constants: - name: STATE_UNSET type: str value: STATE_UNSET - name: STATE_UNSET_INT type: int value: -1 - name: BOND_UNBOUND type: int value: -1 doc: Represents cases when a component must not be bound in a pattern. - name: BOND_BOUND type: int value: -2 doc: Represents bond type !+ in a pattern. - name: BOND_ANY type: int value: -3 doc: Represents bond type !? in a pattern. - name: PARTITION_EDGE_EXTRA_MARGIN_UM type: float value: 0.01 doc: Internal constant used to match partition setup when comparing models against their MDL variant. - name: DEFAULT_COUNT_BUFFER_SIZE type: int value: 100 doc: Internal constant used to initialize buffer size for molecule and reaction counts. - name: ALL_MOLECULES type: str value: "ALL_MOLECULES" - name: ALL_VOLUME_MOLECULES type: str value: "ALL_VOLUME_MOLECULES" - name: ALL_SURFACE_MOLECULES type: str value: "ALL_SURFACE_MOLECULES" - name: DEFAULT_CHECKPOINTS_DIR type: str value: "checkpoints" - name: DEFAULT_SEED_DIR_PREFIX type: str value: "seed_" - name: DEFAULT_SEED_DIR_DIGITS type: int value: 5 - name: DEFAULT_ITERATION_DIR_PREFIX type: str value: "it_" # TODO: maybe rename to AllSpecies ... - name: AllMolecules type: Species value: AllMolecules # object from api/globals.cpp - name: AllVolumeMolecules type: Species value: AllVolumeMolecules # object from api/globals.cpp - name: AllSurfaceMolecules type: Species value: AllSurfaceMolecules # object from api/globals.cpp - name: ID_INVALID type: int value: -1 - name: NUMBER_OF_TRAINS_UNLIMITED type: int value: -1 - name: TIME_INFINITY type: float value: 1e140 - name: INT_UNSET type: int value: INT32_MAX doc: | This is a special integer value that means that an argument was not set, its value is 2147483647. - name: FLT_UNSET type: float value: FLT_MAX doc: | This is a special floating-point value that means that an argument was not set, its value is 3.40282346638528859812e+38F. - name: RNG_SIZE type: int value: 256 doc: | Size of arrays of enums: - name: Orientation doc: Orientation of a Complex. # TODO: consider adding/changing orientation don't care, this might make things a bit clearer values: - name: DOWN value: -1 - name: NONE value: 0 - name: UP value: 1 - name: NOT_SET value: 2 - name: ANY value: 3 - name: DEFAULT value: 4 doc: Value DEFAULT means NONE for volume complexes and UP for surface complexes. - name: Notification values: - name: NONE value: 0 - name: BRIEF value: 1 - name: FULL value: 2 - name: WarningLevel values: - name: IGNORE value: 0 doc: Do something sensible and continue silently. - name: WARNING value: 1 doc: Do something sensible but emit a warning message. - name: ERROR value: 2 doc: Treat the warning as an error and stop. - name: VizMode values: - name: ASCII value: 0 doc: Readable molecule visualization output. - name: CELLBLENDER_V1 value: 1 doc: | Binary molecule visualization output used by MCell3, format v1. Allows only limited length of species name (256 chars) and does not contain molecule IDs. - name: CELLBLENDER value: 2 doc: Binary molecule visualization output, format v2. # other shapes are defined in in release_shape_t but only the spherical one is supported by mcell4 now - name: Shape values: - name: UNSET value: 0 - name: SPHERICAL value: 1 - name: REGION_EXPR value: 2 - name: LIST value: 3 - name: COMPARTMENT value: 4 - name: SurfacePropertyType values: - name: UNSET value: 0 - name: REACTIVE value: 1 doc: | This surface class does not do anything by itself, but it can be used as a reactant in reaction rules. - name: REFLECTIVE value: 2 doc: | If used as a surface property for a volume molecule it is reflected by any surface with this surface class. This is the default behavior for volume molecules. If used for a surface molecule it is reflected by the border of the surface with this surface class. Setting orientation in affected_complex_pattern allows selective reflection of volume molecules from only the front or back of a surface or selective reflection of surface molecules with only a certain orientation from the surface’s border. Using m.ALL_MOLECULES as affected_complex_pattern has the effect that all volume molecules are reflected by surfaces with this surface class and all surface molecules are reflected by the border of the surfaces with this surface class. Using m.ALL_VOLUME_MOLECULES as affected_complex_pattern has the effect that all volume molecules are reflected by surfaces with this surface class. Using m.ALL_SURFACE_MOLECULES as affected_complex_pattern has the effect that all surface molecules are reflected by the border of the surface with this surface class. - name: TRANSPARENT value: 3 doc: | If used as a surface property for a volume molecule it passes through all surfaces with this surface class. If used for a surface molecule it passes through the border of the surface