> From the API documentation I see there are "Get" methods for accessing
> the stereochemistry information of a molecule.  Is there anyway to add
> this information into a instrumented molecule?  I am building
> molecules from scratch, and am missing how to create wedge bonds,
> etc... within Indigo.

> Thanks for the help!

> Corey

> Unfortunately, such functions are not implemented yet, but I think it
> can be added in a short time.

> But there are some difficulties with setting stereochemistry might
> appear. Stereocenters are independent of coordinate representation,
> and it is stored as right handed stereopyramid. You can load molecules
> from SMILES without coordinates, but SMILES notation defines
> stereocenters and cis-trans bonds.

> I see here 3 cases that should be taken into account during
> implementation:
> 1. If molecules doesn't have coordinates then to add a stereocenter
> you need to specify atoms in a right handed stereopyramid. After that
> layout() function will compute coordinates and stereobonds will be
> marked as 'up' or 'down'.
> 2. If molecule has 2D coordinates, then you can mark bonds as 'up',
> 'down', 'either'. Then after defining all bond marks you can call
> buildStereo (not implemented) function to construct actual
> stereocenters (right handed stereopyramids). It would also be possible
> to define right handed stereopyramid and after that call markBonds()
> method to get actual 'up', 'down', or 'either' on some bonds.
> 3. If molecule has 3D coordinates, then the only one possibility would
> be to call buildStereo method to build stereoinformation from 3D
> coordinates. 'up'/'down' marks are not relevant in this case.

> This is what can be implemented in a short time, because internally
> such functionality already exists, but there is no API for it. I would
> be great if you explain your scenario: do you have 2D coordinates? Is
> presented approach with 3 cases acceptable? Or maybe you can suggest
> better approach to set stereocenters?

> With best regards,
> Mikhail Rybalkin

> On Aug 3, 8:37 pm, Corey Dow-Hygelund <godelsthe...@gmail.com> wrote:

> > Hi,

> > From the API documentation I see there are "Get" methods for accessing
> > the stereochemistry information of a molecule.  Is there anyway to add
> > this information into a instrumented molecule?  I am building
> > molecules from scratch, and am missing how to create wedge bonds,
> > etc... within Indigo.

> > Thanks for the help!

> > Corey

> Thank you for your helpful reply!  I didn't get the Google Groups
> response, which is curious, because I have received them in the past.
> I will look into my email settings.

> To answer your question concerning my "use case", I am parsing
> ChemDraw CDX/CDXML files into IndigoObjects to generate MOL files,
> canonical smiles strings, etc...  These files contain stereochemistry
> information at the bond level.  I am not directly using the coordinate
> information, because I am using the layout functionality of Indigo.
> However, the stereochemistry information contained in the ChemDraw
> files is useful for rendering purposes.

> Therefore, for my purposes, only case one is necessary.

> Thanks for your help!

> Corey

> On Aug 3, 2:32 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:

> > Hello Corey,

> > Unfortunately, such functions are not implemented yet, but I think it
> > can be added in a short time.

> > But there are some difficulties with setting stereochemistry might
> > appear. Stereocenters are independent of coordinate representation,
> > and it is stored as right handed stereopyramid. You can load molecules
> > from SMILES without coordinates, but SMILES notation defines
> > stereocenters and cis-trans bonds.

> > I see here 3 cases that should be taken into account during
> > implementation:
> > 1. If molecules doesn't have coordinates then to add a stereocenter
> > you need to specify atoms in a right handed stereopyramid. After that
> > layout() function will compute coordinates and stereobonds will be
> > marked as 'up' or 'down'.
> > 2. If molecule has 2D coordinates, then you can mark bonds as 'up',
> > 'down', 'either'. Then after defining all bond marks you can call
> > buildStereo (not implemented) function to construct actual
> > stereocenters (right handed stereopyramids). It would also be possible
> > to define right handed stereopyramid and after that call markBonds()
> > method to get actual 'up', 'down', or 'either' on some bonds.
> > 3. If molecule has 3D coordinates, then the only one possibility would
> > be to call buildStereo method to build stereoinformation from 3D
> > coordinates. 'up'/'down' marks are not relevant in this case.

> > This is what can be implemented in a short time, because internally
> > such functionality already exists, but there is no API for it. I would
> > be great if you explain your scenario: do you have 2D coordinates? Is
> > presented approach with 3 cases acceptable? Or maybe you can suggest
> > better approach to set stereocenters?

