schrodinger.application.scaffold_enumeration.rdcml module¶
Basic CML reader: http://www.xml-cml.org/
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schrodinger.application.scaffold_enumeration.rdcml.
parse_and_drop_xmlns
(source)¶ Parses
source
viaxml.etree.ElementTree.iterparse
, and removes namespace prefix (if present) from tags and attributes.Parameters: source (str or file-like) – File name or file-like object. Returns: Root of the tree. Return type: xml.etree.ElementTree.Element
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schrodinger.application.scaffold_enumeration.rdcml.
rdk_mol_from_cml_element
(xml_molecule, prop_prefix='cml_')¶ Instantiates
rdkit.Chem.Mol
from the XML element.Parameters: - xml_molecule (
xml.etree.ElementTree.Element
) – XML element that represents CML molecule. - prop_prefix (str) – Prefix to be added to the CML property names.
Returns: RDKit molecule.
Return type: rdkit.Chem.ROMol
- xml_molecule (
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class
schrodinger.application.scaffold_enumeration.rdcml.
CmlFileReader
(filename, prop_prefix='cml_')¶ Bases:
contextlib.AbstractContextManager
Does not need to be context manager (such need may arise in case we switch to a different XML parser).
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__init__
(filename, prop_prefix='cml_')¶ Initialize self. See help(type(self)) for accurate signature.
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