with this surface class. This is the default behavior for surface molecules. Setting orientation in affected_complex_pattern allows selective transparency of volume molecules from only the front or back of a surface or selective transparency for surface molecules with only a certain orientation from the surface’s border. To make a surface with this surface class transparent to all volume molecules, use m.ALL_VOLUME_MOLECULES for affected_complex_pattern. To make a border of the surface with this surface class transparent to all surface molecules, use m.ALL_SURFACE_MOLECULES for the affected_complex_pattern. Using m.ALL_MOLECULES for affected_complex_pattern has the effect that surfaces with this surface class are transparent to all volume molecules and borders of the surfaces with this surface class are transparent to all surface molecules. - name: ABSORPTIVE value: 4 doc: | If affected_complex_pattern refers to a volume molecule it is destroyed if it touches surfaces with this surface class. If affected_complex_pattern refers to a surface molecule it is destroyed if it touches the border of the surface with this surface class, i.e., it is allowed to release surface molecules on absorptive surfaces, they get destroyed only when they touch the border of this surface. Tick marks on name allow destruction from only one side of the surface for volume molecules or selective destruction for surface molecules on the surfaces’s border based on their orientation. To make a surface with this surface class absorptive to all volume molecules, m.ALL_VOLUME_MOLECULES can be used for affected_complex_pattern. To make a border of the surface with this surface class absorptive to all surface molecules, m.ALL_SURFACE_MOLECULES can be used for name. Using m.ALL_MOLECULES as affected_complex_pattern has the effect that surfaces with this surface class are absorptive for all volume molecules and borders of the surfaces with this surface class are absorptive for all surface molecules. - name: CONCENTRATION_CLAMP value: 5 doc: | Clamps concentration at a surface by periodically releasing molecules that correspond to the wall being a transparent boundary to the area with given concentration, and by absorbing all molecules that hit this surface. The molecules matching affected_complex_pattern are destroyed if they touch the surface (as if they had passed through), and new molecules are created at the surface, as if molecules had passed through from the other side at a concentration value (units = M). Orientation marks may be used; in this case, the other side of the surface is reflective. Note that this command is only used to set the effective concentration of a volume molecule at a surface; it is not valid to specify a surface molecule. - name: FLUX_CLAMP value: 6 doc: | Clamps flux at a surface by periodically releasing molecules that correspond to the wall being a transparent boundary to the area with given concentration. The clamped surface reflects these molecules. - name: ExprNodeType doc: Used internally to represent expression trees. values: - name: UNSET value: 0 - name: LEAF value: 1 - name: ADD value: 2 - name: SUB value: 3 - name: RegionNodeType doc: Used internally to represent region trees. values: - name: UNSET value: 0 - name: LEAF_GEOMETRY_OBJECT value: 1 - name: LEAF_SURFACE_REGION value: 2 - name: UNION value: 3 - name: DIFFERENCE value: 4 - name: INTERSECT value: 5 - name: ReactionType doc: Used in reaction callbacks. values: - name: UNSET value: 0 - name: UNIMOL_VOLUME value: 1 - name: UNIMOL_SURFACE value: 2 - name: VOLUME_VOLUME value: 3 - name: VOLUME_SURFACE value: 4 - name: SURFACE_SURFACE value: 5 - name: MoleculeType doc: Used in molecule introspection and internally in checkpointing. values: - name: UNSET value: 0 - name: VOLUME value: 1 - name: SURFACE value: 2 - name: BNGSimulationMethod doc: Specifies simulation method in exported BNGL, used in Model.export_to_bngl. values: - name: NONE value: 0 - name: ODE value: 1 - name: SSA value: 2 - name: PLA value: 3 - name: NF value: 4 - name: CountOutputFormat values: - name: UNSET value: 0 doc: Invalid value. - name: AUTOMATIC_FROM_EXTENSION value: 1 doc: | Output format is determined fom extension - .dat selects DAT file format and .gdat selects GDAT file format. - name: DAT value: 2 doc: | A two-column file with columns time and observable value is created. Each count must have its own unique file name. - name: GDAT value: 3 doc: | A multi-column file with time and observable values is created. The first line of the file is a header that starts with a comment character followed by time and then by the observable names. The order of observables is given by the order in which they were added to the model. Can specify the same output file name for multiple observables.