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OpenBabelDocumentation,Release2.3.1
CanIuseOpenBabelcodeinapersonalproject?
OnecommonmisconceptionabouttheGNUGPLlicenseforOpenBabelisthatitrequiresuserstoreleaseanycode
thatusestheOpenBabellibrary.Thisiscompletelyuntrue.TherearenorestrictionsonuseofOpenBabelcodefor
personalprojects,regardlessofwhereyouwork(academia,industry,...wherever).
However,ifyouintendonreleasingasoftwarepackagethatusesOpenBabelcode,theGPLrequiresthatyourpackage
bereleasedundertheGNUGPLlicense. Thedistinctionisbetweenuseanddistribution. . SeeWhat’sinitformeto
contribute?belowformoreonthelicensingissues.
HowdoIciteOpenBabelinapaper?
TosupportdevelopmentofOpenBabel,pleasecite:
• Hutchisonetal.[obj2011]
• OpenBabel,version2.3.1,http://openbabel.org(accessedOct2011)
ThefirstisapaperdescribingOpenBabel;andthesecondisonewaytociteasoftwarepackageataparticularURL.
Obviously,youshouldincludetheversionnumberofOpenBabelyouused,andthedateyoudownloadedthesoftware
orinstalledOpenBabel.
1.2.2 Features,Formats,Roadmap
Whydon’tyousupportfileformatX?
Thefileformatscurrentlysupportedaresomeofthemorecommonfileformatsand,admittedly,thoseweuseinour
work.Ifyou’dliketoseeotherfileformatsadded,weneedoneof:
• documentationonthefileformat
• workingcodetoreadthefileformatortranslateit
• examplefilesinthenewfileformatandinsomeotherformat
Thelatterobviouslyistheeasiestwithtextfileformats. Binaryfilestakesometimetoreverseengineerwithout
documentationorworkingcode.AlsoconsiderpointingdeveloperstothisFAQandthe“What’sinitforme?”section.
WhenIconvertfromSMILEStoMOL2/PDB/etc.,whyareallofthecoordinateszero?
TheSMILESformatcontains2Dinformationonthemolecule. Thatis,itsayswhichatomsareconnectedtowhich
otheratoms, andwhattypeofbondsarepresent. . MOL2, , PDBandseveralotherformatscontain3Dcoordinate
informationnotpresentintheSMILESformat. SinceOpenBabeldoesnotattempttogenerate3Dstructureby
default,allofthecoordinatesaresettozero.However,itispossibletogenerate3DstructurewiththereleaseofOpen
Babel2.2.0usingthe--gen3doption.
Whatsortsoffeatureswillbeaddedinthefuture?
It’sanopenproject,soiffeaturesaresuggestedordonated,they’llbeconsideredasmuchasanythingelseonthe
drawingboard.Somethingsareprettyclearfromtheroadmap.
1.2. FrequentlyAskedQuestions
5
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OpenBabelDocumentation,Release2.3.1
1.2.3 What’sinitformetocontribute?
What’sinitformychemistrysoftwarecompany?
Ifyourproductisclosed-sourceorotherwiseincompatiblewiththeGPL,youunfortunatelycannotlinkdirectlytothe
codelibrary.Youcan,however,distributeOpenBabelinunmodifiedformwithyourproductstousethecommand-line
interface.ThisisfairlyeasybecausetheOpenBabelbabelprogramallowreadingfromthestandardinputandwriting
tothestandardoutput(functioningasaPOSIXpipe).
Ifyoudecidetodistributebinaries,youshouldeitherofferusersthesourceiftheywant,orpointthemtotheOpen
Babelwebsite. Notethatifyoumodifythesource,youobviouslycan’tpointbacktotheOpenBabelwebsite–the
GPLrequiresthatyoudistributethechangedsource. (Oryoucanconvinceustoincorporatethechangesandpoint
backtous.)
