BioNetGen/Perl2/RateLaw.pm

97             ($param, $err) = $model->ParamList->lookup($rc);
118         $err = $expr1->readString( \$expr_string_1, $model->ParamList );
121         my $name1 = $expr1->getName( $model->ParamList, "_localFuncL", $force_fcn );
123         (my $param1, $err) = $model->ParamList->lookup($name1);
128         my $err = $expr2->readString( \$expr_string_2, $model->ParamList );
131         my $name2 = $expr2->getName( $model->ParamList, "_localFuncR", $force_fcn );
133         (my $param2, $err) = $model->ParamList->lookup($name2);
152         $err = $phi_expr->readString( \$string_left, $model->ParamList, "," );
154         my $phi_name = $phi_expr->getName( $model->ParamList, "_Aphi_" );
155         (my $phi_param, $err) = $model->ParamList->lookup($phi_name);
163         $err = $actE_expr->readString( \$string_left, $model->ParamList );
165         my $actE_name = $actE_expr->getName( $model->ParamList, "_AEact0_" );
166         (my $actE_param, $err) = $model->ParamList->lookup($actE_name);
183         $err = $expr->readString( \$string_left, $model->ParamList, "," );
188         my $name = $expr->getName( $model->ParamList, $basename, $force_fcn );
190         (my $param, $err) = $model->ParamList->lookup($name);
204                 if ( $totalRate   and  $expr->checkLocalDependency($model->ParamList) )
383         my ($param) = $model->ParamList->lookup($rl->Constants->[1]);
387             if ( $fcn->checkLocalDependency($model->ParamList) )
392                 $local_expr = $expr->evaluate_local($model->ParamList);
395 …    $lfcn_fingerprint = $rl->Constants->[0] . "," . $local_expr->toString($model->ParamList, 0, 2);
427 …       {   $arrhenius_expr = Expression::newNumOrVar( $rl->Constants->[1], $model->ParamList );   }
433                 (my $expr, $err) = $epatt->getDeltaEnergy( $rxn, $model->ParamList );
440             {   $deltaG_expr = Expression::operate("+", [@deltaG_terms], $model->ParamList);   }
448                 $phi_expr = Expression::newNumOrVar( $rl->Constants->[0], $model->ParamList );
452                 $phi_expr = Expression::newNumOrVar( $rl->Constants->[0], $model->ParamList );
453                 $phi_expr = Expression::operate( "-", [1, $phi_expr], $model->ParamList );
461 …      my $phi_deltaG_expr = Expression::operate("*", [$phi_expr, $deltaG_expr], $model->ParamList);
462 …arrhenius_expr  = Expression::operate("+", [$arrhenius_expr, $phi_deltaG_expr], $model->ParamList);
466             $arrhenius_expr = Expression::operate("-", [$arrhenius_expr], $model->ParamList);
467 …$arrhenius_expr = Expression::operate("FunctionCall", ["exp", $arrhenius_expr], $model->ParamList);
472             my $local_name = $arrhenius_expr->getName( $model->ParamList, "_${base_name}_local" );
473             (my $local_param, $err) = $model->ParamList->lookup($local_name);
493         (my $rl_param) = $model->ParamList->lookup($rl->Constants->[0]);
500         if ( $fcn->checkLocalDependency($model->ParamList) )
505             my $local_expr = $expr->evaluate_local($model->ParamList);
510             my $fingerprint = $local_expr->toString($model->ParamList, 0, 2);
522                 my $local_name = $local_expr->getName( $model->ParamList, "_${base_name}_local" );
523                 (my $local_param, $err) = $model->ParamList->lookup($local_name);