OpenBabelDocumentation,Release2.3.1
12.4.8 DMol3coordinatesformat(outmol,dmol)
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.4.9 FHIaimsXYZformat(fhiaims)
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.4.10 Fenske-HallZ-Matrixformat(fh)
Note: Thisisawrite-onlyformat.
12.4.11 GAMESSInput(inp,gamin)
WriteOptions
k<keywords>
Usethespecifiedkeywordsforinput
f<file>
Readthefilespecifiedforinputkeywords
12.4.12 GAMESSOutput(gamout,gam,gamess)
Note: Thisisaread-onlyformat.
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
c
Readmultipleconformers
12.4.13 GAMESS-UKInput(gukin)
12.4.14 GAMESS-UKOutput(gukout)
12.4.15 GULPformat(got)
TheformatusedbyGULP(GeneralUtilityLatticeProgram).
12.4. Computationalchemistryformats
125
Pdf no pages selected - Split, seperate PDF into multiple files in C#.net, ASP.NET, MVC, Ajax, WinForms, WPF
Explain How to Split PDF Document in Visual C#.NET Application
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VB.NET PDF Document Splitter Control to Disassemble PDF Document
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OpenBabelDocumentation,Release2.3.1
Note: Thisisaread-onlyformat.
12.4.16 Gaussian98/03Input(gjf,gjc,gau,com)
Note: Thisisawrite-onlyformat.
WriteOptions
b
Outputincludesbonds
k<keywords>
Usethespecifiedkeywordsforinput
f<file>
Readthefilespecifiedforinputkeywords
u
Writethecrystallographicunitcell,ifpresent.
12.4.17 GaussianOutput(g09,g03,g94,g92,g98,gal)
Note: Thisisaread-onlyformat.
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.4.18 GaussianZ-MatrixInput(gzmat)
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
WriteOptions
k<keywords>
Usethespecifiedkeywordsforinput
f<file>
Readthefilespecifiedforinputkeywords
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VB.NET TWAIN: TWAIN Image Scanning in Console Application
First, there is no SelectSourceDialog in VB.NET TWAIN console scanning application. image scanning SDK, like how to scan multiple pages to one PDF or TIFF
add page break to pdf; pdf file specification
VB.NET PowerPoint: Convert & Render PPT into PDF Document
VB.NET programmers can easily render selected PowerPoint slide our VB.NET PowerPoint to PDF conversion add pptx document file independently, no other external
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OpenBabelDocumentation,Release2.3.1
12.4.19 Gaussianformattedcheckpointfileformat(fchk,fch,fck)
AformattedtextfilecontainingtheresultsofaGaussiancalculation
Currentlysupportsreadingmoleculargeometriesfromfchkfiles.Moretocome.
Note: Thisisaread-onlyformat.
ReadOptions
s
Singlebondsonly
b
Nobondperception
12.4.20 HyperChemHINformat(hin)
12.4.21 Jaguarinputformat(jin)
Note: Thisisawrite-onlyformat.
12.4.22 Jaguaroutputformat(jout)
Note: Thisisaread-onlyformat.
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.4.23 MOPACCartesianformat(mopcrt,mpc,mop)
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
WriteOptions
k<keywords>
Usethespecifiedkeywordsforinput
f<file>
Readthefilespecifiedforinputkeywords
u
Writethecrystallographicunitcell,ifpresent.
12.4. Computationalchemistryformats
127
C# HTML5 PDF Viewer SDK deployment on IIS in .NET
the place where you store XDoc.PDF.HTML5 Viewer Bit Applications" in accordance with the selected DLL (x86 site configured in IIS has no sufficient authority
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VB.NET PDF - VB.NET HTML5 PDF Viewer Deployment on IIS
the place where you store XDoc.PDF.HTML5 Viewer Bit Applications" in accordance with the selected DLL (x86 site configured in IIS has no sufficient authority
cannot print pdf file no pages selected; break pdf into multiple pages
OpenBabelDocumentation,Release2.3.1
12.4.24 MOPACInternal(mopin)
WriteOptions
k<keywords>
Usethespecifiedkeywordsforinput
f<file>
Readthefilespecifiedforinputkeywords
12.4.25 MOPACOutputformat(moo,mopout)
Note: Thisisaread-onlyformat.
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.4.26 MPQCoutputformat(mpqc)
Note: Thisisaread-onlyformat.
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.4.27 MPQCsimplifiedinputformat(mpqcin)
Note: Thisisawrite-onlyformat.
12.4.28 Molproinputformat(mp)
Note: Thisisawrite-onlyformat.
12.4.29 Molprooutputformat(mpo)
Note: Thisisaread-onlyformat.
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C# Image: Create C#.NET Windows Document Image Viewer | Online
C# Windows Document Image Viewer Features. No need for viewing multiple document & image formats (PDF, MS Word value of selected drop-down list to switch pages.
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VB.NET TIFF: .NET TIFF Printer Control; Print TIFF Using VB.NET
document printing add-on has no limitation on the function to print multiple TIFF pages by defining powerful & profession imaging controls, PDF document, image
acrobat split pdf; break pdf
OpenBabelDocumentation,Release2.3.1
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.4.30 NWCheminputformat(nw)
Note: Thisisawrite-onlyformat.