What’snottolikewiththisdeal?YoucanhaveOpenBabeltranslateforeignfileformatsforyouandcanpointusers
atthewebsitefordistribution.Youdon’tneedtowritetonsofcodeforalltheseformatsandbugreportscanbepassed
backtous.
Ofcourse, there’sonecatch. . You’llmostlikelyneedtoaddfeature-richsupportforyourfileformats. . Soifyou
contributeasmallamountofcodeundertheGPLtoread/writeyourfiles,everythingelseishandledbyOpenBabel.
It’sawin-winforeveryone. Thecommunitybenefitsbyhavingfeature-richtranslationcodeandopenfileformats.
Yourcompanyanditsprogramsbenefitbytheabilitytoreadjustabouteveryformatimaginable. Usersbenefitby
usingtheprogramstheyneedforthetaskstheyneed.
What’sinitformeasanacademic?
Ifyou’reanacademicdeveloper,youcertainlyshouldreadthepreviousanswertoo.Ittakeslittleworkonyourpartto
interfacewithOpenBabelandyougetalotinreturn.
Butevenifyou’rejustanacademicuser,there’salotofreasonstocontribute. Mostofusdealwithavarietyoffile
formatsinourwork.Soit’susefultotranslatethesecleanly.Ifaformatisn’tcurrentlysupportedbyOpenBabel,see
above. Ifyoufindbugspleasereportthem. Sinceit’sopensource,youcanpatchthecodeyourself,recompileand
havetheproblemfixedveryquickly.
Ifyou’reinclinedtowritecode,theGPLisanexcellentoptionfortheacademic.You’retheoriginalcopyrightholder,
soyoucandowhateveryouwantwiththecode,inadditiontosellingit.Butifyou’vealsolicenseditundertheGPL,
noonecandistributeitasproprietary(i.e.,closed-source)softwarewithoutyouragreement. Fellowacademicscan
useitdirectly,learnfromit,improveitandcontributebacktoyou.Isn’tthatwhymanyofuswentintoscience?
OncelicensedundertheGPL,thecodemustremainfreetointerestedparties.Ifsomeonemodifiesit,thatcodemust
stillremainundertheGPL,freeforall.
What’sinitforanopen-sourcesoftwareproject?
Certainlytheanswersforclosed-sourcesoftwareandacademicsalsoapplyforyou. Beyondthat,ifyourcodeis
compatiblewiththeGPL,youcandirectlyuseOpenBabelandalloftheAPI.Thisisalreadyhappeningwiththe
Avogadromoleculareditor,availableundertheGPL,andmanyothers(seerelatedprojects).There’salotofcodein
OpenBabelbeyondfiletranslationandmoretocome.Whyreinventthewheel?
WhyisthiscoveredundertheGPLinsteadoflicenseX?
TheshortansweristhatOpenEyeScientificSoftwareemploysMattStahl,oneoftheauthorsoftheoriginalBabel.
TheyreleasedalibrarycalledOELibundertheGPLthatdidmanythingsthatBabeldid.Latertheydecidedtorelease
6
Chapter1. Introduction
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OpenBabelDocumentation,Release2.3.1
thenextversionofOELibasaclosed-sourceproject–theirchoicefortheircode. WetooktheversionofOELibstill
underGPLandwentfromthere.
Ifyou’dliketoseeOpenBabellicenseddifferently,we’dsuggestaskingOpenEyeifthey’dconsiderreleasingtheold
codeunderanewlicense,e.g. theLGPL.Atthatpoint,we’dconsiderwhetherOpenBabelshouldberelicensedor
not.Obviouslyallcopyrightholdersmustagreetothenewlicense.
It’sworthnotingthatsinceOpenEyeisdevelopingaclosed-sourcelibrarycalledOEChemandimpliesonereasonfor
purchaseisinclosed-sourcedevelopmentproducts.Sowethinkit’shighlyunlikelythatOpenEyewouldallowOpen
BabeltobecomeacompetitorbyrelicensingundertheLGPL.
