The modelcif.descriptor Python module

Classes to describe the chemistry of custom chemical components.

If a given ihm.ChemComp is not defined in either the wwPDB chemical component dictionary (CCD) or the ModelArchive CCD, its chemistry can be described with one or more of these objects. They are passed as the descriptors argument when creating a new ihm.ChemComp.

class modelcif.descriptor.Descriptor(value, details=None, software=None)[source]

Base class for all descriptors. This class is generally not used directly; instead, a subclass such as IUPACName or InChI is employed.

Parameters:

  • value (str) – The actual name or identifier describing the chemistry.

  • details (str) – Additional details about this descriptor.

  • software (modelcif.Software) – The software used to generate the descriptor, if any.

class modelcif.descriptor.CanonicalSMILES(value, details=None, software=None)[source]

Simplified Molecular-Input Line-Entry System (SMILES) computed from chemical structure devoid of isotopic and stereochemical information.

class modelcif.descriptor.IsomericSMILES(value, details=None, software=None)[source]

Simplified Molecular-Input Line-Entry System (SMILES) computed from chemical structure containing isotopic and stereochemical information.

SMILES written with isotopic and chiral specifications are collectively known as isomeric SMILES.

class modelcif.descriptor.IUPACName(value, details=None, software=None)[source]

Chemical name computed from chemical structure that uses International Union of Pure and Applied Chemistry (IUPAC) nomenclature standards.

class modelcif.descriptor.InChI(value, details=None, software=None)[source]

International Chemical Identifier (InChI) computed from chemical structure using the International Union of Pure and Applied Chemistry (IUPAC) standard.

class modelcif.descriptor.InChIKey(value, details=None, software=None)[source]

International Chemical Identifier hash (InChIKey) computed from chemical structure using the International Union of Pure and Applied Chemistry (IUPAC) standard.

class modelcif.descriptor.PubChemCID(value, details=None, software=None)[source]

PubChem Compound ID.