2D coordinates atomsbonds missing
3D coordinates atomsbonds
adjacency matrix graph
anti-clockwise stereo
aromaticity properties
ASN.1 io
atomic number atomsbonds missing
atom types atomtype
background color depiction
benzene atomsbonds
boiling points cheminfo
bond orders missing
Cambridge Structural Database cheminfo
canonicalization graph
canonical SMILES graph
CAS cheminfo
CASE cheminfo
CDK-JChemPaint depiction
CDKOWLReader ioclasseslist
CDKOWLWriter ioclasseslist
CDKSourceCodeWriter ioclasseslist
Chemical Abstracts Service cheminfo
chemical format io
chemical graph cheminfo
cheminformatics cheminfo
chemometrics cheminfo
chiral atom stereo
CIFReader ioclasseslist
classification methods cheminfo
clockwise stereo
closures writingApps
CMLReader ioclasseslist
CMLWriter ioclasseslist
collinearity cheminfo
complexity cheminfo cheminfo
computer-aided structure elucidation cheminfo
conformations stereo
connected atoms atomsbonds
connected bonds atomsbonds
connectivity layer inchi
coordinates missing
covalent radii missing
covalent radius missing
crambin protein
crystal salts
CrystClustReader ioclasseslist
CrystClustWriter ioclasseslist
CSD cheminfo
CTXReader ioclasseslist
databases cheminfo
DNA protein
ECFP substructure
electronegativity missing
electrons atomsbonds
ethanol atomsbonds
exception descriptor
explicit hydrogens missing
FCFP substructure
ferrocene} cheminfo
Figueras algorithm graph
FixedH option inchi
fixed hydrogen layer inchi
flags atomsbonds
Floyd’s algorithm graph
force field cheminfo
GamessReader ioclasseslist
Gaussian03Reader ioclasseslist
Gaussian98Reader ioclasseslist
Gaussian input file io
GaussianInputWriter ioclasseslist
geometry stereo
GhemicalMMReader ioclasseslist ioclasseslist
graph graph
graph matrices graph
graph theory cheminfo
Groovy writingApps
group missing
gzip io
heavy atoms ctr
HINReader ioclasseslist
HINWriter ioclasseslist
hybridization atomtype
IAtom atomsbonds atomsbonds
IAtomType atomsbonds
IBond atomsbonds
ICrystal salts
identifiers atomsbonds
IElectronContainer atomsbonds unpairedelectrons
IElement atomsbonds
IIsotope atomsbonds
implicit hydrogens missing properties
InChI atom numbers graph
InChI graph inchi
INChIPlainTextReader ioclasseslist
INChIReader ioclasseslist
isomeric SMILES io
IUPAC name cheminfo
Java application writingApps
javac writingApps
JChemPaint depiction
JNI-InChI inchi
line notation io
line notations cheminfo
LogP properties
lone pairs unpairedelectrons
MDLReader ioclasseslist
MDL RXN reaction
MDLRXNReader ioclasseslist
MDLRXNV2000Reader ioclasseslist
MDLRXNV3000Reader ioclasseslist
MDL SD files io
MDLV2000Reader ioclasseslist ioclasseslist
MDLV2000Writer ioclasseslist
MDLV3000Reader ioclasseslist
metabolomics missing
missing hydrogens missing
Mol2Reader ioclasseslist
Mol2Writer ioclasseslist
molecular descriptors cheminfo descriptor
molecular fingerprints substructure
molecular formula atomsbonds missing
molecular mass properties
molecular volume properties
molecule atomsbonds
moment of inertia descriptor
monoisotopic mass missing
Morgan atom numbers graph
multivariate regression cheminfo
notional coordinates atomsbonds
numerical representations cheminfo
OpenSMILES io
parameters descriptor
partial least squares cheminfo
partition coefficient properties
partitioning graph
PCA cheminfo
PCCompoundASNReader ioclasseslist
PCCompoundXMLReader ioclasseslist
PCSubstanceXMLReader ioclasseslist
PDB files protein
PDB io
PDBReader ioclasseslist
PDBWriter ioclasseslist
periodic table missing
period missing
PLS cheminfo
PMPReader ioclasseslist
PNG depiction
principal component analysis cheminfo
products reaction
properties atomsbonds
protein protein
PubChem io
QSAR cheminfo descriptor
QSPR cheminfo
quantum chemical descriptors cheminfo
quantum chemistry cheminfo
radical unpairedelectrons
reactants reaction
reaction reaction
rendering depiction
RGroupQueryReader ioclasseslist
RGroupQueryWriter ioclasseslist
ring bonds graph
ring detection graph
rings graph
RssWriter ioclasseslist
salt salts
SDFWriter ioclasseslist
sequence protein
ShelXReader ioclasseslist
ShelXWriter ioclasseslist
Smallest Set of Smallest Rings graph
SMILES cheminfo io migration
SMILESReader ioclasseslist
SMILESWriter ioclasseslist
SNon option inchi
spanning tree graph
specification descriptor
SSSR graph
Standard InChI inchi inchi
statistical methods cheminfo
stereochemistry inchi
stereoisomerism inchi
superimpose stereo
Sybyl atom type atomtype
Sybyl Line Notation io
symbol missing
tautomerism inchi inchi
tetrahedral chirality stereo
torsion cheminfo
Total Polar Surface Area properties
TPSA properties
unique identifier inchi
unit cell atomsbonds
unpaired electron unpairedelectrons
van der Waals radius missing
van der waals volume properties
VASPReader ioclasseslist
water unpairedelectrons
wedge bonds stereo
Wiswesser Line Notation cheminfo io
XLogP properties
XYZReader ioclasseslist
XYZWriter ioclasseslist
ZMatrixReader ioclasseslist