Hi Jan and Greg,
Thanks for nice suggestion. I think that will serve the purpose. I will do
it tomorrow asap and let you know.
Regards,
Dr. Hitesh Patel
Post-Doctoral Fellow,
Technische Universität Dortmund,
Chemische Biologie,
Otto-Hahn-Straße 6,
44227, Dortmund,
Germany
Room: C1-05-181
Work: 0231 755-4740
Mob.: +49 (0)176 5544 6467
Email: [email protected]
On Sun, Jul 5, 2015 at 10:49 AM, Jan Holst Jensen <[email protected]>
wrote:
> Hi Greg,
>
> I was running with both RDKit 2014.09.2 and 2013.09.1. "V " lines
> accepted and read in input, but no "V " lines produced in mol block
> output.
>
> I downloaded 2015.03.1 and that produces "V " lines in mol block
> output. Another good reason to upgrade :-).
>
> 2014.09.2:
>
> >>> from rdkit import rdBase
> >>> rdBase.rdkitVersion
> '2014.09.2'
> >>> from rdkit import Chem
> >>> m = Chem.MolFromSmiles('CO')
> >>> m.GetAtomWithIdx(0).SetProp('molFileValue','a1')
> >>> print Chem.MolToMolBlock(m)
>
> RDKit
>
> 2 1 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> M END
>
> >>>
>
>
> 2015.03.1:
>
> >>> from rdkit import rdBase
> >>> rdBase.rdkitVersion
> '2015.03.1'
> >>> from rdkit import Chem
> >>> m = Chem.MolFromSmiles('CO')
> >>> m.GetAtomWithIdx(0).SetProp('molFileValue','a1')
> >>> print Chem.MolToMolBlock(m)
>
> RDKit
>
> 2 1 0 0 0 0 0 0 0 0999 V2000
> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> V 1 a1
> M END
>
> >>>
>
> Cheers
> -- Jan
>
> On 2015-07-05 04:59, Greg Landrum wrote:
> > Hmm, that's strange. Unless that atom also has a query associated with
> > it, the atom values definitely should be written. It certainly works
> > at least some of the time:
> >
> > In [5]: m = Chem.MolFromSmiles('CO')
> >
> > In [6]: m.GetAtomWithIdx(0).SetProp('molFileValue','a1')
> >
> > In [7]: mb = Chem.MolToMolBlock(m)
> >
> > In [8]: print(mb)
> >
> > RDKit
> >
> > 2 1 0 0 0 0 0 0 0 0999 V2000
> > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> > 1 2 1 0
> > V 1 a1
> > M END
> >
> > Jan: what version of the RDKit are you using?
> >
> > -greg
> >
> >
> >
> > On Sat, Jul 4, 2015 at 8:08 PM, Jan Holst Jensen
> > <[email protected] <mailto:[email protected]>> wrote:
> >
> > Hi Hitesh,
> >
> > The V2000 molfile format has a feature that can be used to set a
> > simple text value for an atom by adding "V " lines to the
> > molfile. The RDKit molfile *reader* supports this feature as seen
> > below (I have seen this feature used to e.g. tag reactive centers
> > in a molecule when doing RDKit reaction-based enumeration).
> >
> > from rdkit import Chem molfile_with_values =
> >
> > >>> "".join(open("C:/temp/cns-with-values.mol").readlines()) print
> > >>> molfile_with_values
> >
> > -ISIS- 07041519212D
> >
> > 3 2 0 0 0 0 0 0 0 0999 V2000
> > 0.0958 -2.6833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 0.8083 -2.2708 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> > 1.5208 -2.6792 0.0000 <tel:2.6792%20%20%20%200.0000> S 0
> > 0 0 0 0 0 0 0 0 0 0 0
> > 1 2 1 0 0 0 0
> > 2 3 1 0 0 0 0
> > V 1 Carbs
> > V 3 Sulfuric
> > M END
> >
> > m = Chem.MolFromMolBlock(molfile_with_values)
> >
> > >>> m.GetAtoms()[0].GetProp('molFileValue')
> > 'Carbs'
> >
> > m.GetAtoms()[1].GetProp('molFileValue')
> >
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > KeyError: 'molFileValue'
> >
> > m.GetAtoms()[2].GetProp('molFileValue')
> >
> > 'Sulfuric'
> >
> >
> >
> > As you can see, the "V " lines in the molfile are put into RDKit
> > atom "molFileValue" properties.
