Constant Field Values

Contents

• com.chemaxon.*

com.chemaxon.*

com.chemaxon.calculations.io.Segmenters

Modifier and Type	Constant Field	Value
public static final String	SEGMENTER_FORMATS	"\"smiles\", \"sdf\""

com.chemaxon.calculations.util.CmdlineUtils

Modifier and Type	Constant Field	Value
public static final String	UTF8ENCODING	"UTF-8"

com.chemaxon.descriptors.common.BinaryVectors

Modifier and Type	Constant Field	Value
public static final int	BYTES_IN_INT	4
public static final int	BYTES_IN_LONG	8
public static final int	LOG2_BYTES_IN_INT	2
public static final int	LOG2_BYTES_IN_LONG	3

com.chemaxon.descriptors.fingerprints.cfp.CfpParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BITS_TO_SET_FOR_PATTERNS	3
public static final int	DEFAULT_CFP_LENGTH	1024
public static final int	DEFAULT_CFP_MAX_PATTERN_LENGTH	7
public static final boolean	DEFAULT_CONSIDER_RINGS	true

com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_ECFP_DIAMETER	4
public static final int	DEFAULT_ECFP_LENGTH	1024

com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MACCS_LENGTH	192

com.chemaxon.descriptors.vectors.binary.BvParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_LENGTH	1024

com.chemaxon.descriptors.vectors.floats.FvParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_LENGTH	1
public static final double	DEFAULT_SCALED_MAX	1.0
public static final double	DEFAULT_SCALED_MIN	0.0

com.chemaxon.overlap.OverlapAnalysisContextFactory

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_PHARMA_CALC_CONFIG_XML	"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<PharmacophoreFingerprintConfiguration Version=\"\" schemaLocation=\"pharmacophores.xsd\">\n <PharmacophoreDefinition>\n <Search StereoCareChecking=\"false\"/>\n <Functions>\n <Function ID=\"formalcharge\" Class=\"chemaxon.util.expression.function.AtomProperties\">\n <Param Name=\"property\" Value=\"charge\"/>\n <Param Name=\"pH\" Value=\"7\"/> \n </Function> \n </Functions>\n <Plugins>\n <Plugin ID=\"acceptor\" Class=\"chemaxon.marvin.calculations.HBDAPlugin\">\n <Param Name=\"type\" Value=\"acc\"/>\n <Param Name=\"pH\" Value=\"7\"/>\n </Plugin>\n <Plugin ID=\"donor\" Class=\"chemaxon.marvin.calculations.HBDAPlugin\">\n <Param Name=\"type\" Value=\"don\"/>\n <Param Name=\"pH\" Value=\"7\"/>\n </Plugin>\n <Plugin ID=\"ioncharge\" Class=\"chemaxon.marvin.calculations.IonChargePlugin\">\n <Param Name=\"pH\" Value=\"7\"/>\n </Plugin> \n </Plugins>\n <Mols>\n <Mol ID=\"arom\" Structure=\"[*;a]\"/>\n <Mol ID=\"cx\" Structure=\"[C,F,Cl,Br,I,At]\"/>\n </Mols>\n <Pharmacophores>\n <AtomSet ID=\"Aromatic\" Symbol=\"r\">arom</AtomSet>\n <AtomSet ID=\"Cationic\" Symbol=\"+\"><![CDATA[ (formalcharge() > 0) || (ioncharge() > 0.4) ]]></AtomSet>\n <AtomSet ID=\"Anionic\" Symbol=\"-\"><![CDATA[ (formalcharge() < 0) || (ioncharge() < -0.4)]]></AtomSet>\n <AtomSet ID=\"HydrogenBondDonor\" Symbol=\"d\"><![CDATA[ donor() ]]></AtomSet>\n <AtomSet ID=\"HydrogenBondAcceptor\" Symbol=\"a\"><![CDATA[ acceptor() ]]></AtomSet>\n <AtomSet ID=\"Hydrophobic\" Symbol=\"h\"><![CDATA[ cx && !{Aromatic} && !{Cationic} && !{Anionic} && !{HydrogenBondDonor} && !{HydrogenBondAcceptor} ]]></AtomSet>\n </Pharmacophores>\n <PharmacophoreFingerprintParameters MinimalDistance=\"1\" MaximalDistance=\"10\"/>\n </PharmacophoreDefinition>\n\n <StandardizerConfiguration>\n <Actions>\n <Removal ID=\"keepOne\" Method=\"keepLargest\" Measure=\"molMass\"/>\n <Action ID=\"aromatize\" Act=\"aromatize\"/>\n </Actions>\n </StandardizerConfiguration>\n\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=\"100\" />\n </ParametrizedMetrics>\n </ScreeningConfiguration>\n</PharmacophoreFingerprintConfiguration>"
public static final String	DEFAULT_PHARMA_FRAG_CONFIG_XML	"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\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\t <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=\"[H][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\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\n <ScreeningConfiguration>\n <PharmacophorePointColors>\n <Color Symbol=\"+\" Value=\"#cc0000\"/>\n <Color Symbol=\"-\" Value=\"#0000cc\"/>\n <Color Symbol=\"r\" Value=\"#00ff00\"/>\n <Color Symbol=\"h\" Value=\"#000000\"/>\n <Color Symbol=\"d\" Value=\"#0000ff\"/>\n <Color Symbol=\"a\" Value=\"#ff0000\"/>\n <Color Symbol=\"a/d\" Value=\"#ff00ff\"/>\n <Color Symbol=\"+/d\" Value=\"#cc6666\"/>\n <Color Symbol=\"-/a\" Value=\"#ff99cc\"/>\n <Color Symbol=\"a/r\" Value=\"#ffcc00\"/>\n <Color Symbol=\"d/r\" Value=\"#00ccff\"/>\n <Color Symbol=\"h/r\" Value=\"#339933\"/>\n <Color Symbol=\"-/a/d\" Value=\"#33ffff\"/>\n <Color Symbol=\"other\" Value=\"#cc9900\"/>\n <Color Symbol=\"empty\" Value=\"#cccccc\"/>\n </PharmacophorePointColors>\n <ParametrizedMetrics>\n <ParametrizedMetric Name=\"Tanimoto\" ActiveFamily=\"Generic\" Metric=\"Tanimoto\" Threshold=\"0.2\"/>\n <ParametrizedMetric Name=\"Euclidean\" ActiveFamily=\"Generic\" Metric=\"Euclidean\" Threshold=\"15\" />\n </ParametrizedMetrics>\n </ScreeningConfiguration>\n</PharmacophoreFingerprintConfiguration>"
public static final String	STANDARDIZER_DEFAULTAROMA_CONFIG_XML	"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<StandardizerConfiguration Version =\"0.1\" schemaLocation=\"standardize.xsd\">\n <Actions>\n <Action ID=\"aromatize\" Act=\"aromatize\"/>\n </Actions>\n</StandardizerConfiguration>"

