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chemical-mime-database.xml.in
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chemical-mime-database.xml.in
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<?xml version="1.0" encoding="UTF-8"?>
<!--
Document $Id$
Summary The main chemical MIME type database with all information
found about a special MIME type.
Copyright (C) 2004-2006 Egon Willighagen <e.willighagen@science.ru.nl>.
Copyright (C) 2004-2007 Daniel Leidert <daniel.leidert@wgdd.de>.
This file is free software. The copyright owner gives unlimited
permission to copy, distribute and modify it.
-->
<!DOCTYPE mime-info [
<!ELEMENT mime-info (mime-type+)>
<!ATTLIST mime-info xmlns CDATA #FIXED "http://www.freedesktop.org/standards/shared-mime-info">
<!ATTLIST mime-info xmlns:cm CDATA #FIXED "http://chemical-mime.sourceforge.net/chemical-mime">
<!ATTLIST mime-info cm:vcsid CDATA #IMPLIED>
<!ELEMENT mime-type (comment+, (acronym,expanded-acronym)* , (generic-icon? | glob | magic | treemagic | root-XML | alias | sub-class-of)* , cm:icon?, cm:supported-by?, cm:specification*)>
<!ATTLIST mime-type type CDATA #REQUIRED>
<!ATTLIST mime-type cm:support (yes|no) "no">
<!ATTLIST mime-type cm:added CDATA #IMPLIED>
<!-- a comment describing a document with the respective MIME type. Example: "WMV video" -->
<!ELEMENT comment (#PCDATA)>
<!ATTLIST comment xml:lang CDATA #IMPLIED>
<!-- a comment describing the respective unexpanded MIME type acronym. Example: "WMV" -->
<!ELEMENT acronym (#PCDATA)>
<!ATTLIST acronym xml:lang CDATA #IMPLIED>
<!-- a comment describing the respective expanded MIME type acronym. Example: "Windows Media Video" -->
<!ELEMENT expanded-acronym (#PCDATA)>
<!ATTLIST expanded-acronym xml:lang CDATA #IMPLIED>
<!-- a generic icon name as per the Icon Naming Specification, only required if computing
it from the mime-type would not work, See "generic-icon" in the Shared Mime Specification -->
<!ELEMENT generic-icon (#PCDATA)>
<!ATTLIST generic-icon name (application-x-executable|audio-x-generic|font-x-generic|image-x-generic|package-x-generic|text-html|text-x-generic|text-x-generic-template|text-x-script|video-x-generic|x-office-address-book|x-office-calendar|x-office-document|x-office-presentation|x-office-spreadsheet) #IMPLIED>
<!ELEMENT glob (cm:conflicts)*>
<!ATTLIST glob pattern CDATA #REQUIRED>
<!ATTLIST glob weight CDATA #IMPLIED>
<!ATTLIST glob case-sensitive CDATA #IMPLIED>
<!ELEMENT magic (match)+>
<!ATTLIST magic priority CDATA #IMPLIED>
<!ELEMENT match (match)*>
<!ATTLIST match offset CDATA #REQUIRED>
<!ATTLIST match type (string|big16|big32|little16|little32|host16|host32|byte) #REQUIRED>
<!ATTLIST match value CDATA #REQUIRED>
<!ATTLIST match mask CDATA #IMPLIED>
<!ELEMENT treemagic (treematch)+>
<!ATTLIST treemagic priority CDATA #IMPLIED>
<!ELEMENT treematch (treematch)*>
<!ATTLIST treematch path CDATA #REQUIRED>
<!ATTLIST treematch type (file|directory|link) #IMPLIED>
<!ATTLIST treematch match-case (true|false) #IMPLIED>
<!ATTLIST treematch executable (true|false) #IMPLIED>
<!ATTLIST treematch non-empty (true|false) #IMPLIED>
<!ATTLIST treematch mimetype CDATA #IMPLIED>
<!ELEMENT root-XML EMPTY>
<!ATTLIST root-XML namespaceURI CDATA #REQUIRED>
<!ATTLIST root-XML localName CDATA #REQUIRED>
<!ELEMENT alias EMPTY>
<!ATTLIST alias type CDATA #REQUIRED>
<!ELEMENT sub-class-of EMPTY>
<!ATTLIST sub-class-of type CDATA #REQUIRED>
<!-- * Conflicting MIME-type(s). Use the @gnome and/or @kde
* attributes to determine if we will have problems with
* KDE 3.x, GNOME <= 2.4 or both. -->
<!ELEMENT cm:conflicts EMPTY>
<!ATTLIST cm:conflicts type CDATA #REQUIRED>
<!ATTLIST cm:conflicts cmd (yes|no) "no">
<!ATTLIST cm:conflicts fdo (yes|no) "no">
<!ATTLIST cm:conflicts gnome (yes|no) "no">
<!ATTLIST cm:conflicts kde (yes|no) "no">
<!ATTLIST cm:conflicts mimetypes (yes|no) "no">
<!-- * Icon for GNOME 2.4 and/or KDE 3.x system. Use the @gnome and/or
* kde attributes to determine the icon especially for KDE and/or
* GNOME. -->
<!ELEMENT cm:icon EMPTY>
<!ATTLIST cm:icon gnome CDATA #IMPLIED>
<!ATTLIST cm:icon kde CDATA #IMPLIED>
<!-- * Wrapper element for a list of applications supporting the
* respective MIME type. -->
<!ELEMENT cm:supported-by (cm:application+)>
<!-- * Application supporting the respective MIME type. Use the
* read and @write attributes to determine, if the application
* reads and/or writes the specified MIME type. -->
<!ELEMENT cm:application EMPTY>
<!ATTLIST cm:application name CDATA #REQUIRED>
<!ATTLIST cm:application read (yes|no) "no">
