| Modifier and Type | Constant Field | Value |
|---|---|---|
protected final int |
electronCount |
0 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
ACDLABS_LABEL |
"cdk:ACDLabsAtomLabel" |
public static final String |
ALL_RINGS |
"cdk:AllRings" |
public static final String |
ANNOTATIONS |
"cdk:Annotations" |
public static final String |
ATOM_ATOM_MAPPING |
"cdk:AtomAtomMapping" |
public static final String |
AUTONOMNAME |
"cdk:AutonomName" |
public static final String |
BEILSTEINRN |
"cdk:BeilsteinRN" |
public static final String |
CASRN |
"cdk:CasRN" |
public static final String |
CHEMICAL_GROUP_CONSTANT |
"cdk:Chemical Group" |
public static final String |
CIP_DESCRIPTOR |
"cip.label" |
public static final String |
COMMENT |
"cdk:Comment" |
public static final String |
CTAB_SGROUPS |
"cdk:CtabSgroups" |
public static final String |
DESCRIPTION |
"cdk:Description" |
public static final int |
DUMMY_POINTER |
1 |
public static final String |
ESSENTIAL_RINGS |
"cdk:EssentialRings" |
public static final String |
FORMULA |
"cdk:Formula" |
public static final int |
HYBRIDIZATION_SP1 |
1 |
public static final int |
HYBRIDIZATION_SP2 |
2 |
public static final int |
HYBRIDIZATION_SP3 |
3 |
public static final int |
HYBRIDIZATION_SP3D1 |
4 |
public static final int |
HYBRIDIZATION_SP3D2 |
5 |
public static final int |
HYBRIDIZATION_SP3D3 |
6 |
public static final int |
HYBRIDIZATION_SP3D4 |
7 |
public static final int |
HYBRIDIZATION_SP3D5 |
8 |
public static final int |
HYBRIDIZATION_UNSET |
0 |
public static final String |
INCHI |
"cdk:InChI" |
public static final int |
IS_HYDROGENBOND_ACCEPTOR |
512 |
public static final int |
IS_HYDROGENBOND_DONOR |
256 |
public static final int |
IS_TYPEABLE |
2048 |
public static final int |
ISALIPHATIC |
8 |
public static final int |
ISAROMATIC |
32 |
public static final int |
ISCONJUGATED |
64 |
public static final int |
ISINRING |
2 |
public static final int |
ISNOTINRING |
4 |
public static final String |
ISOTROPIC_SHIELDING |
"cdk:IsotropicShielding" |
public static final int |
ISPLACED |
1 |
public static final String |
LONE_PAIR_COUNT |
"cdk:Lone Pair Count" |
public static final int |
MAPPED |
128 |
public static final int |
MAX_FLAG_INDEX |
13 |
public static final int |
MAX_POINTER_INDEX |
1 |
public static final String |
NAMES |
"cdk:Names" |
public static final String |
NMRSHIFT_CARBON |
"carbon nmr shift" |
public static final String |
NMRSHIFT_DEUTERIUM |
"deuterium nmr shift" |
public static final String |
NMRSHIFT_FLUORINE |
"fluorine nmr shift" |
public static final String |
NMRSHIFT_HYDROGEN |
"hydrogen nmr shift" |
public static final String |
NMRSHIFT_NITROGEN |
"nitrogen nmr shift" |
public static final String |
NMRSHIFT_PHOSPORUS |
"phosphorus nmr shift" |
public static final String |
NMRSHIFT_SULFUR |
"sulfur nmr shift" |
public static final String |
NMRSIGNAL_INTENSITY |
"nmr signal intensity" |
public static final String |
NMRSIGNAL_MULTIPLICITY |
"nmr signal multiplicity" |
public static final String |
NMRSPECTYPE_1D |
"1D NMR spectrum" |
public static final String |
NMRSPECTYPE_1D_DEPT135 |
"1D NMR spectrum: DEPT135" |
public static final String |
NMRSPECTYPE_1D_DEPT90 |
"1D NMR spectrum: DEPT90" |
public static final String |
NMRSPECTYPE_2D_HHCOSY |
"2D NMR spectrum: HHCOSY" |
public static final String |
NMRSPECTYPE_2D_HMBC |
"2D NMR spectrum: HMBC" |
public static final String |
NMRSPECTYPE_2D_HSQC |
"2D NMR spectrum: HSQC" |
public static final String |
NMRSPECTYPE_2D_INADEQUATE |
"2D NMR spectrum: INADEQUATE" |
public static final String |
PART_OF_RING_OF_SIZE |
"cdk:Part of ring of size" |
public static final String |
PI_BOND_COUNT |
"cdk:Pi Bond Count" |
public static final String |
REACTION_CONDITIONS |
"cdk:ReactionConditions" |
public static final String |
REACTION_GROUP |
"cdk:ReactionGroup" |
public static final String |
REACTION_ROLE |
"cdk:ReactionRole" |
public static final int |
REACTIVE_CENTER |
1024 |
public static final String |
RELEVANT_RINGS |
"cdk:RelevantRings" |
public static final String |
REMARK |
"cdk:Remark" |
public static final String |
REST_H |
"cdk:RestH" |
public static final String |
RING_CONNECTIONS |
"cdk:RingConnections" |
public static final String |
RING_SIZES |
"cdk:RingSizes" |
public static final String |
SINGLE_ELECTRON_COUNT |
"cdk:Single Electron Count" |
public static final int |
SINGLE_OR_DOUBLE |
4096 |
public static final String |
SMALLEST_RINGS |
"cdk:SmallestRings" |
public static final String |
SMILES |
"cdk:SMILES" |
public static final String |
SPHERICAL_MATCHER |
"cdk:HOSE code spherical matcher" |
public static final String |
SPIN_MULTIPLICITY |
"cdk:SpinMultiplicity" |
public static final int |
STEREO_ATOM_PARITY_MINUS |
-1 |
public static final int |
STEREO_ATOM_PARITY_PLUS |
1 |
public static final int |
STEREO_ATOM_PARITY_UNDEFINED |
0 |
public static final String |
TITLE |
"cdk:Title" |
public static final String |
TOTAL_CONNECTIONS |
"cdk:TotalConnections" |
public static final String |
TOTAL_H_COUNT |
"cdk:TotalHydrogenCount" |
public static final int |
VISITED |
16 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected final int |
electronCount |
2 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final double |
BOHR_TO_ANGSTROM |
0.529177249 |
public static final double |
MASS_ELECTRON |
9.109534E-31 |
public static final double |
