pyrfume.odorants module

Classes for odorants, mixtures, chemical orders, etc.

class pyrfume.odorants.ChemicalOrder(molecule: pyrfume.odorants.Molecule, vendor: pyrfume.odorants.Vendor, part_id: str, purity: float = 1, known_impurities: list = None)

Bases: object

known_impurities = None

molecule = None

part_id = ''

purity = 1

vendor = None

class pyrfume.odorants.Compound(chemical_order: pyrfume.odorants.ChemicalOrder, stock: str = '', date_arrived: datetime.datetime = None, date_opened: datetime.datetime = None, is_solvent: bool = False)

Bases: object

chemical_order = None

date_arrived = None

date_opened = None

is_solvent = False

stock = ''

class pyrfume.odorants.Molecule(cid: int, name: str = None, fill: bool = False)

Bases: object

cas = ''

cid = 0

density = None

fill_details()

get_cid_from_api()

get_name_from_api()

iupac = ''

molar_evaporation_rate

molarity

molecular_weight = None

name = ''

synonyms = ''

vapor_pressure = None

class pyrfume.odorants.Solution(components: dict, date_created: datetime.datetime = None)

Bases: object

components = None

compounds

date_created = None

dilutions

molar_evaporation_rate(molecule)

molar_evaporation_rates

molarities

Returns a dictionary with the molarity of each Molecule

mole_fraction(molecule)

mole_fractions

Returns a dictionary with the mole fraction of each Molecule

molecules

Returns a dictionary with the moles of each Molecule

partial_pressure(molecule)

partial_pressures

Computes partial pressures for each odorant in the mixture using Raoult’s law

total_pressure

Computes total pressure of the vapor using Dalton’s law

vapor_concentration(molecule)

vapor_concentrations

Concentrations of each component in the vapor phase at steady state. Units are fraction of volume. Air is assumed to make up the balance

class pyrfume.odorants.Vendor(name: str, url: str)

Bases: object

name = ''

url = ''

pyrfume.odorants.all_cids()

All CIDs found in the file at ODORANTS_BASIC_INFO_PATH

pyrfume.odorants.all_odorants()

All CIDs, SMILES, Names, and Molecular Weights found in the file at ODORANTS_BASIC_INFO_PATH

pyrfume.odorants.all_smiles()

All SMILES found in the file at ODORANTS_BASIC_INFO_PATH. May contain duplicates (if two CIDs give the same SMILES)

pyrfume.odorants.all_sources()

Whether or not each odorant (by CID) is in each of the data sources

pyrfume.odorants.cactus(identifier: str, output: str = 'cas') → str

pyrfume.odorants.cactus_image(smiles: str) → None

pyrfume.odorants.canonical_smiles(smiles: str, kekulize: bool = False) → str

Use rdkit to convert the smiles string to canonical form

pyrfume.odorants.cas_from_synonyms(synonyms: list) → list

pyrfume.odorants.cids_to_cas(cids: list) → collections.OrderedDict

pyrfume.odorants.cids_to_smiles(cids: list) → dict

Returns an ordered dictionary of SMILES strings with CIDs as keys

pyrfume.odorants.crop_image(img, padding=0)

Crop white out of a PIL image.

pyrfume.odorants.deisomerize_smiles(smiles: str) → str

pyrfume.odorants.display_molecules(molecules: pandas.core.frame.DataFrame, no_of_columns=5, figsize=(15, 15))

pyrfume.odorants.embed_molecules(molecules: pandas.core.frame.DataFrame)

pyrfume.odorants.from_cids(cids: list, property_list: bool = None) → list

pyrfume.odorants.get_cid(identifier: str, kind: str = None, verbose: bool = True, fix_smiles_on_error: bool = True, attempt=0) → int

Return data about a molecule from any synonym, including a chemical name or a CAS. change_kind: Whether to try other kinds if the search fails.

pyrfume.odorants.get_cids(identifiers: list, kind: str = None, verbose: bool = True, wait: float = 0, results: dict = None) → dict

Return CIDs for molecule based on any synonym, including a chemical name or a CAS

pyrfume.odorants.get_compound_odor(cid, raw=False)

pyrfume.odorants.get_compound_summary(cid: int, heading: str)

Get summary info about heading from PubChem for the compound given by cid. Example heading: ‘Physical Description’

pyrfume.odorants.get_kind(identifier: str)

pyrfume.odorants.is_kind(identifier: str, kind: str) → bool

pyrfume.odorants.smiles_to_image(smiles, png=True, b64=False, crop=True, padding=10, size=300)

png: Whether to convert to .png data (or to leave as a PIL image) b64: Whether to base64 encode (only possible for .png data)

pyrfume.odorants.smiles_to_mol(smiles: list, max_attempts: int = 10, use_random_coords: bool = False, deisomerize=False) → dict

pyrfume.odorants.url_to_json(url, verbose=True) → str