<!ATTLIST cm:application write (yes|no) "no">
<!ATTLIST cm:application package CDATA #IMPLIED>
<!-- * URL where to find the MIME/file type specification or
* explanation. -->
<!ELEMENT cm:specification EMPTY>
<!ATTLIST cm:specification url CDATA #REQUIRED>
<!ATTLIST cm:specification title CDATA #IMPLIED>
]>
<mime-info cm:vcsid="'$Id$'">
<mime-type type="application/x-ghemical" cm:support="no">
<_comment>Ghemical QM file</_comment>
<acronym>QM</acronym>
<expanded-acronym>Quantum Mechanics</expanded-acronym>
<glob pattern="*.gpr"/>
<glob pattern="*.mm1gp"/>
<glob pattern="*.qm1gp"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="!Header gpr " offset="0">
<match type="string" value="100\n" offset="12"/>
<match type="string" value="110\n" offset="12"/>
<match type="string" value="111\n" offset="12"/>
</match>
<match type="string" value="!Header mmlgp " offset="0">
<match type="string" value="100\n" offset="14"/>
</match>
</magic>
<cm:supported-by>
<cm:application name="ghemical"/>
</cm:supported-by>
</mime-type>
<mime-type type="application/x-jmol-voxel" cm:support="no">
<_comment>JVXL file</_comment>
<acronym>JVXL</acronym>
<expanded-acronym>Jmol voxel</expanded-acronym>
<glob pattern="*.jvxl"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="JVXL " offset="0"/>
</magic>
<cm:supported-by>
<cm:application name="ghemical"/>
</cm:supported-by>
<cm:specification url="http://www.stolaf.edu/academics/chemapps/jmol/docs/misc/JVXL-format.pdf"/>
</mime-type>
<mime-type type="application/x-xdrawchem" cm:support="no">
<_comment>Native XDrawChem file</_comment>
<glob pattern="*.xdc"/>
<!-- <root-XML namespaceURI="http://www.xdrawchem.org" localName="xdrawchem"/> -->
<sub-class-of type="application/xml"/>
<magic priority="50">
<match type="string" value="<!DOCTYPE xdrawchem" offset="0:256"/>
<match type="string" value="<xdrawchem" offset="0:64"/>
</magic>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
</mime-type>
<mime-type type="chemical/seq-aa-fasta" cm:support="no">
<_comment>Fasta Amino Acid Sequence</_comment>
<glob pattern="*.aa"/>
<!-- see also chemical/x-fasta -->
<sub-class-of type="chemical/x-fasta"/>
<cm:specification url="http://msdlocal.ebi.ac.uk/docs/mimetype.html"/>
<cm:specification url="http://www.ebi.ac.uk/help/formats.html"/>
</mime-type>
<mime-type type="chemical/seq-na-fasta" cm:support="no">
<_comment>Fasta Nucleotide Sequence</_comment>
<glob pattern="*.na"/>
<!-- see also chemical/x-fasta -->
<sub-class-of type="chemical/x-fasta"/>
<cm:specification url="http://msdlocal.ebi.ac.uk/docs/mimetype.html"/>
</mime-type>
<mime-type type="chemical/seq-aa-genpept" cm:support="no">
<_comment>GenPept Flat File</_comment>
<glob pattern="*.gp">
<cm:conflicts type="application/x-gnuplot" fdo="yes"/>
</glob>
<sub-class-of type="text/plain"/>
<cm:specification url="http://msdlocal.ebi.ac.uk/docs/mimetype.html"/>
</mime-type>
<mime-type type="chemical/x-alchemy" cm:support="yes" cm:added="0.1.91">
<_comment>Alchemy file</_comment>
<glob pattern="*.alc"/>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://local.wasp.uwa.edu.au/~pbourke/dataformats/alc/"/>
</mime-type>
<mime-type type="chemical/x-cache" cm:support="yes" cm:added="0.1.91">
<_comment>CAChe MolStruct file</_comment>
<acronym>CAChe</acronym>
<expanded-acronym>Computer Aided Chemistry</expanded-acronym>
<glob pattern="*.cac"/>
<glob pattern="*.cache"/>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
</mime-type>
<mime-type type="chemical/x-cache-csf" cm:support="no">
<_comment>CAChe CSF file</_comment>
<acronym>CAChe</acronym>
<expanded-acronym>Computer Aided Chemistry</expanded-acronym>
<glob pattern="*.csf"/>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
</mime-type>
<mime-type type="chemical/x-cactvs-ascii" cm:support="yes" cm:added="0.1.94">
<_comment>CACTVS ASCII file</_comment>
<acronym>ASCII</acronym>
<expanded-acronym>American Standard Code for Information Interchange</expanded-acronym>
<acronym>CACTVS</acronym>
<expanded-acronym>Chemical Algorithms Construction, Threading and Verification System</expanded-acronym>
<glob pattern="*.cascii"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="#" offset="0">
<match type="string" value="Cactvs NMDSAscii by" offset="0:100"/>
</match>
</magic>
<cm:supported-by>
<cm:application name="csbr" package="cactvs"/>
</cm:supported-by>
</mime-type>
<mime-type type="chemical/x-cactvs-binary" cm:support="yes" cm:added="0.1.94">
<_comment>CACTVS binary file</_comment>
<acronym>CACTVS</acronym>
<expanded-acronym>Chemical Algorithms Construction, Threading and Verification System</expanded-acronym>