MASS_PROTON |
1.6726485E-27 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected final int |
electronCount |
1 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
REQUIRE_EXPLICIT_HYDROGENS |
2 |
public static final int |
REQUIRE_NOTHING |
1 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
MMFF_94_CHARGE |
"MMFF94charge" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
ATOMTYPE_ID_JMOL |
"jmol" |
public static final String |
ATOMTYPE_ID_MODELING |
"modeling" |
public static final String |
ATOMTYPE_ID_STRUCTGEN |
"structgen" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected static final double |
DEFAULT_PADDING_FACTOR |
2.0 |
public static final String |
EPS_FMT |
"eps" |
public static final String |
GIF_FMT |
"gif" |
public static final String |
JPG_FMT |
"jpg" |
protected static final double |
MM_TO_POINT |
2.83464566751 |
public static final String |
PDF_FMT |
"pdf" |
public static final String |
PNG_FMT |
"png" |
public static final String |
PS_FMT |
"ps" |
public static final String |
SVG_FMT |
"svg" |
public static final String |
UNITS_MM |
"mm" |
public static final String |
UNITS_PX |
"px" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
DICTREFPROPERTYNAME |
"org.openscience.cdk.dict" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
CLASS_ECFP0 |
1 |
public static final int |
CLASS_ECFP2 |
2 |
public static final int |
CLASS_ECFP4 |
3 |
public static final int |
CLASS_ECFP6 |
4 |
public static final int |
CLASS_FCFP0 |
5 |
public static final int |
CLASS_FCFP2 |
6 |
public static final int |
CLASS_FCFP4 |
7 |
public static final int |
CLASS_FCFP6 |
8 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
DEFAULT_SEARCH_DEPTH |
7 |
public static final int |
DEFAULT_SIZE |
1024 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
FP_SIZE |
881 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
DEFAULT_SIZE |
1024 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
HYDROGEN |
-1 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final boolean |
DEBUG |
false |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
AtomicMass |
8 |
public static final int |
Default |
0 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final byte |
Ac |
89 |
public static final byte |
Ag |
47 |
public static final byte |
Al |
13 |
public static final byte |
Am |
95 |
public static final byte |
Ar |
18 |
public static final byte |
As |
33 |
public static final byte |
At |
85 |
public static final byte |
Au |
79 |
public static final byte |
B |
5 |
public static final byte |
Ba |
56 |
public static final byte |
Be |
4 |
public static final byte |
Bh |
107 |
public static final byte |
Bi |
83 |
public static final byte |
Bk |
97 |
public static final byte |
Br |
35 |
public static final byte |
C |
6 |
public static final byte |
Ca |
20 |
public static final byte |
Cd |
48 |
public static final byte |
Ce |
58 |
public static final byte |
Cf |
98 |
public static final byte |
Cl |
17 |
public static final byte |
Cm |
96 |
public static final byte |
Cn |
112 |
public static final byte |
Co |
27 |
public static final byte |
Cr |
24 |
public static final byte |
Cs |
55 |
public static final byte |
Cu |
29 |
public static final byte |
Db |
105 |
public static final byte |
Ds |
110 |
public static final byte |
Dy |
66 |
public static final byte |
Er |
68 |
public static final byte |
Es |
99 |
public static final byte |
Eu |
63 |
public static final byte |
F |
9 |
public static final byte |
Fe |
26 |
public static final byte |
Fl |
114 |
public static final byte |
Fm |
100 |
public static final byte |
Fr |
87 |
public static final byte |
Ga |
31 |
public static final byte |
Gd |
64 |
public static final byte |
Ge |
32 |
public static final byte |
H |
1 |
public static final byte |
He |
2 |
public static final byte |
Hf |
72 |
public static final byte |
Hg |
80 |
public static final byte |
Ho |
67 |
public static final byte |
Hs |
108 |
public static final byte |
I |
53 |
public static final byte |
In |
49 |
public static final byte |
Ir |
77 |
public static final byte |
K |
19 |
public static final byte |
Kr |
36 |
public static final byte |
La |
57 |
public static final byte |
Li |
3 |
public static final byte |
Lr |
103 |
public static final byte |
Lu |
71 |
public static final byte |
Lv |
116 |
public static final byte |
Mc |
115 |
public static final byte |
Md |
101 |
public static final byte |
Mg |
12 |
public static final byte |
Mn |
25 |
public static final byte |
Mo |
42 |
public static final byte |
Mt |
109 |
public static final byte |
N |
7 |
public static final byte |
Na |
11 |
public static final byte |
Nb |
41 |
public static final byte |
Nd |
60 |
public static final byte |
Ne |
10 |
public static final byte |
Nh |
113 |
public static final byte |
Ni |
28 |
public static final byte |
No |
102 |
public static final byte |
Np |
93 |
public static final byte |
O |
8 |
public static final byte |
Og |
118 |
public static final byte |
Os |
76 |
public static final byte |
P |
15 |
public static final byte |
Pa |
91 |
public static final byte |
Pb |
82 |
public static final byte |
Pd |
46 |
public static final byte |
Pm |
61 |
public static final byte |
Po |
84 |
public static final byte |
Pr |
59 |
public static final byte |
Pt |
78 |
public static final byte |
Pu |
94 |
public static final byte |
Ra |
88 |
public static final byte |
Rb |
37 |
