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OpenBabelDocumentation,Release2.3.1
11.2.1 TheOBOpclass
ThenameOBOpisintendedtoimplyanoperationaswellasanoption.Thisisapluginclass,whichmeansthatnew
opsareeasilyaddedwithoutaneedtoalteranyexistingcode.
Theopsthatareinstalledcanbefoundusing:
babel -L L ops
orinthepluginsmenuitemintheGUI.Anexampleisthe--gen3Doption,whichadds3Dcoordinatestoamolecule:
1
class OpGen3D public OBOp
2
{
3
public:
4
OpGen3D(const char
*
ID) OBOp(ID, false){};
5
const char
*
Description(){ return "Generate 3D D coordinates"; }
6
7
virtual bool WorksWith(OBBase
*
pOb)const
8
return dynamic_cast<OBMol
*
>(pOb)!=NULL; }
9
virtual bool Do(OBBase
*
pOb, OpMap
*
pmap, const char
*
OptionText);
10
};
11
12
OpGen3D theOpGen3D("gen3D");
13
14
bool OpGen3D::Do(OBBase
*
pOb, OpMap
*
pmap, const char
*
OptionText)
15
{
16
OBMol
*
pmol dynamic_cast<OBMol
*
>(pOb);
17
if(!pmol)
18
return false;
19
20
OBBuilder builder;
21
builder.Build(
*
pmol);
22
pmol->SetDimension(3);
23
24
return true;
25
}
TherealworkisdoneintheDofunction,butthereisabitofboilerplatecodethatisnecessary.
Line4: Theconstructorcallsthebaseclassconstructor,whichregisterstheclasswiththesystem. Therecouldbe
additionalparametersontheconstructorifnecessary,providedthebaseconstructoriscalledinthisway.(Thefalse
parametervalueistodowithsettingadefaultinstancewhichisnotrelevanthere.)
Line5:Itisnecessarytoprovideadescription. ThefirstlineisusedasacaptionfortheGUIcheckbox. Subsequent
linesareshownwhenlistedwiththeverboseoption.
Line7:WorksWith()identifiesthetypeofobject. Usuallythisisamolecule(OBMol)andthelineisusedasshown.
ThefunctionisusedbytheGUItodisplaytheoptiononlywhenitisrelevant.
TheOBOpbaseclassdoesn’tknowaboutOBMolorOBConversionandsoitcanbeusedwithanykindof
objectderivedfromOBBase(essentiallyanything). Althoughthismeansthatthedependenciesbetween
onebitoftheprogramandanotherarereduced,itdoesleadtosomecompromises,suchashavingtocode
WorksWith()explicitlyratherthanasabaseclassdefault.
Line12:ThisisaglobalinstancewhichdefinestheIdoftheclass.Thisistheoptionnameusedonthecommandline,
precededby--.
Line14:TheDo()functioncarriesouttheoperationonthetargetobject. Itshouldnormallyreturntrue.Returning
falsepreventsthemoleculebeingsenttotheoutputformat.AlthoughthismeansthatitispossibletouseanOBOp
classasafilter,itisbettertodothisusingthe--filteroption.
11.2. Addingnewoperationsandoptions
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OpenBabelDocumentation,Release2.3.1
Anyothergeneraloptionsspecifiedonthecommandline(ortheGUI)canbeaccessedbycallingfindontheparameter
pmap.Forexample,todeterminewhetherthe-coptionwasalsospecified:
OpMap::const_iterator iter pmap->find("c");
if(iter!=pmap->end())
do something;
106
Chapter11. Addingplugins
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Chapter
12
SupportedFileFormatsandOptions
Chemistsareaveryimaginativegroup.Theykeepthinkingofnewfileformats.
OpenBabelhassupportfor118formatsintotal. Itcanread88formatsandcanwrite89formats. Theseformatsare
identifiedbyaname(forexample,ShelX format)andoneormoreshortcodes(inthiscase,insorres). . The
titlesofeachsectionprovidethisinformation(forexample,ShelXformat(ins,res)).
