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OpenBabelDocumentation,Release2.3.1
Commonnames Namessuchas“aspirin”or“alcohol”forsubstancesthatareinwidespreaduse.
8.3 SubstructureSearchingwithIndexes
8.3.1 WhatisIndexing?
Indexingispre-computingtheanswerstoportionsofexpectedquestionsbeforethey’reasked,sothatwhenthequestion
comes,itcanbeansweredquickly.
Takeyourfavoritesearchengine(AOL,Yahoo!,Google,MSN,...)forexample. Withoutindexing,theymightwait
untilyouaskfor“JohnHartfordBluegrass”,thenstartsearchingtheweb,andinayearortwofindallthewebpages
aboutthedeceasedbanjo/fiddleplayerandsteamboatcaptain.Thatwouldprobablynotimpressyou.
Instead,thesesearchenginessearchthewebbeforeyouaskyourquestion,andbuildanindexofthewordstheyfind.
Whenyoutypein“BluegrassJohnHartford”,theyalreadyknowallofthepagesthathave“John”,allofthepages
with“Hartford”,andallofthepageswith“Bluegrass”.Insteadofsearching,theyexaminetheirindex,andfindpages
thatareonallthreelists,andquicklyfindyourresults. (NB:It’sactuallyalotmorecomplex,butthisillustratesthe
mainideaofindexing.)
8.3.2 IndexesforChemicals
Insteadofindexingwords,cheminformaticssystemsindexsubstructures.Althoughtherearemanyschemesfordoing
this,cheminformaticssystemsallusethesamefundamentalprinciple:theydecomposethemoleculeintosmallerbits,
andindexthose.
8.3. SubstructureSearchingwithIndexes
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OpenBabelDocumentation,Release2.3.1
Roughlyspeaking,acheminformaticssystemwillindexeachofthesubstructures(fragments)above,sothatevery
moleculethatcontainseachfragmentisknown.
Whenaqueryisentered,thecheminformaticssystembreaksapartthequeryusingthesametechnique,tofindallof
thefragmentsinthequery.Itthenchecksitsindexforeachfragment,andcombinesthelistsitfindstogetonlythose
moleculesthathaveallofthosefragments.
Thisdoesn’tmeanthatallmoleculesreturnedbytheindexactuallyarematches.Inthelanguageofdatabases,wesay
theindexwillreturnfalsepositives,candidatemoleculesthatdon’tactuallymatchthesubstructuresearch.
Considerourexampleofsearchingfor“JohnHartford”-theindexmightreturnmanypagesthathaveboth“John”
and“Hartford”,yethavenothingtodowithbluegrassmusicorsteamboats. Forexample,itmightreturnapage
containing,“PresidentJohnF.KennedyvisitedHartford,Connecticuttoday...”. Toconfirmthatthesearchsystem
hasfoundsomethingrelevant,itmustcheckthepagesreturnfromtheindextoensurethatthespecificphrase“John
Hartford”ispresent. However,noticethatthisismuchfasterthansearchingeverypage,sincetheoverwhelming
majorityofwebpageswereinstantlyrejectedbecausetheyhaveneither“John”nor“Hartford”onthem.
Similarly,achemicalfragmentindexservestofindonlythemostlikelymoleculesforoursubstructurematch-anything
thattheindexdidn’tfindisdefinitelynotamatch.Butwestillhavetoexamineeachofthemoleculesreturnedbythe
indexingsystemandverifythatthecompletesubstructureforwhichwearesearchingispresent.
8.3.3 NP-Complete-ALittleaboutComputability
Searchingthroughapageoftextforthewords“JohnHartford”isprettyeasyforamoderncomputer. Although
falsepositivesreturnedbytheindexareanuisanceandimpairperformance,theyarenotacatastrophe. Notsofor
substructurematching. Unfortunately,substructurematchingfallsintoacategoryof“hard”mathematicalproblems,
whichmeansfalsepositivesfromtheindexareabigproblem.
