mcell/libmcell/definition/constants.yaml

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.