Hi,
I am fairly new to RDKit and I apologize in advance if this question is
rather basic in nature.
I am reading a molecule the following way and trying to display the
properties from the sdf:
[dkeidel-desktop:dkeidel] /emi/doc/sod/villa $ python
Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41)
[GCC 4.4.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import os, sys, copy
>>> from rdkit.Chem import rdDepictor
>>> from rdkit import Geometry
>>>
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem
>>> from rdkit.Chem.Draw import MolDrawing
>>> from rdkit.Chem.AvailDescriptors import descDict
[15:14:22] WARNING: The AvailDescriptors module is deprecated. Please
switch to using the Descriptors module.
>>>
>>> import rdkit.DataStructs
>>> import rdkit.Chem.MACCSkeys
>>> import rdkit.Chem.AtomPairs.Pairs
>>> import rdkit.Chem.AtomPairs.Torsions
>>> suppl = Chem.SDMolSupplier('/emi/doc/sod/villa/R1_060A.sdf')
>>> mb = suppl.GetItemText(0)
>>> nsuppl = Chem.SDMolSupplier()
>>> nsuppl.SetData(mb)
>>> mol = nsuppl.next()
>>> list(mol.GetPropNames(includePrivate=True, includeComputed=True))
['Template', '_MolFileComments', '_MolFileInfo', '_Name',
'_StereochemDone', '__computedProps', 'numArom']
>>> mol.GetProp('Template')
'060A/11'
As you can see I have successfully done this. However, I want to get
access to other properties from the properties block in the sd file.
Here is the sd file I am referring to:
-ISIS- 03241116262D
7 6 0 0 0 0 0 0 0 0999 V2000
7.9102 -2.4208 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.4770 -2.4208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0437 -2.4208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.1916 -2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7583 -2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3292 -2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.9148 -3.2458 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
2 4 1 0 0 0 0
3 5 1 0 0 0 0
4 1 1 0 0 0 0
5 2 1 0 0 0 0
6 3 1 0 0 0 0
1 7 1 0 0 0 0
M RGP 1 7 1
M END
> <Template>
060A/11
$$$$
My question is the following. When I have the RDKit mol object, can I
Get the property M RGP or Set it to something different? Or should I
deal with this information as a string and write it out to a new sdf if
I want to change some numbers on the M RGP line?
Thank you in advance for any help.
Don
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