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[Joelib-devel] Re: [Joelib-help] CML2 and (solved?) AtomTyperProblem
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From: Peter Murray-R. <pm...@ca...> - 2004-03-17 10:17:59
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At 10:46 16/03/2004 +0100, Joerg K. Wegner wrote: >Hi Geoff, > >I've used Egon's code to establish CML2 support for JOELib. (Thank's again >!!!). This includes full stereochemistry support, also for MDL SD were the >missing lines were added to the writer (see attachments)! >pipe: original.sdf -> test.cml -> test.sdf > >As already discussed, this can be a step to 'reproducible' >conversion/descriptorCalculation results. > >CML (metainformations) and SDF (comment) contains now both the ID for the >used chemistry kernel (expert systems). >This number is the hash code for all hard- and soft-coded expert system >informations. >I've modified the JOEGlobalDataBase and all text file definitions. They >contain now all CVS tags: > >VENDOR: http://joelib.sf.net >RELEASE_VERSION: $Revision: 1.4 $ >RELEASE_DATE: $Date: 2004/03/15 13:33:42 $ > >So this is not platform independant, BUT if we can find a way to assign >the same vendor, version and date tag (independent standard organization >or just a combined standard web page for JOELib/OpenBabel!!!) we can get >the same hash codes ! >BTW, the hash code uses the standard hash code calculation for string in Java. This looks very exciting - haven't worked through the details. >So descriptors contain now also a reference to the used kernel, e.g.: > ><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" >title="Number_of_HBD_2">0</cml:scalar> Yes - apart from the dictRef - this is great. At present it is required to add integer if you wish to inform a generic processing engine that this is an integer. Otherwise it defaults to an xsd:string. JOElib itself knows the implied semantics and could omit it. The title is optional - it is for humans - machines simply replicate it. So if you are happy to refer to this by joelib:kernel:715333816 you have everything. The string joelib:kernel:715333816 is an XML QName, so it can't have two colons. The prefix has no semantic value and maps to a URI. So the full spec could be: <cml:cml xmlns:cml="http://www.xml-cml.org/schema/cml2/core" xmlns:jk="http:joelib.sf.net/joelib/kernel/dict"> <cml:scalar dataType="xsd:integer" dictRef="jk:a715333816" title="Number_of_HBD_2">0</cml:scalar> </cml:cml> Note that a QNname must have both components starting with a letter, hence: a715333816 >Peter, is this now correct ? > >I will release a new JOELib version the next hours, then i'm going home, >i'm sick. Hope you get better soon. Best wishes P. MORE comments below: >Kind regards, Joerg >-- >Dipl. Chem. Joerg K. Wegner >Center of Bioinformatics Tuebingen (ZBIT) >Department of Computer Architecture >Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany >Phone: (+49/0) 7071 29 78970 >Fax: (+49/0) 7071 29 5091 >E-Mail: mailto:we...@in... >WWW: http://www-ra.informatik.uni-tuebingen.de >-- >Never mistake motion for action. > (E. Hemingway) > >Never mistake action for meaningful action. > (Hugo Kubinyi,2004) > > > ><?xml version="1.0" encoding="ISO-8859-1"?> ><!DOCTYPE molecule SYSTEM "cml.dtd" []> ><cml:molecule xmlns:cml="http://www.xml-cml.org/schema/cml2/core" >title="Gonan derivate with stereochemistry" id="-2114331329"> IDs must start with a letter ><cml:metadataList title="generated automatically from JOELib"> ><cml:metadata name="dc:creator" content="Used JOELib chemistry kernel ID >is 715333816 and the used CML writer is >joelib.io.types.cml.MoleculeHuge(version 1.2)"></cml:metadata> ><cml:metadata name="dc:description" content="Conversion of legacy filetype >to CML"></cml:metadata> ><cml:metadata name="dc:identifier" content="unknown"></cml:metadata> ><cml:metadata name="dc:content"></cml:metadata> ><cml:metadata name="dc:rights" content="unknown"></cml:metadata> ><cml:metadata name="dc:type" content="chemistry"></cml:metadata> ><cml:metadata name="dc:contributor" content="see http://joelib.sf.net for >a full list of contributors"></cml:metadata> ><cml:metadata name="dc:date" content="16 Mar 2004 08:53:52 >GMT"></cml:metadata> ><cml:metadata name="cmlm:structure" content="yes"></cml:metadata> Looks great ></cml:metadataList> ><cml:scalar dataType="xsd:string" dictRef="joelib:kernel" >title="joelib:kernel:715333816:softCoded:joelib.data.JOEAromaticTyper" >id="joelib:kernel:single:1345017519">joelib.data.JOEAromaticTyper >http://joelib.sf.net joelib/data/plain/aromatic.txt 1.4 >2004-03-15_13-33-42</cml:scalar> This is a compound data field. We are working on how dictionaries can support this. The fields are, I think: classname URI id datetime XSD can support complexContent which describes and validates these. We are looking at how the dictionaries can support this ><cml:scalar dataType="xsd:string" dictRef="joelib:kernel" >title="joelib:kernel:715333816:softCoded:joelib.data.JOEAtomTyper" >id="joelib:kernel:single:331687181">joelib.data.JOEAtomTyper >http://joelib.sf.net joelib/data/plain/atomtype.txt 1.8 >2004-03-15_13-33-42</cml:scalar> ><cml:scalar dataType="xsd:string" dictRef="joelib:kernel" >title="joelib:kernel:715333816" >id="joelib:kernel:715333816">joelib:kernel:single:1345017519, >joelib:kernel:single:331687181, joelib:kernel:single:-349822152, >joelib:kernel:single:1305056389, joelib:kernel:single:2066602532, >joelib:kernel:single:1443728660, joelib:kernel:single:2056739992, >joelib:kernel:single:-465953241, joelib:kernel:single:-752030822, >joelib:kernel:single:-647783807, joelib:kernel:single:1562896312, >joelib:kernel:single:1380529384, joelib:kernel:single:2132350161, >joelib:kernel:single:-1630937171, joelib:kernel:single:862707252, >joelib:kernel:single:-94117937</cml:scalar> I would make this an array and use prefixes: ><cml:array dataType="xsd:QName dictRef="joelib:kernel" >title="joelib:kernel:715333816" id="joelib:kernel:715333816"> jks:a1345017519 jks:331687181 ...</cml:array> But it looks messy. Do you actually want to process these as integers? If so it can be redesigned >joelib:kernel:single:1345017519, joelib:kernel:single:331687181, >joelib:kernel:single:-349822152, joelib:kernel:single:1305056389, >joelib:kernel:single:2066602532, joelib:kernel:single:1443728660, >joelib:kernel:single:2056739992, joelib:kernel:single:-465953241, >joelib:kernel:single:-752030822, joelib:kernel:single:-647783807, >joelib:kernel:single:1562896312, joelib:kernel:single:1380529384, >joelib:kernel:single:2132350161, joelib:kernel:single:-1630937171, >joelib:kernel:single:862707252, joelib:kernel:single:-94117937</cml:scalar> ><cml:atom id="-2114331329:a1"> ><cml:string builtin="elementType">C</cml:string> ><cml:float builtin="x2">13.916500091552734</cml:float> ><cml:float builtin="y2">-7.770199775695801</cml:float> Looks good This is CML1 - I assume you can now use CML2 ><cml:scalar units="units:electron" dataType="xsd:float" >dictRef="joelib:partialCharge">-0.022420638985526313</cml:scalar> Yes. this is great. I am hoping to get some hierarchy for units so they don't need constant reiteration. And if space matters you can use CML2array ><cml:integer builtin="hydrogenCount">5</cml:integer> ></cml:atom> ><cml:atom id="-2114331329:a2"> ><cml:string builtin="elementType">C</cml:string> ><cml:float builtin="x2">13.916500091552734</cml:float> ><cml:name convention="trivial">Gonan derivate with stereochemistry</cml:name> ><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" >title="Fraction_of_rotatable_bonds">4.3478260869565216E-2</cml:scalar> ><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" >title="Geometrical_shape_coefficient">9.202824265150003</cml:scalar> ><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" >title="Molecular_weight">2.452599936723709E2</cml:scalar> ><cml:scalar dataType="xsd:string" title="RDF"><![CDATA[Gasteiger_Marsili >50<1.5940199183282508E-16,3.5320351902369007E-12,1.0787560326377212E-8,4.562926679481138E-6,2.6872124085373483E-4,2.2069047752468125E-3,2.303245111884276E-3,-5.436356512771221E-4,-3.2478281395112424E-4,4.918651334382971E-5,1.536251324560617E-3,2.277435169742313E-3,1.300816511980075E-3,6.126140107135232E-4,-4.1824716100300705E-4,-1.368863814540861E-3,-8.208339192751625E-4,5.3376461771753E-4,1.534072562138197E-3,1.7908914501277423E-3,5.507175720486667E-6,-5.763211262243748E-4,1.4132473231521047E-4,8.686437677244833E-4,1.5090055350379477E-3,1.6546296948737362E-3,8.647678978194836E-4,2.500403657505191E-4,-8.328990776669339E-5,3.4797339389094526E-4,1.0482630671704465E-3,3.57933385516601E-4,-9.243630247315901E-5,-1.6374118268106688E-4,-6.744686206966648E-4,-7.3563670708480915E-6,1.0783852781926621E-3,1.1659437942465932E-3,5.3669116363927E-4,-1.1314694263345528E-4,-6.928623677582942E-4,-4.119554183357553E-4,2.042136965559031E-5,2.119917715225437E-4,2.94531451807724E-4,-6.505797814441567 E >-4,-2.9527826356305804E-4,6.187696472975766E-5,1.1298076477827559E-4,9.012712526200434E-5>]]></cml:scalar> You could use array and xsd:float for this. CDATA isn't needed unless you expect < or & in your content ><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" >title="Number_of_rotatable_bonds">1</cml:scalar> ><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" >title="Number_of_HBD_2">0</cml:scalar> ><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" >title="Number_of_HBD_1">0</cml:scalar> ><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" >title="MolarRefractivity">9.199900000000002E1</cml:scalar> ><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" >title="Number_of_aromatic_bonds">0</cml:scalar> ><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" >title="Zagreb_group_index_2">1.8E2</cml:scalar> ><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" >title="Zagreb_group_index_1">1.47E2</cml:scalar> ><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" >title="PolarSurfaceArea">0.0</cml:scalar> This needs structuring... ><cml:scalar dataType="xsd:string" title="Topological_atom_pair"><