public static final byte |
Re |
75 |
public static final byte |
Rf |
104 |
public static final byte |
Rg |
111 |
public static final byte |
Rh |
45 |
public static final byte |
Rn |
86 |
public static final byte |
Ru |
44 |
public static final byte |
S |
16 |
public static final byte |
Sb |
51 |
public static final byte |
Sc |
21 |
public static final byte |
Se |
34 |
public static final byte |
Sg |
106 |
public static final byte |
Si |
14 |
public static final byte |
Sm |
62 |
public static final byte |
Sn |
50 |
public static final byte |
Sr |
38 |
public static final byte |
Ta |
73 |
public static final byte |
Tb |
65 |
public static final byte |
Tc |
43 |
public static final byte |
Te |
52 |
public static final byte |
Th |
90 |
public static final byte |
Ti |
22 |
public static final byte |
Tl |
81 |
public static final byte |
Tm |
69 |
public static final byte |
Ts |
117 |
public static final byte |
U |
92 |
public static final byte |
V |
23 |
public static final byte |
W |
74 |
public static final byte |
Wildcard |
0 |
public static final byte |
Xe |
54 |
public static final byte |
Y |
39 |
public static final byte |
Yb |
70 |
public static final byte |
Zn |
30 |
public static final byte |
Zr |
40 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
AL |
17152 |
public static final int |
Allenal |
17152 |
public static final int |
AT |
17408 |
public static final int |
Atropisomeric |
17408 |
public static final int |
CFG_MASK |
255 |
public static final int |
CisTrans |
8448 |
public static final int |
CLS_MASK |
65280 |
public static final int |
CT |
8448 |
public static final int |
CU |
8704 |
public static final int |
Cumulene |
8704 |
public static final int |
GRP_ABS |
0 |
public static final int |
GRP_MASK |
16711680 |
public static final int |
GRP_NUM_MASK |
16515072 |
public static final int |
GRP_NUM_SHIFT |
18 |
public static final int |
GRP_RAC |
65536 |
public static final int |
GRP_RAC1 |
327680 |
public static final int |
GRP_RAC2 |
589824 |
public static final int |
GRP_RAC3 |
851968 |
public static final int |
GRP_RAC4 |
1114112 |
public static final int |
GRP_RAC5 |
1376256 |
public static final int |
GRP_REL |
131072 |
public static final int |
GRP_REL1 |
393216 |
public static final int |
GRP_REL2 |
655360 |
public static final int |
GRP_REL3 |
917504 |
public static final int |
GRP_REL4 |
1179648 |
public static final int |
GRP_REL5 |
1441792 |
public static final int |
GRP_TYPE_MASK |
196608 |
public static final int |
HBPY8 |
33024 |
public static final int |
HBPY9 |
37120 |
public static final int |
HeptagonalBipyramidal |
37120 |
public static final int |
HexagonalBipyramidal |
33024 |
public static final int |
LEFT |
1 |
public static final int |
OC |
24832 |
public static final int |
Octahedral |
24832 |
public static final int |
OPPOSITE |
1 |
public static final int |
PBPY |
28928 |
public static final int |
PentagonalBipyramidal |
28928 |
public static final int |
RIGHT |
2 |
public static final int |
SP |
17664 |
public static final int |
SP4 |
17666 |
public static final int |
SPU |
17665 |
public static final int |
SPY |
20736 |
public static final int |
SPZ |
17667 |
public static final int |
SquarePlanar |
17664 |
public static final int |
SquarePyramidal |
20736 |
public static final int |
TBPY |
20992 |
public static final int |
Tetrahedral |
16896 |
public static final int |
TH |
16896 |
public static final int |
TOGETHER |
2 |
public static final int |
TrigonalBipyramidal |
20992 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final boolean |
ANGSTROM_UNIT |
false |
public static final double |
BOHR_TO_ANGSTROM |
0.529177249 |
public static final boolean |
BOHR_UNIT |
true |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
OptWriteAgents |
"WriteAgents" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
OptForceWriteAs2DCoordinates |
"ForceWriteAs2DCoordinates" |
public static final String |
OptProgramName |
"ProgramName" |
public static final String |
OptWriteAromaticBondTypes |
"WriteAromaticBondTypes" |
public static final String |
OptWriteDefaultProperties |
"WriteDefaultProperties" |
public static final String |
OptWriteMajorIsotopes |
"WriteMajorIsotopes" |
public static final String |
OptWriteQueryFormatValencies |
"WriteQueryFormatValencies" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public final String |
ATOM_NAME_FORMAT |
"%-5s" |
public final String |
POSITION_FORMAT |
"%8.3f" |
public final String |
RESIDUE_FORMAT |
"%s" |
public final String |
SERIAL_FORMAT |
"%5d" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
OptAlwaysV3000 |
"writeV3000" |
public static final String |
OptTruncateLongData |
"TruncateLongData" |
public static final String |
OptWriteData |
"writeProperties" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected final String |
SYSTEMID |
"CML-1999-05-15" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
BAD_SMILES_INPUT |
"bad.smiles.input" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
EL_ATOM_CONFORMER |
"PC-Conformer" |
public static final String |
EL_ATOM_CONFORMER_X |
"PC-Conformer_x" |
public static final String |
EL_ATOM_CONFORMER_XE |
"PC-Conformer_x_E" |
public static final String |
EL_ATOM_CONFORMER_Y |
"PC-Conformer_y" |
public static final String |
EL_ATOM_CONFORMER_YE |
"PC-Conformer_y_E" |
public static final String |
EL_ATOM_CONFORMER_Z |