WherecanIreadmoreabouttheGNUGPL?
TheFreeSoftwareFoundationmaintainsaFAQlistabouttheGNUGPL.TheFAQattemptstoaddress common
questionsinaneasy-to-read(i.e.,notinlegallanguage)form.
1.3 Thanks
OpenBabelwouldnotbewhatitiswithoutthehelpofacastofmany. Wearefundamentallyacommunityproject
andaimtoofferopendevelopment,responsivetousersandcontributorsalike.
Inadditiontocontributorsofallsorts,avarietyofrelatedprojectskeepusonourtoes. Wewouldalsoliketothank
everyonewhohascitedOpenBabelinacademicandtechnicalliterature,posters,andpresentations.
Credits(inalphabeticalorder)
• RichApodaca
• JoshuaBallanco
• MichaelBanck
• RossBraithwaite
• DaniilBratashov
• FrancescoBresciani
• JeanBrefort
• AlexClark
• JoeCorkery
• SteveConstable
• DonaldCurtis
• AndrewDalke
• DaendeLeon
• MennoDeij
• ChristianEhrlicher
• NickEngland
• VincentFavre-Nicolin
• MaximFedorovsky
• FabienFontaine
• MalcolmGillies
• RichardGillilan
• BrianGoldman
• RajarshiGuha
• RichardHall
• BobHanson
• MarcusHanwell
1.3. Thanks
7
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OpenBabelDocumentation,Release2.3.1
• TommiHassinen
• BryanHerger
• DavidHoekman
• GeoffreyHutchison
• BenoîtJacob
• CraigJames
• MikaelJohansson
• StefanKebekus
• ElmarKrieger
• ErikKruus
• DanielLeidert
• ChristianLaggner
• GregLandrum
• EugeneLeitl
• TengLin
• ZhiguoLiu
• DanielMansfield
• DavidMathog
• GerdeMenche
• DominikMierzejewski
• ChrisMorley
• PaulMortenson
• PeterMurray-Rust
• CarstenNiehaus
• AnthonyNicholls
• NoelO’Boyle
• SergeiPatchkovskii
• FrankPeters
• SteffenReith
• LouisRichard
• RogerSayle
• Ernst-GeorgSchmid
• AjayShah
• KevinShepherd
• SangwooShim
• AndrewSmellie
• MattSprague
• MattStahl
• ChrisSwain
• SJoshuaSwamidass
• BobTolbert
• SergeyTrepalin
• TimVandermeersch
• UgoVaretto
• MartinVogt
• IzharWallach
• FredrikWallner
• PatWalters
• PawelWolinski
• JoergKurtWegner
ThereareprobablymanymorewhohavecontributedtoBabel,OBabel,OELibordirectlytoOpenBabelwhoarenot
listedhere.Pleasehelpuskeepthislistupdated.THANKS!
8
Chapter1. Introduction
C# PDF: C#.NET PDF Document Merging & Splitting Control SDK
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Chapter
2
InstallOpenBabel
OpenBabelrunsonWindows,LinuxandMacOSX.Youcaneitherinstallabinarypackage(theeasiestoption)or
compileOpenBabelyourself(alsoeasy,butmuchmoregeekcred).
2.1 Installabinarypackage
2.1.1 Windows
OpenBabelisavailableasabinaryinstallerforWindows.Itincludesseveralcommand-linetoolsaswellasagraphical
userinterface(GUI).
AdvancedusersmaybeinterestedincompilingOpenBabelthemselves(seeCompilingOpenBabel).
2.1.2 Linux
OpenBabelbinarypackagesareavailablefrommanyLinuxdistributionsincludingUbuntu,OpenSUSEandFedora.
Ingeneral,werecommendusingthelatestreleaseofOpenBabel(currently2.3.1). Ifthisisnotavailableforyour
Linuxdistribution,youshouldcompileOpenBabelyourself.