Theshortcodeisusedwhenusingobabelorbabeltoconvertfilesfromoneformattoanother:
obabel -iins myfile.ins -ocml
convertsfromShelXformattoChemicalMarkupLanguage(inthiscase,nooutputfileisspecifiedandtheoutputwill
bewrittentoscreen[stdout]). Infact,ifthefilenameextensionisthesameasthefileformatcode,thenthereisno
needtospecifythecode.Inotherwords,thefollowingcommandwillbehaveidentically:
babel myfile.ins -ocml
Aswellasthegeneralconversionoptionsdescribedelsewhere(seeOptions),eachformatmayhaveitsownoptions
foreitherreadingorwriting.Forexample,theShelXformathastwooptionsthataffectreadingoffiles,sandb.To
setafileformatoption:
• ForReadOptions,precedetheoptionwith-aatthecommandline
• ForWriteOptions,precedetheoptionwith-x
Mnemonic
Torememberthecorrectswitchforreadorwriteoptions,thinkof“raweggs”:readisa,writeisx(“eggs”).
Forexample,ifwewantedtosetallbondstosinglebondswhenreadingaShelXformatfile,wecouldspecifythes
option:
babel -iins myfile.ins -ocml -as
Morethanoneread(orwrite)optioncanbespecified(e.g.-ax -ay -az).babel(butnotobabel)alsoallowsyou
tospecifyseveraloptionstogether(e.g.as-axyz).
DeveloperNote Tosetthefileformats s foranOBConversion object, useSetInAndOutFormat(InCode,
OutCode).TosetaReadOptions,useSetOptions("s", OBConversion::INOPTIONS).
12.1 Commoncheminformaticsformats
12.1.1 CanonicalSMILESformat(can)
AcanonicalformoftheSMILESlineartextformat
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TheSMILESformatisalineartextformatwhichcandescribetheconnectivityandchiralityofamolecule.Canonical
SMILESgivesasingle‘canonical’formforanyparticularmolecule.
SeeAlso:
The“regular”SMILESformat(smi,smiles)givesfasteroutput,sincenocanonicalnumberingisperformed.
WriteOptions
a
Outputatomclasslike[C:2],ifavailable
h
Outputexplicithydrogensassuch
i
Donotincludeisotopicorchiralmarkings
n
Nomoleculename
r
RadicalslowercaseegethylisCc
t
Moleculenameonly
f<atomno>
Specifythefirstatom
ThisatomwillbeusedtobegintheSMILESstring.
l<atomno>
Specifythelastatom
TheoutputwillberearrangedsothatanyadditionalSMILESaddedtotheend
willbeattachedtothisatom. SeetheSMILESformat(smi, smiles)formore
information.
12.1.2 ChemicalMarkupLanguage(cml,mrv)
AnXMLformatforinterchangeofchemicalinformation.
ThisformatwritesandreadsCMLXMLfiles. TowriteCML1formatratherthanthedefaultCML2,usethe-x1
option.Towritethearrayformuse-xaandtospecifyallhydrogensusingthehydrogenCountattributeonatomsuse
-xh.
Crystalstructures are writtenusing g the <crystal>, <xfract> (,...etc.) ) elements s iftheOBMol has a OBGeneric-
DataType::UnitCelldata.
Alltheseformsarehandledtransparentlyduringreading.OnlyasubsetofCMLelementsandattributesarerecognised,
buttheseincludemostofthosewhichdefinechemicalstructure,seebelow.