"PC-Conformer_z" |
public static final String |
EL_ATOM_CONFORMER_ZE |
"PC-Conformer_z_E" |
public static final String |
EL_ATOMBLOCK |
"PC-Atoms" |
public static final String |
EL_ATOMINT |
"PC-AtomInt" |
public static final String |
EL_ATOMINT_AID |
"PC-AtomInt_aid" |
public static final String |
EL_ATOMINT_VALUE |
"PC-AtomInt_value" |
public static final String |
EL_ATOMSCHARGE |
"PC-Atoms_charge" |
public static final String |
EL_ATOMSELEMENT |
"PC-Atoms_element" |
public static final String |
EL_BONDBLOCK |
"PC-Bonds" |
public static final String |
EL_BONDID1 |
"PC-Bonds_aid1" |
public static final String |
EL_BONDID2 |
"PC-Bonds_aid2" |
public static final String |
EL_BONDORDER |
"PC-Bonds_order" |
public static final String |
EL_COORDINATES_AID |
"PC-Coordinates_aid" |
public static final String |
EL_COORDINATES_AIDE |
"PC-Coordinates_aid_E" |
public static final String |
EL_COORDINATESBLOCK |
"PC-Compound_coords" |
public static final String |
EL_ELEMENT |
"PC-Element" |
public static final String |
EL_PCCOMPOUND |
"PC-Compound" |
public static final String |
EL_PCCOMPOUND_CID |
"PC-CompoundType_id_cid" |
public static final String |
EL_PCCOMPOUND_ID |
"PC-Compound_id" |
public static final String |
EL_PCCOMPOUNDS |
"PC-Compounds" |
public static final String |
EL_PCID_ID |
"PC-ID_id" |
public static final String |
EL_PCSUBSTANCE |
"PC-Substance" |
public static final String |
EL_PCSUBSTANCE_SID |
"PC-Substance_sid" |
public static final String |
EL_PROPS_BVAL |
"PC-InfoData_value_binary" |
public static final String |
EL_PROPS_FVAL |
"PC-InfoData_value_fval" |
public static final String |
EL_PROPS_INFODATA |
"PC-InfoData" |
public static final String |
EL_PROPS_SVAL |
"PC-InfoData_value_sval" |
public static final String |
EL_PROPS_URNLABEL |
"PC-Urn_label" |
public static final String |
EL_PROPS_URNNAME |
"PC-Urn_name" |
public static final String |
EL_PROPSBLOCK |
"PC-Compound_props" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
UNKNOWN_STEREO |
-1 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
ROOT_LABEL |
"Root structure" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
DEFAULT_OCCURRENCE |
">0" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
ROLE_AGENT |
2 |
public static final int |
ROLE_ANY |
7 |
public static final int |
ROLE_PRODUCT |
4 |
public static final int |
ROLE_REACTANT |
1 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
A |
25 |
public static final int |
ACTINIUM |
69 |
public static final int |
AL |
49 |
public static final int |
ALUMINIUM |
103 |
public static final int |
ALUMINO |
41 |
public static final int |
AMERCIUM |
135 |
public static final int |
AMIDE |
50 |
public static final int |
AMINE |
51 |
public static final int |
AMINO |
40 |
public static final int |
AN |
27 |
public static final int |
ANTIMONY |
111 |
public static final int |
ARSENIC |
110 |
public static final int |
BARIUM |
64 |
public static final int |
BERKELIUM |
137 |
public static final int |
BERYLLIUM |
60 |
public static final int |
BISMUTH |
112 |
public static final int |
BOHRIUM |
85 |
public static final int |
BROMO |
35 |
public static final int |
BUT |
9 |
public static final int |
CADMIUM |
101 |
public static final int |
CALCIUM |
62 |
public static final int |
CALIFORNIUM |
138 |
public static final int |
CERIUM |
116 |
public static final int |
CESIUM |
58 |
public static final int |
CHLORO |
33 |
public static final int |
CHROMIUM |
78 |
public static final int |
COBALT |
90 |
public static final int |
COMMA |
5 |
public static final int |
CONSTANT |
2 |
public static final int |
CONT |
24 |
public static final int |
COPPER |
97 |
public static final int |
COS |
23 |
public static final int |
CURIUM |
136 |
public static final int |
CYCLO |
32 |
public static final int |
DASH |
4 |
public static final int |
DEC |
22 |
public static final int |
DEFAULT |
0 |
public static final int |
DI |
31 |
public static final int |
DIGIT |
3 |
public static final int |
DO |
14 |
public static final int |
DUBNIUM |
77 |
public static final int |
DYSPROSIUM |
124 |
public static final int |
E |
44 |
public static final int |
EICOS |
11 |
public static final int |
EINSTEINIUM |
139 |
public static final int |
EN |
28 |
public static final int |
EOF |
0 |
public static final int |
EOL |
1 |
public static final int |
ERBIUM |
126 |
public static final int |
ETH |
7 |
public static final int |
EUROPIUM |
121 |
public static final int |
FERMIUM |
140 |
public static final int |
FLUORO |
34 |
public static final int |
FRANCIUM |
59 |
public static final int |
GADOLINIUM |
122 |
public static final int |
GALLIUM |
104 |
public static final int |
GERMAINIUM |
107 |
public static final int |
GOLD |
99 |
public static final int |
HAFNIUM |
72 |
public static final int |
HASSIUM |
89 |
public static final int |
HEN |
13 |
public static final int |
HENICOS |
12 |
public static final int |
HEPT |
19 |
public static final int |
HEX |
18 |
public static final int |
HOLMIUM |
125 |
public static final int |
HYDROXY |
43 |
public static final int |
INDIUM |
105 |
public static final int |
IODO |
36 |
public static final int |
IRIDIUM |
92 |
public static final int |
IRON |
86 |
public static final int |
LANTHANUM |
68 |
public static final int |
LAWRENCIUM |
143 |
public static final int |
LEAD |
109 |
public static final int |
LITHIUM |
54 |