Substructurematching(findingacertainfunctionalgroupwithinamolecule)isanexampleofwhatmathematicians
callgraphisomorphism,andisinaclassofproblemscalledNPComplete. Roughlyspeaking,thismeansthetime
ittakestodoasubstructuresearchisnon-polynomial,i.e. exponentialinthenumberofatomsandbonds. Tosee
whythisisacomputationaldisaster,comparetwotasks,onethattakespolynomialtime,k
1
*N2,versusonethattakes
exponentialtimek
2
*2N.Ourpolynomialtaskisbadenough:IfwedoubleN,ittakesfourtimesaslongtosolve.But
theexponentialtaskisworse:Everytimeweaddanatomitdoubles.Sogoingfromoneatomtotwodoublesthetime,
andgoingfrom100atomsto101atomsdoublesthetime.Evenifwecangetk
2
downtoamillionthofk
1
,we’restill
introuble-amillionisjust2
20
ortwentyatomsaway.
IthasbeenmathematicallyproventhatsubstructuresearchingisinthesetofNPCompleteproblems,sothere’sno
pointwastingourtimesearchingforapolynomialalgorithm.Thegoodnewsisthatmostmoleculeshave“lowcon-
nectivity”,meaningmostatomshavefewerthanfourbonds,unliketheweirdandtwistedgraphsthatmathematicians
consider.Inpractice,mostsubstructurematchingcanbedoneinpolynomialtimearoundN
2
orN
3
.Butevenwiththis
improvement,substructurematchingisan“expensive”time-consumingtaskforacomputer.
Thekeypointisthatindexingisparticularlyimportantforcheminformaticssystems. Thetypicalmoderncomputer
canonlyexamineafewthousandmoleculespersecond,soexaminingmillionsofmoleculesone-by-oneisoutofthe
question.Theindexingdonebyamoderncheminformaticssystemisthekeytoitsperformance.
8.4 MolecularSimilarity
Substructuresearchingisaverypowerfultechnique,butsometimesitmissesanswersforseeminglytrivialdifferences.
Wesawthisearlierwiththefollowing:
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Chapter8. Cheminformatics101
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OpenBabelDocumentation,Release2.3.1
Query
Target
We’relookingforsteroids...
Butwedon’tfindthisonebecauseofthedoublebond
Itissomewhatlikesearchingfor“221bBakerStreet”andfindingnothingbecausethedatabasecontains“221BBaker
Street”andthesystemdoesn’tconsider“b”and“B”amatch.
Agoodsimilaritysearchwouldfindthetargetstructureshownabove,becauseeventhoughitisnotasubstructure
match,itishighlysimilartoourquery.
Therearemanywaystomeasuresimilarity.
2Dtopology Thebest-knownandmostwidelyusedsimilaritymetricscomparethetwo-dimensionaltopology,that
is,theyonlyusethemolecule’satomsandbondswithoutconsideringitsshape.
Tanimotosimilarityisperhapsthebestknownasitiseasytoimplementandfasttocompute. Anexcellent
summaryof2Dsimilaritymetricscanbefoundinsection5.3oftheDaylightTheoryManual.
3Dconfiguration Oneofthemostimportantusesofsimilarityisinthediscoveryofnewdrugs,andamolecule’s
shapeiscriticaltoit’smedicinalvalue(seeQSAR).
3Dsimilaritysearches comparetheconfiguration n (alsocalledthe “conformation”) ofa molecule to other
molecules. The“electronicsurface”ofthemoleculeistheimportantbit-thepartthatcaninteractwithother
molecules.3Dsearchescomparethesurfacesoftwomolecules,andhowpolarizedorpolarizableeachbitofthe
surfaceis.
3Dsimilaritysearchesareuncommon,fortworeasons:It’sdifficultandit’sslow.Thedifficultycomesfromthe
complexityofmolecularinteractions-amoleculeisnotafixedshape,butratheradynamicobjectthatchanges
accordingtoitsenvironment. Andtheslownesscomesfromthedifficulty: : Togetbetterresults, , scientists
employmoreandmorecomplexprograms.
PhysicalProperties Theabove2Dand3Dsimilarityarebasedonthemolecule’sstructure.Anothertechniquecom-
parestheproperties-eithercomputedormeasuredorboth-anddeclaresthatmoleculeswithmanyproperties
incommonarelikelytohavesimilarstructure.ItistheideaofQSARtakentothedatabase.