2.2 CompilingOpenBabel
OpenBabeliswritteninC++. CompilingistheprocessofturningthisC++intoinstructionsthatthecomputer’s
processorcanunderstand,machinecode.
Althoughpre-compiled(or“binary”)packagesareavailableforseveralplatforms,thereareseveralreasonsyoumight
wanttocompileOpenBabelyourself:
• Thecurrentrelease(2.3.1)ofOpenBabelisnotavailableforyourplatform. . Werecommendalwaysusingthe
latestrelease.
• Youwantmorecontroloverthefeaturesavailable.Forexample,perhapsyouwantthePythonbindingsbutthese
werenotincludedinyourdistribution.
• Youwanttousethelatestdevelopmentcode.
• Youwanttoaddanewfeature. ItiseasytoaddnewformatsoroperationstoOpenBabelasithasaplugin
architecture(seeAddingplugins).
• Youjustwanttocompilestuffyourself.Weunderstand.
OpenBabelcanbecompiledonLinux, MacOSX, BSDsandotherUnixes,andalsoonWindows (withCygwin,
MinGWorMSVC).
9
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VB.NET Word: Merge Multiple Word Files & Split Word Document
destnPath As [String]) DOCXDocument.Combine(docList, destnPath and encode created sub-documents into stream or profession imaging controls, PDF document, image
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OpenBabelDocumentation,Release2.3.1
2.2.1 Requirements
TobuildOpenBabel,youneedthefollowing:
• ThesourcecodeforthelatestreleaseofOpenBabel
• AC++compiler
OpenBabeliswritteninstandards-compliantC++. Thebest-supportedcompilersareGCC4and
MSVC++2008,butitalsocompileswithClangandIntelCompiler11.
• CMake2.4ornewer
OpenBabelusesCMakeasitsbuildsystem.CMakeisanopensourcecross-platformbuildsystem
fromKitWare.
YouneedtoinstallCMake2.4ornewer. ThisisavailableasabinarypackagefromtheKitWare
website;alternatively,itmaybeavailablethroughyourpackagemanager(onLinux). Ifnecessary,
youcanalsocompileityourselffromthesourcecode.
IfyouwanttobuildtheGUI(GraphicalUserInterface),youneedthefollowinginaddition:
• wxWidgets2.8(ornewer)
Binarypackagesmaybeavailablethroughyourpackagemanager(wx-common,wx2.8-headersand
libwxbase2.8-devonUbuntu)orfromhttp://www.wxwidgets.org/downloads/.Otherwise,youcould
trycompilingityourselffromthesourcecode.
ThefollowingareoptionalwhencompilingOpenBabel,butifnotavailablesomefeatureswillbemissing:
• libxml2developmentheadersarerequiredtoread/writeCMLfilesandotherXMLformats(thelibxml2-dev
packageinUbuntu)
• zlibdevelopmentlibrariesarerequiredtosupportreadinggzippedfiles(thezlib1g-devpackageinUbuntu)
• Eigenversion2isrequiredifusingthelanguagebindingsintherelease. Inaddition,ifitnotpresent,some
APIclasses(OBAlign,OBConformerSearch)andplugins(theQEqandQTPIEchargemodels,theconformer
operation)willnotbeavailable.
Eigenmaybeavailablethroughyourpackagemanager(thelibeigen2-devpackageinUbuntu). Alternatively,
Eigenisavailablefromhttp://eigen.tuxfamily.org.Itdoesn’tneedtobecompiledorinstalled.Justunzipitand
specifyitslocationwhenconfiguringcmake(seebelow)using-DEIGEN2_INCLUDE_DIR=whereever.