public static final int |
LITHO |
42 |
public static final int |
LUTETIUM |
129 |
public static final int |
MAGNESIUM |
61 |
public static final int |
MANGANESE |
82 |
public static final int |
MECURY |
102 |
public static final int |
MEITMERIUM |
93 |
public static final int |
MENDELEVIUM |
141 |
public static final int |
METH |
6 |
public static final int |
MOLYBDENUM |
79 |
public static final int |
NEODYMIUM |
118 |
public static final int |
NEPTUNIUM |
133 |
public static final int |
NICKEL |
94 |
public static final int |
NIOBIUM |
75 |
public static final int |
NITRILE |
48 |
public static final int |
NITRO |
37 |
public static final int |
NOBELIUM |
142 |
public static final int |
NON |
21 |
public static final int |
OATE |
53 |
public static final int |
OCT |
20 |
public static final int |
OICACID |
46 |
public static final int |
OL |
45 |
public static final int |
ONE |
52 |
public static final int |
OSMIUM |
88 |
public static final int |
OXO |
38 |
public static final int |
OYLCHLORIDE |
47 |
public static final int |
PALLADIUM |
95 |
public static final int |
PENT |
17 |
public static final int |
PHENYL |
39 |
public static final int |
PLATINUM |
96 |
public static final int |
PLUTONIUM |
134 |
public static final int |
POLONIUM |
115 |
public static final int |
POTASSIUM |
56 |
public static final int |
PRASEODYMIUM |
117 |
public static final int |
PROMETHIUM |
119 |
public static final int |
PROP |
8 |
public static final int |
PROTACTINIUM |
131 |
public static final int |
RADIUM |
65 |
public static final int |
RHENIUM |
84 |
public static final int |
RHODIUM |
91 |
public static final int |
RUBIDIUM |
57 |
public static final int |
RUTHENIUM |
87 |
public static final int |
RUTHERFORDIUM |
73 |
public static final int |
SANARIUM |
120 |
public static final int |
SCANDIUM |
66 |
public static final int |
SEABORGIUM |
81 |
public static final int |
SELENIUM |
113 |
public static final int |
SILVER |
98 |
public static final int |
SODIUM |
55 |
public static final int |
SPACE |
26 |
public static final int |
STRONTIUM |
63 |
public static final int |
TANTALUM |
76 |
public static final int |
TECHNETIUM |
83 |
public static final int |
TELLURIUM |
114 |
public static final int |
TERBIUM |
123 |
public static final int |
TETR |
16 |
public static final int |
THALLIUM |
106 |
public static final int |
THORIUM |
130 |
public static final int |
THULIUM |
127 |
public static final int |
TIN |
108 |
public static final int |
TITANIUM |
70 |
public static final int |
TRI |
15 |
public static final int |
TUNGSTEN |
80 |
public static final int |
UNDEC |
10 |
public static final int |
URANIUM |
132 |
public static final int |
VANADIUM |
74 |
public static final int |
YL |
30 |
public static final int |
YN |
29 |
public static final int |
YTTERBIUM |
128 |
public static final int |
YTTRIUM |
67 |
public static final int |
ZINC |
100 |
public static final int |
ZIRCONIUM |
71 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final boolean |
staticFlag |
false |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final boolean |
debug |
true |
public static final String |
PRIORITY |
"Weight" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
NS_CML |
"http://www.xml-cml.org/schema" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
URI |
"http://cdk.sourceforge.net/model.owl#" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final double |
DEFAULT_BOND_LENGTH_H |
1.0 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
TEMPLATE_PATH |
"data/ringTemplateStructures.sdf.gz" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
HELIX |
"helix" |
public static final String |
SHEET |
"sheet" |
public static final String |
TURN |
"turn" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
CHECK_RING_SYSTEM |
"checkRingSystem" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
MDEC11 |
0 |
public static final int |
MDEC12 |
1 |
public static final int |
MDEC13 |
2 |
public static final int |
MDEC14 |
3 |
public static final int |
MDEC22 |
4 |
public static final int |
MDEC23 |
5 |
public static final int |
MDEC24 |
6 |
public static final int |
MDEC33 |
7 |
public static final int |
MDEC34 |
8 |
public static final int |
MDEC44 |
9 |
public static final int |
MDEN11 |
13 |
public static final int |
MDEN12 |
14 |
public static final int |
MDEN13 |
15 |
public static final int |
MDEN22 |
16 |
public static final int |
MDEN23 |
17 |
public static final int |
MDEN33 |
18 |
public static final int |
MDEO11 |
10 |
public static final int |
MDEO12 |
11 |
public static final int |
MDEO22 |
12 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final double |
DEFAULT_SCALE |
30.0 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
BELOWAREA |
1 |
public static final int |
NORMAL |
0 |
public static final int |
OVERAREA |
2 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
WIND_EVEN_ODD |
0 |
public static final int |
WIND_NON_ZERO |
1 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
ID_MAP |
"cdk.highlight.id" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
ANNOTATION_LABEL |
"stdgen.annotation.label" |
public static final String |
HIDDEN |
"stdgen.hidden" |
public static final String |
HIDDEN_FULLY |
"stdgen.hidden.fully" |
public static final String |
HIGHLIGHT_COLOR |
"stdgen.highlight.color" |
public static final String |
ITALIC_DISPLAY_PREFIX |