Clustering “Clustering”istheprocessofdifferentiatingasetofthingsintogroupswhereeachgrouphascommon
features.Moleculescanbeclusteredusingavarietyoftechniques,suchascommon2Dand/or3Dfeatures.
Notethatclusteringisnotasimilaritymetricperse(thetopicofthissection),butitmayusevarioussimilarity
metricswhencomputingclusters.Itisincludedherebecauseitcanbeusedasa“cheapsubstitute”.Thatis,when
someonewantstofindcompoundssimilartoaknowncompound,youcanshowthemthegroup(thecluster)to
whichthecompoundbelongs.Itallowsyoutopre-computetheclusters,spendinglotsofcomputationaltimeup
front,andthengiveanswersveryquickly.
Manycheminformaticsdatabaseshaveoneormoresimilaritysearchesavailable.
8.5 ChemicalRegistrationSystems
ChemicalRegistrationisthe“bigbrother”ofcheminformatics.
8.5. ChemicalRegistrationSystems
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OpenBabelDocumentation,Release2.3.1
Acheminformaticssystemisprimarilydevotedtorecordingchemicalstructure. ChemicalRegistrationsystemsare
additionallyconcernedwith:
• Structuralnovelty-ensurethateachcompoundisonlyregisteredonce
• Structuralnormalization-ensurethat structures s withalternative representations(suchasnitrogroups, fer-
rocenes,andtautomers)areenteredinauniformway.
• Structuredrawing-ensurethatcompoundsaredrawninauniformfashion,sothattheycanbequicklyrecog-
nized“byeye”.
• Maintainingrelationshipsamongrelatedcompounds. . Forexample, , allsaltformsofacompoundshouldbe
recognizedasbeingrelatedtooneanother,andcompoundsindifferentsolvatesarealsorelated.
• Registeringmixtures,formulationsandalternativestructures.
• Registeringcompoundsthestructureofwhichisunknown.
• Roles,responsibilities,security,andcompanyworkflow.
• Updates,amendmentsandcorrections,andcontrollingpropagationofchanges(e.g.doeschangingacompound
changeamixturecontainingthatcompound?)
ThescopeofChemicalRegistrationSystemsisfarbeyondthegoalsofthisbriefintroductiontocheminformatics.
However,toillustratejustoneofthepointsabove,let’sconsiderstructuralnovelty.Inreallife,chemicalstructurecan
beveryambiguous.Imagineyouhavefivebottlesofaparticularcompoundthathasastereocenter:
1. Thecontentsofthefirstbottlewerecarefullyanalyzed,andfoundtobeasinglestereoisomer.
2. Thecontentsofthe e secondbottlewere carefullyanalyzedandfoundtocontaina racemicmixtureofthe
stereoisomers.
3. Thestereoisomersofthethirdbottleareunknown. . Itmaybepure, , orhaveonepredominantform,orbea
racemicmixture.
4. Thefourthbottlewasobtainedbyrunningpartofthecontentsofbottle#2throughachromatographicseparation.
Itisisotopicallypure,butyoudon’tknowwhichstereoisomer.
5. Thefifthbottleistheotherfractionfromthesameseparationof#4. Itisalsoisotopicallypure,butyoudon’t
knowwhichstereoisomer,butyouknowit’stheoppositeof#4.
Whichofthesefivebottlescontainthesamecompound, andwhicharedifferent? ? Thatistheessentialtaskofa
chemicalregistrysystem,whichwouldconsiderallfivetobedifferent. Afterall,youprobablyhavedataabouteach
bottle(that’swhyyouhavethem),andyoumustbeabletorecorditandnotconfuseitwiththeotherbottles.
Inthisexampleabove,considerwhatisknownandnotknown:
Bottle
Known
NotKnown
1
Everything
Nothing
2
Everything
Nothing
3
Compoundisknown
Stereochemistry
4
Compoundandpurityknown,stereochemistryisoppositeof#5
Specificstereochemistry
5
Compoundandpurityknown,stereochemistryisoppositeof#4
Specificstereochemistry
Acheminformaticssystemhasnowaytorecordthecontentsofthefivebottles;itisonlyconcernedwithstructure.
Bycontrast,achemicalregistrationsystemcanrecordbothwhatisknownaswellaswhatisnotknown. Thisisthe
criticaldifferencebetweenthetwo.