12.4.31 NWChemoutputformat(nwo)
Note: Thisisaread-onlyformat.
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.4.32 PWscfformat(pwscf)
TheformatusedbyPWscf,partofQuantumEspresso.
Note: Thisisaread-onlyformat.
12.4.33 ParallelQuantumSolutionsformat(pqs)
12.4.34 Q-Cheminputformat(qcin)
Note: Thisisawrite-onlyformat.
WriteOptions
k<keywords>
Usethespecifiedkeywordsforinput
f<file>
Readthefilespecifiedforinputkeywords
12.4.35 Q-Chemoutputformat(qcout)
Note: Thisisaread-onlyformat.
12.4. Computationalchemistryformats
129
VB.NET Word: Use VB.NET Code to Convert Word Document to TIFF
Render one or multiple selected DOCXPage instances into to TIFF image converting application, no external Word user guides with RasteEdge .NET PDF SDK using VB
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C# Word: C#.NET Word Rotator, How to Rotate and Reorient Word Page
Remarkably, no other external products, including Microsoft Office rotate all MS Word document pages by 90 & profession imaging controls, PDF document, image
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OpenBabelDocumentation,Release2.3.1
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.4.36 TurboMoleCoordinateformat(tmol)
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
a
InputinAngstroms
WriteOptions
a
OutputAngstroms
12.4.37 VASPformat(CONTCAR,POSCAR)
ReadsindatafromPOSCARandCONTCARtoobtaininformationfromVASPcalculations.
DuetolimitationsinOpenBabel’sfilehandling,readinginVASPfilescanbeabittricky;theclientthatisusingOpen
BabelmustuseOBConversion::ReadFile()tobegintheconversion.Thischangeisusuallytrivial.Also,thecomplete
pathtotheCONTCARfilemustbeprovided,otherwisetheotherfilesneededwillnotbefound.
Note: Thisisaread-onlyformat.
12.4.38 ZINDOinputformat(zin)
Theinputformatforthesemiempiricalquantum-mechanicsprogramZINDO.
Note: Thisisawrite-onlyformat.
WriteOptions
c
WriteaninputfilefortheCNDO/INDOprogram.
12.5 Crystallographyformats
12.5.1 ACRformat(acr)
CaRIneASCIICrystalformat(ACR)
Note: Thisisaread-onlyformat.
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OpenBabelDocumentation,Release2.3.1
ReadOptions
s
Considersinglebondsonly
12.5.2 CSDCSSRformat(cssr)
Note: Thisisawrite-onlyformat.
12.5.3 CrystallographicInformationFile(cif)
TheCIFfileformatisthestandardinterchangeformatforsmall-moleculecrystalstructures
Fractionalcoordinatesareconvertedtocartesianonesusingthefollowingconvention:
• Thexaxisisparalleltoa
• Theyaxisisinthe(a,b)plane
• Thezaxisisalongc*
Ref:Int.TablesforCrystallography(2006),vol.B,sec3.3.1.1.1 (thematrixusedisthe2ndformlisted)
ReadOptions
v
VerboseCIFconversion
s
Outputsinglebondsonly
b
Disablebondingentirely
B
UsebondslistedinCIFfilefrom_geom_bond_etcrecords(overridesoptionb)
12.5.4 FreeFormFractionalformat(fract)
Generalpurposecrystallographicformat
The“free-form”fractionalformatattemptstoallowforinputfromarangeoffractional/crystallographyfileformats.
Assuch,ithasonlyafewrestrictionsoninput:
• Lineoneofthefilecontainsatitleorcomment.
• Linetwoofthefilecontainstheunitcellparametersseparatedbywhitespaceand/orcommas(i.e.“abcalpha
betagamma”).
• Anyremaininglinesareparsedforatominformation.Linesstartwiththeelementsymbol,followedbyfractional
X,Y,andZcoordinates(inangstroms)separatedbywhitespace.
Anynumericinput(i.e.,unitcellparameters,XYZcoordinates)canincludedesignationsoferrors,althoughthisis
currentlyignored.Forexample:
C 1.00067(3) 2.75(2) ) 3.0678(12)
willbeparsedas:
C 1.00067 7 2.75 3.0678
12.5. Crystallographyformats
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OpenBabelDocumentation,Release2.3.1
Whenusedasanoutputformat,Thefirstlinewrittenisthetitleofthemoleculeorthefilenameifnotitleisdefined.
Ifamoleculehasadefinedunitcell,thenthesecondlinewillbeformattedas:
a b b c c alpha beta gamma
wherea,b,caretheunitcellvectorlengths,andalpha,beta,andgammaaretheanglesbetweenthem.Thesenumbers
areformattedas“10.5”,whichmeansthat5decimalplaceswillbeoutputforallnumbers.Inthecasewherenounit
cellisdefinedforthemolecule,thevectorlengthswillbedefinedas1.0,andtheanglesto90.0degrees.
