API

PubChem.get_compound — Function

get_compound(name::AbstractString | cid::Integer)

Retrieve PubChem's JSON compound record by name or compound identifier.

Arguments

name::AbstractString: A PubChem-recognized compound name, such as "water".
cid::Integer: A PubChem Compound Identifier (CID), such as 962 for water.

Returns

A JSON object represented by Julia dictionaries and vectors.

Throws

KeyError: The PubChem endpoint responds with HTTP 404 for name or cid.
Downloads.RequestError: The request cannot be completed for another HTTP or network reason.

Examples

water = get_compound(962)
properties = extract_properties(water)
properties["Molecular_formula"] # "H2O"

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PubChem.extract_properties — Function

extract_properties(data)

Extract PubChem compound properties from the JSON object returned by get_compound.

Arguments

data: A compound record returned by get_compound, with the PubChem PUG JSON layout.

Returns

A Dict whose available keys are "IUPAC_Name_Preferred", "IUPAC_Name_Traditional", "Molecular_weight", "Molecular_formula", "Molecular_mass", "Smiles", and "Charge". PubChem omits some properties for some compounds, so all keys except "Charge" are conditional on the response.

Examples

properties = extract_properties(get_compound("water"))
properties["IUPAC_Name_Preferred"] # "oxidane"

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PubChem.@attach_metadata — Macro

@attach_metadata species [name_or_cid]

Fetch chemical properties from PubChem and attach them as ModelingToolkit metadata to species.

Arguments

species: A ModelingToolkit or Catalyst symbolic species variable.
name_or_cid: Optional AbstractString, Symbol, or integer CID identifying the compound. When omitted, the species name is used as the PubChem query.

Returns

The macro expands to an assignment that replaces species with a metadata-annotated symbolic variable. The attached properties can be read with chemical_properties.

Examples

@variables t
@species H2(t)
@attach_metadata H2
chemical_properties(H2)["Molecular_formula"] # "H2"

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PubChem.molar_ratio — Function

molar_ratio(reaction::Reaction, species1, species2)

Return the stoichiometric ratio of species1 to species2 in reaction.

Arguments

reaction::Reaction: A Catalyst reaction containing both species.
species1: The numerator species.
species2: The denominator species.

Returns

A Rational equal to the stoichiometric coefficient of species1 divided by that of species2.

Throws

ErrorException: Either species is not a substrate or product of reaction.

Examples

molar_ratio(reaction, Al, Cl2) # 2//3 for 2Al + 3Cl2 -> 2AlCl3

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PubChem.moles_by_mass — Function

moles_by_mass(species, mass)

Calculate the amount of species from a supplied mass.

Arguments

species: A metadata-annotated symbolic species, compound name, or PubChem CID accepted by molecular_weight.
mass: Mass in grams.

Returns

mass / molecular_weight(species) in moles.

Examples

@variables t
@species MnO2(t)
@attach_metadata MnO2

moles_by_mass(MnO2, 95)

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PubChem.moles_by_volume — Function

moles_by_volume(molarity, volume)

Calculate the number of moles in a solution from molarity and volume.

Arguments

molarity: Amount concentration in mol/L.
volume: Solution volume in L.

Returns

The product molarity * volume, preserving the arithmetic type selected by the input values.

Examples

moles_by_volume(0.400, 0.300) == 0.120

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PubChem.limiting_reagent — Function

limiting_reagent(reaction::Reaction, masses::AbstractVector)

Find the substrate with the fewest available moles in a reaction.

Arguments

reaction::Reaction: A balanced Catalyst reaction.
masses::AbstractVector: Substrate masses in grams, in the same order as reaction.substrates.

Returns

A tuple (limiting_species, moles), where moles is the available amount of that species.

Throws

ArgumentError: masses does not support fast scalar indexing. GPU arrays are not supported because the calculation scans values on the host.

Examples

limiting_reagent(reaction, [2.8, 4.15]) # (Cl2, 0.0585...)

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PubChem.theoretical_yield — Function

theoretical_yield(reaction::Reaction, masses::AbstractVector, product::Num)

Calculate the theoretical mass yield of a product from substrate masses.

Arguments

reaction::Reaction: A balanced Catalyst reaction.
masses::AbstractVector: Substrate masses in grams, ordered as reaction.substrates.
product::Num: A product symbolic species in reaction.

Returns

The theoretical product mass in grams.

Throws

ArgumentError: masses does not support fast scalar indexing.
ErrorException: product is not in reaction.

Examples

theoretical_yield(reaction, [2.8, 4.15], AlCl3) # 5.2032...

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PubChem.chemical_properties — Function

chemical_properties(species)

Return PubChem chemical properties for a symbolic species or a PubChem query.

Arguments

species: A metadata-annotated Catalyst or ModelingToolkit symbolic species, an AbstractString compound name, or an integer PubChem CID.

Returns

A Dict of the properties returned by extract_properties. Symbolic species are read from their attached metadata; names and CIDs are retrieved from PubChem.

Examples

chemical_properties("water")["Molecular_formula"] # "H2O"

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PubChem.molecular_weight — Function

molecular_weight(species)

Return the molecular weight of species in g/mol.

Arguments

species: Any value accepted by chemical_properties.

Returns

The "Molecular_weight" property from PubChem.

Throws

ErrorException: The available properties do not contain a molecular weight.

Examples

molecular_weight("water") # 18.015

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PubChem.molecular_formula — Function

molecular_formula(species)

Return the molecular formula of species.

Arguments

species: Any value accepted by chemical_properties.

Returns

The "Molecular_formula" property from PubChem.

Throws

ErrorException: The available properties do not contain a molecular formula.

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PubChem.molecular_mass — Function

molecular_mass(species)

Return the molecular mass of species in unified atomic mass units.

Arguments

species: Any value accepted by chemical_properties.

Returns

The "Molecular_mass" property from PubChem.

Throws

ErrorException: The available properties do not contain a molecular mass.

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PubChem.IUPAC_Name_Preferred — Function

IUPAC_Name_Preferred(species)

Return the preferred IUPAC name of species.

Arguments

species: Any value accepted by chemical_properties.

Returns

The "IUPAC_Name_Preferred" property from PubChem.

Throws

ErrorException: The available properties do not contain a preferred IUPAC name.

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PubChem.IUPAC_Name_Traditional — Function

IUPAC_Name_Traditional(species)

Return the traditional IUPAC name of species.

Arguments

species: Any value accepted by chemical_properties.

Returns

The "IUPAC_Name_Traditional" property from PubChem.

Throws

ErrorException: The available properties do not contain a traditional IUPAC name.

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PubChem.smiles — Function

smiles(species)

Return the SMILES representation of species.

Arguments

species: Any value accepted by chemical_properties.

Returns

The "Smiles" property from PubChem.

Throws

ErrorException: The available properties do not contain a SMILES string.

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PubChem.charge — Function

charge(species)

Return the formal charge of species.

Arguments

species: Any value accepted by chemical_properties.

Returns

The "Charge" property from PubChem.

Throws

ErrorException: The available properties do not contain a charge.

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