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Chapter8. Cheminformatics101
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Chapter
9
RadicalsandSMILESextensions
9.1 Theneedforradicalsandimplicithydrogentocoexist
Hydrogendeficientmolecules,radicals,carbenes,etc.,arenotwellcateredforbychemicalsoftwareaimedatphar-
maceuticals.Butradicalsareimportantreactionintermediatesinlivingsystemsaswellasmanyotherfields,suchas
polymers,paints,oils,combustionandatmosphericchemistry.Theexamplesgivenherearesmallmolecules,relevant
tothelasttwoapplications.
Chemistrysoftwaretohandle radicalsis complicatedbythecommonuse ofimplicithydrogenwhendescribing
molecules. Howistheprogram m toknowwhenyoutype“O”whetheryoumeananoxygenatom orwater? ? This
ambiguityleadssometosaythathydrogensshouldalwaysbeexplicitinanychemicaldescription.Butthisisnotthe
waythatmostchemistswork.Astraightparaffinicchainfromwhichahydrogenhadbeenabstractedmightcommonly
berepresentedbysomethinglike:
Thisusesimplicithydrogensandanexplicitradicalcentre.Butsometimesthehydrogensareexplicitandtheradical
centreimplicit,aswhenCH
3
isusedtorepresentthemethylradical.
9.2 HowOpenBabeldoesit
OpenBabelacceptsmoleculeswithexplicitorimplicithydrogensandcanconvertbetweenthetwo.Itwillalsohandle
radicals(andotherhydrogen-deficientspecies)withimplicithydrogenbyusinginternallyapropertyofanatom,
_spinmultiplicity,modelledontheRADpropertyinMDLMOLfilesandalsousedinCML.Thiscanberegardedin
thepresentcontextasameasureofthehydrogendeficiencyofanatom.Itsvalueis:
• 0fornormalatoms,
• 2forradical(missingonehydrogen)and
• 1or3forcarbenesandnitrenes(missingtwohydrogens).
Ithappensthatforsomedoublydeficientspecies,likecarbeneCH
2
andoxygenatoms,thesingletandtripletspecies
arefairlycloseinenergyandbothmaybesignificantincertainapplicationssuchas combustion, atmosphericor
preparativeorganicchemistry,soitisconvenientthattheycanbedescribedseparately. Thereareofcourseanin-
finityofotherelectronicconfigurationsofmoleculesbutOpenBabelhasnospecialdescriptorsforthem. However,
evenmorehydrogen-deficientatomsareindicatedbythehighestpossiblevalueofspinmultiplicity(Catomhasspin
multiplicityof5).(ThisextendsMDL’sRADpropertywhichhasamaximumvalueof3.)
Ifthespinmultiplicityofanatomisnotinputexplicitly,itisset(inOBMol::AssignSpinMultiplicity())whentheinput
formatisMOL,SMI,CMLorTherm.Thisroutineiscalledafteralltheatomsandbondsofthemoleculeareknown.
Itdetectshydrogendeficiencyinanatomandassignsspinmultiplicityappropriately. Butbecausehydrogenmaybe
implicititonlydoesthisforatomswhichhaveatleastoneexplicithydrogenoronatomswhichhavehadForceNoH()
calledforthem-whichiseffectivelyzeroexplicithydrogens. Thelatterisused,forinstance,whenSMILESinputs
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OpenBabelDocumentation,Release2.3.1
[O]toensurethatitisseenasanoxygenatom(spinmultiplicity=3)ratherthanwater. Otherwise,atomswithno
explicithydrogenareassumedtohaveaspinmultiplicityof0,i.ewithfullcomplementofimplicithydrogens.
Indecidingwhichatomsshouldbehavespinmultiplicityassigned,hydrogenatomswhichhaveanisotopespecifica-
tion(D,Toreven1H)donotcount. SoSMILESN[2H]isNH
2
D(spinmultiplicityleftat0,sowithafullcontent
ofimplicithydrogens),whereasN[H]isNH(spinmultiplicity=3). AdeuteratedradicallikeNHDisrepresentedby
[NH][2H].
