chemaxon.calculations.*

  • chemaxon.calculations.dipole.DipoleResult
    Modifier and Type
    Constant Field
    Value
    protected static final double
    0.20822678
  • chemaxon.calculations.stereo.Stereochemistry
    Modifier and Type
    Constant Field
    Value
    public static final int
    2
    public static final int
    1

chemaxon.checkers.*

chemaxon.core.*

  • chemaxon.core.ChemConst
    Modifier and Type
    Constant Field
    Value
    public static final int
    89
    public static final int
    47
    public static final int
    13
    public static final int
    95
    public static final int
    18
    public static final int
    33
    public static final int
    85
    public static final int
    79
    public static final int
    5
    public static final int
    56
    public static final int
    4
    public static final int
    107
    public static final int
    83
    public static final int
    97
    public static final int
    35
    public static final int
    6
    public static final int
    20
    public static final int
    48
    public static final int
    58
    public static final int
    98
    public static final int
    17
    public static final int
    96
    public static final int
    112
    public static final int
    27
    public static final int
    24
    public static final int
    55
    public static final int
    29
    public static final int
    105
    public static final int
    110
    public static final int
    66
    public static final int
    118
    public static final int
    68
    public static final int
    99
    public static final int
    63
    public static final int
    9
    public static final int
    26
    public static final int
    114
    public static final int
    100
    public static final int
    87
    public static final int
    31
    public static final int
    64
    public static final int
    32
    public static final int
    1
    public static final int
    2
    public static final int
    72
    public static final int
    80
    public static final int
    67
    public static final int
    108
    public static final int
    53
    public static final int
    49
    public static final int
    77
    public static final int
    19
    public static final int
    36
    public static final int
    57
    public static final int
    3
    public static final int
    103
    public static final int
    71
    public static final int
    116
    public static final int
    115
    public static final int
    101
    public static final int
    12
    public static final int
    25
    public static final int
    42
    public static final int
    109
    public static final int
    7
    public static final int
    11
    public static final int
    41
    public static final int
    60
    public static final int
    10
    public static final int
    113
    public static final int
    28
    public static final int
    102
    public static final int
    93
    public static final int
    8
    public static final int
    118
    public static final int
    76
    public static final int
    15
    public static final int
    91
    public static final int
    82
    public static final int
    46
    public static final int
    61
    public static final int
    84
    public static final int
    59
    public static final int
    78
    public static final int
    94
    public static final int
    88
    public static final int
    37
    public static final int
    75
    public static final int
    104
    public static final int
    111
    public static final int
    45
    public static final int
    86
    public static final int
    44
    public static final int
    16
    public static final int
    51
    public static final int
    21
    public static final int
    34
    public static final int
    106
    public static final int
    14
    public static final int
    62
    public static final int
    50
    public static final int
    38
    public static final int
    73
    public static final int
    65
    public static final int
    43
    public static final int
    52
    public static final int
    90
    public static final int
    22
    public static final int
    81
    public static final int
    69
    public static final int
    117
    public static final int
    92
    public static final int
    23
    public static final int
    74
    public static final int
    54
    public static final int
    39
    public static final int
    70
    public static final int
    30
    public static final int
    40
  • chemaxon.core.util.BondTable
    Modifier and Type
    Constant Field
    Value
    public static final int
    -1