• CairodevelopmentlibrariesarerequiredtosupportPNGdepiction(thelibcairo2-devpackageinUbuntu)
• IfusingGCC3.xtocompile(andnotGCC4.x),thentheBoostheadersarerequiredforcertainformats(CML,
Chemkin,ChemdrawCDX,MDLRXNandRSMI)
IfyouwanttouseOpenBabelusingoneofthesupportedlanguagebindings,thenthefollowingnotesmayapply:
• YouneedthethePythondevelopmentlibrariestocompilethePythonbindings(packagepython-devinUbuntu)
• YouneedthethePerldevelopmentlibrariestocompilethePerlbindings(packagelibperl-devinUbuntu)
2.2.2 Basicbuildprocedure
Thebasicbuildprocedureisthesameforallplatformsandwillbedescribedfirst.Afterthis,wewilllookatvariations
forparticularplatforms.
1. TherecommendedwaytobuildOpenBabelis s tousea separate source andbuilddirectory; forexample,
openbabel-2.3.1andbuild.Thefirststepistocreatethesedirectories:
10
Chapter2. InstallOpenBabel
C# PowerPoint: C# Codes to Combine & Split PowerPoint Documents
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OpenBabelDocumentation,Release2.3.1
tar zxf openbabel-2.3.1.tar.gz
# (this creates s openbabel-2.3.1)
mkdir build
2. Nowyouneedtoruncmaketoconfigurethebuild. . Thefollowingwillconfigurethebuildtouseallofthe
defaultoptions:
cd build
cmake ../openbabel-2.3.1
3. Ifyouneedtospecifyanoption,usethe-Dswitchtocmake.Forexample,thefollowinglinesetsthevalueof
CMAKE_INSTALL_PREFIXandCMAKE_BUILD_TYPE:
cmake ../openbabel-2.3.1 1 -DCMAKE_INSTALL_PREFIX=~/Tools -DCMAKE_BUILD_TYPE=DEBUG
Wewilldiscussvariouspossibleoptionslater.
4. Atthispoint,itwouldbeagoodideatocompileOpenBabel:
make
Haveacoffeewhilethemagichappens. Ifyouhaveamulti-processormachineandwouldpreferanexpresso,
tryaparallelbuildinstead:
make -j4
# parallel l build across 4 4 processors
5. Andfinally,asroot(orusingsudo)youshouldinstallit:
make install
2.2.3 Localbuild
LookMa,noinstall!
Withtherightsortofenvironmentvariablemagic(seebelow),youcanactuallyuseOpenBabelstraightfrom
thebuildfolder.Butlifeisabiteasierifyouinstallitsomewhere,eithersystem-wideorlocally.
Bydefault,OpenBabelisinstalledin/usr/local/onaUnix-likesystem. Thisrequiresrootaccess(orsudo).
Evenifyoudohaverootaccess,youmaynotwanttooverwriteanexistinginstallationoryoumaywanttoavoid
conflictswithaversionofOpenBabelinstalledbyyourpackagemanager.
Thesolutiontoalloftheseproblemsistodoalocalinstallintoadirectorysomewhereinyourhomefolder. An
additionaladvantageofalocalinstallisthatifyoueverwanttouninstallit,allyouneedtodoisdeletetheinstallation
directory;removingthefilesfromaglobalinstallismorework.
1. Toconfigurecmaketoinstallinto~/Tools/openbabel-install,forexample,youwoulddothefollow-
ing:
cmake ../openbabel-2.3.1 1 -DCMAKE_INSTALL_PREFIX=~/Tools/openbabel-install
2. Thenyoucanrunmakeandmakeinstallwithoutneedingrootaccess:
make && make install
2.2. CompilingOpenBabel
11
OpenBabelDocumentation,Release2.3.1
2.2.4 CompiletheGUI
TheGUIisbuiltusingthewxWidgetstoolkit.Assumingthatyouhavealreadyinstalledthis(seeRequirementsabove),
youjustneedtoconfigurecmakeasfollows:
cmake ../openbabel-2.3.1 1 -DBUILD_GUI=ON
Whenyourunmakeandmake install,theGUIwillbeautomaticallybuiltandinstalledalongsidethemainOpen
Babellibraryandtools.
