BioMoleculeValue

BioMoleculeValue[biomol,prop]

returns the value of the property prop for the BioMolecule biomol.

BioMoleculeValue[biomolpart,prop]

returns the property value association with part of biomol.

Details

  • For inputs of the form BioMoleculeValue[biomolpart,prop], part should be an Association whose keys and default values are given by:
  • "Model"1which model to use
    "Chains"Allwhich chains to include
    "Residues"Allwhich residues to include
    "Atoms"Allwhich atoms to include
  • The following general properties are available:
  • "Name"biomolecule name
    "BioSequence"a BioSequence with type "HybridStrand"
    "ModelCount"number of models (usually one)
    "Models"a list of BioMolecule objects with one model each
    "AssemblyCount"number of assemblies
    "AssemblyData"data for assemblies
    "Assemblies"a list of BioMolecule objects with one assembly each
    "CrystallographicSpaceGroup"crystallographic space group
    "ComputedStructureQ"gives True if biomol is a predicted structure
    "PDBString"a string representing biomol in the "PDB" format
    "MMCIFString"a string representing biomol in the "MMCIF" format
  • The following properties apply at the model level:
  • "ChainCount"number of chains
    "ChainLabels"list of chain labels, e.g. {"A","B",…}
    "PolymerChainCount"number of polymer chains
    "PolymerChainLabels"list of labels for polymer chains
    "ResidueCount"number of residues in all chains
  • The following properties apply at the chain level, and the results are returned in an Association whose keys are the chain labels:
  • "ResidueCounts"number of residues per chain
    "ResidueLabels"list of residue labels, e.g. {"GLY","PRO",…}
    "ResidueIDs"numeric identifiers
    "AtomCounts"number of atoms per chain
  • The following properties apply at the residue level, and the results are returned in an Association whose keys are the chain labels and whose values are lists of lists, one for each residue:
  • "AtomicSymbols"symbols for the atoms
    "AtomCoordinates"atom coordinates with units, wrapped in QuantityArray
    "AtomCoordianteValues"numeric atom coordinates in angstroms
    "AtomLabels"labels for each atom, e.g. {"CA","CB",…}

Examples

Basic Examples  (1)

Create a biomolecule from an ExternalIdentifier:

Find the number of models:

Find the atom coordinate for the first atom in residue 3 for each model:

Visualize the atom positions:

Wolfram Research (2024), BioMoleculeValue, Wolfram Language function, https://reference.wolfram.com/language/ref/BioMoleculeValue.html.

Text

Wolfram Research (2024), BioMoleculeValue, Wolfram Language function, https://reference.wolfram.com/language/ref/BioMoleculeValue.html.

CMS

Wolfram Language. 2024. "BioMoleculeValue." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/BioMoleculeValue.html.

APA

Wolfram Language. (2024). BioMoleculeValue. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/BioMoleculeValue.html

BibTeX

@misc{reference.wolfram_2024_biomoleculevalue, author="Wolfram Research", title="{BioMoleculeValue}", year="2024", howpublished="\url{https://reference.wolfram.com/language/ref/BioMoleculeValue.html}", note=[Accessed: 22-November-2024 ]}

BibLaTeX

@online{reference.wolfram_2024_biomoleculevalue, organization={Wolfram Research}, title={BioMoleculeValue}, year={2024}, url={https://reference.wolfram.com/language/ref/BioMoleculeValue.html}, note=[Accessed: 22-November-2024 ]}