Thank you all again for the great responses! :)
There seems to be a consensus between Andrew and Pavel that the solution is
with SetBondDir(). I've tried Pavel's functions get_unspec_double_bonds()
and set_double_bond_stereo() in python 2 (couldn't figure out how to get
RDkit set up in python 3, but it seems like python 3 is only used for
read_input). In python 2 get_unspec_double_bonds() worked, but
set_double_bond_stereo() did not change the stereo of the bond. I've also
tried the SetBondDir() function myself with no avail.
However, Brian's answer makes the logical sense with setStereo(). I did not
find a function like that in python (It is in the C++ code however:
http://www.rdkit.org/C++_Docs/Bond_8h_source.html#l00278). Oddly enough
there is the GetStereo() function for python.
I'm wondering if maybe I could use SetProp() to do this? I couldn't find
how exactly GetStereo() works, if it is a property that is set or
calculated. But I would assume if it was a property I could do something
like the following: SetProp("d_stereo","STEREOE"). However, I did not find
the right property name to do this.
Again, thank you all for the help. It is very much appreciated!
- James
On Fri, Dec 9, 2016 at 11:46 PM, Pavel Polishchuk <pavel_polishc...@ukr.net>
wrote:
> I just want to share my script, which I use for enumeration of
> stereoisomers. Enumeration of double bonds was added quite recently and
> thus I didn't test it extensively.
> I put it on github: <https://github.com/DrrDom/rdk>
> https://github.com/DrrDom/rdk
> It seems to work well on quite complex queries like
> CC1CCC(CC1)C1CC=C(C\C(=C/I)C(=CF)C1C1C[C@@H](C)CC=C1)C1CC[C@H](O)C(Br)C1
>
> to generate all possible stereoisomers:
> gen_stereo_rdkit3.py -i input.smi -o output.smi -t -d
>
> to discard compounds with more than 4 undefined centers/double bonds:
> gen_stereo_rdkit3.py -i input.smi -o output.smi -t -d -u 4
>
> Try it on your own risk :)
> If you will find mistakes let me know.
>
> Pavel.
>
>
> On 12/10/2016 03:44 AM, Brian Cole wrote:
>
> So I may need a little guidance on this one from someone with a little
> more historical knowledge of RDKit.
>
> I found the findPotentialStereoBonds function inside Chirality.cpp that
> appears to do what we want, detect double bonds with unspecified E/Z stereo
> chemistry. That's at least what the comment in the file leads me to
> believe:
>
> // Find bonds than can be cis/trans in a molecule and mark them as "any"
> ...
> void findPotentialStereoBonds(ROMol &mol, bool cleanIt) {
>
>
> But when you look at the code, it's not setting bonds to Bond::STEREOANY,
> it's setting them to Bond::STEREONONE here:
>
> ...
> // proceed only if we either want to clean the stereocode on this
> bond
> // or if none is set on it yet
>
> if (cleanIt || dblBond->getStereo() == Bond::STEREONONE) {
> dblBond->setStereo(Bond::STEREONONE);
> ...
>
> Seems odd to me check that the stereo is Bond::STEREONONE, and then set it
> to that value.
>
> While findPotentialStereoBonds isn't exposed in Python, there is some Java
> docs written for it in the Java wrappers:
> %javamethodmodifiers RDKit::MolOps::findPotentialStereoBonds (
> ROMol & mol, bool cleanIt = false )
> "
> /**
> <p>
> finds bonds that could be cis/trans in a molecule and mark them as
> Bond::STEREONONE
> <p>
>
>
> So that documentation is actually correct. It does find bonds that could
> be cis/trans and mark them as Bond::STEREONONE. That just isn't very useful
> since all bonds are marked Bond::STEREONONE by default.
>
> The only direct test case of findPotentialStereoBonds I can find is the
> following:
>
> MolOps::findPotentialStereoBonds(*m, false);
> TEST_ASSERT(m->getNumAtoms() == 15);
> TEST_ASSERT(m->getBondWithIdx(1)->getBondType() == Bond::DOUBLE);
> TEST_ASSERT(m->getBondWithIdx(1)->getStereoAtoms().size() == 2);
> TEST_ASSERT(m->getBondWithIdx(3)->getBondType() == Bond::DOUBLE);
> TEST_ASSERT(m->getBondWithIdx(3)->getStereoAtoms().size() == 2);
>
> That doesn't even test the getStereo() return value. Though it does test
> getStereoAtoms() return value. So it looks like the proper thing to do to
> detect unspecified bond stereo is to check for a non-empty getStereoAtoms()
> vector?
>
> So ideally, I would like to write an bond stereo enumerator that tests if
> a double bond has unspecified stereo (testing the size of getStereoAtoms()
> would work) and then sets the stereo, that is:
>
> bond.SetStereo(Bond::STEREOE);
> or
> bond.SetStereo(Bond::STEREOZ);
>
> And then hopefully the Chem.MolToSmiles will "do the right thing".
> However, this commented out code in the wrapper has given me pause:
>
> // this is no longer exposed because it requires that stereo atoms
> // be set. This is a task that is tricky and "dangerous".