2.2.5 Compilelanguagebindings
Eigen2required
Ifyouwishtocompilethelanguagebindingssuppliedintherelease, Eigen2isrequired(seeRequirements
above).
1. WhenconfiguringCMake,includeoptionssuchas-DPYTHON_BINDINGS=ON N -DRUBY_BINDINGS=ON
forwhicheverbindingsyouwishtobuild(validnamesarePYTHON,CSHARP, PERL, JAVAorRUBY)or
-DALL_BINDINGS=ONtobuildthemall.Thebindingswillthenbebuiltandinstalledalongwiththerestof
OpenBabel.YoushouldnoteanywarningmessagesintheCMakeoutput.
2. IfCMakecannotfindJava,youshouldsetthevalueoftheenvironmentvariableJAVA_HOMEtothedirectory
containingtheJavabinandlibdirectories. Forexample,ifyoudownloadtheJDKfromSunandrunthe
self-extracting.binfile,itcreatesadirectoryjdk1.6.0_21(orsimilar);youshouldsetJAVA_HOMEtothe
fullpathtothisdirectory.
3. If f CMake e cannot find d the e Perl l libraries s (which h happens on Ubuntu 10.10, , surprisingly), , you
need to o configure CMake with something g like e -DPERL_LIBRARY=/usr/lib/libperl.so.5.10
-DPERL_INCLUDE_PATH=/usr/lib/perl/5.10.1/CORE.
4. IfyouarecompilingtheCSharpbindings,youshouldspecifytheCSharpcompilertousewithsomethinglike
-DCSHARP_EXECUTABLE=C:\Windows\Microsoft.NET\Framework\v3.5\csc.exe.
5. Whenyourunmake e install,allofthebindingswillbeinstalledtothesamelocationastheOpenBabel
libraries(typically/usr/local/lib).
6. To prepare e tousethebindings, , addtheinstalldirectorytothe e frontofthe appropriate environmentvari-
able: PYTHONPATHfor r Python, PERL5LIB forPerl, RUBYLIB forRuby, CLASSPATHforJava, and
MONO_PATHforMono.
Forexample,forPython:
cmake ../openbabel-2.3.1 1 -DPYTHON_BINDINGS=ON
make
make install
export PYTHONPATH=/usr/local/lib:$PYTHONPATH
2.2.6 Cygwin
ThebasicbuildinstructionsupaboveworkjustfinesolongasyouusetheCMakeprovidedbyCygwinratherthana
nativeWindowsinstallation.
Ifyougetanerroraboutundefined reference to ’_xmlFreeTextReader’, , youneedtospecifythe
locationoftheXMLlibrarieswiththe-DLIBXML2_LIBRARIESoption:
12
Chapter2. InstallOpenBabel
OpenBabelDocumentation,Release2.3.1
cmake ../openbabel-2.3.1 1 -DLIBXML2_LIBRARIES=/usr/lib/libxml2.dll.a
Thelanguagebindingsdon’tseemtoworkunderCygwin.Ifyoucangetthemtowork,letusknow.Alsoremember
thatanythingthatusesCygwinrunsslowerthananativebuildusingMinGWorMSVC++,soifspeedisanissueyou
mightprefertocompilewithMinGWorMSVC++.
2.2.7 MinGW
OpenBabelbuildsoutoftheboxwithMinGW.It’sanawkwardsystemtosetupthough,soherearesomestep-by-step
instructions...TODO
2.2.8 Windows(MSVC)
ThemainWindowsbuildusedbyOpenBabelusestheMicrosoftVisualC++compiler(MSVC).
1. Setupthefollowingenvironmentvariables:
(a) AddtheCMakebindirectorytothePATH.
(b) (Optional,seeRequirementsabove)SetEIGEN2_INCLUDE_DIRtothelocationofthetoplevelEigen
directory(ifinstalled).
