[Rdkit-discuss] Functions to call to generate wedge information when given 3D coordinates (C++)

[Shubbey McBean]

Hello again!

RDKit nicely provides several functions to accept molecule input under the
FileParsers module.  For example, we have MolFileToMol(), MolBlockToMol(),
Mol2FileToMol(), and so forth.  Each of these parses the input and then
does various cleanup to generate stereochemistry and such.

In my case, my input is passed simply as raw molecule information (elems +
3D coordinates). So I generate the molecule manually, as follows:

RWMol mol;
// my info in atom and bond structs
for(int i=0;isetAtomPos(i, RDGeom::Point3D(atom[i].x,atom[i].y,atom[i].z));
  }
  mol.addConformer(confp,true);

At this point I have a molecule but it isn't cleaned up.  My question is,
what is the most concise order of operations I need to generate a 2D
depiction, including wedge information, from this setup?  I have tried a
few different approaches and am getting mixed results-- some approaches
produce better results than others, but it isn't consistent (one method may
get a better result on one molecule, but worse on another).  I posted more
about this in a bug report (may not be a bug) here:
https://github.com/rdkit/rdkit/issues/1379

So here is an example of something I've tried:

Kekulize(mol);
assignChiralTypesFrom3D(mol);
assignStereochemistry(mol,true,true);
compute2DCoords(mol);

const Conformer  = mol.getConformer();
WedgeMolBonds(mol,);

As noted in the github post, the assignStereochemistry() part can sometimes
cause wedging to disappear completely.  I chose this particular order by
groking through the FileParser routines to see how they handled molecules
post-3D input.

I feel like I am overcomplicating this.  Is there a recommended approach?

Thanks!
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Re: [Rdkit-discuss] Trouble with conda build in Docker

[Markus Sitzmann]

Thanks Riccardo for your reply

I tried both master and development - both with your Dockerscript (which
starts from centos) and mine (which starts from Debian:jessie). Same result
everywhere. I haven't built it in a while, too, but since I updated to
Docker CE, Version 17.03, it triggered this rebuild.

I hope it isn't my setup (well, that is actually what I wanted to find out
:-), if somebody else has problems). It isn't urgent, also :-)


Markus

On Thu, Apr 6, 2017 at 8:50 AM, Riccardo Vianello <
riccardo.viane...@gmail.com> wrote:

> Hi Markus,
>
> On Thu, Apr 6, 2017 at 12:03 AM, Markus Sitzmann <
> markus.sitzm...@gmail.com> wrote:
>
>> Hi (Riccardo).
>>
>> I have trouble with the conda build in Docker (I just updated to the most
>> recent version which triggered the new build) - below is the error trace. I
>> took the original Docker file and just edited out all non-Python35 builds -
>> so it does only the Python35 builds and ends somewhere when
>> rdkit-postgres95 is built. Does somebody have the same problem?
>>
>
> I couldn't work on this during the last few months so I didn't test any
> recent builds. I might be able to have a closer look and run some tests
> next week. What branch of the conda-rdkit repository are you using (master
> or development)?
>
> Best,
> Riccardo
>
>
>>
>> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
>> 1491429385957/work/postgresql-9.5.2/src/port'
>> make -C ../backend submake-errcodes
>> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
>> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
>> cd ../../../src/include/catalog && /bin/sh ../../../config/missing perl
>> ./duplicate_oids
>> make -C utils probes.h
>> ***
>> ERROR: Perl is missing on your system. It is needed unless you are
>> building
>> from an unmodified official distribution of PostgreSQL.
>> ***
>> make[3]: Leaving directory `/home/rdkit/bld/postgresql95_
>> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
>>
>>
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Re: [Rdkit-discuss] Trouble with conda build in Docker

[Riccardo Vianello]

Hi Markus,

On Thu, Apr 6, 2017 at 12:03 AM, Markus Sitzmann 
wrote:

> Hi (Riccardo).
>
> I have trouble with the conda build in Docker (I just updated to the most
> recent version which triggered the new build) - below is the error trace. I
> took the original Docker file and just edited out all non-Python35 builds -
> so it does only the Python35 builds and ends somewhere when
> rdkit-postgres95 is built. Does somebody have the same problem?
>

I couldn't work on this during the last few months so I didn't test any
recent builds. I might be able to have a closer look and run some tests
next week. What branch of the conda-rdkit repository are you using (master
or development)?

Best,
Riccardo


>
> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
> 1491429385957/work/postgresql-9.5.2/src/port'
> make -C ../backend submake-errcodes
> make[3]: Entering directory `/home/rdkit/bld/postgresql95_
> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
> cd ../../../src/include/catalog && /bin/sh ../../../config/missing perl
> ./duplicate_oids
> make -C utils probes.h
> ***
> ERROR: Perl is missing on your system. It is needed unless you are building
> from an unmodified official distribution of PostgreSQL.
> ***
> make[3]: Leaving directory `/home/rdkit/bld/postgresql95_
> 1491429385957/work/postgresql-9.5.2/src/backend/catalog'
>
>
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