Re: [Cdk-devel] some questions about DTD's

[Egon W. <ego...@gm...>]

Hi,

On 9/25/07, Rajarshi Guha <rg...@in...> wrote:
> I'm working on a DTD for pharmacophore description files. The
> description file would be of the form

Please forget DTD, go for RelaxNG or XML Schema. I would suggest the
former, which is closer in syntax to DTDs.

> <pharmacophore label="5HT1 receptor">
>    <group label="H" description="Hydrophobic groups">SMARTS</group>
>    <group label="D" description="Hydrogen bond donor">SMARTS</group>
>    <group label="P" description="Positive groups">SMARTS</group>
>    <constraint type="distance" units="???" groupRef="H D">1.234</
> constraint>
>    <constraint type="distance" units="???" groupRef="H P">3.456</
> constraint>
> </pharmacophore>
>
> My DTD would look like
>
> <!ELEMENT pharmacophore (group, constraint)+>
> <!ATTLIST pharmacophore label CDATA #REQUIRED>
>
> <!ELEMENT group (#CDATA)>
> <!ATTLIST group
>            label CDATA #REQUIRED
>            description CDATA #IMPLIED>
>
> <!ELEMENT constraint (#PCDATA)>
> <!ATTLIST constraint
>            type (distance | angle | torsion) "distance"
>           units PCDATA #REQUIRED
>           groupRefs CDATA #REQUIRED>

You need to add a root element, to hold more than one pcore in one file...

> A few questions
>
> * Can I use an arbitrary namespace? Would it be possible to make this
> part of the BO and then use a BO namespace such as http://
> www.blueobelisk.org/dtd/pharmacophore.dtd?

DTDs do not support namespaces.

> * How should I specify units? Do I need to import another DTD for that?

Another reason not to use DTD... DTD does not have an easy way to
reuse other specifications.

> * In the constraint element I used groupRefs in the same way that the
> bond element in CML uses atomRefs. However what I'd like to have is
> to be able to use groupRefs as subelements of constraint, rather than
> attributes and also enforce cardinality of groupRefs based on the
> type of the constraint. So for example I'd like to be able to write a
> distance constraint element as
>
> <constraint type="distance" units="???" value="1.234">
>    <groupRef id="H" />
>    <groupRef id="P" />
> </constraint>
>
> but an angle constraint would be
>
> <constraint type="angle" units="???" value="34">
>    <groupRef id="H" />
>    <groupRef id="P" />
>    <groupRef id="D" />
> </constraint>

Because the list of possible constraints is limited, I would go for:

<angleConstraint>,  <distanceConstraint> etc

> More over , how does one indicate that the value of the id attribute
> must be a valid group (i.e., there must be a group element that has a
> label equal to the id of the groupRef)?

You cannot do that with any of the above, but Schematron allows you to
define such rules.

Egon

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