From: E.L. W. <eg...@sc...> - 2004-05-21 09:50:34
|
=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Friday 21 May 2004 11:16, Peter Murray-Rust wrote: > The coordinates are in the well-known unit - the "arbitrary". There are no > semantics associated with them. They may be often be screen units but may > also be (IMO incorrectly) scaled to some sort of pseudo angstroms. > > There is a different problem with CML units. The hardcoded units are > angstrom.=20 So CDK needs to make a unitRef (have to look how that works) to overwrite t= his=20 default? > It is not easy to define methods for other units, but we shall > need to for certain compChem problems. I am thinking of adding a > lengthUnits attribute on atomArray but it is potentially fragile. I would > value comments. > > ><bondArray id=3D"b6"> > > <bond atomRefs2=3D"a2 a1"><scalar dataType=3D"xsd:float" > >title=3D"order">1.5</scalar></bond> > > <bond atomRefs2=3D"a3 a2"><scalar dataType=3D"xsd:float" > >title=3D"order">1.5</scalar></bond> > > <bond atomRefs2=3D"a4 a3"><scalar dataType=3D"xsd:float" > >title=3D"order">1.5</scalar></bond> > > <bond atomRefs2=3D"a5 a4"><scalar dataType=3D"xsd:float" > >title=3D"order">1.5</scalar></bond> > > <bond atomRefs2=3D"a6 a5"><scalar dataType=3D"xsd:float" > >title=3D"order">1.5</scalar></bond> > > <bond atomRefs2=3D"a6 a1"><scalar dataType=3D"xsd:float" > >title=3D"order">1.5</scalar></bond> > ></bondArray> > > The CML convention for aromatic bonds is > > > <bond atomRefs2=3D"a6 a1" order=3D"A"/> Yes, the CMLWrite did use that for bonds that were flaged aromatic, but in= =20 this case they were not, and did only use a bond order =3D=3D 1.5. I've upd= ated=20 the CDK2CML convertor to use A in that case too... > The syntax above is valid CML but the semantics are undefined. If the user > wishes to communicate a bond order they could use: <bond > atomRefs2=3D"a6 a1"> > <scalar dataType=3D"xsd:float" title=3D"order" > dictRef=3D"foo:myBondOrder">1.5</scalar> > </bond> > > which would assert that there was a foo dictionary defining what > myBondOrder means. I overlooked this... it should actually use a namespaced dictRef here: cdk:bondOrder... I'll check why this is not the case... Egon =2D --=20 eg...@sc... PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFArdDgd9R8I9Yza6YRAkxwAJwN142QA6Bt6AzSfqb5C2c7hR670QCfckt6 t3Krxk3U36GB6rdUYRi0Rhw=3D =3DATGu =2D----END PGP SIGNATURE----- |