"std.itl:" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final boolean |
debug |
false |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected final int |
electronCount |
2 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
HELIX |
"helix" |
public static final String |
SHEET |
"sheet" |
public static final String |
TURN |
"turn" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
LARGE_FIRST |
1 |
public static final int |
SMALL_FIRST |
2 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected final int |
electronCount |
1 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
FLAVOR_CACTVS |
4 |
public static final int |
FLAVOR_CDK |
1 |
public static final int |
FLAVOR_CDK_LEGACY |
64 |
public static final int |
FLAVOR_DAYLIGHT |
2 |
public static final int |
FLAVOR_LOOSE |
1 |
public static final int |
FLAVOR_MOE |
8 |
public static final int |
FLAVOR_OECHEM |
16 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
MODE_EXACT |
2 |
public static final int |
MODE_JCOMPOUNDMAPPER |
1 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
CANONICAL_LABEL |
"CanonicalLabel" |
public static final String |
INVARIANCE_PAIR |
"InvariancePair" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
Absolute |
1801 |
public static final int |
AtomAtomMap |
4 |
public static final int |
AtomAtomMapRenumber |
33554437 |
public static final int |
AtomicMass |
8 |
public static final int |
AtomicMassStrict |
2048 |
public static final int |
Canonical |
1 |
public static final int |
Cx2dCoordinates |
4096 |
public static final int |
Cx3dCoordinates |
8192 |
public static final int |
CxAtomLabel |
32768 |
public static final int |
CxAtomValue |
65536 |
public static final int |
CxCoordinates |
12288 |
public static final int |
CxDataSgroups |
4194304 |
public static final int |
CxEnhancedStereo |
8388864 |
public static final int |
CxFragmentGroup |
1048576 |
public static final int |
CxLigandOrder |
2097152 |
public static final int |
CxMulticenter |
262144 |
public static final int |
CxPolymer |
524288 |
public static final int |
CxRadical |
131072 |
public static final int |
CxSmiles |
12550400 |
public static final int |
CxSmilesWithCoords |
12562688 |
public static final int |
Default |
12551944 |
public static final int |
Generic |
0 |
public static final int |
InChILabelling |
3 |
public static final int |
Isomeric |
1800 |
public static final int |
Stereo |
1792 |
public static final int |
StereoCisTrans |
512 |
public static final int |
StereoExCisTrans |
1280 |
public static final int |
StereoExTetrahedral |
1024 |
public static final int |
StereoTetrahedral |
256 |
public static final int |
Unique |
1 |
public static final int |
UniversalSmiles |
1803 |
public static final int |
UseAromaticSymbols |
16 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final boolean |
staticFlag |
false |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
a |
34 |
public static final int |
A |
35 |
public static final int |
AC |
117 |
public static final int |
AG |
90 |
public static final int |
AL |
61 |
public static final int |
AM |
122 |
public static final int |
ANY_BOND |
14 |
public static final int |
AR |
63 |
public static final int |
AR_BOND |
13 |
public static final int |
as |
21 |
public static final int |
AS |
77 |
public static final int |
AT |
113 |
public static final int |
ATOM_EXPRESSION |
0 |
public static final int |
AU |
107 |
public static final int |
B |
23 |
public static final int |
BA |
98 |
public static final int |
BE |
57 |
public static final int |
BI |
111 |
public static final int |
BK |
124 |
public static final int |
BR |
31 |
public static final int |
c |
16 |
public static final int |
C |
24 |
public static final int |
CA |
65 |
public static final int |
CARET |
36 |
public static final int |
CD |
91 |
public static final int |
CE |
132 |
public static final int |
CF |
125 |
public static final int |
CL |
30 |
public static final int |
CM |
123 |
public static final int |
CO |
71 |
public static final int |
CR |
68 |
public static final int |
CS |
97 |
public static final int |
CU |
73 |
public static final int |
D |
46 |
public static final int |
D_BOND |
11 |
public static final int |
DEFAULT |
1 |
public static final int |
DIGIT |
38 |
public static final int |
DN_OR_UNSPECIFIED_S_BOND |
10 |
public static final int |
DN_S_BOND |
8 |
public static final int |
DOLLAR |
43 |
public static final int |
DY |
139 |
public static final int |
EOF |
0 |
public static final int |
ER |
141 |
public static final int |
ES |
126 |
public static final int |
EU |
136 |
public static final int |
F |
27 |
public static final int |
FE |
70 |
public static final int |
FM |
127 |
public static final int |
FR |
115 |
public static final int |
G |
52 |
public static final int |
GA |
75 |
public static final int |
GD |
137 |
public static final int |
GE |
76 |
public static final int |
h |
45 |
public static final int |
H |
54 |
public static final int |
H_AND |
3 |
public static final int |
HE |
55 |
public static final int |
HF |
100 |
public static final int |
HG |
108 |
public static final int |
HO |
140 |
public static final int |
HX |
53 |
public static final int |
I |
32 |
public static final int |
IN |
92 |
public static final int |
IR |
105 |
public static final int |
K |
64 |
public static final int |
KR |
79 |
public static final int |
L_AND |