> >
> > Unfortunately, the atom values are not written when RDKit outputs
> > a molfile:
> >
> > print Chem.MolToMolBlock(m)
> >
> >
> > RDKit 2D
> >
> > 3 2 0 0 0 0 0 0 0 0999 V2000
> > 0.0958 -2.6833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 0.8083 -2.2708 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> > 1.5208 -2.6792 0.0000 <tel:2.6792%20%20%20%200.0000> S 0
> > 0 0 0 0 0 0 0 0 0 0 0
> > 1 2 1 0
> > 2 3 1 0
> > M END
> >
> >
> >
> > But, it is fairly easy to add them with this function:
> >
> > def MolToMolBlock_WithAtomValues(mol):
> > mol_block = Chem.MolToMolBlock(mol).split("\n")
> > # Delete the "M END" line.
> > mol_block = mol_block[:-2]
> > # Add appropriate "V" lines.
> > for atom in mol.GetAtoms():
> > if atom.HasProp("molFileValue"):
> > mol_block.append("V %3d %s" % (atom.GetIdx() + 1,
> > atom.GetProp("molFileValue")))
> >
> > mol_block.append("M END")
> > return "\n".join(mol_block)
> >
> > This lets you persist atom text values. Disclaimer: I have no idea
> > if this will break in the presence of other property lines, e.g.
> > "M CHG" etc., but ... it's a start.
> >
> > As an example, let's first create the "CNS" molecule without atom
> > values.
> >
> > m = Chem.MolFromSmiles("CNS") print
> >
> > >>> MolToMolBlock_WithAtomValues(m)
> >
> > RDKit
> >
> > 3 2 0 0 0 0 0 0 0 0999 V2000
> > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> > 0.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
> > 1 2 1 0
> > 2 3 1 0
> > M END
> >
> >
> >
> > Add two atom values and use the new function to persist the atom
> > values to the V2000 molfile output:
> >
> > m.GetAtoms()[0].SetProp("molFileValue", "C-atom")
> >
> > >>> m.GetAtoms()[2].SetProp("molFileValue", "Here is an S-atom")
> > >>> print MolToMolBlock_WithAtomValues(m)
> >
> > RDKit
> >
> > 3 2 0 0 0 0 0 0 0 0999 V2000
> > 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> > 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> > 0.0000 0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
> > 1 2 1 0
> > 2 3 1 0
> > V 1 C-atom
> > V 3 Here is an S-atom
> > M END
> >
> >
> >
> > Check that the output can be read back in:
> >
> > molblock_test = MolToMolBlock_WithAtomValues(m) m_test =
> >
> > >>> Chem.MolFromMolBlock(molblock_test)
> > >>> m_test.GetAtoms()[0].GetProp("molFileValue")
> > 'C-atom'
> >
> > m_test.GetAtoms()[1].GetProp("molFileValue")
> >
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > KeyError: 'molFileValue'
> >
> > m_test.GetAtoms()[2].GetProp("molFileValue")
> >
> > 'Here is an S-atom'
> >
> >
> >
> > If you have multiple properties they would have to be encoded into
> > the text value as e.g. key-value pairs. The text values are in
> > principle limited to max. 70-80 characters (72 ?) by the MDL
> > molfile specification, but RDKit probably accepts longer strings
> > (I would guess, but have not tried).
> >
> > A more generic solution would be to map RDKit atom and bond
> > properties to molfile S-group data - but that's a bit more
> > involved and is not supported at the moment.
> >
> > Cheers
> > -- Jan Holst Jensen
> >
> > On 2015-07-04 18:28, Greg Landrum wrote:
> >
> > Hi,
> >
> > >
> > > On Friday, July 3, 2015, Hitesh Patel <[email protected]
> > <mailto:[email protected]>
> > > <mailto:[email protected]
> > <mailto:[email protected]>>> wrote:
> > >
> > > Hi Greg,
> > >
> > > At first priority, I will use mol2 format. A s shown in mol2 format
> > > explanation, we can set user specified atom attributes. I copied
> the
> > > text below for your convenience. See the bold text.
