<div dir="ltr">One additional comment that I forgot yesterday:<div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Nov 21, 2013 at 10:08 PM, Teemu Murtola <span dir="ltr"><<a href="mailto:teemu.murtola@gmail.com" target="_blank">teemu.murtola@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div class="gmail_extra"><div class="gmail_quote"><div class="im">On Mon, Nov 18, 2013 at 5:23 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Looks like a good start! Thanks.<div><br></div>
<div>I'm not sure whether <span style="font-size:13px;font-family:arial,sans-serif"><gromacs xmlns:gmx="</span><a href="http://www.gromacs.org/schemas" style="font-size:13px;font-family:arial,sans-serif" target="_blank">http://www.gromacs.<u></u>org/schemas</a><span style="font-size:13px;font-family:arial,sans-serif">"> should name a schema file, or a place to look up a schema file. Does anyone know?</span></div>
</div></blockquote><div><br></div></div><div>As Erik said, it's just a string with no direct semantics. And there is no strict correspondence between schemas and namespaces, either. I'm not an expert on this, but at least it is possible to have multiple schemas that all declare parts of the same namespace, and composite schemas created from these. A single schema can also reference multiple namespaces (but must in such a case import schemas for the other namespaces). And the location of the schema is often declared using a separate attribute (xsi:schemaLocation, with suitably defined xsi:), separately from the namespace. Don't know exactly what kind of look-up rules different parsers use for the schema locations.</div>
<div><br></div><div>If we want to publish the schemas on the web page, we also need to consider versioning. What is going to happen if, say, Gromacs 6.0 needs to change these schemas somehow? If we just replace them on the web page, earlier files are going to break. It's unrealistic to assume that we can design something that is going to remain static forever, in particular if we start from a corner like this instead from a central concept like the topology representation.</div>
<div><br></div><div>For the units, I don't have a strong opinion, but do we really want to implement a mini-language that we then must parse and validate to be able to specify arbitrary units and arbitrary unit conversions, and force the users to type them everywhere? One simple alternative would be to just encode the expected unit in the name of the element.</div>
</div></div></div></div></blockquote><div><br></div><div>Is it a good idea to have a root-level <gromacs> element instead of starting directly with <sfactors>? The root element being in a Gromacs-specific namespace should be enough indication that this is a Gromacs file, and that <gromacs> element makes it difficult to use this file as part of a larger entity through inclusion, which at least Erik was suggesting. Also, if all files would have the same root element, it is somewhat difficult (but probably not impossible) to compose a schema for that element from parts that could be used independently. Similarly, extra code is needed to check that the file actually contains the expected subelement and/or extract the relevant element; we may need that code in the future anyways, though, if we want to allow composite XML files.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div class="im"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr"><div><span style="font-size:13px;font-family:arial,sans-serif"> In the past I have seem XML files with namespace-specific content like</span></div>
<div><span style="font-size:13px;font-family:arial,sans-serif"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px"> <gmx:sfactors type="Fourier" force_field="any" displaced_solvent="true" reference=""></span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px"> <gmx:sfactor residue="ALA" atom="MW" type="1"></span><br style="font-family:arial,sans-serif;font-size:13px"><span style="font-size:13px;font-family:arial,sans-serif"><br>
</span></div><div><span style="font-size:13px;font-family:arial,sans-serif">which I'm sure we'd like to avoid. Does David's suggestion achieve that?</span></div></div></blockquote><div><br></div></div><div>It doesn't. It declares that anything prefixed with gmx: is in the given namespace, but doesn't actually use that prefix for anything. If you want to declare that unqualified elements go into a specific namespace, you need to use xmlns="…".</div>
</div></div></div></blockquote><div><br></div><div>Regards,</div><div>Teemu </div></div></div></div>