Am Freitag, den 12.12.2008, 18:03 +0100 schrieb Steffen Moeller: > Hello, > > I am so busy that I followed my attention deficit disorder a bit and came up > with those > magic for the "file" command. They seem to work. Before I place a wishlist to > file, please > be so kind to check them for me a bit: > > > sudo cat >> /etc/magic <<EOMAGIC > # Sybil mol2 format > 0 string @<TRIPOS> Sybil Mol2 molecular coordinates
There can be comments before this string. But one can search for a string with file. > # Ghemical gpr format > 0 string !Header\ gpr ghemical molecular coordinates One of the possible patterns for this format. > # Protein Data Bank > 0 string HEADER\ \ \ \ PDB structure That's pretty much generic. However, the PDB format is not very strict (and there are a lot of applications, which produce, broken PDB). So it is hard to detect. > EOMAGIC > > Extensions welcome The chemical-mime project already creates these magic entries from the database. But there is no way to "extend" files magic database. Everything has to be written into /etc/magic(.mime) by hand. I currently prepare the pattern directly from the shared-mime-info database entries for these files. But this is some kind of pain (although it runs automatically). Maybe I will simply write a plain text file and distribute it with the next cmd release. Here is the overview for chemical file types (inlcuding pattern): http://chemical-mime.sourceforge.net/chemical-mime-data.html And attached the produced magic file. PS: I'm currently not in favour of asking for an official addition of these magic pattern to file project, because the chemical MIME types have never been registered with the IANA. PPS: Hope, you are fine! Regards, Daniel
# This file is part of the chemical-mime-data package. # It is distributed under the GNU Lesser General Public License version 2.1. # # Database: '$Id: chemical-mime-database.xml.in 150 2008-02-16 02:47:40Z dleidert $' # This file was created automatically by cmd_file-magic.xsl. # Copy or append its content to file(1)'s MIME magic database (on # Debian systems, it's the file /etc/magic.mime. # chemical/x-pdb 85 0 string HEADER\ \ \ \ chemical/x-pdb 0 string HEADER\ \ \ \ chemical/x-pdb 0 string TITLE\ \ \ \ \ chemical/x-pdb 0 string REMARK\ chemical/x-pdb 0 string AUTHOR\ \ \ \ chemical/x-pdb 0 string COMPND\ \ \ \ chemical/x-pdb 0 string MODEL\ \ \ \ \ \ \ \ 1 chemical/x-pdb 0 string TER\ \ \ \ \ \ \ 1\ \ \ \ \ \ chemical/x-pdb 0 string CRYST1\ \ \ \ chemical/x-pdb 0 string ATOM\ \ \ \ \ \ 1\ chemical/x-pdb 0 string HETATM\ \ \ \ 1\ chemical/x-pdb # chemical/x-cmtx 80 0 string TITL >5 search/76 NOTE chemical/x-cmtx 0 string MOLE >5 search/76 TITL >>10 search/151 NOTE chemical/x-cmtx # chemical/x-gamess-input 80 0 search/80 $CONTRL >8 search/72 AIMPAC chemical/x-gamess-input >8 search/72 CCTYP chemical/x-gamess-input >8 search/72 CITYP chemical/x-gamess-input >8 search/72 COORD chemical/x-gamess-input >8 search/72 DFTTYP chemical/x-gamess-input >8 search/72 EXETYP chemical/x-gamess-input >8 search/72 FRIEND chemical/x-gamess-input >8 search/72 GEOM chemical/x-gamess-input >8 search/72 GRDTYP chemical/x-gamess-input >8 search/72 ICHARG chemical/x-gamess-input >8 search/72 ICUT chemical/x-gamess-input >8 search/72 INTTYP chemical/x-gamess-input >8 search/72 ISPHER chemical/x-gamess-input >8 search/72 ITOL chemical/x-gamess-input >8 search/72 LOCAL chemical/x-gamess-input >8 search/72 MAXIT chemical/x-gamess-input >8 search/72 MOLPLT chemical/x-gamess-input >8 search/72 MPLEVEL chemical/x-gamess-input >8 search/72 MULT chemical/x-gamess-input >8 search/72 NPRINT chemical/x-gamess-input >8 search/72 NORMF chemical/x-gamess-input >8 search/72 NORMP chemical/x-gamess-input >8 