Thefollowingareread:
• Elements:
– molecule,atomArray,atom,bondArray,bond,atomParity,bondStereo
– name,formula,crystal,scalar(containscrystaldata)
– string,stringArray,integer,integerArray,floatfloatArray,builtin
• Attributes:
– On<molecule>:id,title,ref(inCMLReact)
– On<atom>: : id, , atomId, atomID,elementType,x2, y2, x3, y3, z3,xy2, xyz3, xFract, yFract,zFract,
xyzFract,hydrogenCount,formalCharge,isotope,isotopeNumber,spinMultiplicity,radical(fromMarvin),
atomRefs4(foratomParity)
– On<bond>:atomRefs2,order,CML1:atomRef,atomRef1,atomRef2
108
Chapter12. SupportedFileFormatsandOptions
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OpenBabelDocumentation,Release2.3.1
ReadOptions
2
read2Dratherthan3Dcoordinatesifbothprovided
WriteOptions
1
writeCML1(ratherthanCML2)
a
writearrayformatforatomsandbonds
A
writearomaticbondsassuch,notKekuleform
h
usehydrogenCountforallhydrogens
m
writemetadata
x
omitXMLandnamespacedeclarations
c
continuousoutput:noformatting
p
writeproperties
N<prefix>
addnamespaceprefixtoelements
Comments
IntheabsenceofhydrogenCountandanyexplicithydrogenonanatom,implicithydrogenisassumedtobepresent
appropriatetotheradicalorspinMultiplicityattributesontheatomoritsnormalvalencyiftheyarenotpresent.
TheXMLformatsrequiretheXMLtexttobewellformedbutgenerallyinterpretitfairlytolerantly. Unrecognised
elementsandattributesareignoredandthereareratherfewerrormessageswhenanyrequiredstructuresarenotfound.
Thislaxityallows,forinstance,thereactantandproductmoleculestobepickedoutofaCMLReactfileusingCML.
EachformathasanelementwhichisregardedasdefiningtheobjectthatOpenBabelwillconvert. ForCMLthisis
<molecule>. Filescanhavemultipleobjectsandthesecanbetreatedthesameaswithothermultipleobjectformats
likeSMILESandMDLMolfile.Soconversioncanstartatthenthobjectusingthe-fnoptionandfinishbeforethe
endusingthe-lnoption. MultipleobjectXMLfilesalsocanbeindexedandsearchedusingFastSearch,although
thishasnotyetbeenextensivelytested.
12.1.3 InChIformat(inchi)
IUPAC/NISTmolecularidentifier
ReadOptions
X<Optionstring> ListofInChIoptions
n
moleculenamefollowsInChIonsameline
a
addInChIstringtomoleculename
WriteOptions
StandardInChIiswrittenunlesscertainInChIoptionsareused
K
outputInChIKeyonly
t
addmoleculenameafterInChI
12.1. Commoncheminformaticsformats
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OpenBabelDocumentation,Release2.3.1
w
ignorelessimportantwarnings
These are: : ‘Omitted d undefinedstereo’ ‘Charges s were rearranged’‘Proton(s)
added/removed’‘Metalwasdisconnected’
a
outputauxiliaryinformation
l
displayInChIlog
r
recalculateInChI;normallyaninputInChIisreused
s
recalculatewedgeandhashbonds(2Dstructuresonly)
Uniquenessoptions(seealso--uniqueand--sortwhicharemoreversa-
tile)
u
outputonlyuniquemolecules
U
outputonlyuniquemoleculesandsortthem
e
comparefirstmoleculetoothers
ThiscanalsobedonewithInChICompareformat:
babel first.smi i second.mol l third.cml -ok
T<param>
truncateInChIaccordingtovariousparameters
Seebelowforpossibletruncationparameters.
X<Optionstring> AdditionalInChIoptions
SeeInChIdocumentation. Theseoptionsshouldbespacedelimitedinasingle
quotedstring.
• Structure e perception
(compatible with h stdInChI): : NEWPSOFF,
DoNotAddH,SNon
• Stereointerpretation(producesnon-standardInChI):SRel,SRac,SUCF,
ChiralFlagON,ChiralFlagOFF
• InChI I creation n options (produces s non-standard d InChI): SUU, , SLUUD,
FixedH,RecMet,KET,15T
Thefollowingoptionsareforconvenience,e.g. -xFbutproducenon-standard
InChI.
