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CMDL Groups

WARNING

CMDL is undergoing significant revisions to improve conciseness and ease of use. This page will be undergoing updates as the type of CMDL groups is revised.

Chemical


  • Description: Describes a small-molecule chemical reference for use in an experiment.

  • Member Of: None

  • Reference Group Properties: None

  • Properties:

  • Example:

    cmdl
    chemical lLactide {
        molecular_weight: 144.12 g/mol;
        state: "solid";
        smiles: "C[C@H]1C(=O)O[C@H](C(=O)O1)C";
    }

Complex


Component


  • Description: Describes a physical component in a continuous flow reactor.

  • Member Of:

  • Reference Group Properties: None

  • Properties:

  • Example:

    Note: The following illustrate valid arrangements of the component group. For more detailed description of a reactor_graph setup see the flow reaction tutorial.

    cmdl
    reactor_graph FlowReactorA {
        reactor PolymerizationReactor {
            component Mixer {
                description: "PEEK T-Mixer (0.05 cm ID)";
                inner_diameter: 0.05 cm;
            };
    
            component Reactor_Tubing {
                description: "PFA Reactor Tubing (14 cm, 0.05 cm ID)";
                inner_diameter: 0.05 cm;
                length: 14 cm;
                volume: 0.02749 ml;
            };
        };
    }
    cmdl
    reactor_graph FlowReactorA {
        component Monomer_Syringe {
          description: "NormJect Syringe (10 mL)";
    	    volume: 10 ml;
    	    target: @Monomer_Pump;
      };
    }

Container


  • Description: Describes a container group in a polymer_graph representation. Contains references to edges, nodes, and other container groups for describing the polymer structure

  • Member Of:

  • Reference Group Properties: None

  • Properties:

  • Example:

    cmdl
    polymer_graph mPEG_Graph {
        nodes: [ @eg_MeO ];
        <@eg_MeO.R => @PEG_Block.p_PEO.R>;
    
        container PEG_Block {
            nodes: [ @p_PEO ]
            <@p_PEO.Q => @p_PEO.R>;
        };
    }

Flow Reaction


  • Description:
  • Member Of:
  • Properties:
  • Example:

Polymer


  • Description: Defines a polymer reference for use within an experiment record.

  • Member Of: None

  • Reference Group Properties: None

  • Properties:

  • Example:

    cmdl
      polymer mPEG-OH {
          tree: @PEG_BASE;
          mn_avg: 5000 g/mol;
    
          @PEG_BASE.PEG_Block.p_PEO {
              degree_poly: 112.8
          };
      }

Polymer Graph


  • Description: Defines a graph representation for a polymeric material.

  • Member Of: None

  • Reference Group Properties: None

  • Properties:

  • Example:

    cmdl
    polymer_graph PEG_PLLA_Base {
        nodes: [ @eg_MeO ];
        <@eg_MeO.R => @PEG_Block.p_PEO.R>;
    
        container PEG_Block {
            nodes: [ @p_PEO ];
            <@p_PEO.Q => @p_PEO.R>;
        };
    
        container PLLA_Block {
            nodes: [ @p_Llac ];
            <@p_Llac.Q => @p_Llac.R>;
        };
    }

Reaction


  • Description: Defines a batch reaction for an experimental record.

  • Member Of: None

  • Reference Group Properties:

  • Properties:

  • Example:

    cmdl
    reaction BatchRxn {
        temperature: 22 degC;
        reaction_time: 10 s;
    
        @mPEG-OH {
            mass: 5 mg;
            roles: [ "initiator" ];
            limiting: true;
        };
    
        @kOtBu {
            mass: 5 mg;
            roles: [ "catalyst", "reagent" ];
        };
    
        @lLactide {
            mass: 1440 mg;
            roles: [ "monomer" ];
        };
    
        @THF {
            volume: 2 ml;
            roles: [ "solvent" ];
        };
    
        @mPEG-PLLA {
            roles: [ "product" ];
        };
    }

Reactor


  • Description: Defines a container for component elements that belong to a single reactor element within a reactor graph. Treated as a single volume for computing residence times and stoichiometry.

  • Member Of:

  • Reference Group Properties: None

  • Properties: None

  • Example:

    Note: The following example would be nested inside a reactor graph

    cmdl
    reactor PolymerizationReactor {
        component Mixer {
            description: "PEEK T-Mixer (0.05 cm ID)";
            inner_diameter: 0.05 cm;
        };
    
        component Reactor_Tubing {
            description: "PFA Reactor Tubing (14 cm, 0.05 cm ID)";
            inner_diameter: 0.05 cm;
            length: 14 cm;
            volume: 0.02749 ml;
        };
    };

Reactor Graph


  • Description: Defines a reactor graph representation that can be used within a flow reaction group.

  • Member Of: None

  • Reference Group Properties: None

  • Properties: None

  • Example:

    cmdl
    reactor_graph FlowReactorA {
        reactor PolymerizationReactor {
            component Mixer {
                description: "PEEK T-Mixer (0.05 cm ID)";
                inner_diameter: 0.05 cm;
            };
    
            component Reactor_Tubing {
                description: "PFA Reactor Tubing (14 cm, 0.05 cm ID)";
                inner_diameter: 0.05 cm;
                length: 14 cm;
                volume: 0.02749 ml;
            };
        };
    }

Solution


  • Description: Describes a stock solution of reagents for use in a flow reaction.

  • Member Of: None

  • Reference Group Properties:

  • Properties: None

  • Example:

    cmdl
      solution Catalyst_Solution {
          @KOMe {
              mass: 144 mg;
              roles: [ "catalyst" ];
          };
    
          @UreaCatalyst {
              mass: 500 mg;
              roles: [ "catalyst" ];
          };
    
          @THF {
              volume: 8 ml;
              roles: [ "solvent" ];
          };
      }