> > >
> > >
> > > The rdkit does not yet have a mol2 writer, so that isn't an option.
> > >
> > >
> > > For second priority, I can use mol files. There I have to set
> > > Properties block:
> > >
> > > * |M ALS| - atom list and exclusive list * |M APO| - Rgroup
> > > attachment point * |M CHG| - charge * .....
> > >
> > > But, I am not sure, whether the user defined property block is
> > > allowed or not.
> > >
> > >
> > > M CHG and M ALS are already used by the rdkit when atoms have
> > charges
> > > or there are list queries. M APO is not used, but that's because I
> > > have never managed to figure out how to adapt the MDL R Group
> > idea to
> > > something sensible in the context of the rdkit.
> > >
> > > Which one looks feasible??
> > >
> > >
> > > I'm still not sure of what kind of custom properties you are
> looking
> > > to write.
> > >
> > > -greg
> > >
> > >
> > >
> > >
> > >
> > > On Fri, Jul 3, 2015 at 4:45 PM Greg Landrum
> > <[email protected] <mailto:[email protected]>
> > > <javascript:_e(%7B%7D,'cvml','[email protected]
> > <mailto:[email protected]>');>> wrote:
> > >
> > > Hitesh,
> > >
> > > It is certainly possible to set atom properties. I don't think
> > any of
> > > the output formats the rdkit can generate really support atom
> > > properties though. What format did you envision writing and how
> > would
> > > the atom properties be encoded?
> > >
> > > -greg
> > >
> > >
> > > On Friday, July 3, 2015, Hitesh Patel <[email protected]
> > <mailto:[email protected]>
> > > <javascript:_e(%7B%7D,'cvml','[email protected]
> > <mailto:[email protected]>');>> wrote:
> > >
> > > Hi Josh, Thanks for your quick reply. But, sorry, I want to set
> atom
> > > properties, not molecule properties. Like,
> > >
> > > atom = m.GetAtomWithIdx(5) atom.SetProp('my_property',
> > > 'value_of_my_property')
> > >
> > > I want to save this property associated with each atom.
> > >
> > > Regards,
> > >
> > > Hitesh Patel
> > >
> > > On Fri, Jul 3, 2015 at 3:41 PM, Campbell J.E.
> > <[email protected] <mailto:[email protected]>>
> > > wrote:
> > >
> > > Hi Hitesh
> > >
> > >
> > >
> > > I use the PropertyMol object to save molecules with properties,
> > > setting a property for a molecule is fairly simple,
> > >
> > >
> > >
> > > m.SetProp("_Name",”mol_name")
> > >
> > >
> > >
> > > for m in mol_lst:
> > >
> > > pm = AllChem.PropertyMol(m)
> > >
> > > pm.SetProp("_Name", name)
> > >
> > > pm.SetProp("_Energy", None)
> > >
> > > dump_list.append(pm)
> > >
> > > cPickle.dump(dump_list, open(p_name, "w+"))
> > >
> > >
> > >
> > > Then something like this will allow you to act on the molecules
> > > again.
> > >
> > >
> > >
> > > mol_list = cPickle.load( open(p_name, "rb" ) )
> > >
> > >
> > >
> > > Hope this helps.
> > >
> > >
> > >
> > > Josh Campbell
> > >
> > >
> > >
> > > *From:*Hitesh Patel [mailto:[email protected]
> > <mailto:[email protected]>] *Sent:* 03 July
> > > 2015 14:21 *To:* [email protected]
> > <mailto:[email protected]> *Subject:*
> >
> > > [Rdkit-discuss] Save files with new atom properties and read again
> > >
> > >
> > >
> > > Hi there,
> > >
> > > I am new to RDkti.
> > >
> > > Is there a way to save custom property for each atoms and save that
> > > to any file format and use it again?
> > >
> > >
> > > --
> > >
> > > Regards,
> > >
> > > Dr. Hitesh Patel Post-Doctoral Fellow, Technische Universität
> > > Dortmund, Chemische Biologie, Otto-Hahn-Straße 6, 44227, Dortmund,
> > > Germany
> > >
> >
> >
> >
>
>
>
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