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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:
cmdlchemical lLactide { molecular_weight: 144.12 g/mol; state: "solid"; smiles: "C[C@H]1C(=O)O[C@H](C(=O)O1)C"; }
Complex
- Description: Describes a reference of a macromolecular complex for use in experiments and assays. May consist of both polymeric and small-molecule components.
- Member Of: None
- Reference Group Properties:
- Properties:
- Example:
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 areactor_graph
setup see the flow reaction tutorial.cmdlreactor_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; }; }; }
cmdlreactor_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 othercontainer
groups for describing the polymer structureMember Of:
Reference Group Properties: None
Properties:
Example:
cmdlpolymer_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:
cmdlpolymer 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:
cmdlpolymer_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:
cmdlreaction 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
cmdlreactor 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:
cmdlreactor_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:
cmdlsolution Catalyst_Solution { @KOMe { mass: 144 mg; roles: [ "catalyst" ]; }; @UreaCatalyst { mass: 500 mg; roles: [ "catalyst" ]; }; @THF { volume: 8 ml; roles: [ "solvent" ]; }; }