<glob pattern="*.cbin"/>
<!-- Byte 0:7 -> 8 Byte header by XDR? -->
<!-- Byte 0:7 -> Can it be specified? -->
<magic priority="50">
<match type="byte" value="07" offset="8">
<match type="string" value="CACTVSBIN" offset="9"/>
</match>
</magic>
<cm:supported-by>
<cm:application name="csbr" package="cactvs"/>
</cm:supported-by>
</mime-type>
<mime-type type="chemical/x-cactvs-table" cm:support="yes" cm:added="0.1.94">
<_comment>CACTVS table file</_comment>
<acronym>CACTVS</acronym>
<expanded-acronym>Chemical Algorithms Construction, Threading and Verification System</expanded-acronym>
<glob pattern="*.ctab"/>
<magic priority="50">
<match type="string" value="CACTVS QSAR Table" offset="0"/>
</magic>
<cm:supported-by>
<cm:application name="csbr" package="cactvs"/>
</cm:supported-by>
</mime-type>
<mime-type type="chemical/x-cdx" cm:support="yes" cm:added="0.1.91">
<_comment>CDX binary file</_comment>
<acronym>CDX</acronym>
<expanded-acronym>ChemDraw eXchange</expanded-acronym>
<glob pattern="*.cdx"/>
<magic priority="50">
<match type="string" value="VjCD0100" offset="0">
<match type="little32" value="0x01020304" offset="8">
<match type="little32" value="0x00000000" offset="12">
<match type="little32" value="0x00000000" offset="16">
<match type="little32" value="0x80000000" offset="20"/>
<match type="little32" value="0x00000000" offset="20"/>
</match>
</match>
</match>
</match>
</magic>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.camsoft.com/plugins/"/>
<cm:specification url="http://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/index.htm"/>
<cm:specification url="http://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/IntroCDX.htm"/>
</mime-type>
<!-- probably not official -->
<mime-type type="chemical/x-cdxml" cm:support="yes" cm:added="0.1.94">
<_comment>CDXML document</_comment>
<acronym>CDXML</acronym>
<expanded-acronym>ChemDraw eXchangeable XML</expanded-acronym>
<glob pattern="*.cdxml"/>
<!-- <root-XML namespaceURI="http://www.camsoft.com" localName="CDXML"/> -->
<sub-class-of type="application/xml"/>
<magic priority="50">
<match type="string" value="<!DOCTYPE CDXML" offset="0:256"/>
<match type="string" value="<CDXML" offset="0:64"/>
</magic>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.camsoft.com/plugins/"/>
<cm:specification url="http://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/index.htm"/>
<cm:specification url="http://www.cambridgesoft.com/services/documentation/sdk/chemdraw/cdx/IntroCDXML.htm"/>
</mime-type>
<mime-type type="chemical/x-cerius" cm:support="no">
<_comment>MSI Cerius II file</_comment>
<acronym>MSI</acronym>
<expanded-acronym>Molecular Simulations Inc.</expanded-acronym>
<glob pattern="*.cer">
<cm:conflicts type="application/x-x509-ca-cert" fdo="yes" kde="yes"/>
</glob>
<sub-class-of type="text/plain"/>
</mime-type>
<mime-type type="chemical/x-chemdraw" cm:support="no">
<_comment>ChemDraw file</_comment>
<glob pattern="*.chm">
<cm:conflicts type="application/chm" kde="yes"/>
<cm:conflicts type="application/x-chm" fdo="yes" gnome="yes"/>
</glob>
<alias type="application/x-chemdraw"/>
</mime-type>
<mime-type type="chemical/x-chem3d" cm:support="yes" cm:added="0.1.91">
<_comment>Chem3D binary file</_comment>
<glob pattern="*.c3d"/>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.camsoft.com/plugins/"/>
</mime-type>
<mime-type type="chemical/x-chem3d-xml" cm:support="no">
<_comment>Chem3D XML file</_comment>
<glob pattern="*.c3xml"/>
<!-- <root-XML namespaceURI="http://www.camsoft.com" localName="C3XML"/> -->
<sub-class-of type="application/xml"/>
<magic priority="50">
<match type="string" value="<!DOCTYPE C3XML" offset="0:256"/>
<match type="string" value="<C3XML" offset="0:64"/>
</magic>
<cm:specification url="http://www.camsoft.com/plugins/"/>
</mime-type>
<mime-type type="chemical/x-cif" cm:support="yes" cm:added="0.1.91">
<_comment>CIF document</_comment>
<acronym>CIF</acronym>
<expanded-acronym>Crystallographic Information File</expanded-acronym>
<glob pattern="*.cif"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="#\\#CIF_1.1" offset="0">
<match type="byte" value="9" offset="10"/>
<match type="byte" value="10" offset="10"/>
<match type="byte" value="13" offset="10"/>
</match>
</magic>
<cm:supported-by>
<cm:application name="gdis"/>
<cm:application name="jmol"/>
</cm:supported-by>
<cm:specification url="http://www.iucr.org/iucr-top/cif/spec/"/>
<cm:specification url="http://www.iucr.org/iucr-top/cif/standard/cifstd1.html"/>
<cm:specification url="http://www.iucr.org/iucr-top/cif/spec/version1.1/index.html"/>
