From: Miguel <mi...@jm...> - 2004-03-31 23:05:53
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I am trying to learn about CML There are only a few examples of .cml files in the Jmol samples directory. Q: Can someone look at these files and tell me whether or not they are good examples for me to be working with? Q: Can someone take the existing files and save them in CML format with the same coordinates? samples/caffeine.xyz samples/aspirina.mol samples/1crn.pdb Q: Where can I find other .cml files? samples/estron.cml and samples/glycine-crystal.cml have 'charge' values that are decimal values. When I look at http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/concatenated.xml I see 'formalCharge' references which are integers. Q: Can someone give me 25 word definitions of 'charge' vs. 'formal charge'? Q: Why are there no references to 'charge' in concatenated.xml? I am looking at cmlCore.pdf When I look up the element 'atom' I see interesting attributes like 'formalCharge' and 'occupancy'. But I do not see these defined in cmlCore.pdf as elements. Q: Is this just a documentation problem? I can search cmlCore.xsd and fine these attributes. Q: Is there a tool that I should use to browse/read cmlCore.xsd? Miguel |
From: E.L. W. <eg...@sc...> - 2004-04-01 06:07:52
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Thursday 01 April 2004 01:05, Miguel wrote: > I am trying to learn about CML > > There are only a few examples of .cml files in the Jmol samples directory. > > Q: Can someone look at these files and tell me whether or not they are > good examples for me to be working with? > Q: Can someone take the existing files and save them in CML format with > the same coordinates? > samples/caffeine.xyz > samples/aspirina.mol > samples/1crn.pdb Will do at the end of today... > Q: Where can I find other .cml files? cdk/data/cml* *And* cdk/src/org/openscience/cdk/test/io/cml/cmlTestFramework.xml The latter validates if opened with jEdit which has the XML plugin installe= d. > samples/estron.cml and samples/glycine-crystal.cml have 'charge' values > that are decimal values. When I look at > http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/concatenated.xml I see > 'formalCharge' references which are integers. > > Q: Can someone give me 25 word definitions of 'charge' vs. 'formal charge= '? The formal charge is a charge indication given by humans, but molecules spr= ead=20 this charge over the atoms, leading to 'partial charges'. "Charge" can be=20 both, but if having a decimal expect it to be a partial charge. > Q: Why are there no references to 'charge' in concatenated.xml? Don't know. > I am looking at cmlCore.pdf > When I look up the element 'atom' I see interesting attributes like > 'formalCharge' and 'occupancy'. But I do not see these defined in > cmlCore.pdf as elements. Elements are different than attributes... like in HTML <atom occupancy=3D"0.5"/> Element atom has attribute occupancy. > Q: Is this just a documentation problem? > > I can search cmlCore.xsd and fine these attributes. > > Q: Is there a tool that I should use to browse/read cmlCore.xsd? The cmlCore schema is very big, but you could use jEdit with the XML plugin= =20 installed and the plugin which has the Structure Browser plugin window... T= he=20 latter will give you a very nice browsing tree... 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) iD8DBQFAa7C+d9R8I9Yza6YRAhwiAJ9luThxHFVz8s/13NWoBojjlvDaywCgvW6q 8okWMh6A1dK4H+2Yn42mJTM=3D =3DnB+s =2D----END PGP SIGNATURE----- |
From: Peter Murray-R. <pm...@ca...> - 2004-04-03 13:40:09
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At 08:03 01/04/2004 +0200, E.L. Willighagen wrote: >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > >On Thursday 01 April 2004 01:05, Miguel wrote: > > I am trying to learn about CML > > Excellent! :-) > > There are only a few examples of .cml files in the Jmol samples directory. > > > > Q: Can someone look at these files and tell me whether or not they are > > good examples for me to be working with? > > Q: Can someone take the existing files and save them in CML format with > > the same coordinates? > > samples/caffeine.xyz > > samples/aspirina.mol > > samples/1crn.pdb These can also be converted to CML with OpenBabel. (http://openbabel.sf.net) This contains a complete set of examples of conversion to and from the various dialects of CML. The dialects are: CML-1 deprecated for new applications but supported CML-1-array deprecated for new applications but supported CML-2 probably the commonest now CML-2-array There are two syntaxes for CML2. The first is more explicit and easier to parse while the second is more compact. I have people who will not use CML unless it is in array form and people who are the exact opposite. Fortunately modern XML tools make this fairly easy to support. OpenBabel has a complete set of roundtrips between all formats. That is probably a good place to start. >Will do at the end of today... > > > Q: Where can I find other .cml files? See http://www.xml-cml.org and http://wwmm.ch.cam.ac.uk/moin/ChemicalMarkupLanguage. These pages will have the complete and emerging specs >cdk/data/cml* > >*And* cdk/src/org/openscience/cdk/test/io/cml/cmlTestFramework.xml > >The latter validates if opened with jEdit which has the XML plugin installed. > > > samples/estron.cml and samples/glycine-crystal.cml have 'charge' values > > that are decimal values. When I look at > > http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/concatenated.xml I see > > 'formalCharge' references which are integers. > > > > Q: Can someone give me 25 word definitions of 'charge' vs. 