search/72 NOSYM chemical/x-gamess-input >8 search/72 NUMGRD chemical/x-gamess-input >8 search/72 NZVAR chemical/x-gamess-input >8 search/72 PLTORB chemical/x-gamess-input >8 search/72 PP chemical/x-gamess-input >8 search/72 QMTTOL chemical/x-gamess-input >8 search/72 RELWFN chemical/x-gamess-input >8 search/72 RUNTYP chemical/x-gamess-input >8 search/72 SCFTYP chemical/x-gamess-input >8 search/72 TDDFT chemical/x-gamess-input >8 search/72 TREST chemical/x-gamess-input >8 search/72 UNITS chemical/x-gamess-input >8 search/72 $END chemical/x-gamess-input # chemical/x-genbank 80 0 string \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ GENETIC\ SEQ >&0 string UENCE\ DATA\ BANK chemical/x-genbank 0 string LOCUS\ \ \ \ \ \ \ chemical/x-genbank # chemical/x-shelx 80 0 string TITL >5 search/76 CELL chemical/x-shelx # application/x-chemtool 50 0 string Chemtool\ Version\ application/x-chemtool # application/x-ghemical 50 0 string \!Header\ gpr\ >12 string 100\n application/x-ghemical >12 string 110\n application/x-ghemical >12 string 111\n application/x-ghemical 0 string \!Header\ mmlgp\ >14 string 100\n application/x-ghemical # application/x-jmol-voxel 50 0 string JVXL\ application/x-jmol-voxel # application/x-xdrawchem 50 0 search/256 \<\!DOCTYPE\ xdrawchem application/x-xdrawchem 0 search/64 \<xdrawchem application/x-xdrawchem # chemical/x-cactvs-ascii 50 0 string # >0 search/100 Cactvs\ NMDSAscii\ by chemical/x-cactvs-ascii # chemical/x-cactvs-binary 50 8 byte 07 >9 string CACTVSBIN chemical/x-cactvs-binary # chemical/x-cactvs-table 50 0 string CACTVS\ QSAR\ Table chemical/x-cactvs-table # chemical/x-cdx 50 0 string VjCD0100 >8 lelong 0x01020304 >>12 lelong 0x00000000 >>>16 lelong 0x00000000 >>>>20 lelong 0x80000000 chemical/x-cdx >>>>20 lelong 0x00000000 chemical/x-cdx # chemical/x-cdxml 50 0 search/256 \<\!DOCTYPE\ CDXML chemical/x-cdxml 0 search/64 \<CDXML chemical/x-cdxml # chemical/x-chem3d-xml 50 0 search/256 \<\!DOCTYPE\ C3XML chemical/x-chem3d-xml 0 search/64 \<C3XML chemical/x-chem3d-xml # chemical/x-cif 50 0 string #\\#CIF_1.1 >10 byte 9 chemical/x-cif >10 byte 10 chemical/x-cif >10 byte 13 chemical/x-cif # chemical/x-cmdf 50 0 string CMDFCrystalMakerM chemical/x-cmdf 0 string CMD5(CrystalMaker) chemical/x-cmdf # chemical/x-cml 50 0 search/256 \<\!DOCTYPE\ cml chemical/x-cml 0 search/256 \<\!DOCTYPE\ molecule chemical/x-cml 0 search/64 \<cml chemical/x-cml 0 search/64 \<molecule chemical/x-cml # chemical/x-cmmf 50 0 string CMMFCrystalMakerM chemical/x-cmmf 0 string CMM5(CrystalMaker) chemical/x-cmmf # chemical/x-ctx 50 0 string \ /IDENT\ \ \ \ \ \ \ \ chemical/x-ctx # chemical/x-embl-dl-nucleotide 50 0 string ID\ \ \ chemical/x-embl-dl-nucleotide # chemical/x-fasta 50 0 string \> >1 string bbs| chemical/x-fasta >1 string gi| chemical/x-fasta >1 string gnl| chemical/x-fasta >1 string lcl| chemical/x-fasta >1 string pat| chemical/x-fasta >1 string pdb| chemical/x-fasta >1 string pir|| chemical/x-fasta >1 string prf|| chemical/x-fasta >1 string ref| chemical/x-fasta >1 string sp| chemical/x-fasta # chemical/x-gamess-output 50 0 string -----\ GAMESS\ execution\ script\ >&0 string ----- chemical/x-gamess-output 65 search/65 GAMESS\ VERSION\ = >584 search/1 \n\n\ EXECUTION\ OF\ GAMESS\ BEGUN >chemical/x-gamess-output # chemical/x-gaussian-log 50 1 string Entering\ Gaussian\ System,\ Link >&0 string \ 0= chemical/x-gaussian-log # chemical/x-gcg8-sequence 50 0 string \!\!AA_SEQUENCE\ 1.0\n chemical/x-gcg8-sequence 0 string \!