Constant Field Values

Contents

• org.helm.*

org.helm.*

org.helm.notation2.Attachment

Modifier and Type	Constant Field	Value
public static final String	BACKBONE_MONOMER_BRANCH_ATTACHEMENT	"R3"
public static final String	BACKBONE_MONOMER_LEFT_ATTACHEMENT	"R1"
public static final String	BACKBONE_MONOMER_RIGHT_ATTACHEMENT	"R2"
public static final String	BRANCH_MONOMER_ATTACHEMENT	"R1"
public static final String	CAP_GROUP_H	"H"
public static final String	CAP_GROUP_OH	"OH"
public static final String	PAIR_ATTACHMENT	"pair"
public static final String	STARTING_MONOMER_ATTACHEMENT	"Starting"

org.helm.notation2.Monomer

Modifier and Type	Constant Field	Value
public static final String	ATTACHMENT_LIST_DELIMITER	"$"
public static final String	BACKBONE_MOMONER_TYPE	"Backbone"
public static final String	BRANCH_MOMONER_TYPE	"Branch"
public static final String	CHEMICAL_POLYMER_TYPE	"CHEM"
public static final String	ID_A	"A"
public static final String	ID_ALA	"Ala"
public static final String	ID_ARG	"Arg"
public static final String	ID_ASN	"Asn"
public static final String	ID_ASP	"Asp"
public static final String	ID_C	"C"
public static final String	ID_CHEMICAL_STRUCTURE	"chemical structure"
public static final String	ID_CYS	"Cys"
public static final String	ID_dR	"dR"
public static final String	ID_G	"G"
public static final String	ID_GLN	"Gln"
public static final String	ID_GLU	"Glu"
public static final String	ID_GLY	"Gly"
public static final String	ID_HIS	"His"
public static final String	ID_ILE	"Ile"
public static final String	ID_LEU	"Leu"
public static final String	ID_LYS	"Lys"
public static final String	ID_MET	"Met"
public static final String	ID_P	"P"
public static final String	ID_PHE	"Phe"
public static final String	ID_PRO	"Pro"
public static final String	ID_R	"R"
public static final String	ID_SER	"Ser"
public static final String	ID_T	"T"
public static final String	ID_THR	"Thr"
public static final String	ID_TRP	"Trp"
public static final String	ID_TYR	"Tyr"
public static final String	ID_U	"U"
public static final String	ID_VAL	"Val"
public static final String	ID_X	"X"
public static final String	NUCLIEC_ACID_POLYMER_TYPE	"RNA"
public static final String	PEPTIDE_POLYMER_TYPE	"PEPTIDE"
public static final String	STARTING_NAME	"5"
public static final String	UNDEFINED_MOMONER_TYPE	"Undefined"

org.helm.notation2.MonomerFactory

Modifier and Type	Constant Field	Value
public static final String	ATTACHMENT_LIST_ELEMENT	"AttachmentList"
public static final String	ATTACHMENTS_RESOURCE	"resources/Attachments.json"
public static final String	DEFAULT_NAME_SPACE	"lmr"
public static final String	EXTERNAL_SCHEMA_LOCATION_KEY	"http://apache.org/xml/properties/schema/external-schemaLocation"
public static final String	MONOMER_CACHE_FILE_NAME	"MonomerCache.ser"
public static final String	MONOMER_DB_FILE_NAME	"MonomerDBGZEncoded.xml"
public static final String	MONOMER_DB_SCHEMA_RESOURCE	"resources/MonomerDBSchema.xsd"
public static final String	MONOMER_DB_XML_RESOURCE	"resources/MonomerDBGZEncoded.xml"
public static final String	POLYMER_ELEMENT	"Polymer"
public static final String	POLYMER_LIST_ELEMENT	"PolymerList"
public static final String	POLYMER_TYPE_ATTRIBUTE	"polymerType"
public static final String	XML_SCHEMA_VALIDATION_FEATURE	"http://apache.org/xml/features/validation/schema"

org.helm.notation2.NotationConstant

Modifier and Type	Constant Field	Value
public static final int	MONOMER_COUNT_THRESHOLD	200
public static final int	MONOMER_GROUP_COUNT_INTERVAL	20
public static final String	NOTATION_SOURCE	"HELM Notation"

