cdkbook

CDK OWL (N3)

Preferred Extension: n3 MIME type: text/n3 XML Based?: No

CDKOWLReader

This reader supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

CDKOWLWriter

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

CDK Source Code

Preferred Extension: java XML Based?: No

CDKSourceCodeWriter

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

This writer has these IO settings:

Name	Desc
write3DCoordinates	Should 3D coordinates be added? [Default: true]
builder	Which IChemObjectBuilder should be used? [Default: DefaultChemObjectBuilder]
write2DCoordinates	Should 2D coordinates be added? [Default: true]

CML enriched RSS

XML Based?: Yes

RssWriter

This writer supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	true
ChemSequence	true
Reaction	true
ReactionSet	true
isomorphism.matchers.RGroupQuery	true
Crystal	true

CTX

Preferred Extension: ctx MIME type: chemical/x-ctx XML Based?: No

CTXReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

Chemical Markup Language

Extensions: [cml, xml] Preferred Extension: cml MIME type: chemical/x-cml XML Based?: Yes

CMLReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

CMLWriter

This writer supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false
ChemSequence	true
Reaction	true
ReactionSet	true
Crystal	true

This writer has these IO settings:

Name	Desc
CMLIDs	Should the output use CML identifiers? [Default: true]
NamespacedOutput	Should the output use namespaced output? [Default: true]
NamespacePrefix	What should the namespace prefix be? [empty is no prefix] [Default: ]
Indenting	Should the output be indented? [Default: true]
SchemaInstance	Should the output use the Schema-Instance attribute? [Default: false]
XMLDeclaration	Should the output contain an XML declaration? [Default: true]
InstanceLocation	Where is the schema found? [Default: ]

CrystClust

Preferred Extension: crystclust XML Based?: No

CrystClustReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

CrystClustWriter

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	false
ChemSequence	true
Crystal	true

Crystallographic Interchange Format

Preferred Extension: cif MIME type: chemical/x-cif XML Based?: No

CIFReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

GAMESS log file

Extensions: [gam, gamin, inp, gamout] Preferred Extension: gam MIME type: chemical/x-gamess-output XML Based?: No

GamessReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

Gaussian 2003

MIME type: chemical/x-gaussian-log XML Based?: No

Gaussian03Reader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false
ChemSequence	true

Gaussian Input

Extensions: [gau, com] Preferred Extension: gau MIME type: chemical/x-gaussian-input XML Based?: No

GaussianInputWriter

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

This writer has these IO settings:

Name	Desc
OpenShell	Should the calculation be open shell? [Default: false]
Comment	What comment should be put in the file? [Default: Created with CDK (http://cdk.sf.net/)]
Memory	How much memory do you want to use? [Default: unset]
Command	What kind of job do you want to perform? [Default: energy calculation]
ProcessorCount	How many processors should be used by Gaussian? [Default: 1]

Gaussian98

MIME type: chemical/x-gaussian-log XML Based?: No

Gaussian98Reader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

This reader has these IO settings:

Name	Desc
ReadOptimizedStructureOnly	Should I only read the optimized structure from a geometry optimization? [Default: false]

Ghemical Quantum/Molecular Mechanics Model

Preferred Extension: gpr MIME type: application/x-ghemical XML Based?: No

GhemicalMMReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

Ghemical Simplified Protein Model

XML Based?: No

GhemicalMMReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

HyperChem HIN

Preferred Extension: hin MIME type: chemical/x-hin XML Based?: No

HINReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

HINWriter

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true

IUPAC-NIST Chemical Identifier (Plain Text)

MIME type: chemical/x-inchi XML Based?: No

INChIPlainTextReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

IUPAC-NIST Chemical Identifier (XML)

Preferred Extension: inchi MIME type: chemical/x-inchi-xml XML Based?: Yes

INChIReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

MDL Mol/SDF V3000

MIME type: chemical/x-mdl-molfile XML Based?: No

MDLV3000Reader

This reader supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

This reader has these IO settings:

Name	Desc
AddStereo0d	Allow stereo created from parity value when no coordinates [Default: true]
AddStereoElements	Detect and create IStereoElements for the input. [Default: true]
InterpretHydrogenIsotopes	Should D and T be interpreted as hydrogen isotopes? [Default: true]
ForceReadAs3DCoordinates	Should coordinates always be read as 3D? [Default: false]

MDLV3000Writer

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	false

This writer has these IO settings:

Name	Desc
ProgramName	Program name to write at the top of the molfile header, should be exactly 8 characters long [Default: CDK]
writeProperties	Should molecule properties be written as non-structural data [Default: false]
TruncateLongData	Truncate long data files >200 characters [Default: false]

MDL Molfile

Preferred Extension: mol MIME type: chemical/x-mdl-molfile XML Based?: No

MDLReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	true
Crystal	true

This reader has these IO settings:

Name	Desc
ForceReadAs3DCoordinates	Should coordinates always be read as 3D? [Default: false]

MDL Molfile V2000

Preferred Extension: mol MIME type: chemical/x-mdl-molfile XML Based?: No

MDLV2000Reader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	true
Crystal	true

This reader has these IO settings:

Name	Desc
AddStereo0d	Allow stereo created from parity value when no coordinates [Default: true]
AddStereoElements	Detect and create IStereoElements for the input. [Default: true]
InterpretHydrogenIsotopes	Should D and T be interpreted as hydrogen isotopes? [Default: true]
ForceReadAs3DCoordinates	Should coordinates always be read as 3D? [Default: false]

MDLV2000Writer

This writer supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	true
Crystal	true

This writer has these IO settings:

Name	Desc
WriteAromaticBondTypes	Should aromatic bonds be written as bond type 4? [Default: false]
WriteMajorIsotopes	Write atomic mass of any non-null atomic mass including major isotopes (e.g. [12]C) [Default: true]
writeProperties	Should molecule properties be written as non-structural data [Default: false]
WriteQueryFormatValencies	Should valencies be written in the MDL Query format? (deprecated) [Default: false]
TruncateLongData	Truncate long data files >200 characters [Default: false]
ProgramName	Program name to write at the top of the molfile header, should be exactly 8 characters long [Default: CDK]
ForceWriteAs2DCoordinates	Should coordinates always be written as 2D? [Default: false]
WriteDefaultProperties	Write trailing zero's on atom/bond property blocks even if they're not used. [Default: true]

MDL RXN V2000

Preferred Extension: rxn MIME type: chemical/x-mdl-rxnfile XML Based?: No

MDLRXNV2000Reader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false
Reaction	true

MDL RXN V3000

Preferred Extension: rxn MIME type: chemical/x-mdl-rxnfile XML Based?: No

MDLRXNV3000Reader

This reader supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	false
Reaction	true

MDL Reaction format

Preferred Extension: rxn MIME type: chemical/x-mdl-rxnfile XML Based?: No

MDLRXNReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false
Reaction	true
ReactionSet	true

MDL Structure-data file

Extensions: [sdf, sd] Preferred Extension: sdf MIME type: chemical/x-mdl-sdfile XML Based?: No

MDLV2000Reader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	true
Crystal	true

This reader has these IO settings:

Name	Desc
AddStereo0d	Allow stereo created from parity value when no coordinates [Default: true]
AddStereoElements	Detect and create IStereoElements for the input. [Default: true]
InterpretHydrogenIsotopes	Should D and T be interpreted as hydrogen isotopes? [Default: true]
ForceReadAs3DCoordinates	Should coordinates always be read as 3D? [Default: false]

SDFWriter

This writer supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	true
Crystal	true

This writer has these IO settings:

Name	Desc
WriteAromaticBondTypes	Should aromatic bonds be written as bond type 4? [Default: false]
WriteMajorIsotopes	Write atomic mass of any non-null atomic mass including major isotopes (e.g. [12]C) [Default: true]
writeProperties	Should molecule properties be written as non-structural data [Default: true]
WriteQueryFormatValencies	Should valencies be written in the MDL Query format? (deprecated) [Default: false]
TruncateLongData	Truncate long data files >200 characters [Default: false]
ProgramName	Program name to write at the top of the molfile header, should be exactly 8 characters long [Default: CDK]
ForceWriteAs2DCoordinates	Should coordinates always be written as 2D? [Default: false]
WriteDefaultProperties	Write trailing zero's on atom/bond property blocks even if they're not used. [Default: true]
writeV3000	Write all records as V3000 [Default: false]

Mol2 (Sybyl)

Preferred Extension: mol2 MIME type: chemical/x-mol2 XML Based?: No

Mol2Reader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	true
Crystal	true

Mol2Writer

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

PolyMorph Predictor (Cerius)

Preferred Extension: pmp XML Based?: No

PMPReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

Protein Brookhave Database (PDB)

Extensions: [pdb, ent] Preferred Extension: pdb MIME type: chemical/x-pdb XML Based?: No

PDBReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

This reader has these IO settings:

Name	Desc
UseRebondTool	Should the PDBReader deduce bonding patterns? [Default: false]
ReadConnectSection	Should the CONECT be read? [Default: true]
UseHetDictionary	Should the PDBReader use the HETATM dictionary for atom types? [Default: false]

PDBWriter

This writer supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	true
Crystal	true

This writer has these IO settings:

Name	Desc
WriteCONECT	Should the bonds be written as CONECT records? [Default: true]
UseElementSymbolAsAtomName	Should the element symbol be written as the atom name [Default: false]
WriteTER	Should a TER record be put at the end of the atoms? [Default: false]
WriteEND	Should an END record be put at the end of the file? [Default: true]
WriteAsHET	Should the output file use HETATM [Default: false]

PubChem Compound ASN

Preferred Extension: asn XML Based?: No

PCCompoundASNReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

PubChem Compound XML

Preferred Extension: xml XML Based?: Yes

PCCompoundXMLReader

This reader supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

PubChem Substance XML

Preferred Extension: xml XML Based?: Yes

PCSubstanceXMLReader

This reader supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

SMILES

Preferred Extension: smi MIME type: chemical/x-daylight-smiles XML Based?: No

SMILESReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

SMILESWriter

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

This writer has these IO settings:

Name	Desc
SmilesFlavor	Output SMILES flavor, binary option [Default: 230655752]
WriteTitle	Write the molecule title after the SMILES [Default: true]
UseAromaticity	Should aromaticity information be stored in the SMILES? [Default: false]

ShelXL

Extensions: [ins, res] Preferred Extension: ins MIME type: chemical/x-shelx XML Based?: No

ShelXReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false
Crystal	true

ShelXWriter

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	false
Crystal	true

Symyx Rgroup query files

Extensions: [mol, rgp] Preferred Extension: mol XML Based?: No

RGroupQueryReader

This reader supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	false
isomorphism.matchers.RGroupQuery	true

RGroupQueryWriter

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	false
isomorphism.matchers.RGroupQuery	true

VASP

XML Based?: No

VASPReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

XYZ

Preferred Extension: xyz MIME type: chemical/x-xyz XML Based?: No

XYZReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

XYZWriter

This writer supports these data objects:

Class	Accepted
ChemFile	false
AtomContainer	true
Crystal	true

ZMatrix

XML Based?: No

ZMatrixReader

This reader supports these data objects:

Class	Accepted
ChemFile	true
AtomContainer	false

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