rdkit.Chem.PropertyMol module

class rdkit.Chem.PropertyMol.PropertyMol(self)
class rdkit.Chem.PropertyMol.PropertyMol(self, pklString: bytes)
class rdkit.Chem.PropertyMol.PropertyMol(self, pklString: bytes, propertyFlags: int)
class rdkit.Chem.PropertyMol.PropertyMol(self, pklString: str)
class rdkit.Chem.PropertyMol.PropertyMol(self, pklString: str, propertyFlags: int)
class rdkit.Chem.PropertyMol.PropertyMol(self, mol: rdkit.Chem.rdchem.Mol, quickCopy: bool = False, confId: int = -1)

Bases: Mol

allows rdkit molecules to be pickled with their properties saved.

>>> import os
>>> import pickle
>>> from rdkit import RDConfig
>>> m = Chem.MolFromMolFile(os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data/benzene.mol'))
>>> m.GetProp('_Name')
'benzene.mol'

by default pickling removes properties:

>>> m2 = pickle.loads(pickle.dumps(m))
>>> m2.HasProp('_Name')
0

Property mols solve this:

>>> pm = PropertyMol(m)
>>> pm.GetProp('_Name')
'benzene.mol'
>>> pm.SetProp('MyProp','foo')
>>> pm.HasProp('MyProp')
1

>>> pm2 = pickle.loads(pickle.dumps(pm))
>>> Chem.MolToSmiles(pm2)
'c1ccccc1'
>>> pm2.GetProp('_Name')
'benzene.mol'
>>> pm2.HasProp('MyProp')
1
>>> pm2.GetProp('MyProp')
'foo'
>>> pm2.HasProp('MissingProp')
0

Property mols are a bit more permissive about the types of property values:

>>> pm.SetProp('IntVal',1)

That wouldn’t work with a standard mol

but the Property mols still convert all values to strings before storing:

>>> pm.GetProp('IntVal')
'1'

This is a test for sf.net issue 2880943: make sure properties end up in SD files:

>>> import tempfile, os
>>> fn = tempfile.NamedTemporaryFile(suffix='.sdf', delete=False).name
>>> w = Chem.SDWriter(fn)
>>> w.write(pm)
>>> w=None
>>> with open(fn,'r') as inf:
...   txt = inf.read()
>>> '<IntVal>' in txt
True
>>> try:
...   os.unlink(fn)
... except Exception:
...   pass

The next level of that bug: does writing a depickled propertymol to an SD file include properties:

>>> fn = tempfile.NamedTemporaryFile(suffix='.sdf', delete=False).name
>>> w = Chem.SDWriter(fn)
>>> pm = pickle.loads(pickle.dumps(pm))
>>> w.write(pm)
>>> w=None
>>> with open(fn,'r') as inf:
...   txt = inf.read()
>>> '<IntVal>' in txt
True
>>> try:
...   os.unlink(fn)
... except Exception:
...   pass

Overloaded function.

  1. __init__(self) -> None

Constructor, takes no arguments

  1. __init__(self, pklString: bytes) -> None

Constructor from a binary string

  1. __init__(self, pklString: bytes, propertyFlags: int) -> None

Constructor from a binary string with property flags

  1. __init__(self, pklString: str) -> None

Constructor from a binary string

  1. __init__(self, pklString: str, propertyFlags: int) -> None

Constructor from a binary string with property flags

  1. __init__(self, mol: rdkit.Chem.rdchem.Mol, quickCopy: bool = False, confId: int = -1) -> None

Constructor from another molecule

SetProp(self, key: str, val: str, computed: bool = False) → None

Sets a molecular property

ARGUMENTS:

  • key: the name of the property to be set (a string).

  • value: the property value (a string).

  • computed: (optional) marks the property as being computed.

    Defaults to False.