[Jmol-developers] Re: Display of properties

[Miguel H. <mt...@mt...>]

Christoph had previously inquired off-list about displaying arbitrary ato=
m
properties in labels. Text of that message is below.

Christoph,

I have completed the work to allow the display of arbitrary user-defined
properties using the 'label' tags in Jmol. This should allow you to
display your nmrshift property ... or any other property associated with =
a
cdk.Atom object.

The syntax is:
  label My custom property value is %=7BpropertyName=7D

The curly brackets are required to delimit the property name.

Currently, only the CDKJmolModelAdapter implements this method.

Q: Are there file types that store arbitrary property values for atoms?


Miguel


>> Miguel,
>>
>> if I want to keep my plugin code as application-independent as
>> possible,
>>  I cannot include code for sending script commands to Jmol, since
>> JChemPaint e.g. will not be able to understand them.
>
> OK
>
>> If course, the user can be instructed to use these script command once=

>> a
>>  certain structure was loaded in order to activate display of certain
>> atom properties. These atom or better ChemObject properties *are*
>> already part of a ChemFile passed to Jmol, but there is not way to
>> acces
>>  them.
>
> Well, yes and no.
>
> Jmol does not use the ChemFile/ChemObjects directly. Rather, Jmol
> extracts the data that it wants, builds its own data structures, and
> releases the references. All of this happens when the molecule first
> gets loaded.
>
>> Of course, one would need a placeholder like %n for nmr shifts,
>> which again doesn't make much sense since there could be tons of
>> potential properties for which we will not want to make %-tags each.
>
> Agreed.
>
>> The solution would be a script command to display cdk.ChemObject
>> properties by label:
>>
>> select carbon; label =22nmr shift =3D %nmrshift=22
>
> That is a good suggestion.
>
>> where the latter is a dynamically generated variable based on an
>> existing cdk.ChemObject property. Do you think this is doable?
>
> I think that there should be a way to handle this.
>
> I will need to think about extending the JmolModelAdapter interface so
> that it can support user-defined properties.
>
>
>> BTW, sending an EditBus command =22showChemFile()=22  (or so) does not=

>> work in the current HEAD (stackTrace attached). If I walk down this
>> hierarchy, I do indeed not find any code for handling cdk.ChemFiles.
>> It worked in b6.
>
> I have never looked at the EditBus code ... Egon probably needs to take=

> a look at it.
>
>
> Miguel


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Miguel Howard                   miguel=40howards.org
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