get_dsd_header_strGet the DSD script header
get_dsd_species_strGet the DSD definition of a species
get_first_partGet the first part of a reaction.
get_MReturns the matrix M.
get_neuron_AND_gate_hjeGet a AND neuron gate
get_neuron_binding_hjeGet a binding of two neurons
get_neuron_generic_gate_hjeGet a generic neuron gate with n inputs and 1 output
get_neuron_hjeGet a neuron based on Hjelmfelt A. et al. '[1]' approach
get_neuron_majority_gateGet a majority gate
get_neuron_OR_gate_hjeGet a OR neuron gate
get_onespecies_countGet the count of occurrences of a given species in a reaction...
get_productsGet the products of a given reaction
get_reactantsGet the reactants of a given reaction
get_second_partGet the second part of a reaction.
get_speciesGet the species of a reaction part
get_stoichiometry_allGet the stoichiometry of a reaction
get_stoichiometry_onespeciesGet the stoichiometry of a specific species in a reaction.
get_stoichiometry_partIt returns the stoichiometry of part of a reaction.
is_bimolecularCheck if a reaction is bimolecular.
is_degradationCheck if a reaction is of the degradation type
isempty_partCheck if part of a reaction is equal to 0.
is_formationCheck if a reaction is of the formation type
is_unimolecularCheck if a reaction is unimolecular.
jnHelper function to concatenate strings
load_behavior_csvLoad a reaction behavior
nrmseCalculate the normalized root-mean-square error of two data...
plot_behaviorPlot the behavior of a CRN.
prepare_dsd_4d_moduleBinds the module function with its parameters.
reactSimulate a CRN
react_4domainTranslate a formal CRN into a set of DNA based reactions...
reactants_in_reactionCheck which species are reactants in a given reaction
relation_operatorGets the relation operator of the reaction
remove_stoichiometryRemove the stoichiometry of a species string.
replace_module_markersReplaces markers on a template string by other strings
rmseCalculate the root-mean-square error of two data sets
save_behavior_csvSave a reaction behavior
save_dsd_scriptExport a DSD script for a CRN
save_reactions_txtSave the reactions in a formatted text file
select_dsd_4d_moduleSelects a module based on the reaction stoichiometry
update_crn_4domainAutomatically modify a CRN to make it compatible with the DNA...
update_neuron_input_hjeUpdate the neuron input according to the bindings
DanielKneipp/DNAr documentation built on May 14, 2019, 2:32 p.m.