diff --git a/vcell-core/src/test/resources/cbit/vcell/biomodel/Spring_reactions_bad.vcml b/vcell-core/src/test/resources/cbit/vcell/biomodel/Spring_reactions_bad.vcml new file mode 100644 index 0000000000..802af546e2 --- /dev/null +++ b/vcell-core/src/test/resources/cbit/vcell/biomodel/Spring_reactions_bad.vcml @@ -0,0 +1,1010 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2.0 + 0.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1.0 + 0.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.4 + 0.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + 0.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.7 + 0.2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.6 + 0.2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.3 + 0.2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.7 + 0.2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.7 + 0.2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0 + 0.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0 + 0.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0 + 0.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + 0.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.5 + 0.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0 + 0.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0.0 + 0.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Mixed binding / transitoning reactions are not permitted. + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Transition bound reactions always show, by convention, 2 molecules. One + depicts the binding condition, the other depicts the state transition. + Here, the binding molecule is missing. + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Mixed binding / transitoning reactions are not permitted. + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + In a Decay reaction, the product must be the reserved molecule 'Sink' + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Binding cannot be defined within the same molecule. Such a connection, + if exist, must be defined as an internal Link. + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Transition bound reactions always show, by convention, 2 molecules. One + depicts the binding condition, the other depicts the state transition. + Here, the binding condition is missing. + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + The non-transitioning sites must be, by convention, marked as bond + 'Possible' and state 'Any' + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + In a Creation reaction, the reactant must be the reserved molecule + 'Source' + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Only one site with allosteric state condition is allowed + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Binding cannot be defined within the same molecule. Such a connection, + if exist, must be defined as an internal Link. + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Transition bound reactions always show, by convention, 2 molecules. One + depicts the binding condition, the other depicts the state transition. + Here, the binding condition is missing. + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Only one binding is allowed per Binding reaction + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + Transition bound reactions always show, by convention, 2 molecules. One + depicts the binding condition, the other depicts the state transition. + Here, binding condition and the state transition are depicted on the + same molecule + </p> + </body> +</html> + + + <html> + <head> + + </head> + <body> + <p style="margin-top: 0"> + The non-transitioning sites must be, by convention, marked as bond + 'Unbound' and state 'Any' + </p> + </body> +</html> + + + + + + +