org.helm.notation2.Nucleotide

Modifier and Type	Constant Field	Value
public static final int	ENDING_POSITION_TYPE	3
public static final int	MIDDLE_POSITION_TYPE	2
public static final int	STARTING_POSITION_TYPE	1

org.helm.notation2.NucleotideFactory

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_NAME_SPACE	"lmr"
public static final String	EXTERNAL_SCHEMA_LOCATION_KEY	"http://apache.org/xml/properties/schema/external-schemaLocation"
public static final String	LOCAL_NUCLEOTIDE_TEMPLATE_FILE_NAME	"NucleotideTemplates.xml"
public static final String	NUCLEOTIDE_TEMPLATE_SCHEMA_RESOURCE	"resources/NucleotideTemplateSchema.xsd"
public static final String	NUCLEOTIDE_TEMPLATE_XML_RESOURCE	"resources/NucleotideTemplates.xml"
public static final String	XML_SCHEMA_VALIDATION_FEATURE	"http://apache.org/xml/features/validation/schema"

org.helm.notation2.calculation.ExtinctionCoefficient

Modifier and Type	Constant Field	Value
public static final int	PEPTIDE_UNIT_TYPE	2
public static final int	RNA_UNIT_TYPE	1

org.helm.notation2.tools.HELM2NotationUtils

Modifier and Type	Constant Field	Value
public static final String	DEFAULT_BASE_PAIR_CHAR	"|"
public static final String	DEFAULT_PADDING_CHAR	" "

org.helm.notation2.tools.MonomerParser

Modifier and Type	Constant Field	Value
public static final String	ATTACHEMENT_ELEMENT	"Attachment"
public static final String	ATTACHEMENT_ID_ELEMENT	"AttachmentID"
public static final String	ATTACHEMENT_LABEL_ELEMENT	"AttachmentLabel"
public static final String	ATTACHEMENTS_ELEMENT	"Attachments"
public static final String	ATTACHEMENTS_LIST_ELEMENT	"AttachmentList"
public static final String	CAP_GROUP_NAME_ELEMENT	"CapGroupName"
public static final String	CAP_GROUP_SMILES_ELEMENT	"CapGroupSmiles"
public static final String	MONOMER_ELEMENT	"Monomer"
public static final String	MONOMER_ID_ELEMENT	"MonomerID"
public static final String	MONOMER_MOL_FILE_ELEMENT	"MonomerMolFile"
public static final String	MONOMER_NAME_ELEMENT	"MonomerName"
public static final String	MONOMER_SMILES_ELEMENT	"MonomerSmiles"
public static final String	MONOMER_TYPE_ELEMENT	"MonomerType"
public static final String	NATURAL_ANALOG_ELEMENT	"NaturalAnalog"
public static final String	POLYMER_TYPE_ELEMENT	"PolymerType"
protected static final String	SMILES_EXTENSION_SEPARATOR_REGEX	"\\|"

org.helm.notation2.tools.NucleotideParser

Modifier and Type	Constant Field	Value
public static final char	BRANCH_END_SYMBOL	41
public static final char	BRANCH_START_SYMBOL	40
public static final String	DEFAULT_NOTATION_SOURCE	"HELM Notation"
public static final int	MINUMUM_MATCH_FRAGMENT_LENGTH	2
public static final char	MODIFICATION_END_SYMBOL	93
public static final char	MODIFICATION_START_SYMBOL	91
public static final String	RNA_DESIGN_DICER_27_L	"DICER_27_L"
public static final String	RNA_DESIGN_DICER_27_R	"DICER_27_R"
public static final String	RNA_DESIGN_NONE	"NONE"
public static final String	RNA_DESIGN_TUSCHL_19_PLUS_2	"TUSCHL_19_PLUS_2"

org.helm.notation2.tools.RNAUtils

Modifier and Type	Constant Field	Value
public static final int	MINUMUM_MATCH_FRAGMENT_LENGTH	2

org.helm.notation2.tools.xHelmNotationExporter

Modifier and Type	Constant Field	Value
public static final String	HELM_NOTATION_ELEMENT	"HelmNotation"
public static final String	MONOMER_ELEMENT	"Monomer"
public static final String	MONOMER_LIST_ELEMENT	"Monomers"
public static final String	XHELM_ELEMENT	"Xhelm"