\!NA_SEQUENCE\ 1.0\n chemical/x-gcg8-sequence 0 string GCG8\ format\ protein\ sequence\n >&0 string \nGCG8 chemical/x-gcg8-sequence # chemical/x-gulp 50 81 search/79 GENERAL\ UTILITY\ LATTICE\ PROGRA >161 search/79 Julian\ Gale >>241 search/79 Nanochemistry\ Research\ Institu >>>&0 string te >>>>321 search/79 Curtin\ University\ of\ Technolog >>>>>&0 string y,\ Western\ Australia chemical/x-gulp >161 search/79 Julian\ Gale,\ NRI,\ Curtin\ Unive >>&0 string rsity chemical/x-gulp # chemical/x-hin 50 0 string mol\ 1\ >6 search/58 .hin >>12 search/116 atom\ 1 chemical/x-hin # chemical/x-inchi 50 0 string InChI= chemical/x-inchi # chemical/x-inchi-xml 50 0 search/64 \<INChI chemical/x-inchi-xml # chemical/x-isostar 50 0 string #\ Isostar\ Scatter\ Plot chemical/x-isostar # chemical/x-kinemage 50 0 string \<title\> >17 search/223 \...@text chemical/x-kinemage >17 search/223 \...@kinemage chemical/x-kinemage 0 string @text chemical/x-kinemage 0 string @kinemage chemical/x-kinemage # chemical/x-mdl-rdfile 50 0 string $RDFILE\ 1\n >10 string $DATM chemical/x-mdl-rdfile # chemical/x-mdl-rxnfile 50 0 string $RXN\n chemical/x-mdl-rxnfile 0 string $RXN\ V3000\n chemical/x-mdl-rxnfile # chemical/x-mdl-xdfile 50 0 search/64 \<XDfile chemical/x-mdl-xdfile # chemical/x-mol2 50 0 search/800 @\<TRIPOS\>MOLECULE\x0D chemical/x-mol2 # chemical/x-mopac-out 50 81 search/79 MOPAC >81 search/79 (c)\ Fujitsu chemical/x-mopac-out 81 search/79 MOPAC chemical/x-mopac-out # chemical/x-msi-car 50 0 string \!BIOSYM\ archive\ chemical/x-msi-car # chemical/x-msi-hessian 50 0 string $hessian chemical/x-msi-hessian # chemical/x-msi-mdf 50 0 string \!BIOSYM\ molecular_data\ chemical/x-msi-mdf # chemical/x-msi-msi 50 0 string #\ MSI\ CERIUS2\ DataModel\ File\ V >&0 string ersion\ chemical/x-msi-msi # chemical/x-ncbi-asn1 50 0 string PC-AssayContainer chemical/x-ncbi-asn1 0 string PC-Compound chemical/x-ncbi-asn1 0 string PC-InfoData chemical/x-ncbi-asn1 0 string PC-ID chemical/x-ncbi-asn1 0 string PC-Source chemical/x-ncbi-asn1 0 string PC-Substance chemical/x-ncbi-asn1 0 string PC-XRefData chemical/x-ncbi-asn1 # chemical/x-ncbi-asn1-binary 50 0 lelong 0x803080A0 >4 lelong 0x80308030 chemical/x-ncbi-asn1-binary 0 lelong 0x80308030 >4 lelong 0x803080A0 chemical/x-ncbi-asn1-binary # chemical/x-ncbi-asn1-xml 50 0 search/64 \<PC-AssayContainer chemical/x-ncbi-asn1-xml 0 search/64 \<PC-Compound chemical/x-ncbi-asn1-xml 0 search/64 \<PC-ID chemical/x-ncbi-asn1-xml 0 search/64 \<PC-InfoData chemical/x-ncbi-asn1-xml 0 search/64 \<PC-Source chemical/x-ncbi-asn1-xml 0 search/64 \<PC-Substance chemical/x-ncbi-asn1-xml 0 search/64 \<PC-XRefData chemical/x-ncbi-asn1-xml # chemical/x-pdbml 50 0 search/64 \<PDBx:datablock chemical/x-pdbml 0 search/64 \<datablock chemical/x-pdbml # chemical/x-qchem-output 50 20 string Welcome\ to\ Q-Chem >41 string A\ Quantum\ Leap\ Into\ The\ Future >>&0 string \ Of\ Chemistry chemical/x-qchem-output # chemical/x-swissprot 50 0 string ID\ \ \ chemical/x-swissprot # chemical/x-turbomole-basis 50 0 string $basis\n chemical/x-turbomole-basis # chemical/x-turbomole-control 50 0 string $title\n chemical/x-turbomole-control 0 string $operating\ system\ unix\n chemical/x-turbomole-control # chemical/x-turbomole-coord 50 0 string $coord\n chemical/x-turbomole-coord # chemical/x-turbomole-grad 50 0 string $grad\ chemical/x-turbomole-grad # chemical/x-turbomole-input 50 0 string %method\n >8 string ENRGY\ ::\ chemical/x-turbomole-input >8 string FORCE\ ::\ chemical/x-turbomole-input >8 string GEOMY\ ::\ chemical/x-turbomole-input >8 string GRADI\ ::\ chemical/x-turbomole-input # chemical/x-turbomole-jbas 50 0 string $jbas\ chemical/x-turbomole-jbas # chemical/x-turbomole-scfmo 50 0 string $scfmo\ chemical/x-turbomole-scfmo # chemical/x-vamas-iso14976 50 0 string VAMAS\ Surface\ Chemical\ Analysi >&0 string s\ Standard\ Data\ Transfer\ Forma >>&0 string t\ 1988\ May\ 4 chemical/x-vamas-iso14976 # chemical/x-vmd 50
