cdkbook

File Formats

This appendix lists of file formats the CDK knows about. For each format, it indicated if the CDK has a reader (R) and/or a writer (W) for it. It also indicates which formats can be detected from the file content. Chemical file format definitions implementations in the CDK implement the IChemFormatMatcher class for that.

This script was used to create this list:

Script 24.1 code/ListAllFileFormats.groovy

formats = new ArrayList<IChemFormat>();
reader =
  this.getClass().getClassLoader().getResourceAsStream(
    "io-formats.set"
  )
reader.eachLine { formatName ->
  try {
    Class<? extends Object> formatClass =
      this.getClass().getClassLoader().
        loadClass(formatName);
    Method getinstanceMethod =
      formatClass.getMethod(
        "getInstance", new Class[0]
      );
    format = getinstanceMethod.invoke(
      null, new Object[0]
    );
    formats.add(format);
  } catch (ClassNotFoundException exception) {
  } catch (Exception exception) {
  }
}
formats.sort{ it.formatName }
for (format in formats) {
  if (format instanceof IChemFormat &&
      format.getReaderClassName() != null) {
    output.append("R");
  }
  if (format instanceof IChemFormat &&
      format.getWriterClassName() != null) {
    output.append("W");
  }
  if (format instanceof IChemFormatMatcher) {
    output.append("M");
  }
  output.append(format.getFormatName())
}

Read/Write	Matcher	File Format
	M	ABINIT
	M	ADF
	M	Aces2
		Alchemy
		Ball and Stick
	M	CAChe MolStruct
RW	M	CDK OWL (N3)
W		CDK Source Code
W		CML enriched RSS
R	M	CTX
		Cacao Cartesian
		Cacao Internal
		Chem3D Cartesian 1
		Chem3D Cartesian 2
		ChemDraw eXchange file
RW	M	Chemical Markup Language
		Chemical Resource Kit 2D
		Chemical Resource Kit 3D
		Chemtool
RW	M	CrystClust
R	M	Crystallographic Interchange Format
		DMol3
	M	Dalton
		Dock 5 Box
		Fenske-Hall Z-Matrix
		Fingerprint
R	M	GAMESS log file
		GROMOS96
R	M	Gaussian 2003
W		Gaussian Input
	M	Gaussian90
	M	Gaussian92
	M	Gaussian94
	M	Gaussian95
R	M	Gaussian98
R	M	Ghemical Quantum/Molecular Mechanics Model
R	M	Ghemical Simplified Protein Model
RW	M	HyperChem HIN
R	M	IUPAC-NIST Chemical Identifier (Plain Text)
R	M	IUPAC-NIST Chemical Identifier (XML)
		JME
	M	Jaguar
R	M	MDL Mol/SDF V3000
R	M	MDL Molfile
RW	M	MDL Molfile V2000
R	M	MDL RXN V2000
R	M	MDL RXN V3000
R	M	MDL Reaction format
RW	M	MDL Structure-data file
	M	MOPAC 2002
	M	MOPAC 2007
	M	MOPAC 2009
	M	MOPAC 2012
	M	MOPAC 93
	M	MOPAC 97
	M	MOPAC7
	M	MOPAC7 Input
		MSI BGF
		MacroModel
		MacroModel
		Massively Parallel Quantum Chemistry Program
	M	MoSS Output Format
RW	M	Mol2 (Sybyl)
	M	NWChem
		PCModel
		POV Ray
		Parallel Quantum Solutions
R	M	PolyMorph Predictor (Cerius)
RW	M	Protein Brookhave Database (PDB)
		Protein Data Bank Markup Language (PDBML)
		PubChem
R	M	PubChem Compound ASN
R	M	PubChem Compound XML
	M	PubChem Compounds XML
R	M	PubChem Substance XML
	M	PubChem Substances ASN
	M	PubChem Substances XML
	M	Q-Chem
		Raw Copy
		SMARTS
RW		SMILES
		SMILES FIX
		Scalable Vector Graphics
RW	M	ShelXL
	M	Spartan Quantum Mechanics Program
		Sybyl descriptor
RW	M	Symyx Rgroup query files
		Tinker MM2
		Tinker XYZ
		TurboMole
		UniChemXYZ
R	M	VASP
		Viewmol
		XED
RW		XYZ
		Yasara
R	M	ZMatrix
		Zindo

The Readers and Writers

Additionally, for all formats we can list information about the readers and writers, again by iterating over all formats:

Script 24.2 code/ListAllIOClassesByFormat.groovy

for (format in formats) {
  if (format instanceof IChemFormat &&
      (format.getReaderClassName() != null ||
       format.getWriterClassName() != null)) {
    output.append(
      "## " + format.formatName + "\n"
    )
    // output some further format details
    if (format.readerClassName != null) {
      reader = format.readerClassName.substring(
        format.readerClassName.lastIndexOf(".") + 1
      )
      output.append(
        "### <topic type=\"class\">" + reader + "</topic>\n"
      )
    }
    if (format.writerClassName != null) {
      writer = format.writerClassName.substring(
        format.writerClassName.lastIndexOf(".") + 1
      )
      output.append(
        "### <topic type=\"class\">" + writer + "</topic>\n"
      )
    }
  }
}

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]

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
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]
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]
WriteDefaultProperties	Write trailing zero's on atom/bond property blocks even if they're not used. [Default: true]
WriteQueryFormatValencies	Should valencies be written in the MDL Query format? (deprecated) [Default: false]

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: 12551944]
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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