Re: [Rdkit-discuss] Atom Symbol Case in MolFile?

2016-01-20 Thread John M 
Correct message thread this time:

The joys of the molfile - was curious whether it was accepted/correctly
> interpreted:


>
> ISIS Draw 2.5 Yes (arguably the arbitrator of the format)
> ChemDraw 15 Yes
> ChemDoodle No (accepted but only as a text label 'CL' no conversion)
> MarvinSketch Yes
> CDK Yes
> OEChem Yes
> Open Babel Yes
> Indigo Yes


J


On 20 January 2016 at 05:26, Greg Landrum  wrote:

> Paul,
>
> On Tue, Jan 19, 2016 at 7:59 PM, Paul Emsley 
> wrote:
>
>>
>> Thanks for that.
>>
>> Why do I ask?  Because the sdf files [1] distributed by the wwPDB, such
>> as this one:
>>
>> http://www.rcsb.org/pdb/files/ligand/CQ8_ideal.sdf
>>
>> from this page:
>>
>> http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CQ8
>>
>> are upper-cased.  I didn't know whether that was right or not (and, as
>> you imply, RDKit will not parse it).  I'll get in touch with them and see
>> if they can get it changed.
>>
>
> It's an important data source, so it would be great if they were supplying
> data that's correctly formatted (assuming, of course, that my reading of
> that "spec" is correct). In the meantime, it would be pretty easy to modify
> the RDKit to handle these cases correctly when the "strictParsing" option
> is set to false. I'll add a github issue for this and get it in there.
>
>
>> [1] I thought that they were molfiles when I wrote the mail - and I
>> suppose the same thinking applies.
>>
>
> Yeah, the format of the CTAB piece is identical for mol files and SDFs.
>
> -greg
>
>
>
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Re: [Rdkit-discuss] Atom Symbol Case in MolFile?

2016-01-19 Thread Paul Emsley 

Hi Greg,

Thanks for that.

Why do I ask?  Because the sdf files [1] distributed by the wwPDB, such 
as this one:


http://www.rcsb.org/pdb/files/ligand/CQ8_ideal.sdf

from this page:

http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CQ8

are upper-cased.  I didn't know whether that was right or not (and, as 
you imply, RDKit will not parse it).  I'll get in touch with them and 
see if they can get it changed.


Paul.

[1] I thought that they were molfiles when I wrote the mail - and I 
suppose the same thinking applies.


On 18/01/2016 20:59, Greg Landrum wrote:

Hi Paul,

ctfile.pdf says: "entry in periodic table"
I interpret this to mean "Cl", since that's what one finds in the 
typical periodic table.


The RDKit, curiously, agrees with me. ;-)


:-)



-greg


On Mon, Jan 18, 2016 at 8:45 AM, Paul Emsley 
> wrote:



Dear RDKitters,

Is is clear what the case of the second character of an atom symbol in
the atom block of a MolFile should be? i.e. "CL", "Cl" or either?

Thanks,

Paul.



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Re: [Rdkit-discuss] Atom Symbol Case in MolFile?

2016-01-19 Thread Greg Landrum 
Paul,

On Tue, Jan 19, 2016 at 7:59 PM, Paul Emsley 
wrote:

>
> Thanks for that.
>
> Why do I ask?  Because the sdf files [1] distributed by the wwPDB, such as
> this one:
>
> http://www.rcsb.org/pdb/files/ligand/CQ8_ideal.sdf
>
> from this page:
>
> http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CQ8
>
> are upper-cased.  I didn't know whether that was right or not (and, as you
> imply, RDKit will not parse it).  I'll get in touch with them and see if
> they can get it changed.
>

It's an important data source, so it would be great if they were supplying
data that's correctly formatted (assuming, of course, that my reading of
that "spec" is correct). In the meantime, it would be pretty easy to modify
the RDKit to handle these cases correctly when the "strictParsing" option
is set to false. I'll add a github issue for this and get it in there.


> [1] I thought that they were molfiles when I wrote the mail - and I
> suppose the same thinking applies.
>

Yeah, the format of the CTAB piece is identical for mol files and SDFs.

-greg
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Re: [Rdkit-discuss] Atom Symbol Case in MolFile?

2016-01-18 Thread Greg Landrum 
Hi Paul,

ctfile.pdf says: "entry in periodic table"
I interpret this to mean "Cl", since that's what one finds in the typical
periodic table.

The RDKit, curiously, agrees with me. ;-)

-greg


On Mon, Jan 18, 2016 at 8:45 AM, Paul Emsley 
wrote:

>
> Dear RDKitters,
>
> Is is clear what the case of the second character of an atom symbol in
> the atom block of a MolFile should be? i.e. "CL", "Cl" or either?
>
> Thanks,
>
> Paul.
>
>
>
> --
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>
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