> > With best regards,
> > Mikhail Rybalkin

> > On Aug 3, 8:37 pm, Corey Dow-Hygelund <godelsthe...@gmail.com> wrote:

> > > Hi,

> > > From the API documentation I see there are "Get" methods for accessing
> > > the stereochemistry information of a molecule.  Is there anyway to add
> > > this information into a instrumented molecule?  I am building
> > > molecules from scratch, and am missing how to create wedge bonds,
> > > etc... within Indigo.

> > > Thanks for the help!

> > > Corey

> I have just uploaded an updated Indigo version 1.1-beta5. There is an
> additional method to add a stereocenters by specifing stereopyramid.
> Code snippet is here:
>       IndigoObject m = indigo.createMolecule();
>       IndigoObject a0 = m.addAtom("C");
>       IndigoObject a1 = m.addAtom("N");
>       IndigoObject a2 = m.addAtom("O");
>       IndigoObject a3 = m.addAtom("P");

>       a0.addBond(a1, 1);
>       a0.addBond(a2, 1);
>       a0.addBond(a3, 1);

>       System.out.println(m.smiles());
>       a0.addStereocenter(Indigo.ABS, a1.index(), a2.index(),
> a3.index());
>       System.out.println(m.smiles());

> This interface might be not the best, and I think we will improve this
> interface to support both atoms andatom indices, and to do it better.
> All advices and suggestions are welcome.

> There is no method to get a stereopyramid yet. Such methods are
> planned to be added into the next
> version: get stereocenter pyramid; change stereocenter group, type;
> add cis-trans bonds, and etc.
> On the next week I will be on vacation, but in case you have questions
> my colleagues will try to answer them.

> With best regards,
> Mikhail Rybalkin

> On Aug 11, 10:19 pm, Corey Dow-Hygelund <godelsthe...@gmail.com>
> wrote:

> > Hi Mikhail,

> > Thank you for your helpful reply!  I didn't get the Google Groups
> > response, which is curious, because I have received them in the past.
> > I will look into my email settings.

> > To answer your question concerning my "use case", I am parsing
> > ChemDraw CDX/CDXML files into IndigoObjects to generate MOL files,
> > canonical smiles strings, etc...  These files contain stereochemistry
> > information at the bond level.  I am not directly using the coordinate
> > information, because I am using the layout functionality of Indigo.
> > However, the stereochemistry information contained in the ChemDraw
> > files is useful for rendering purposes.

> > Therefore, for my purposes, only case one is necessary.

> > Thanks for your help!

> > Corey

> > On Aug 3, 2:32 pm, Mikhail Rybalkin <rybal...@ggasoftware.com> wrote:

> > > Hello Corey,

> > > Unfortunately, such functions are not implemented yet, but I think it
> > > can be added in a short time.

> > > But there are some difficulties with setting stereochemistry might
> > > appear. Stereocenters are independent of coordinate representation,
> > > and it is stored as right handed stereopyramid. You can load molecules
> > > from SMILES without coordinates, but SMILES notation defines
> > > stereocenters and cis-trans bonds.

> > > I see here 3 cases that should be taken into account during
> > > implementation:
> > > 1. If molecules doesn't have coordinates then to add a stereocenter
> > > you need to specify atoms in a right handed stereopyramid. After that
> > > layout() function will compute coordinates and stereobonds will be
> > > marked as 'up' or 'down'.
> > > 2. If molecule has 2D coordinates, then you can mark bonds as 'up',
> > > 'down', 'either'. Then after defining all bond marks you can call
> > > buildStereo (not implemented) function to construct actual
> > > stereocenters (right handed stereopyramids). It would also be possible
> > > to define right handed stereopyramid and after that call markBonds()
> > > method to get actual 'up', 'down', or 'either' on some bonds.
> > > 3. If molecule has 3D coordinates, then the only one possibility would
> > > be to call buildStereo method to build stereoinformation from 3D
> > > coordinates. 'up'/'down' marks are not relevant in this case.

> > > This is what can be implemented in a short time, because internally
> > > such functionality already exists, but there is no API for it. I would
> > > be great if you explain your scenario: do you have 2D coordinates? Is
> > > presented approach with 3 cases acceptable? Or maybe you can suggest
> > > better approach to set stereocenters?

> > > With best regards,
> > > Mikhail Rybalkin

> > > On Aug 3, 8:37 pm, Corey Dow-Hygelund <godelsthe...@gmail.com> wrote:

> > > > Hi,

> > > > From the API documentation I see there are "Get" methods for accessing
> > > > the stereochemistry information of a molecule.  Is there anyway to add
> > > > this information into a instrumented molecule?  I am building
> > > > molecules from scratch, and am missing how to create wedge bonds,
> > > > etc... within Indigo.

> > > > Thanks for the help!

> > > > Corey