</mime-type>
<mime-type type="chemical/x-cmdf" cm:support="no">
<_comment>CrystalMaker binary crystal file</_comment>
<glob pattern="*.cmdf"/>
<glob pattern="*.cmd5"/><!-- old format -->
<magic priority="50">
<match type="string" value="CMDFCrystalMakerM" offset="0"/>
<match type="string" value="CMD5(CrystalMaker)" offset="0"/>
</magic>
<cm:specification url="http://www.crystalmaker.com/library/index.html"/>
</mime-type>
<mime-type type="chemical/x-cml" cm:support="yes" cm:added="0.1.90">
<_comment>CML document</_comment>
<acronym>CML</acronym>
<expanded-acronym>Chemical Markup Language</expanded-acronym>
<glob pattern="*.cml"/>
<root-XML namespaceURI="http://www.xml-cml.org/schema" localName="cml"/>
<root-XML namespaceURI="http://www.xml-cml.org/schema/cml2/core" localName="cml"/>
<sub-class-of type="application/xml"/>
<alias type="chemical/cml"/>
<magic priority="50">
<match type="string" value="<!DOCTYPE cml" offset="0:256"/>
<match type="string" value="<!DOCTYPE molecule" offset="0:256"/>
<match type="string" value="<cml" offset="0:64"/>
<match type="string" value="<molecule" offset="0:64"/>
</magic>
<cm:supported-by>
<cm:application name="gchempaint"/>
<cm:application name="jmol"/>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.xml-cml.org/"/>
</mime-type>
<mime-type type="chemical/x-cmmf" cm:support="no">
<_comment>CrystalMaker binary molecule file</_comment>
<glob pattern="*.cmmf"/>
<glob pattern="*.cmm5"/><!-- old format -->
<magic priority="50">
<match type="string" value="CMMFCrystalMakerM" offset="0"/>
<match type="string" value="CMM5(CrystalMaker)" offset="0"/>
</magic>
<cm:specification url="http://www.crystalmaker.com/library/proteins.html"/>
</mime-type>
<mime-type type="chemical/x-cmtx" cm:support="no">
<_comment>CrystalMaker crystal/molecule text file</_comment>
<glob pattern="*.cmtx"/>
<magic priority="80">
<match type="string" value="TITL" offset="0">
<match type="string" value="NOTE" offset="5:81"/>
</match>
<!-- molecule files begin with ^MOLE -->
<match type="string" value="MOLE" offset="0">
<match type="string" value="TITL" offset="5:81">
<match type="string" value="NOTE" offset="10:161"/>
</match>
</match>
</magic>
<cm:specification url="http://www.crystalmaker.co.uk/downloads/CM_Users_Guide.pdf"/>
</mime-type>
<mime-type type="chemical/x-compass" cm:support="no">
<_comment>COMPASS Program of the Takahashi</_comment>
<glob pattern="*.cpa"/>
</mime-type>
<mime-type type="chemical/x-crossfire" cm:support="no">
<_comment>CrossFire file</_comment>
<glob pattern="*.bsd"/>
</mime-type>
<mime-type type="chemical/x-csml" cm:support="no">
<_comment>CSML document</_comment>
<acronym>CSML</acronym>
<expanded-acronym>Chemical Style Markup Language</expanded-acronym>
<glob pattern="*.csm"/>
<glob pattern="*.csml"/>
</mime-type>
<mime-type type="chemical/x-ctx" cm:support="no">
<_comment>Gasteiger ClearText file</_comment>
<glob pattern="*.ctx"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value=" /IDENT " offset="0"/>
</magic>
</mime-type>
<mime-type type="chemical/x-cxf" cm:support="no">
<_comment>CXF file</_comment>
<acronym>CXF</acronym>
<expanded-acronym>Chemical eXchange Format</expanded-acronym>
<glob pattern="*.cef"/>
<glob pattern="*.cxf"/>
</mime-type>
<mime-type type="chemical/x-daylight-smiles" cm:support="yes" cm:added="0.1.91">
<_comment>SMILES formula</_comment>
<acronym>SMILES</acronym>
<expanded-acronym>Simplified Molecular Input Line Entry Specification</expanded-acronym>
<glob pattern="*.smi">
<cm:conflicts type="application/smil" fdo="yes" kde="yes" mimetypes="yes"/>
<cm:conflicts type="application/x-sami" fdo="yes"/>
<cm:conflicts type="application/x-smil" gnome="yes"/>
</glob>
<glob pattern="*.smiles"/>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="csbr" package="cactvs"/>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.daylight.com/smiles/"/>
</mime-type>
<mime-type type="chemical/x-dmol" cm:support="yes" cm:added="0.1.91">
<_comment>DMol Output Format</_comment>
<glob pattern="*.dmol"/>
<glob pattern="*.outmol"/>
<sub-class-of type="text/plain"/>
<cm:icon kde="qc"/>
<cm:supported-by>
<cm:application name="viewmol"/>
</cm:supported-by>
</mime-type>
<mime-type type="chemical/x-embl-dl-nucleotide" cm:support="no">
<_comment>EMBL nucleotide file</_comment>
<acronym>EMBL</acronym>
<expanded-acronym>European Molecular Biology Laboratory</expanded-acronym>
<glob pattern="*.emb"/>
<glob pattern="*.embl"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="ID " offset="0"/>
</magic>
<cm:specification url="http://mercury.ebi.ac.uk/"/>
