zero Z-coordinates in MDLV2000 reader

[Rajarshi Guha-3]

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Hi, it appears that the MDLV2000 reader assumes that if all Z-
coordinates are 0, then the molecule has no 3D coordinates and the  
coordinates are considered to be 2D.

However for something like a polcyclic aromatic compound, the  
molecule is meant to be flat and hence the z-coordinates are all 0.  
However perceiving these as 2D coordinates and not 3D is wrong.

Does anybody know why this decision was made? I think it'd be a good  
idea to either

1) drop the conversion of the 3D coords to null if sum of z-coords  = 0

or

2) keep 3D coordinates and at the same time use them as 2D coordinates

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Rajarshi Guha  <rguha@...>
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[Egon Willighagen-5]

On Wed, Jul 23, 2008 at 4:55 AM, Rajarshi Guha <rguha@...> wrote:
> Hi, it appears that the MDLV2000 reader assumes that if all Z-
> coordinates are 0, then the molecule has no 3D coordinates and the
> coordinates are considered to be 2D.

MDL molfiles can contain 2D and 3D coordinates, but lacks the means of
indicating the coordinates are 2D or 3D.

> However for something like a polcyclic aromatic compound, the
> molecule is meant to be flat and hence the z-coordinates are all 0.
> However perceiving these as 2D coordinates and not 3D is wrong.

Yes, that's an unfortunate confounding.

> Does anybody know why this decision was made? I think it'd be a good
> idea to either

Yes, because treating 2D coordinates as if 3D is even worse, than the
occasional flat molecule is 2D.

> 1) drop the conversion of the 3D coords to null if sum of z-coords  = 0
>
> or
>
> 2) keep 3D coordinates and at the same time use them as 2D coordinates

I disagree with both solutions, because of the above argument.

There are two options:

1. Use the IO option to force reading as 3D coordinates

2. Add some logic to detect the outliers

The only outlier are the flat aromatic ring systems (benzene, etc),
where the program decided that it was convenient to have the z
coordinate as zero, instead of using some other 3D orientation where
at least z coordinates are non zero. (Who came up with that brilliant
idea??)

I would be happy with a solution where we do:

1. copy, and strip hydrogens (if any)
2. determine ring atoms using the SpanningTree
3. decide if the molecule might be a flat PAH

This is btw why I like semantic file formats.

Egon

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[Rajarshi Guha-3]

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On Jul 23, 2008, at 2:40 AM, Egon Willighagen wrote:

> There are two options:
>
> 1. Use the IO option to force reading as 3D coordinates

Can you provide an example of how I'd do this with IteratingMDLReader?

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Rajarshi Guha  <rguha@...>
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[Egon Willighagen-5]

On Wed, Jul 23, 2008 at 2:37 PM, Rajarshi Guha <rguha@...> wrote:
> On Jul 23, 2008, at 2:40 AM, Egon Willighagen wrote:
>> 1. Use the IO option to force reading as 3D coordinates
>
> Can you provide an example of how I'd do this with IteratingMDLReader?

Good point. You currently can't. Please file a bug report, and then
I'll fix that.

Egon

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[Rajarshi Guha-3]

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On Jul 23, 2008, at 8:40 AM, Egon Willighagen wrote:

> On Wed, Jul 23, 2008 at 2:37 PM, Rajarshi Guha <rguha@...>  
> wrote:
>> On Jul 23, 2008, at 2:40 AM, Egon Willighagen wrote:
>>> 1. Use the IO option to force reading as 3D coordinates
>>
>> Can you provide an example of how I'd do this with  
>> IteratingMDLReader?
>
> Good point. You currently can't. Please file a bug report, and then
> I'll fix that.

Hi, I took a look at your commit for this. The code has

  setting.setSetting(forceReadAs3DCoords.getSetting());

where settings is the input argument. Is this correct? Or should it  
be the other way around?

Also can you provide an example of how this is used

Thanks,

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[Matt Sprague]

I agree that we should do something about this. It adding coordinates
as 2D causes problems when running planar molecules through the
symmetry perception classes.

-Matt

On Tue, Jul 22, 2008 at 8:55 PM, Rajarshi Guha <rguha@...> wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi, it appears that the MDLV2000 reader assumes that if all Z-
> coordinates are 0, then the molecule has no 3D coordinates and the
> coordinates are considered to be 2D.
>
> However for something like a polcyclic aromatic compound, the
> molecule is meant to be flat and hence the z-coordinates are all 0.
> However perceiving these as 2D coordinates and not 3D is wrong.
>
> Does anybody know why this decision was made? I think it'd be a good
> idea to either
>
> 1) drop the conversion of the 3D coords to null if sum of z-coords  = 0
>
> or
>
> 2) keep 3D coordinates and at the same time use them as 2D coordinates
>
> - -------------------------------------------------------------------
> Rajarshi Guha  <rguha@...>
> GPG Fingerprint: D070 5427 CC5B 7938 929C  DD13 66A1 922C 51E7 9E84
> - -------------------------------------------------------------------
> All great ideas are controversial, or have been at one time.
>
>
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> =8jr6
> -----END PGP SIGNATURE-----
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[Egon Willighagen-5]

On Thu, Jul 24, 2008 at 1:36 AM, Rajarshi Guha <rguha@...> wrote:
> Hi, I took a look at your commit for this. The code has
>
>  setting.setSetting(forceReadAs3DCoords.getSetting());

forceReadAs3DCoords is the IteratingMDLRreader setting, which needs to
be propagated to the MDLV2000Reader (the MDLV3000Reader does not
support forceReadAs3DCoords yet). 'setting' is the MDLV2000Reader
setting.

> where settings is the input argument. Is this correct? Or should it be the
> other way around?

No, I think this is OK.

> Also can you provide an example of how this is used

The MDLV2000Reader (or any reader) will fire IOSetting questions when
needed, typically just before a file is saved. So, it calls the
processIOSetting() method. This is they way the setting is set. Google
for 'CDK News IOSetting' and read the PDF.

Egon

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