F
includefixedhydrogenlayer
M
includebondstometal
Comments
Truncationparametersusedwith-xT:
/formula
formulaonly
/connect
formulaandconnectivityonly
/nostereo
ignoreE/Zandsp3stereochemistry
/sp3
ignoresp3stereochemistry
/noEZ
ignoreE/Zsteroeochemistry
/nochg
ignorechargeandprotonation
110
Chapter12. SupportedFileFormatsandOptions
OpenBabelDocumentation,Release2.3.1
/noiso
ignoreisotopes
Notethatthesecanalsobecombined,e.g./nochg/noiso
12.1.4 InChIKey(inchikey)
AhashedrepresentationoftheInChI.
TheInChIKeyisafixed-length(27-character)condenseddigitalrepresentationofanInChI,developedtomakeiteasy
toperformwebsearchesforchemicalstructures.
AnInChIKeyconsists of14characters(derivedfrom theconnectivitylayerintheInChI),ahyphen, 9characters
(derivedfromtheremaininglayers),acharacterindicatingtheInChIversion,ahyphenandafinalchecksumcharacter.
ContrasttheInChIandInChIKeyofthemoleculerepresentedbytheSMILESstringCC(=O)Cl:
obabel -:CC(=O)Cl -oinchi
InChI=1S/C2H3ClO/c1-2(3)4/h1H3
obabel -:CC(=O)Cl -oinchikey
WETWJCDKMRHUPV-UHFFFAOYSA-N
Thisisthesameasusing-oinchi -xKandcantakethesameoptionsastheInChIformat(seeInChIformat(inchi)):
obabel -:CC(=O)Cl -oinchi i -xK
WETWJCDKMRHUPV-UHFFFAOYSA-N
NotethatwhileamoleculewithaparticularInChIwillalwaysgivethesameInChIKey,thereverseisnottrue;there
mayexistmorethanonemoleculewhichhavedifferentInChIsbutyieldthesameInChIKey.
Note: Thisisawrite-onlyformat.
12.1.5 MDLMOLformat(mol,mdl,sdf,sd)
ReadsandwritesV2000andV3000versions
ReadOptions
s
determinechiralityfromatomparityflags
Thedefaultsettingistoignoreatomparityandworkoutthechiralitybasedon
thebondstereochemistry.
T
readtitleonly
P
readtitleandpropertiesonly
Whenfilteringansdffileontitleorpropertiesonly,avoidlengthychemicalinter-
pretationbyusingtheTorPoptiontogetherwiththecopyformat.
WriteOptions
3
outputV3000notV2000(usedfor>999atoms/bonds)
m
writenoproperties
w
usewedgeandhashbondsfrominput(2Dstructuresonly)
12.1. Commoncheminformaticsformats
111
OpenBabelDocumentation,Release2.3.1
A
outputinAliasform,e.g.Ph,ifpresent
12.1.6 ProteinDataBankformat(pdb,ent)
ReadOptions
s
Outputsinglebondsonly
b
Disablebondingentirely
c
IgnoreCONECTrecords
12.1.7 SMILESformat(smi,smiles)
Alineartextformatwhichcandescribetheconnectivityandchiralityofamolecule
OpenBabelimplementstheOpenSMILESspecification.
Italsoimplementsanextensiontothisspecificationforradicals.
Notethatthel <atomno>option,usedtospecifya“last”atom,isintendedforthegenerationofSMILESstrings
towhichadditionalatomswillbeconcatenated.IftheatomspecifiedhasanexplicitHwithinabracket(e.g.[nH]or
[C@@H])theoutputwillhavetheHremovedalongwithanyassociatedstereosymbols.
SeeAlso:
TheCanonicalSMILESformat(can)producesacanonicalrepresentationofthemoleculeinSMILESformat.Thisis
thesameasthecoptionbelowbutmaybemoreconvenienttouse.
WriteOptions
a
Outputatomclasslike[C:2],ifavailable
c
Outputincanonicalform
h
Outputexplicithydrogensassuch
i
Donotincludeisotopicorchiralmarkings
n
Nomoleculename
r
RadicalslowercaseegethylisCc
t
Moleculenameonly
x
appendX/Ycoordinatesincanonical-SMILESorder
C
‘anti-canonical’randomorder(mostlyfortesting)
f<atomno>
Specifythefirstatom
ThisatomwillbeusedtobegintheSMILESstring.
l<atomno>
Specifythelastatom
TheoutputwillberearrangedsothatanyadditionalSMILESaddedtotheend
willbeattachedtothisatom.