chemaxon.descriptors.*

  • chemaxon.descriptors.CDParameters
    Modifier and Type
    Constant Field
    Value
    public static final int
    0
    public static final int
    2
    public static final int
    1
  • chemaxon.descriptors.CFParameters
    Modifier and Type
    Constant Field
    Value
    public static final int
    2
    public static final int
    7
    public static final int
    1024
  • chemaxon.descriptors.ECFPParameters
    Modifier and Type
    Constant Field
    Value
    public static final int
    4
    public static final int
    1024
  • chemaxon.descriptors.MDParameters
    Modifier and Type
    Constant Field
    Value
    public static final float
    0.0f
    public static final int
    2
    public static final float
    1.0f
    public static final float
    1.0f
  • chemaxon.descriptors.MetricsType
    Modifier and Type
    Constant Field
    Value
    public static final String
    ":"
  • chemaxon.descriptors.PFParameters
    Modifier and Type
    Constant Field
    Value
    public static final float
    1.0f
    public static final float
    10.0f
    public static final int
    1
    public static final int
    1
    public static final String
    "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<!-- Pharmacophore configuration file -->\n<PharmacophoreFingerprintConfiguration Version =\"0.3\" schemaLocation=\"pharmacophores.xsd\">\n <PharmacophoreDefinition>\n <Search StereoCareChecking=\"false\"/>\n <Mols>\n <Mol ID=\"pos\" Structure=\"[*+]\"/>\n <Mol ID=\"nitro\" Structure=\"[O:2]~[N:1]=[O:3]\"/>\n <Mol ID=\"amine\" Structure=\"C[N:1]\"/>\n <Mol ID=\"tertamine\" Structure=\"C[N:1](C)C\"/>\n <Mol ID=\"aniline\" Structure=\"c[N:1]\"/>\n <Mol ID=\"amide\" Structure=\"[#7:1][C,P,S:2]=O\"/>\n <Mol ID=\"hydrazine\" Structure=\"NN\"/>\n <Mol ID=\"phenylhydrazine\" Structure=\"c[N:1][N:2]\"/>\n <Mol ID=\"hydrazide\" Structure=\"[#7:1]NC=O\"/>\n <Mol ID=\"amidine\" Structure=\"[#7:2][C,P,S:1]=[N:3]\"/>\n <Mol ID=\"neg\" Structure=\"[*-]\"/>\n <Mol ID=\"carbox\" Structure=\"[H][O:3][C:1]=[O:2]\"/>\n <Mol ID=\"carboxylate\" Structure=\"[O-3][C:1]=[O:2]\"/>\n <Mol ID=\"sulfonyl\" Structure=\"[H][O:3][S:1](=[O:2])=[O:4]\"/>\n <Mol ID=\"sulfonate\" Structure=\"[O-:3][S:1](=[O:4])=[O:2]\"/>\n <Mol ID=\"phosphonyl\" Structure=\"[H][O:4][P:1]([O:2])=[O:3]\"/>\n <Mol ID=\"phosphonate\" Structure=\"[O:4][P:1]([O-:2])=[O:3]\"/>\n <Mol ID=\"arom\" Structure=\"[*;a]\"/>\n <Mol ID=\"cx\" Structure=\"[C,F,Cl,Br,I,At]\"/>\n <Mol ID=\"nos\" Structure=\"[#7,#8,#16]\"/>\n <Mol ID=\"pyr\" Structure=\"[nX3]\"/>\n <Mol ID=\"qh\" Structure=\"[!#1!#6:1][H]\"/>\n </Mols>\n <Pharmacophores>\n <AtomSet ID=\"Aromatic\" Symbol=\"r\">arom</AtomSet>\n <AtomSet ID=\"Cationic\" Symbol=\"+\">\n <![CDATA[ !neg && ((pos && !nitro:1) || ((amine:1 || hydrazine || amidine:2,3) && !(tertamine:1 || amide:1 || nitro:1 || aniline:1 || phenylhydrazine:2))) ]]>\n </AtomSet>\n <AtomSet ID=\"Anionic\" Symbol=\"-\">\n <![CDATA[ !pos && ((neg && !nitro:2,3) || carbox:2,3 || carboxylate:2,3 || sulfonyl:2,3,4 || sulfonate || phosphonyl:2,3,4 || phosphonate) ]]>\n </AtomSet>\n <AtomSet ID=\"HydrogenBondDonor\" Symbol=\"d\">\n <![CDATA[ qh:1 || tertamine:1 && !{Anionic}]]>\n </AtomSet>\n <AtomSet ID=\"HydrogenBondAcceptor\" Symbol=\"a\">\n <![CDATA[ nos && !tertamine:1 && !pyr && !amide:1,2 && !aniline:1 && !sulfonyl:1 && !sulfonate:1 && !{Cationic} && !nitro:1 ]]>\n </AtomSet>\n <AtomSet ID=\"Hydrophobic\" Symbol=\"h\">\n <![CDATA[ cx && !{Aromatic} && !{Cationic} && !{Anionic} && !{HydrogenBondDonor} && !{HydrogenBondAcceptor} ]]>\n </AtomSet>\n </Pharmacophores>\n <PharmacophoreFingerprintParameters MinimalDistance=\"1\" MaximalDistance=\"10\" />\n </PharmacophoreDefinition>\n <StandardizerConfiguration Version =\"0.1\">\n <Actions> \n <Removal ID=\"keepOne\" Method=\"keepLargest\" Measure=\"molMass\"/>\n <Action ID=\"aromatize\" Act=\"aromatize\"/>\n </Actions>\n </StandardizerConfiguration>\n <ScreeningConfiguration>\n <PharmacophorePointColors>\n <Color Symbol=\"+\" Value=\"red\"/>\n <Color Symbol=\"-\" Value=\"blue\"/>\n <Color Symbol=\"r\" Value=\"green\"/>\n <Color Symbol=\"h\" Value=\"black\"/>\n <Color Symbol=\"d\" Value=\"navy\"/>\n <Color Symbol=\"a\" Value=\"maroon\"/>\n <Color Symbol=\"a/d\" Value=\"purple\"/>\n <Color Symbol=\"+/d\" Value=\"lime\"/>\n <Color Symbol=\"-/a\" Value=\"aqua\"/>\n <Color Symbol=\"empty\" Value=\"gray\"/>\n <Color Symbol=\"other\" Value=\"fuchsia\"/>\n </PharmacophorePointColors> \n <ParametrizedMetrics>\n <ParametrizedMetric Name=\"Tanimoto\" ActiveFamily=\"Generic\" \n Metric=\"Tanimoto\" Threshold=\"0.2\"/>\n <ParametrizedMetric Name=\"Euclidean\" ActiveFamily=\"Generic\" \n Metric=\"Euclidean\" Threshold=\"15\" />\n <ParametrizedMetric Name=\"Tversky\" ActiveFamily=\"Generic\"\n Metric=\"Tversky\" Threshold=\"0.5\" TverskyAlpha=\"1\" TverskyBeta=\"1\"/>\n <ParametrizedMetric Name=\"UnityTversky\" ActiveFamily=\"Generic\"\n Metric=\"Tversky\" Threshold=\"0.5\" TverskyAlpha=\"0.\" TverskyBeta=\"0.\"/>\n </ParametrizedMetrics>\n </ScreeningConfiguration>\n</PharmacophoreFingerprintConfiguration>\n"
  • chemaxon.descriptors.RFParameters
    Modifier and Type
    Constant Field
    Value
    public static final int
    2
    public static final int
    6
    public static final int
    2048
  • chemaxon.descriptors.SimilarityCalculatorFactory
    Modifier and Type
    Constant Field
    Value
    public static final String
    ";"