<cm:specification url="http://www.ebi.ac.uk/help/formats.html"/>
<cm:specification url="http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#FORMAT"/>
<cm:specification url="http://www.biobind.com/faq/emboss/formats.html"/>
<cm:specification url="http://www.psc.edu/general/software/packages/seq-intro/emblfile.html"/>
</mime-type>
<mime-type type="chemical/x-fasta" cm:support="no">
<_comment>Fasta file</_comment>
<glob pattern="*.fa"/>
<glob pattern="*.fna"/>
<glob pattern="*.fsa"/>
<glob pattern="*.fasta"/>
<glob pattern="*.mpfa"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<!-- overview: http://en.wikipedia.org/wiki/Fasta_format -->
<match type="string" value=">" offset="0">
<!-- GenInfo Backbone Id -->
<match type="string" value="bbs|" offset="1"/>
<!-- GenBank/EMBL Data Library/DDBJ, DNA Database of Japan/NCBI Reference Sequence/SWISS-PROT -->
<match type="string" value="gi|" offset="1"/>
<!-- General database identifier -->
<match type="string" value="gnl|" offset="1"/>
<!-- Local Sequence identifier -->
<match type="string" value="lcl|" offset="1"/>
<!-- Patents -->
<match type="string" value="pat|" offset="1"/>
<!-- Brookhaven Protein Data Bank -->
<match type="string" value="pdb|" offset="1"/>
<!-- NBRF PIR -->
<match type="string" value="pir||" offset="1"/>
<!-- Protein Research Foundation -->
<match type="string" value="prf||" offset="1"/>
<!-- NCBI Reference Sequence -->
<match type="string" value="ref|" offset="1"/>
<!-- SWISS-PROT -->
<match type="string" value="sp|" offset="1"/>
</match>
</magic>
<cm:specification url="http://www.ncbi.nlm.nih.gov/blast/fasta.shtml"/>
<cm:specification url="http://www.ebi.ac.uk/help/formats.html"/>
<cm:specification url="http://en.wikipedia.org/wiki/Fasta_format"/>
</mime-type>
<mime-type type="chemical/x-galactic-spc" cm:support="no">
<_comment>Galactic SPC data</_comment>
<acronym>SPC</acronym>
<expanded-acronym>Spectral and Chromatographic</expanded-acronym>
<!-- <glob pattern="*.fir"/> -->
<!-- <glob pattern="*.rmn"/> -->
<glob pattern="*.spc"/>
<cm:specification url="https://ftirsearch.com/features/converters/SPCFileFormat.htm"/>
<cm:specification url="http://web.archive.org/web/20021201230302/www.galactic.com/instruments/spc.htm"/>
<cm:specification url="http://www.adeptscience.co.uk/products/lab/grams32/instruments/gspc_udf.pdf"/>
</mime-type>
<mime-type type="chemical/x-gamess-input" cm:support="yes" cm:added="0.1.93">
<_comment>GAMESS input</_comment>
<acronym>GAMESS</acronym>
<expanded-acronym>General Atomic and Molecular Electronic Structure System</expanded-acronym>
<glob pattern="*.gamin"/>
<glob pattern="*.inp"/>
<sub-class-of type="text/plain"/>
<magic priority="80">
<!-- These patterns will not hit files with large -->
<!-- comments at their beginning. -->
<match type="string" value="$CONTRL" offset="0:80">
<match type="string" value="AIMPAC" offset="8:80"/>
<match type="string" value="CCTYP" offset="8:80"/>
<match type="string" value="CITYP" offset="8:80"/>
<match type="string" value="COORD" offset="8:80"/>
<match type="string" value="DFTTYP" offset="8:80"/>
<match type="string" value="EXETYP" offset="8:80"/>
<match type="string" value="FRIEND" offset="8:80"/>
<match type="string" value="GEOM" offset="8:80"/>
<match type="string" value="GRDTYP" offset="8:80"/>
<match type="string" value="ICHARG" offset="8:80"/>
<match type="string" value="ICUT" offset="8:80"/>
<match type="string" value="INTTYP" offset="8:80"/>
<match type="string" value="ISPHER" offset="8:80"/>
<match type="string" value="ITOL" offset="8:80"/>
<match type="string" value="LOCAL" offset="8:80"/>
<match type="string" value="MAXIT" offset="8:80"/>
<match type="string" value="MOLPLT" offset="8:80"/>
<match type="string" value="MPLEVEL" offset="8:80"/>
<match type="string" value="MULT" offset="8:80"/>
<match type="string" value="NPRINT" offset="8:80"/>
<match type="string" value="NORMF" offset="8:80"/>
<match type="string" value="NORMP" offset="8:80"/>
<match type="string" value="NOSYM" offset="8:80"/>
<match type="string" value="NUMGRD" offset="8:80"/>
<match type="string" value="NZVAR" offset="8:80"/>
<match type="string" value="PLTORB" offset="8:80"/>
<match type="string" value="PP" offset="8:80"/>
<match type="string" value="QMTTOL" offset="8:80"/>
<match type="string" value="RELWFN" offset="8:80"/>
<match type="string" value="RUNTYP" offset="8:80"/>
<match type="string" value="SCFTYP" offset="8:80"/>
<match type="string" value="TDDFT" offset="8:80"/>
<match type="string" value="TREST" offset="8:80"/>
<match type="string" value="UNITS" offset="8:80"/>