(c) (Optional,requiredforGUI)SetWXWINtothetopleveldirectoryofwxWidgets(ifinstalled).
2. InstalltheMicrosoftVisualC++2008(ornewer)compiler.
WeusetheVisualC++2008(9.0)Express Edition(available forfree). . IfyouuseMSVC++2010, , open
windows-vc2008/default_build.batinatexteditorandchangetheVisual Studio 9 2008
toVisual Studio o 10.
3. Openacommandprompt,andchangedirectorytothewindows-vc2008subdirectory.Toconfigurecmake,
andgeneratetheVC++projectfiles,rundefault_build.bat.
4. Double-clickonwindows-vc2008/build/openbabel.slntostartMSVC++.Atthetopofthewindow
justbelowthemenubar,chooseReleaseinthedrop-downbox.
5. Ontheleft-handside,right-clickontheALL_BUILDtarget,andchooseBuild.
2.2.9 Troubleshootingbuildproblems
CMakecachessomevariablesfromrun-to-run.HowcanIwipethecachetostartfromscratch?
DeleteCMakeCache.txtinthebuilddirectory.Thisisalsoaveryusefulfiletolookintoifyouhaveanyproblems.
HowdoIspecifythelocationoftheXMLlibraries?
CMakeshouldfindtheseautomaticallyiftheyareinstalledsystem-wide. Ifyouneedtospecifythem,tryusing
the-DLIBXML2_LIBRARIES=whereveroptionwithCMaketospecifythelocationoftheDLLorSOfile,and
-DLIBXML2_INCLUDE_DIR=wherevertospecifythelocationoftheheaderfiles.
2.2. CompilingOpenBabel
13
OpenBabelDocumentation,Release2.3.1
HowdoIspecifythelocationoftheZLIBlibraries?
CMake should findtheseautomaticallyiftheyareinstalledsystem-wide. . If f youneedtospecifythem, , try y us-
ingthe-DZLIB_LIBRARY=whereveroptionwithCMaketospecifythelocationoftheDLL orSOfile, and
-DZLIB_INCLUDE_DIR=wherevertospecifythelocationoftheheaderfiles.
WhatenvironmentvariablesaffecthowOpenBabelfindsformats,pluginsandlibraries?
LD_LIBRARY_PATH-Usedtofindthelocationofthelibopenbabel.sofile. Youshouldsetthisifyouget
errormessagesaboutnotbeingabletofindlibopenbabel.so.
BABEL_LIBDIR-Usedtofindpluginssuchasthefileformats Ifobabel l -L formatsdoesnotlistanyfile
formats,thenyouneedtosetthisenvironmentvariabletothedirectorywherethefileformatswereinstalled,
typically/usr/local/lib/openbabel/.
BABEL_DATADIR-Usedtofindthelocationofthedatafilesusedforfingerprints,forcefields,etc. If f you get
errors about t not t being able e to find d some e .txt files, , then n you u should set t this s to the name e of the
folder containing g files s such as patterns.txt and MACCS.txt. . These e are typically installed to
/usr/local/share/openbabel.
2.2.10 Advancedbuildoptions
HowdoIcontrolwhetherthetestsarebuilt?
TheCMakeoption-DENABLE_TESTS=ONorOFFwilllookafterthis.Toactuallyrunthetests,usemake tests.
HowdoIdoadebugbuild?
-DCMAKE_BUILD_TYPE=Debug does a a debug g build d (gcc c -g).
To revert to o a a regular build use
-DCMAKE_BUILD_TYPE=Release.
HowdoIseewhatcommandscmakeisusingtobuild?
RunMakeasfollows:
VERBOSE=1 make
HowdoIbuildonespecifictarget?
JustspecifythetargetwhenrunningMake.ThefollowingjustbuildsthePythonbindings:
make _openbabel
Tospeedthingsup,youcanaskMaketoignoredependencies:
make _openbabel/fast
14
Chapter2. InstallOpenBabel
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