2 |
public static final int |
L_BRACKET |
39 |
public static final int |
L_PAREN |
40 |
public static final int |
LA |
99 |
public static final int |
LI |
56 |
public static final int |
LR |
130 |
public static final int |
LU |
144 |
public static final int |
MD |
128 |
public static final int |
MG |
60 |
public static final int |
MN |
69 |
public static final int |
MO |
85 |
public static final int |
n |
17 |
public static final int |
N |
25 |
public static final int |
NA |
59 |
public static final int |
NB |
84 |
public static final int |
ND |
133 |
public static final int |
NE |
58 |
public static final int |
NI |
72 |
public static final int |
NO |
129 |
public static final int |
NOT |
5 |
public static final int |
NP |
131 |
public static final int |
o |
18 |
public static final int |
O |
26 |
public static final int |
OR |
4 |
public static final int |
OS |
104 |
public static final int |
p |
20 |
public static final int |
P |
28 |
public static final int |
PA |
119 |
public static final int |
PB |
110 |
public static final int |
PD |
89 |
public static final int |
PLUS |
44 |
public static final int |
PM |
134 |
public static final int |
PO |
112 |
public static final int |
PR |
145 |
public static final int |
PT |
106 |
public static final int |
PU |
121 |
public static final int |
Q_MARK |
37 |
public static final int |
r |
48 |
public static final int |
R |
47 |
public static final int |
R_BOND |
15 |
public static final int |
R_BRACKET |
42 |
public static final int |
R_PAREN |
41 |
public static final int |
RA |
116 |
public static final int |
RB |
80 |
public static final int |
RE |
103 |
public static final int |
RH |
88 |
public static final int |
RN |
114 |
public static final int |
RU |
87 |
public static final int |
s |
19 |
public static final int |
S |
29 |
public static final int |
S_BOND |
6 |
public static final int |
SB |
94 |
public static final int |
SC |
146 |
public static final int |
se |
22 |
public static final int |
SE |
78 |
public static final int |
SI |
62 |
public static final int |
SM |
135 |
public static final int |
SN |
93 |
public static final int |
SR |
81 |
public static final int |
T_BOND |
12 |
public static final int |
TA |
101 |
public static final int |
TB |
138 |
public static final int |
TC |
86 |
public static final int |
TE |
95 |
public static final int |
TH |
118 |
public static final int |
TI |
66 |
public static final int |
TL |
109 |
public static final int |
TM |
142 |
public static final int |
U |
120 |
public static final int |
UP_OR_UNSPECIFIED_S_BOND |
9 |
public static final int |
UP_S_BOND |
7 |
public static final int |
v |
49 |
public static final int |
V |
67 |
public static final int |
W |
102 |
public static final int |
WILDCARD |
33 |
public static final int |
WS |
1 |
public static final int |
x |
51 |
public static final int |
X |
50 |
public static final int |
XE |
96 |
public static final int |
Y |
82 |
public static final int |
YB |
143 |
public static final int |
ZN |
74 |
public static final int |
ZR |
83 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
JJTALIPHATIC |
31 |
public static final int |
JJTANYATOM |
34 |
public static final int |
JJTAROMATIC |
33 |
public static final int |
JJTATOM |
4 |
public static final int |
JJTATOMICMASS |
35 |
public static final int |
JJTATOMICNUMBER |
22 |
public static final int |
JJTCHARGE |
24 |
public static final int |
JJTCHIRALITY |
37 |
public static final int |
JJTELEMENT |
38 |
public static final int |
JJTEXPLICITATOM |
11 |
public static final int |
JJTEXPLICITCONNECTIVITY |
21 |
public static final int |
JJTEXPLICITHIGHANDBOND |
7 |
public static final int |
JJTEXPLICITHIGHANDEXPRESSION |
14 |
public static final int |
JJTGROUP |
2 |
public static final int |
JJTHYBRDIZATIONNUMBER |
23 |
public static final int |
JJTIMPLICITHCOUNT |
20 |
public static final int |
JJTIMPLICITHIGHANDBOND |
8 |
public static final int |
JJTIMPLICITHIGHANDEXPRESSION |
15 |
public static final int |
JJTLOWANDBOND |
5 |
public static final int |
JJTLOWANDEXPRESSION |
12 |
public static final int |
JJTNONCHHEAVYATOM |
32 |
public static final int |
JJTNOTBOND |
9 |
public static final int |
JJTNOTEXPRESSION |
16 |
public static final int |
JJTORBOND |
6 |
public static final int |
JJTOREXPRESSION |
13 |
public static final int |
JJTPERIODICGROUPNUMBER |
26 |
public static final int |
JJTREACTION |
1 |
public static final int |
JJTRECURSIVESMARTSEXPRESSION |
17 |
public static final int |
JJTRINGCONNECTIVITY |
25 |
public static final int |
JJTRINGIDENTIFIER |
36 |
public static final int |
JJTRINGMEMBERSHIP |
29 |
public static final int |
JJTSIMPLEBOND |
10 |
public static final int |
JJTSMALLESTRINGSIZE |
30 |
public static final int |
JJTSMARTS |
3 |
public static final int |
JJTSTART |
0 |
public static final int |
JJTTOTALCONNECTIVITY |
27 |
public static final int |
JJTTOTALHCOUNT |
19 |
public static final int |
JJTVALENCE |
28 |
public static final int |
JJTVOID |
18 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected static final int |
A |
0 |
protected static final int |
B |
1 |
protected static final int |
C |
2 |
protected static final int |
D |
3 |
protected static final int |
E |
4 |
protected static final int |
F |
5 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected static final int |
A |
0 |
protected static final int |
B |
1 |