> //.def("SetStereo",&Bond::setStereo,
> // "Set the CIP-classification of the bond as a
> BondStereo\n")
>
> So apparently I shouldn't expose an "easy" way to do this. What is the
> trickiness and dangerousness of this API? And could we make an easy way to
> enumerate bond stereo?
>
> Thanks!
>
>
>
> On Fri, Dec 9, 2016 at 5:44 PM, Brian Cole <col...@gmail.com> wrote:
>
>> This has me quite curious now, how do we detect unspecified bond stereo
>> chemistry in RDKit?
>>
>> m = Chem.MolFromSmiles("FC=CF")
>> assert m.HasProp("_StereochemDone")
>> for bond in m.GetBonds():
>> print(bond.GetBondDir(), bond.GetStereo())
>>
>> Yields:
>>
>> (rdkit.Chem.rdchem.BondDir.NONE, rdkit.Chem.rdchem.BondStereo.STEREONONE)
>> (rdkit.Chem.rdchem.BondDir.NONE, rdkit.Chem.rdchem.BondStereo.STEREONONE)
>> (rdkit.Chem.rdchem.BondDir.NONE, rdkit.Chem.rdchem.BondStereo.STEREONONE)
>>
>> Trying to force the issue:
>>
>> Chem.AssignStereochemistry(m, cleanIt=True, force=True,
>> flagPossibleStereoCenters=True)
>>
>> assert m.HasProp("_StereochemDone")
>> for bond in m.GetBonds():
>> print(bond.GetBondDir(), bond.GetStereo())
>>
>> Still yields:
>>
>> (rdkit.Chem.rdchem.BondDir.NONE, rdkit.Chem.rdchem.BondStereo.STEREONONE)
>> (rdkit.Chem.rdchem.BondDir.NONE, rdkit.Chem.rdchem.BondStereo.STEREONONE)
>> (rdkit.Chem.rdchem.BondDir.NONE, rdkit.Chem.rdchem.BondStereo.STEREONONE)
>>
>> I can see the setStereo(Bond::STEREOANY) in the code here:
>>
>> if ((*bondIt)->getBondDir() == Bond::EITHERDOUBLE) {
>> (*bondIt)->setStereo(Bond::STEREOANY);
>>
>> Guess I have to figure out how to detect EITHERDOUBLE?
>>
>> -Brian
>>
>> On Fri, Dec 9, 2016 at 5:03 PM, Andrew Dalke <da...@dalkescientific.com>
>> wrote:
>>>
>>> On Dec 9, 2016, at 9:50 PM, Brian Kelley wrote: > >>> from rdkit import
>>> Chem > >>> m = Chem.MolFromSmiles("F/C=C/F") > >>> for bond in
>>> m.GetBonds(): > ... print bond.GetStereo() > ... > STEREONONE > STEREOE
>>> > STEREONONE > > However, setting bond stereo doesn't appear to be exposed.
>>> > I
>>> thought I knew a way to change it, via GetBondDir()/SetBondDir() on the
>>> directional bonds. It doesn't seem to work. First, get the existing bond
>>> directions: >>> from rdkit import Chem >>> mol =
>>> Chem.MolFromSmiles("F/C=C/F") >>> for bond in mol.GetBonds(): ...
>>> print(bond.GetBondDir()) ... ENDUPRIGHT NONE ENDUPRIGHT I'll change the
>>> first "/" to a "\" (That's "\\" when escaped for a normal Python string.)
>>> >>> mol.GetBondWithIdx(0) <rdkit.Chem.rdchem.Bond object at 0x10fe26600>
>>> >>> mol.GetBondWithIdx(0).GetBondDir() rdkit.Chem.rdchem.BondDir.ENDUPRIGHT
>>> >>> mol.GetBondWithIdx(0).SetBondDir(Chem.BondDir.ENDDOWNRIGHT) If I
>>> generate the SMILES I see the old "F/C=C/F" instead of the new direction. I
>>> need to clear internal computed properties when I make structure edits: >>>
>>> Chem.MolToSmiles(mol, isomericSmiles=True) 'F/C=C/F' >>>
>>> mol.ClearComputedProps() >>> Chem.MolToSmiles(mol, isomericSmiles=True)
>>> 'F/C=C\\F' I'll set the directions to "NONE" and clear computed properties.
>>> The SMILES is correct: >>>
>>> mol.GetBondWithIdx(0).SetBondDir(Chem.BondDir.NONE)
>>> >>> mol.GetBondWithIdx(2).SetBondDir(Chem.BondDir.NONE) >>>
>>> mol.ClearComputedProps() >>> Chem.MolToSmiles(mol, isomericSmiles=True)
>>> 'FC=CF' although the stereo setting is unchanged: >>> for bond in
>>> mol.GetBonds(): ... print(bond.GetStereo()) ... STEREONONE STEREOE
>>> STEREONONE I expected it to give me all STEREONONEs, as if it were the same
>>> as the following: >>> mol2 = Chem.MolFromSmiles("FC=CF") >>> for bond in
>>> mol2.GetBonds(): ... print(bond.GetStereo()) ... STEREONONE STEREONONE
>>> STEREONONE Andrew
>>> da...@dalkescientific.com
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