<!-- $CONTROL ... $END -->
<match type="string" value="$END" offset="8:80"/>
</match>
</magic>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.msg.ameslab.gov/GAMESS/doc.menu.html"/>
<cm:specification url="http://www.msg.ameslab.gov/GAMESS/Graphics/MacMolPlt.shtml"/>
<cm:specification url="http://www.msg.ameslab.gov/FTP/GAMESS_Manual/input.pdf"/>
</mime-type>
<mime-type type="chemical/x-gamess-output" cm:support="yes" cm:added="0.1.94">
<_comment>GAMESS output</_comment>
<acronym>GAMESS</acronym>
<expanded-acronym>General Atomic and Molecular Electronic Structure System</expanded-acronym>
<glob pattern="*.gam"/>
<glob pattern="*.gamout"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="----- GAMESS execution script -----" offset="0"/>
<match type="string" value="GAMESS VERSION =" offset="65:130">
<match type="string" value="\n\n EXECUTION OF GAMESS BEGUN" offset="584:585"/>
</match>
</magic>
<cm:supported-by>
<cm:application name="gausssum" write="no"/>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.msg.ameslab.gov/GAMESS/doc.menu.html"/>
<cm:specification url="http://www.msg.ameslab.gov/GAMESS/Graphics/MacMolPlt.shtml"/>
</mime-type>
<mime-type type="chemical/x-gaussian-checkpoint" cm:support="no">
<_comment>Gaussian Checkpoint file</_comment>
<glob pattern="*.fch"/>
<glob pattern="*.fchk"/>
<sub-class-of type="text/plain"/>
<cm:specification url="http://gaussian.com/tech_top_level.htm"/>
</mime-type>
<mime-type type="chemical/x-gaussian-cube" cm:support="no">
<_comment>Gaussian Cube (wavefunction) file</_comment>
<glob pattern="*.cub"/>
<cm:specification url="http://gaussian.com/tech_top_level.htm"/>
<cm:specification url="http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm"/>
<cm:specification url="http://local.wasp.uwa.edu.au/~pbourke/dataformats/cube/"/>
</mime-type>
<mime-type type="chemical/x-gaussian-input" cm:support="yes" cm:added="0.1.91">
<_comment>Gaussian input</_comment>
<!-- <glob pattern="*.com"/> -->
<glob pattern="*.gau"/>
<glob pattern="*.gjc"/>
<glob pattern="*.gjf"/>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="cs3d" package="cactvs"/>
<cm:application name="jmol"/>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://gaussian.com/tech_top_level.htm"/>
<cm:specification url="http://www.gaussian.com/g_ur/m_input.htm"/>
</mime-type>
<mime-type type="chemical/x-gaussian-log" cm:support="yes" cm:added="0.1.91">
<_comment>Gaussian log/output</_comment>
<glob pattern="*.g92"/>
<glob pattern="*.g94"/>
<glob pattern="*.g98"/>
<glob pattern="*.g03"/>
<glob pattern="*.gal"/>
<glob pattern="*.log">
<cm:conflicts type="text/x-log" fdo="yes" kde="yes"/>
</glob>
<glob pattern="*.out"/>
<sub-class-of type="text/plain"/>
<!-- Seems there are some weired MIME types. -->
<alias type="chemical/x-gaussian"/>
<alias type="chemical/x-gaussian-output"/>
<alias type="chemical/x-gaussian92-output"/>
<alias type="chemical/x-gaussian94-output"/>
<alias type="chemical/x-gaussian98-output"/>
<alias type="chemical/x-gaussian03-output"/>
<magic priority="50">
<!-- Also seen some stuff before this line sometimes. -->
<!-- Ignore this case here. We start directly at offset 1. -->
<match type="string" value="Entering Gaussian System, Link 0=" offset="1"/>
</magic>
<cm:supported-by>
<cm:application name="gausssum" write="no"/>
<cm:application name="molden"/>
<cm:application name="viewmol"/>
<cm:application name="xmol"/>
</cm:supported-by>
<cm:specification url="http://gaussian.com/tech_top_level.htm"/>
</mime-type>
<mime-type type="chemical/x-gcg8-sequence" cm:support="no">
<_comment>GCG 8 sequence file</_comment>
<glob pattern="*.gcg"/>
<glob pattern="*.gcg8"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="!!AA_SEQUENCE 1.0\n" offset="0"/>
<match type="string" value="!!NA_SEQUENCE 1.0\n" offset="0"/>
<match type="string" value="GCG8 format protein sequence\n\nGCG8" offset="0"/>
</magic>
<cm:specification url="http://www.biobind.com/faq/emboss/formats.html"/>
</mime-type>
<mime-type type="chemical/x-genbank" cm:support="yes" cm:added="0.1.93">
<_comment>GenBank flat file</_comment>
<acronym>GenBank</acronym>
<expanded-acronym>National Genetic Sequence Data Base</expanded-acronym>
<glob pattern="*.gb">
<cm:conflicts type="application/x-gameboy-rom" fdo="yes" gnome="yes"/>
</glob>
<glob pattern="*.gen">
<cm:conflicts type="application/x-genesis-rom" fdo="yes" gnome="yes"/>
</glob>
<sub-class-of type="text/plain"/>
<alias type="chemical/seq-na-genbank"/>
<magic priority="80">
<match type="string" value=" GENETIC SEQUENCE DATA BANK" offset="0"/>