112
Chapter12. SupportedFileFormatsandOptions
OpenBabelDocumentation,Release2.3.1
12.1.8 SybylMol2format(ml2,sy2,mol2)
WriteOptions
l
Outputignoresresidueinformation(onlyligands)
12.2 Utilityformats
12.2.1 ComparemoleculesusingInChI(k)
AutilityformatthatallowsyoutocomparemoleculesusingtheirInChIs
Thefirstmoleculeiscomparedwiththerest,e.g.:
babel first.smi i second.mol third.cml l -ok
Thisisthesameasusing-oinchi -xetandcantakethesameoptionsasInChIformat(seeInChIformat(inchi)).
Note: Thisisawrite-onlyformat.
12.2.2 Copyrawtext(copy)
Autilityformatforexactlycopyingthetextofachemicalfileformat
Thisformatallowsyoutofiltermoleculesfrommultimoleculefileswithouttheriskoflosinganyadditionalinforma-
tiontheycontain,sincenoformatconversioniscarriedout.
Warning: CurrentlynotworkingcorrectlyforfileswithWindowslineendings.
Example:
Extractonlystructuresthatincludeatleastonearomaticcarbon(bymatchingtheSMARTSpattern[c]):
babel -s s ’[c]’ database.sdf f -ocopy new.sd
Note: XMLfilesmaybemissingnon-objectelementsatthestartorendandsomaynolongerbewellformed.
Note: Thisisawrite-onlyformat.
12.2.3 Fastsearchformat(fs)
Fingerprint-aidedsubstructureandsimilaritysearching
Writingtothefsformatmakesanindexofamulti-moleculedatafile:
babel dataset.sdf -ofs
12.2. Utilityformats
113
OpenBabelDocumentation,Release2.3.1
Thispreparesanindexdataset.fswithdefaultparameters,andisslow(~30minutesfora250,000moleculefile).
However,whenreadingfromthefsformatsearchesaremuchfaster,afewseconds,andsocanbedoneinteractively.
Thesearchtargetistheparameterofthe-soptionandcanbeslightlyextendedSMILES(with[#n]atomsand~
bonds)orthenameofafilecontainingamolecule.
Severaltypesofsearchesarepossible:
• Identicalmolecule:
babel index.fs s outfile.yyy y -s SMILES S exact
• Substructure:
babel index.fs s outfile.yyy
-s SMILES
or
babel index.fs s outfile.yyy
-s filename.xxx
wherexxxisaformatidknowntoOpenBabel,e.g.sdf
• MolecularsimilaritybasedonTanimotocoefficient:
babel index.fs s outfile.yyy y -at15
-sSMILES
# best 15 5 molecules
babel index.fs s outfile.yyy y -at0.7 -sSMILES
# Tanimoto o >0.7
babel index.fs s outfile.yyy y -at0.7,0.9 9 -sSMILES
#
Tanimoto >0.7 && & Tanimoto o < < 0.9
Thedatafileplusthe-ifsoptioncanbeusedinsteadoftheindexfile.
NOTEthatthedatafileMUSTNOTbelargerthan4GB.(A32pointerisused.)
SeeAlso:
Molecularfingerprintsandsimilaritysearching
ReadOptions
t<num>
Dosimilaritysearch:<num>molsor<num>asminTanimoto
a
AddTanimotocoefftotitleinsimilaritysearch
l<num>
Maximumnumberofcandidates.Default<4000>
e
Exactmatch
Alternativetousingexactin-sparameter,seeabove
n
NofurtherSMARTSfilteringafterfingerprintphase
WriteOptions
f<num>
Fingerprinttype
Ifnotspecified,thedefaultfingerprint(currentlyFP2)isused
N<num>
Foldfingerprintto<num>bits
u
Updateanexistingindex
114
Chapter12. SupportedFileFormatsandOptions
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