Remaininglinesdefinetheatomsinthefile.Thefirstcolumnistheatomicsymbol,followedbytheXYZcoordinates
in10.5format(inangstroms).
Hereisanexamplefile:
ZnO test file
3.14 3.24 4 5.18 90.0 0 90.0 120.0
O 0.66667
0.33333
0.3750
O 0.33333
0.66667
0.8750
Zn 0.66667
0.33333
0.0000
Zn 0.33333
0.66667
0.5000
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.5.5 MacromolecularCrystallographicInfo(mmcif,mcif)
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.5.6 ShelXformat(ins,res)
Note: Thisisaread-onlyformat.
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
12.6 Reactionformats
12.6.1 CMLReactionformat(cmlr)
AminimalimplementationoftheCMLReactionformat
Thisimplementationuseslibxml2.
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OpenBabelDocumentation,Release2.3.1
WriteOptions
1
outputCML1(ratherthanCML2)
a
outputarrayformatforatomsandbonds
l
moleculesNOTinMoleculeList
h
usehydrogenCountforallhydrogens
x
omitXMLdeclaration
r
omitrateconstantdata
N<prefix>
addnamespaceprefixtoelements
M
addobrprefixonnon-CMLReactelements
p
addpropertiestomolecules
Comments
TheimplementationofthisformatwhichreadsandwritestoandfromOBReactionobjectsisfairlyminimalatpresent.
(CurrentlytheonlyotherreactionformatinOpenBabelisRXN.)Duringreading,onlytheelements<reaction>,<re-
actant>,<product>and<molecule>areactedupon(thelastthroughCML).Themoleculescanbecollectedtogether
inalistatthestartofthefileandreferencedinthereactantandproductviae.g.<moleculeref=”mol1”>.
Onwriting,thelistformatcanbespecifiedwiththe-xloption.Thelistcontainersare<moleculeList>and<reaction-
List>andtheoverallwrapperis<mechanism>.Thesearenon-standardCMLReactelementnamesandwouldhaveto
bechanged(inthecode)to<list>,<list>and<cml>ifthiswasunacceptable.
12.6.2 MDLRXNformat(rxn)
TheMDLreactionformatisusedtostoreinformationonchemicalreactions.
OutputOptions,e.g.-xA AoutputinAliasform,e.g.Ph,ifpresent
12.6.3 ReactionSMILESformat(rsmi)
WriteOptions
r
radicalslowercaseegethylisCc
12.7 Imageformats
12.7.1 PNG2Ddepiction(png)
2Ddepictionofasinglemolecule,oradd/extractachemicalstructurefroma.pngfile
ThePNGformathasseveraluses. Themostcommonistogeneratea.pngfileforasinglestructure(whichmay
containseveraldisconnectedcomponents).2Dcoordinatesaregeneratedifnotpresent:
obabel mymol.smi -O image.png
Chemicalstructuredatacanbeembeddedinthe.pngfile(inatEXtchunk):
12.7. Imageformats
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obabel mymol.mol -O image.png -xO molfile
Theparameterofthe-xOoptionspecifiestheformat(“file”canbeadded).Notethatifyouintendtoembeda2Dor
3Dformat,youmayhavetocall--gen2dor--gen3dtogeneratetherequiredcoordinatesiftheyarenotpresent
intheinput.
MoleculescanalsobeembeddedinanexistingPNGfile:
obabel existing.png mymol1.smi mymol2.mol -O O augmented.png g -xO mol
ReadingfromaPNGfilewillextractanyembeddedchemicalstructuredata:
obabel augmented.png g -O O contents.sdf
ReadOptions
y<additionalchunkID> LookalsoinchunkswithspecifiedID
WriteOptions
p<pixels>
imagesize,default300
O<formatID>
Formatofembeddedtext
Forexample,molfileorsmi.
y<additionalchunkID> WritetoachunkwithspecifiedID
12.7.2 PNG2format(png2)
2Ddepictionofasinglemoleculeasa.pngfile
ThePNG2formatisused‘behindthescenes’bythePNGformatifgeneratingimagefiles,andthebestwaytouse
itisactuallythroughthePNGformat. Whileitpossibletogeneratea.pngfiledirectlyusingthePNG2formatas
follows...:
obabel -:"CC(=O)Cl" -opng2 2 -O O mymol.png
...itismuchbettertogenerateitusingthePNGformatasthisallowsyoutoembedachemicalstructureinthe.png
fileheaderwhichyoucanlaterextract:
$ obabel l -:"CC(=O)Cl" -O O mymol.png -xO O smi
$ obabel l mymol.png g -osmi
CC(=O)Cl
ThePNG2formatusestheCairolibrarytogeneratethe.pngfiles. IfCairowasnotfoundwhenOpenBabelwas
compiled,thenthisformatwillbeunavailable.However,itwillstillbepossibletousethePNGformattoread.png
filesiftheycontainembeddedinformation.
SeeAlso:
PNG2Ddepiction(png)
Note: Thisisawrite-onlyformat.
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Chapter12. SupportedFileFormatsandOptions
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