<match type="string" value="LOCUS " offset="0"/>
</magic>
<cm:supported-by>
<cm:application name="biojava"/>
<cm:application name="bioperl"/>
<cm:application name="biopython"/>
<cm:application name="emboss"/>
<cm:application name="kfile_plugin"/>
</cm:supported-by>
<cm:specification url="http://www.psc.edu/general/software/packages/seq-intro/genbankfile.html"/>
<cm:specification url="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html"/>
<cm:specification url="http://msdlocal.ebi.ac.uk/docs/mimetype.html"/>
<cm:specification url="http://www.ebi.ac.uk/help/formats.html"/>
</mime-type>
<mime-type type="chemical/x-gulp-input" cm:support="no">
<_comment>GULP input</_comment>
<acronym>GULP</acronym>
<expanded-acronym>General Utility Lattice Program</expanded-acronym>
<glob pattern="*.gin"/>
<sub-class-of type="text/plain"/>
<cm:specification url="http://www.ivec.org/GULP/help/gulp_30_manual/gulpnode55.html"/>
<cm:specification url="http://www.ivec.org/GULP/help/examples.html"/>
</mime-type>
<mime-type type="chemical/x-gulp" cm:support="yes" cm:added="0.1.94">
<_comment>GULP output</_comment>
<acronym>GULP</acronym>
<expanded-acronym>General Utility Lattice Program</expanded-acronym>
<glob pattern="*.got"/>
<!-- <glob pattern="*.gulp"/> -->
<glob pattern="*.out"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="GENERAL UTILITY LATTICE PROGRAM" offset="81:160">
<match type="string" value="Julian Gale" offset="161:240">
<match type="string" value="Nanochemistry Research Institute" offset="241:320">
<match type="string" value="Curtin University of Technology, Western Australia" offset="321:400"/>
</match>
</match>
<match type="string" value="Julian Gale, NRI, Curtin University" offset="161:240"/>
</match>
</magic>
<cm:supported-by>
<cm:application name="viewmol"/>
</cm:supported-by>
<cm:specification url="http://www.ivec.org/GULP/help/gulp_30_manual/gulpnode55.html"/>
<cm:specification url="http://www.ivec.org/GULP/help/examples.html"/>
</mime-type>
<mime-type type="chemical/x-hin" cm:support="yes" cm:added="0.1.91">
<_comment>HyperChem molecule file</_comment>
<glob pattern="*.hin"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="mol 1 " offset="0">
<match type="string" value=".hin" offset="6:64">
<match type="string" value="atom 1" offset="12:128"/>
</match>
</match>
</magic>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
</mime-type>
<mime-type type="chemical/x-inchi" cm:support="yes" cm:added="0.1.93">
<_comment>IUPAC InChI string(s)</_comment>
<acronym>InChI</acronym>
<expanded-acronym>International Chemical Identifier</expanded-acronym>
<acronym>IUPAC</acronym>
<expanded-acronym>International Union of Pure and Applied Chemistry</expanded-acronym>
<glob pattern="*.inchi"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<match type="string" value="InChI=" offset="0"/>
</magic>
<cm:supported-by>
<cm:application name="bkchem"/>
<cm:application name="kfile_plugin"/>
<cm:application name="openbabel"/>
</cm:supported-by>
<cm:specification url="http://www.iupac.org/inchi/"/>
</mime-type>
<mime-type type="chemical/x-inchi-xml" cm:support="yes" cm:added="0.1.93">
<_comment>IUPAC InChI XML file</_comment>
<acronym>InChI</acronym>
<expanded-acronym>International Chemical Identifier</expanded-acronym>
<acronym>IUPAC</acronym>
<expanded-acronym>International Union of Pure and Applied Chemistry</expanded-acronym>
<glob pattern="*.inchix"/>
<sub-class-of type="application/xml"/>
<magic priority="50">
<match type="string" value="<INChI" offset="0:64"/>
</magic>
<cm:supported-by>
<cm:application name="bkchem"/>
<cm:application name="kfile_plugin"/>
<cm:application name="openbabel"/>
</cm:supported-by>
<cm:specification url="http://www.iupac.org/inchi/"/>
</mime-type>
<mime-type type="chemical/x-isostar" cm:support="no">
<_comment>IsoStar Library of Intermolecular Interactions</_comment>
<glob pattern="*.ist"/>
<glob pattern="*.istr"/>
<sub-class-of type="chemical/x-mol2"/>
<magic priority="50">
<match type="string" value="# Isostar Scatter Plot" offset="0"/>
</magic>
<cm:specification url="http://www.ccdc.cam.ac.uk/products/csd_system/isostar/"/>
<cm:specification url="http://www.ccdc.cam.ac.uk/support/documentation/isostar/portable/isostar_portable-3-074.html"/>
</mime-type>
<mime-type type="chemical/x-jcamp-dx" cm:support="yes" cm:added="0.1.93">
<_comment>JCAMP Spectroscopic Data Exchange file</_comment>
<acronym>JCAMP</acronym>
<expanded-acronym>Joint Committee on Atomic and Molecular Physical Data</expanded-acronym>
<glob pattern="*.dx"/>
<glob pattern="*.jdx"/>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="csir" package="cactvs"/>