'formal charge'? > >The formal charge is a charge indication given by humans, but molecules >spread >this charge over the atoms, leading to 'partial charges'. "Charge" can be >both, but if having a decimal expect it to be a partial charge. "formalCharge" is an attribute of atom in CML and has precisely defined semantics. "charge" is not part of CML and would have to have a non CML namespace. So a file with a charge attribute is invalid. It would be allowed to write something like: <atom elementType="N" id="c23" formalCharge="1" jmol:charge="0.123" xmlns:jmol="http://jmol.sf.net/attributes"/> The reason for this is that there are probably 50+ ways of describing charge. So there has to be a dictionary entry describing what they are. A typical > > Q: Why are there no references to 'charge' in concatenated.xml? > >Don't know. Because it is not part of CML. See the pages at: http://wwmm.ch.cam.ac.uk/moin/CmlSchemaComponents for all allowed CML names (elements and attributes) > > I am looking at cmlCore.pdf > > When I look up the element 'atom' I see interesting attributes like > > 'formalCharge' and 'occupancy'. But I do not see these defined in > > cmlCore.pdf as elements. Where did you get cmlCore.pdf from? If it doesn't have these attributes then either it is broken or you need a newer version. Bother those attributes should be there >Elements are different than attributes... like in HTML > ><atom occupancy="0.5"/> This is valid CML >Element atom has attribute occupancy. > > > Q: Is this just a documentation problem? I hope so > > > > I can search cmlCore.xsd and fine these attributes. In that case the cmlCore.pdf is incorrect or out of date > > > > Q: Is there a tool that I should use to browse/read cmlCore.xsd? XML-spy has a demo version which you can use for a limited period. Have a look on the http://www.w3.org pages fro XML schema. But we should have a proper version of the PDF mounted >The cmlCore schema is very big, but you could use jEdit with the XML plugin >installed and the plugin which has the Structure Browser plugin window... The >latter will give you a very nice browsing tree... Best, P. >Egon > >- -- >eg...@sc... >PhD on Molecular Representation in Chemometrics >Nijmegen University >http://www.cac.sci.kun.nl/people/egonw/ >GPG: 1024D/D6336BA6 > >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1.0.7 (SunOS) > >iD8DBQFAa7C+d9R8I9Yza6YRAhwiAJ9luThxHFVz8s/13NWoBojjlvDaywCgvW6q >8okWMh6A1dK4H+2Yn42mJTM= >=nB+s >-----END PGP SIGNATURE----- > > > >------------------------------------------------------- >This SF.Net email is sponsored by: IBM Linux Tutorials >Free Linux tutorial presented by Daniel Robbins, President and CEO of >GenToo technologies. Learn everything from fundamentals to system >administration. >_______________________________________________ >Jmol-developers mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-developers Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |
From: Miguel <mi...@jm...> - 2004-04-11 16:06:00
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>> > Q: Can someone take the existing files and save them in CML format >> with >> > the same coordinates? >> > samples/caffeine.xyz >> > samples/aspirina.mol >> > samples/1crn.pdb > > These can also be converted to CML with OpenBabel. Well, I have never compiled openbabel either ... another *barrier to entry*. > (http://openbabel.sf.net) This contains a complete set of examples of > conversion to and from the various dialects of CML. The dialects are: > > CML-1 deprecated for new applications but supported > CML-1-array deprecated for new applications but supported > > CML-2 probably the commonest now > CML-2-array > > There are two syntaxes for CML2. The first is more explicit and easier to > parse while the second is more compact. I have people who will not use CML > unless it is in array form and people who are the exact opposite. > Fortunately modern XML tools make this fairly easy to support. OK >> > Q: Where can I find other .cml files? > > See http://www.xml-cml.org I looked here about 10 days ago. As I recall I only saw fragments and small samples. Will look again. > and > > http://wwmm.ch.cam.ac.uk/moin/ChemicalMarkupLanguage. These pages will > have > the complete and emerging specs OK >> > Q: Can someone give me 25 word definitions of 'charge' vs. 'formal >> charge'? >> >>The formal charge is a charge indication given by humans, but molecules >>spread >>this charge over the atoms, leading to 'partial charges'. "Charge" can be >>both, but if having a decimal expect it to be a partial charge. > > "formalCharge" is an attribute of atom in CML and has precisely defined > semantics. "charge" is not part of CML and would have to have a non CML > namespace. So a file with a charge attribute is invalid. Good. Jmol cannot deal with fractional charge values anyway. >> > I am looking at cmlCore.pdf >> > When I look up the element 'atom' I see interesting attributes like >> > 'formalCharge' and 'occupancy'. But I do not see these defined in >> > cmlCore.pdf as elements. > > Where did you get cmlCore.pdf from? www.xml-cml.org >> > Q: Is there a tool that I should use to browse/read cmlCore.xsd? > > XML-spy has a demo version which you can use for a limited period. Have a > look on the http://www.w3.org pages fro XML schema. But we should have a > proper version of the PDF mounted OK Uhhh ... this is probably not news to you ... but I am finding the learning curve and the tools/infrastructure support for CML rather steep. Miguel |
From: Egon W. <eg...@sc...> - 2004-04-12 11:11:33
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On Sunday 11 April 2004 18:05, Miguel wrote: > >>The formal charge is a charge indication given by humans, but molecules > >>spread > >>this charge over the atoms, leading to 'partial charges'. "Charge" can be > >>both, but if having a decimal expect it to be a partial charge. > > > > "formalCharge" is an attribute of atom in CML and has precisely defined > > semantics. "charge" is not part of CML and would have to have a non CML > > namespace. So a file with a charge attribute is invalid. > > Good. Jmol cannot deal with fractional charge values anyway. I think it can... what about coloring by charge? Those are fractional charges. I thought this was available in HEAD too... Egon |
From: Miguel <mi...@jm...> - 2004-04-12 11:21:48
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>> Good. Jmol cannot deal with fractional charge values anyway. > > I think it can... what about coloring by charge? Those are fractional > charges. > I thought this was available in HEAD too... The color by charge that is in HEAD only deals with integer charge values. Miguel |