9.3 Inradicalseitherthehydrogenorthespinmultiplicitycanbeim-
plicit
Oncethespinmultiplicityhasbeensetonanatom,thehydrogenscanbeimplicitevenifitisaradical.Forinstance,
thefollowingmolfile,withexplicithydrogens,isonewayofrepresentingtheethylradical:
ethyl radical
OpenBabel04010617172D
Has explicit t hydrogen n and implicit t spin multiplicity
7
6
0
0
0
0
0
0
0
0999 V2000
0.0000
0.0000
0.0000 C
0
0
0
0
0
0.0000
0.0000
0.0000 C
0
0
0
0
0
0.0000
0.0000
0.0000 H
0
0
0
0
0
0.0000
0.0000
0.0000 H
0
0
0
0
0
0.0000
0.0000
0.0000 H
0
0
0
0
0
0.0000
0.0000
0.0000 H
0
0
0
0
0
0.0000
0.0000
0.0000 H
0
0
0
0
0
1
2
1
0
0
0
1
3
1
0
0
0
1
4
1
0
0
0
1
5
1
0
0
0
2
6
1
0
0
0
2
7
1
0
0
0
M
END
WhenreadbyOpenBabelthespinmultiplicityissetto2ontheCatom2.Ifthehydrogensaremadeimplicit,perhaps
bythe-doption,andthemoleculeoutputagain,analternativerepresentationisproduced:
ethyl radical
OpenBabel04010617192D
Has explicit t spin multiplicity and implicit t hydrogen
2
1
0
0
0
0
0
0
0
0999 V2000
0.0000
0.0000
0.0000 C
0
0
0
0
0
0.0000
0.0000
0.0000 C
0
0
0
0
0
1
2
1
0
0
0
M
RAD
1
2
2
M
END
9.4 SMILESextensionsforradicals
AlthoughradicalstructurescanberepresentedinSMILESbyspecifyingthehydrogensexplicitly, e.g. . [CH3]is
themethylradical,somechemistshaveapparentlyfelttheneedtodevisenon-standardextensionsthatrepresentthe
radicalcentreexplicitly. OpenBabelwillrecognizeC[O.]aswellasC[O]asthemethoxyradicalCH
3
Oduring
input,butthenon-standardformisnotsupportedinoutput.
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Chapter9. RadicalsandSMILESextensions
OpenBabelDocumentation,Release2.3.1
Bydefault,radicalcentresareoutputinexplicthydrogenform,e.g.C[CH2]fortheethylradical.Alltheatomswill
beinexplictHform,i.e.[CH3][CH2],ifAddHydrogens()orthe-hoptionhasbeenspecified.Theoutputisalways
standardSMILES,althoughotherprogramsmaynotinterpretradicalscorrectly.
OpenBabelsupportsanotherSMILESextensionforbothinputandoutput:theuseoflowercaseatomicsymbolsto
representradicalcentres.(ThisissupportedontheACCORDChemistryControlandmaybeelsewhere.)Sotheethyl
radicalisCcandthemethoxyradicalisCo. Thisformisinputtransparentlyandcanbeoutputbyusingthe-xr
option“radicalslowercase”.Itisausefulshorthandinwritingradicals,andinmanycasesiseasiertoreadsincethe
emphasisisontheradicalcentreratherthanthenumberofhydrogenswhichislesschemicallysignificant.
In addition, , this s extension interprets s multiple lower case e c c without ring closure as s a a conju-
gated carbon n chain, , so o that cccc is s input t as s 1,3-butadiene.
Lycopene (the red in n tomatoes) is
Cc(C)cCCc(C)cccc(C)cccc(C)ccccc(C)cccc(C)cccc(C)CCcc(C)C (without t the stereochemical
specifications). Thisconjugatedchainformisnotusedonoutput-exceptinthestandardSMILESaromaticform,
c1ccccc1benzene.
Itisinterestingtonotethatthelowercaseextensionactuallyimprovesthechemicalrepresentationinafewcases.The
allylradicalC
3
H
5
wouldbeconventionally[CH2]=[CH][CH2](initsexplictHform),butcouldberepresented
ascccwiththeextendedsyntax. Thelattermoreaccuratelyrepresentsthesymmetryofthemoleculecausedby
delocalisation.
ThisextensionisnotasrobustorascarefullyconsideredasstandardSMILESandshouldbeusedwithrestraint.
