--- search: boost: 10.0 --- # Class: MoleculeID _Identifiers of a molecule type in the simulated system._
URI: [https://CCPBioSim.ac.uk/biosim-schema/MoleculeID](https://CCPBioSim.ac.uk/biosim-schema/MoleculeID) ```{mermaid} classDiagram class MoleculeID click MoleculeID href "../../classes/MoleculeID/" MoleculeID : alphafold_ID MoleculeID : atom_count MoleculeID : InChI MoleculeID : InChIKey MoleculeID : modified MoleculeID : molecular_formula MoleculeID : molecular_weight MoleculeID --> "0..1" MassQuantity : molecular_weight click MassQuantity href "../../classes/MassQuantity/" MoleculeID : molecule_charge MoleculeID --> "0..1" ChargeQuantity : molecule_charge click ChargeQuantity href "../../classes/ChargeQuantity/" MoleculeID : molecule_count MoleculeID : monomer_count MoleculeID : nucleic_sequence MoleculeID : PDB_ID MoleculeID : predicted_structure MoleculeID : protein_sequence MoleculeID : PubChem_CID MoleculeID : SMILES MoleculeID : UNIPROT_ID ``` ## Slots | Name | Cardinality and Range | Description | Inheritance | | --- | --- | --- | --- | | [PDB_ID](../slots/PDB_ID.md) | 0..1
[string](../types/string.md) | Protein Data Bank identifier | direct | | [UNIPROT_ID](../slots/UNIPROT_ID.md) | 0..1
[string](../types/string.md) | UniProt accession ID | direct | | [SMILES](../slots/SMILES.md) | 0..1
[string](../types/string.md) | Simplified Molecular Input Line Entry System (SMILES) ASCII-based line notati... | direct | | [InChI](../slots/InChI.md) | 0..1
[string](../types/string.md) | The International Chemical Identifier (InChi) is a textual identifier for che... | direct | | [InChIKey](../slots/InChIKey.md) | 0..1
[string](../types/string.md) | The condensed, 27 character InChIKey, which is a hashed version of the full I... | direct | | [alphafold_ID](../slots/alphafold_ID.md) | 0..1
[string](../types/string.md) | AlphaFold predicted protein structure identifier (AlphaFold DB, EMBL-EBI) | direct | | [PubChem_CID](../slots/PubChem_CID.md) | 0..1
[string](../types/string.md) | PubChem CID of chemical molecules and their activities against biological ass... | direct | | [protein_sequence](../slots/protein_sequence.md) | 0..1
[string](../types/string.md) | One letter sequence for protein amino acids | direct | | [nucleic_sequence](../slots/nucleic_sequence.md) | 0..1
[string](../types/string.md) | One letter sequence for nucleic acid nucleotides | direct | | [predicted_structure](../slots/predicted_structure.md) | 0..1
[boolean](../types/boolean.md) | Are the molecule positions derived from a prediction? | direct | | [modified](../slots/modified.md) | 0..1
[boolean](../types/boolean.md) | Has the initial model been modified from the original? | direct | | [molecular_formula](../slots/molecular_formula.md) | 0..1
[string](../types/string.md) | The molecular formula of a molecule\ | direct | | [molecular_weight](../slots/molecular_weight.md) | 0..1
[MassQuantity](../classes/MassQuantity.md) | The molecular weight of a molecule | direct | | [molecule_charge](../slots/molecule_charge.md) | 0..1
[ChargeQuantity](../classes/ChargeQuantity.md) | Electrostatic charge of a molecule | direct | | [molecule_count](../slots/molecule_count.md) | 0..1
[integer](../types/integer.md) | Number of instances of a given molecule, defined as bonded atoms or beads | direct | | [atom_count](../slots/atom_count.md) | 0..1
[integer](../types/integer.md) | Number of atoms in a molecule | direct | | [monomer_count](../slots/monomer_count.md) | 0..1
[integer](../types/integer.md) | Number of monomeric units in a polymer(e | direct | ## Usages | used by | used in | type | used | | --- | --- | --- | --- | | [SystemComposition](../classes/SystemComposition.md) | [molecule_ID](../slots/molecule_ID.md) | range | [MoleculeID](../classes/MoleculeID.md) | ## Identifier and Mapping Information ### Schema Source * from schema: https://CCPBioSim.ac.uk/biosim-schema/ ## Mappings | Mapping Type | Mapped Value | | --- | --- | | self | https://CCPBioSim.ac.uk/biosim-schema/MoleculeID | | native | https://CCPBioSim.ac.uk/biosim-schema/MoleculeID | ## LinkML Source ### Direct ```yaml name: MoleculeID description: Identifiers of a molecule type in the simulated system. from_schema: https://CCPBioSim.ac.uk/biosim-schema/ slots: - PDB_ID - UNIPROT_ID - SMILES - InChI - InChIKey - alphafold_ID - PubChem_CID - protein_sequence - nucleic_sequence - predicted_structure - modified - molecular_formula - molecular_weight - molecule_charge - molecule_count - atom_count - monomer_count ``` ### Induced ```yaml name: MoleculeID description: Identifiers of a molecule type in the simulated system. from_schema: https://CCPBioSim.ac.uk/biosim-schema/ attributes: PDB_ID: name: PDB_ID annotations: database: tag: database value: PDB prefix: tag: prefix value: pdb base_uri: tag: base_uri value: 'https://identifiers.org/pdb:' description: Protein Data Bank identifier examples: - value: 2VB1 from_schema: https://CCPBioSim.ac.uk/biosim-schema/ aliases: - PDB ID rank: 1000 is_a: identifier owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^[0-9A-Za-z]{4}$ UNIPROT_ID: name: UNIPROT_ID annotations: database: tag: database value: UNIPROT prefix: tag: prefix value: uniprot base_uri: tag: base_uri value: 'https://identifiers.org/uniprot:' description: UniProt accession ID examples: - value: P0DP23 from_schema: https://CCPBioSim.ac.uk/biosim-schema/ aliases: - UNIPROT ID rank: 1000 is_a: identifier owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^[A-Z0-9]{6,10}$ SMILES: name: SMILES annotations: engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: SMILES description: