mcell/libmcell/definition/geometry.yaml

Color:
  superclass: BaseDataClass
  doc: | 
     Represents color with alpha component.
     Provides two means to set value, either red, green, blue and alpha, 
     or rgba. If both color individual components and rgba are set in initialization,
     the individual components are used.
      
  items:
  - name: red
    type: float
    default: unset
    doc: Red component in range 0-1.

  - name: green
    type: float
    default: unset
    doc: Green component in range 0-1.

  - name: blue
    type: float
    default: unset
    doc: Blue component in range 0-1.

  - name: alpha
    type: float
    default: 1
    doc: Alpha component in range 0-1. 1 means nontransparent.
      
  - name: rgba
    type: uint32
    default: 0
    doc: | 
       This attribute provides an alternative way of defining colors by supplying a 
       32-bit unsigned integer representation of the color with an aplha channel. 
       In hexadecimal notation the first 2 digits are value for red, second 2 digits are 
       green, third 2 digits are blue and the last two digits are alpha. 
       The range for each component is thus 0x0-0xFF (0-255). 
       Example\: 0x0000ffcc represents the same color as rgba(0, 0, 100%, 80%).
       All values are valid.
          

Region:
  superclass: BaseDataClass
  doc: Represents region construted from 1 or more multiple, usually unnamed? 
  items:
  - name: node_type
    type: RegionNodeType
    default: RegionNodeType.UNSET
    doc: | 
      When this values is LeafGeometryObject, then this object is of class GeometryObject,
      when LeafSurfaceRegion, then it is of class SurfaceRegion.

  - name: left_node
    type: Region*
    default: unset
    doc: Internal, do not use. When node_type is not Leaf, this is the left operand 

  - name: right_node
    type: Region*
    default: unset
    doc: Internal, do not use. When node_type is not Leaf, this is the right operand 
    
  methods:
  - name: __add__
    doc: Computes union of two regions, use with Python operator '+'. 
    return_type: Region*
    params:
    - name: other
      type: Region* 
          
  - name: __sub__
    doc: Computes difference of two regions, use with Python operator '-'.
    return_type: Region*
    params:
    - name: other
      type: Region* 

  - name: __mul__
    doc: Computes intersection of two regions, use with Python operator '*'.
    return_type: Region*
    params:
    - name: other
      type: Region* 
    
    
SurfaceRegion:
  superclass: Region
  doc: |
     Defines a region on the object. The extent of a region is given by the wall_indices list. 
     Molecules can be added and surface properties can be set with the optional regional surface commands. 
     You can have an arbitrary number of regions on an object, and they may overlap if
     you wish. Molecules added to overlapping regions accumulate. Triangles belonging to 
     multiple regions inherit all parent regions’ surface properties. Users
     have to make sure that in case of overlapped regions their surface properties
     are compatible. 
  examples: tests/pymcell4_positive/1700_linear_conc_gradient_w_conc_clamp/geometry.py
  items:
  - name: name
    type: str
    doc: Name of this region.
    
  - name: wall_indices
    type: List[int]
    doc: |
      Surface region must be a part of a GeometryObject, items in this list are indices to 
      its wall_list array.

  - name: surface_class
    type: SurfaceClass*
    default: unset
    doc: | 
       Optional surface class assigned to this surface region.
       If not set, it is inherited from the parent geometry object's surface_class.

  - name: initial_surface_releases
    type: List[InitialSurfaceRelease*]
    default: empty
    doc: |
      Each item of this list defines either density or number of molecules to be released on this surface 
      regions when simulation starts.
    internal: Equivalent to MDL's MODIFY_SURFACE_REGIONS/MOLECULE_DENSITY or MOLECULE_NUMBER. 
    
  - name: initial_color
    type: Color*
    default: unset
    doc: Initial color for this specific surface region. If not set, color of the parent's GeometryObject is used. 
    
GeometryObject:
  superclass: Region
  doc: Class represents geometry objects defined by triangular surface elements.
  examples: tests/pymcell4_positive/1330_get_wall/geometry.py 
  items:
  - name: name
    type: str
    doc: | 
       Name of the object. Also represents BNGL compartment name if 'is_bngl_compartment' is True.

  - name: vertex_list
    type: List[List[float]]
    doc: | 
       List of [x,y,z] triplets specifying positions of individual vertices of each triangle.
        
  - name: wall_list
    type: List[List[int]]
    doc: | 
       List of [a,b,c] triplets specifying each wall, individual values are indices into the 
       vertex_list attribute.
       
  - name: is_bngl_compartment
    type: bool
    default: false
    doc: |
       Set to True if this object represents a 3D BNGL compartment. 
       Its name will be then the BNGL compartment name.       

  - name: surface_compartment_name
    type: str
    default: unset
    doc: |
       When is_bngl_compartment is True, this attribute can be set to specify its 
       membrane (2D) compartment name.

  - name: surface_regions
    type: List[SurfaceRegion*]
    default: empty
    doc: |
       All surface regions associated with this geometry object.
       
  - name: surface_class
    type: SurfaceClass*
    default: unset
    doc: |
      Surface class for the whole object's surface. It is applied to the whole surface of this object 
      except for those surface regions that have their specific surface class set explicitly.

  - name: initial_surface_releases
    type: List[InitialSurfaceRelease*]
    default: empty
    doc: |
      Each item in this list defines either density or number of molecules to be released on this surface 
      regions when simulation starts.
    internal: Shouldn't we be inheriting this from Region?
    
  - name: initial_color
    type: Color*
    default: unset
    doc: | 
       Initial color for this geometry object. If a surface region has its color set, its value 
       is used for the walls of that surface region.
    
  methods:
  - name: translate
    doc: | 
       Move object by a specified vector. 
       Cannot be called after model was initialized.
    examples: tests/pymcell4_positive/1400_object_translate/model.py
    params:
    - name: move
      type: List[float]
      doc: 3D vector [x, y, z] that will be added to each vertex of this object.