com.chemaxon.overlap.bruteforce.UnguardedPagedOverlap<T extends Serializable>

Modifier and Type	Constant Field	Value
public static final int	MAX_QUEUE_SIZE	200

com.chemaxon.overlap.context.OverlapAnalysisContext<D extends Descriptor,T extends Serializable>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_PAGESIZE	50
public static final int	DEFAULT_QUERY_PAGESIZE	2000

com.chemaxon.overlap.io.MasterStorages

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_IMPORT_PAGESIZE	50
public static final int	MAX_QUEUE_SIZE	300

com.chemaxon.overlap.storage.PagedDescriptorStorage<D extends Descriptor>

Modifier and Type	Constant Field	Value
public static final int	MAX_RESULT_QUEUE_SIZE	100

com.chemaxon.overlap.wui.application.Status

Modifier and Type	Constant Field	Value
public static final int	ACCEPTED	202
public static final int	CREATED	201
public static final int	NO_CONTENT	204

com.chemaxon.overlap.wui.dto.SizeInfoMethod

Modifier and Type	Constant Field	Value
public static final int	MAX_TRAVERSAL_DEPTH	20

com.chemaxon.virtuallib.sc.model.sdf.RgFrag

Modifier and Type	Constant Field	Value
public static final String	REACTANT_ID_SDFIELD	"Reactant_ID"

com.chemaxon.virtuallib.sc.model.sdf.Scaffold

Modifier and Type	Constant Field	Value
public static final String	COMMENT_SDFIELD	"Comment"
public static final String	LIB_ID_SDFIELD	"Library_ID"
public static final String	RXN_ID_SDFIELD	"Rxn_ID"