Astructurethatusescasaradicalcentreclosetoaromaticcarbonscanbeconfusingtoread,andOpenBabel’s
SMILESparsercanalsobeconfused. Forexample,itrecognizesc1ccccc1casthebenzylradical,butitdoesn’t
likec1cc(c)ccc1.Radicalcentresshouldnotbeinvolvedinringclosure:forcyclohexylradicalC1cCCCC1isok,
butc1CCCCC1isnot.
9.4. SMILESextensionsforradicals
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Chapter9. RadicalsandSMILESextensions
Chapter
10
ContributingtoOpenBabel
10.1 Overview
OpenBabelis developedusingopen, community-orienteddevelopmentmadepossiblebyanactivecommunity–
developers,testers,writers,implementersandmostofallusers.Nomatterwhich‘er’youhappentobe,orhowmuch
timeyoucanprovide,youcanmakevaluablecontributions.
Notsurewheretostart?Thissectionaimstogiveyousomeideas.
Provideinput
Youcanhelpusby:
• helpingtoanswerquestionsonourmailinglist
• suggestingnewfeatures
• suggestingneededfileformats
• reportingbugs
Spreadtheword
IfyoufindOpenBabeluseful,there’sachancethatotherswillalso.Youcanhelpusby:
• promotingandcitingOpenBabelintalksandpublications
• writingblogpostsaboutOpenBabel
• helpingwithdocumentationandourwebsite
• buildingyourownsoftwareonOpenBabel
Togetstarted,justsendanemailtoourmailinglist.
Codeastorm
Asanopensourceproject,OpenBabelhasaveryopendevelopmentprocess.Thismeansthatmanycontributorshave
helpedwiththeprojectwithavarietyofhelp–someforlongperiodsoftime,andsomewithsmall,singlechanges.
Alltypesofassistancehasbeenvaluabletothegrowthoftheprojectovertheyears.
NewdevelopersarealwaysverywelcometoOpenBabelsoifyou’reinterested,justsendanemailtothedeveloperlist
(joinhere)aboutwhatyouwouldliketoworkon,orelsewecancomeupwithsomeideasforareaswhereyoucould
contribute.Herearesomepossibilities:
93
OpenBabelDocumentation,Release2.3.1
• Implementthelatestalgorithmsdescribedintheliterature
• Addanewfileformat(seeHowtoaddanewfileformat)
• Perform‘softwarearchaeology’(seeSoftwareArchaeology)
• Fixsomebugs
• Addarequestedfeature
• Addsupportforadditionaldatatypes
• Implementafeaturefromourroadmap
10.2 DevelopingOpenBabel
Duetoitsopennatureofitsdevelopment,OpenBabelcontainscodecontributedbyawidevarietyofdevelopers(see
Thanks).Thissectiondescribessomegeneralguidelinesand“bestpractices”forcodedevelopers.
10.2.1 DeveloperResources
Fornewandexistingdevelopersherearesomeusefulresources:
• SourceForgeprojectpage
• DevelopmentversionAPIdocumentationanddocumentationbugs
• Nightlybuildandtestdashboard
• RSSfeedforSVNcommitsatCIA.vc
10.2.2 WorkingwiththeDevelopmentCode
TodownloadandupdatethelatestversionoftheOpenBabelsourcecode,youneedSubversion.Subversion(orSVN)
isthenameoftheprojectusedtomaintaintheOpenBabelversioncontrolrepository. Therearemanyclientsfor
Subversion,includingcommand-lineandGUIapplications(forexample,onWindows,TortoiseSVN).Formorelinks,
seetheSubversionwebsite.There’salsoagreatbookaboutusingSubversion,whichisavailableonline.
KeepinguptodatewithSubversion
1. Checkoutthelatestdevelopmentversion:
svn co https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk
Thiscreatesadirectorycalledtrunk,whichcontainsthelatestsourcecodefromOpenBabel.
2. ConfigureandcompilethisusingCMake(seeCompilingOpenBabel).
3. Aftersometimepasses,andyouwantthelatestbugfixesornewfeatures,youmaywanttoupdateyoursource
code.Todothis,gointothetrunkdirectoryyoucreatedabove,andtype:
svn update
4. Dostep(2)again.
94
Chapter10. ContributingtoOpenBabel
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