Simplified Molecular Input Line Entry System (SMILES) ASCII-based line notation used to describe chemical structures. It represents molecular graphs with atoms and bonds, allowing software to convert these short strings into 2D or 3D models. examples: - value: CN1C=NC2=C1C(=O)N(C(=O)N2C)C from_schema: https://CCPBioSim.ac.uk/biosim-schema/ aliases: - SMILES rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^[A-Za-z0-9@+\-\[\]()=#$:./\\%*]+$ InChI: name: InChI annotations: engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: InChI description: The International Chemical Identifier (InChi) is a textual identifier for chemical substances, designed to provide a standard way to encode molecular information examples: - value: InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 from_schema: https://CCPBioSim.ac.uk/biosim-schema/ aliases: - InChI rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^InChI=1S?/[A-Za-z0-9.+\-]+(/[a-z][^/]*)*$ InChIKey: name: InChIKey annotations: database: tag: database value: IUPAC prefix: tag: prefix value: inchikey base_uri: tag: base_uri value: 'https://identifiers.org/inchikey:' engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: InChIKey description: The condensed, 27 character InChIKey, which is a hashed version of the full InChI (using the SHA-256 algorithm), designed to allow for easy web searches of chemical compounds. examples: - value: RYYVLZVUVIJVGH-UHFFFAOYSA-N from_schema: https://CCPBioSim.ac.uk/biosim-schema/ aliases: - InChIKey rank: 1000 is_a: identifier owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^[A-Z]{14}-[A-Z]{10}(-[A-Z])?$ alphafold_ID: name: alphafold_ID annotations: database: tag: database value: AlphaFoldDB base_uri: tag: base_uri value: https://alphafold.ebi.ac.uk/entry/ description: AlphaFold predicted protein structure identifier (AlphaFold DB, EMBL-EBI) examples: - value: AF-P12345-F1 from_schema: https://CCPBioSim.ac.uk/biosim-schema/ aliases: - AlphaFold ID rank: 1000 is_a: identifier owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^AF-[A-Z0-9]+-F1$ PubChem_CID: name: PubChem_CID annotations: database: tag: database value: PubChem prefix: tag: prefix value: pubchem.compound base_uri: tag: base_uri value: 'https://identifiers.org/pubchem.compound:' description: PubChem CID of chemical molecules and their activities against biological assays. examples: - value: '100101' from_schema: https://CCPBioSim.ac.uk/biosim-schema/ aliases: - PubChem CID rank: 1000 is_a: identifier owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^\d+$ protein_sequence: name: protein_sequence annotations: textarea: tag: textarea value: true engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: protein_sequence description: One letter sequence for protein amino acids. examples: - value: DRVYIHPF from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^[ACDEFGHIKLMNPQRSTVWY]+$ nucleic_sequence: name: nucleic_sequence annotations: textarea: tag: textarea value: true engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: nucleic_sequence description: One letter sequence for nucleic acid nucleotides. examples: - value: ATGCATCGATCGATCGATCG from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^[ACGTURYSWKMBDHVN]+$ predicted_structure: name: predicted_structure description: Are the molecule positions derived from a prediction? from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: boolean modified: name: modified description: Has the initial model been modified from the original? from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID - WaterPotential - ProteinPotential - LipidPotential - NucleicPotential - CarbohydratePotential - PolymerPotential - GeneralPotential - MachineLearnedPotential range: boolean molecular_formula: name: molecular_formula annotations: engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: molecular_formula description: The molecular formula of a molecule\ examples: - value: C8H10N4O2 from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: string pattern: ^([A-Z][a-z]?\d*)+$ molecular_weight: name: molecular_weight annotations: engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: molecular_weight unit: g/mol description: The molecular weight of a molecule. examples: - value: '18.0' from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: MassQuantity molecule_charge: name: molecule_charge annotations: engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: molecule_charge unit: e description: Electrostatic charge of a molecule. examples: - value: '-1.0' from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: ChargeQuantity pattern: ^[+-]?\d+(\.\d+)?$ molecule_count: name: molecule_count annotations: engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: molecule_count description: Number of instances of a given molecule, defined as bonded atoms or beads. examples: - value: '1' from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: integer minimum_value: 0 atom_count: name: atom_count annotations: engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: atom_count description: Number of atoms in a molecule. examples: - value: '1' from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: integer minimum_value: 0 monomer_count: name: monomer_count annotations: engine_mapping: tag: engine_mapping value: - engine: toptrajparser key: monomer_count description: Number of monomeric units in a polymer(e.g. protein or nucleic acid). examples: - value: '1' from_schema: https://CCPBioSim.ac.uk/biosim-schema/ rank: 1000 owner: MoleculeID domain_of: - MoleculeID range: integer minimum_value: 0 ```