chemaxon.fixers.*

chemaxon.formats.*

  • chemaxon.formats.recognizer.AbbrevGroupRecognizer
    Modifier and Type
    Constant Field
    Value
    public static final int
    1
    public static final int
    0
    public static final int
    2
  • chemaxon.formats.recognizer.PDBRecognizer
    Modifier and Type
    Constant Field
    Value
    public static final int
    1
    public static final int
    0
    public static final int
    2

chemaxon.jep.*

chemaxon.marvin.*

  • chemaxon.marvin.alignment.MinMaxDistance
    Modifier and Type
    Constant Field
    Value
    public static final double
    1.0
  • chemaxon.marvin.alignment.Pharmacophore3D
    Modifier and Type
    Constant Field
    Value
    public static final int
    4
    public static final int
    1024
    public static final int
    2048
    public static final int
    8
    public static final int
    512
    public static final int
    1
    public static final int
    256
    public static final int
    16
    public static final int
    128
    public static final int
    64
    public static final int
    32
  • chemaxon.marvin.io.MRecord
    Modifier and Type
    Constant Field
    Value
    public static final int
    1

chemaxon.naming.*

chemaxon.sss.*

chemaxon.standardizer.*

chemaxon.struc.*

chemaxon.structurechecker.*

chemaxon.util.*

com.chemaxon.*