protected static final int |
C |
2 |
protected static final int |
D |
3 |
protected static final int |
E |
4 |
protected static final int |
F |
5 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected static final int |
A |
0 |
protected static final int |
B |
1 |
protected static final int |
C |
2 |
protected static final int |
D |
3 |
protected static final int |
E |
4 |
protected static final int |
F |
5 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected static final int |
A |
0 |
protected static final int |
B |
1 |
protected static final int |
C |
2 |
protected static final int |
D |
3 |
protected static final int |
E |
4 |
protected static final int |
F |
5 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected static final int |
A |
0 |
protected static final int |
B |
1 |
protected static final int |
C |
2 |
protected static final int |
D |
3 |
protected static final int |
E |
4 |
protected static final int |
F |
5 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected static final int |
A |
0 |
protected static final int |
B |
1 |
protected static final int |
C |
2 |
protected static final int |
D |
3 |
protected static final int |
E |
4 |
protected static final int |
F |
5 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final double |
MAX_AXIS_ANGLE |
0.95 |
public static final double |
MIN_COLINEAR_NORMAL |
0.05 |
public static final double |
PLANE_TOLERANCE |
0.05 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected static final int |
A |
0 |
protected static final int |
B |
1 |
protected static final int |
C |
2 |
protected static final int |
D |
3 |
protected static final int |
E |
4 |
protected static final int |
F |
5 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
protected static final int |
A |
0 |
protected static final int |
B |
1 |
protected static final int |
C |
2 |
protected static final int |
D |
3 |
protected static final int |
E |
4 |
protected static final int |
F |
5 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
SPLIT_MODE_BREADTH_FIRST |
2 |
public static final int |
SPLIT_MODE_DEPTH_FIRST |
1 |
public static final int |
SPLIT_MODE_RADNDOM |
0 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
KETO_ENOL |
1 |
public static final int |
ONE_FIVE_SHIFT |
2 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
ID |
"id" |
public static final String |
NO_ATOMS |
"noOfAtoms" |
public static final String |
NO_BONDS |
"noOfBonds" |
public static final String |
RESIDUE_NAME |
"residueName" |
public static final String |
RESIDUE_NAME_SHORT |
"residueNameShort" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
BENZENE_RING |
5 |
public static final int |
FURAN_RING |
6 |
public static final int |
PYRIDINE_RING |
10 |
public static final int |
PYRIMIDINE_RING |
12 |
public static final int |
PYROLE_RING |
4 |
public static final int |
THIOPHENE_RING |
8 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
HAS_2D_COORDINATES |
1 |
public static final int |
HAS_3D_COORDINATES |
2 |
public static final int |
HAS_ATOM_ELEMENT_SYMBOL |
8 |
public static final int |
HAS_ATOM_FORMAL_CHARGES |
32 |
public static final int |
HAS_ATOM_HYBRIDIZATIONS |
64 |
public static final int |
HAS_ATOM_ISOTOPE_NUMBERS |
256 |
public static final int |
HAS_ATOM_MASS_NUMBERS |
128 |
public static final int |
HAS_ATOM_PARTIAL_CHARGES |
16 |
public static final int |
HAS_DIETZ_REPRESENTATION |
1024 |
public static final int |
HAS_FRACTIONAL_CRYSTAL_COORDINATES |
4 |
public static final int |
HAS_GRAPH_REPRESENTATION |
512 |
public static final int |
HAS_REACTIONS |
4096 |
public static final int |
HAS_UNITCELL_PARAMETERS |
2048 |
public static final int |
NONE |
0 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
OBJECT_UNIQUE_POLICY |
1 |
public static final int |
SET_UNIQUE_POLICY |
0 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
DEBUG |
1 |
public static final int |
DEFAULT_STACK_LENGTH |
5 |
public static final int |
ERROR |
4 |
public static final int |
FATAL |
5 |
public static final int |
INFO |
2 |
public static final int |
TRACE |
0 |
public static final int |
WARN |
3 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public final int |
DEFAULT_STACK_LENGTH |
5 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
DEFAULT_LOGGING_TOOL_CLASS |
"org.openscience.cdk.tools.LoggingTool" |
public static final String |
STDOUT_LOGGING_TOOL_CLASS |
"org.openscience.cdk.tools.SystemOutLoggingTool" |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final boolean |
debug |
false |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
MolWeight |
1 |
public static final int |
MolWeightIgnoreSpecified |
2 |
public static final int |
MonoIsotopic |
3 |
public static final int |
MostAbundant |
4 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
MolWeight |
1 |
public static final int |
MolWeightIgnoreSpecified |
2 |
public static final int |
MonoIsotopic |
3 |
public static final int |
MostAbundant |
4 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final int |
LARGE_FIRST |
1 |
public static final int |
SMALL_FIRST |
2 |
| Modifier and Type | Constant Field | Value |
|---|---|---|
public static final String |
ERROR_MARKER |
"org.openscience.cdk.validate.error" |
public static final String |
WARNING_MARKER |
"org.openscience.cdk.validate.warning" |
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