<cm:application name="jcamp-dx"/>
<cm:application name="kfile_plugin"/>
</cm:supported-by>
<cm:specification url="http://old.iupac.org/standing/cpep/wp_jcamp_dx.html"/>
</mime-type>
<mime-type type="chemical/x-kinemage" cm:support="no">
<_comment>Kinemage protein image</_comment>
<glob pattern="*.kin"/>
<sub-class-of type="text/plain"/>
<alias type="application/kinemage"/>
<magic priority="50">
<!-- probably, this needs to be refined -->
<match type="string" value="<title>" offset="0">
<match type="string" value="\n@text" offset="17:240"/>
<match type="string" value="\n@kinemage" offset="17:240"/>
</match>
<match type="string" value="@text" offset="0"/>
<match type="string" value="@kinemage" offset="0"/>
</magic>
<cm:specification url="http://kinemage.biochem.duke.edu/kinemage/magepage.php"/>
<cm:specification url="http://kinemage.biochem.duke.edu/kinemage/magehelp.php#pt50"/>
<cm:specification url="http://suna.biochem.duke.edu/downloads/PDFs/format-kinemage.pdf"/>
</mime-type>
<mime-type type="chemical/x-macmolecule" cm:support="no">
<_comment>MacMolecule file</_comment>
<glob pattern="*.mcm"/>
<sub-class-of type="text/plain"/>
<cm:specification url="http://web.archive.org/web/20020224015619/http://www.molvent.com/support/filespec.html"/>
</mime-type>
<mime-type type="chemical/x-macromodel-input" cm:support="yes" cm:added="0.1.91">
<_comment>MacroModel input</_comment>
<glob pattern="*.mmd"/>
<glob pattern="*.mmod"/>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.columbia.edu/cu/chemistry/mmod/mmod.html"/>
</mime-type>
<mime-type type="chemical/x-macromodel-output" cm:support="no">
<_comment>MacroModel output</_comment>
<glob pattern="*.dat">
<cm:conflicts type="chemical/x-mopac-input" cmd="yes"/>
<cm:conflicts type="video/mpeg" gnome="yes"/>
</glob>
<glob pattern="*.out"/>
<sub-class-of type="text/plain"/>
<cm:specification url="http://www.columbia.edu/cu/chemistry/mmod/mmod.html"/>
</mime-type>
<mime-type type="chemical/x-mdl-molfile" cm:support="yes" cm:added="0.1.91">
<_comment>MDL molecule file</_comment>
<acronym>MDL</acronym>
<expanded-acronym>Molecular Design Ltd.</expanded-acronym>
<glob pattern="*.mdl"/>
<glob pattern="*.mol"/>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="csbr" package="cactvs"/>
<cm:application name="csed" package="cactvs"/>
<cm:application name="gchem3d-viewer" package="gnome-chemistry-utils"/>
<cm:application name="gchempaint"/>
<cm:application name="jmol"/>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.mdl.com/downloads/public/ctfile/ctfile.pdf"
title="MDL CTFile Formats - Chapter 4: Molfiles"/>
</mime-type>
<mime-type type="chemical/x-mdl-rdfile" cm:support="yes" cm:added="0.1.91">
<_comment>MDL reaction data file</_comment>
<acronym>MDL</acronym>
<expanded-acronym>Molecular Design Ltd.</expanded-acronym>
<glob pattern="*.rd"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<!-- the so-called RDfile Header -->
<match type="string" value="$RDFILE 1\n" offset="0">
<match type="string" value="$DATM" offset="10"/>
</match>
</magic>
<cm:supported-by>
<cm:application name="csbr" package="cactvs"/>
</cm:supported-by>
<cm:specification url="http://www.mdl.com/downloads/public/ctfile/ctfile.pdf"
title="MDL CTFile Formats - Chapter 8: RDfiles"/>
</mime-type>
<mime-type type="chemical/x-mdl-rxnfile" cm:support="yes" cm:added="0.1.91">
<_comment>MDL reaction file</_comment>
<acronym>MDL</acronym>
<expanded-acronym>Molecular Design Ltd.</expanded-acronym>
<glob pattern="*.rxn"/>
<sub-class-of type="text/plain"/>
<magic priority="50">
<!-- the so-called RXNfile header block -->
<match type="string" value="$RXN\n" offset="0"/>
<match type="string" value="$RXN V3000\n" offset="0"/>
</magic>
<cm:supported-by>
<cm:application name="csbr" package="cactvs"/>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.mdl.com/downloads/public/ctfile/ctfile.pdf"
title="MDL CTFile Formats - Chapter 7: RXNfiles"/>
</mime-type>
<mime-type type="chemical/x-mdl-sdfile" cm:support="yes" cm:added="0.1.91">
<_comment>MDL structure data</_comment>
<acronym>MDL</acronym>
<expanded-acronym>Molecular Design Ltd.</expanded-acronym>
<glob pattern="*.sd"/>
<glob pattern="*.sdf">
<cm:conflicts type="application/vnd.stardivision.math" kde="yes" mimetypes="yes"/>
</glob>
<sub-class-of type="text/plain"/>
<cm:supported-by>
<cm:application name="csbr" package="cactvs"/>
<cm:application name="gchempaint"/>
<cm:application name="xdrawchem"/>
</cm:supported-by>
<cm:specification url="http://www.mdl.com/downloads/public/ctfile/ctfile.pdf"