A B C D E F G H I L M N O P R S T U V
All Classes All Packages

A

ACETYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset

addAtomLinkage(StructureAtomLinkage) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

Add a linkage.

addAtomLinkage(StructureAtomLinkage) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

addAtomLinkages(Collection<StructureAtomLinkage>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

Add a collections of linkages.

addAtomLinkages(Collection<StructureAtomLinkage>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

addKeyword(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Add a keyword associate with the PTM.

addKeywords(Collection<String>) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

allComponents() - Static method in class org.biojava.nbio.protmod.Component

allComponents() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

allIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

allKeywords() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

allModifications() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

allPdbccIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

allPsimodIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

allResidIds() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

ARTIFACTUAL - org.biojava.nbio.protmod.ModificationOccurrenceType

ATTACHMENT - org.biojava.nbio.protmod.ModificationCategory

B

build() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Builder(String, ModificationCategory, ModificationOccurrenceType, ModificationCondition) - Constructor for class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Builder(ProteinModification) - Constructor for class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Create a Builder from an existing ProteinModification.

C

CHEMICAL_MODIFICATION - org.biojava.nbio.protmod.ModificationCategory

compareTo(ProteinModification) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

compareTo(ModifiedCompound) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

compareTo(StructureGroup) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

Component - Class in org.biojava.nbio.protmod

contains information about a certain Component.

ComponentXMLConverter - Class in org.biojava.nbio.protmod.io

ComponentXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ComponentXMLConverter

copyFile(File, File) - Static method in class org.biojava.nbio.phosphosite.Dataset

CROSS_LINK_1 - org.biojava.nbio.protmod.ModificationCategory

CROSS_LINK_2 - org.biojava.nbio.protmod.ModificationCategory

CROSS_LINK_3 - org.biojava.nbio.protmod.ModificationCategory

CROSS_LINK_4 - org.biojava.nbio.protmod.ModificationCategory

CROSS_LINK_5 - org.biojava.nbio.protmod.ModificationCategory

CROSS_LINK_6 - org.biojava.nbio.protmod.ModificationCategory

CROSS_LINK_7 - org.biojava.nbio.protmod.ModificationCategory

CROSS_LINK_8_OR_LARGE - org.biojava.nbio.protmod.ModificationCategory

crossChains() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

crossChains() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

D

Dataset - Class in org.biojava.nbio.phosphosite

Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from http://www.phosphosite.org/staticDownloads.do Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations.

Dataset() - Constructor for class org.biojava.nbio.phosphosite.Dataset

description() - Method in enum org.biojava.nbio.protmod.ModificationCategory

destroy() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

DISEASE_ASSOC - Static variable in class org.biojava.nbio.phosphosite.Dataset

download() - Method in class org.biojava.nbio.phosphosite.Dataset

downloadFile(URL, File) - Method in class org.biojava.nbio.phosphosite.Dataset

E

equals(Object) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

equals(Object) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtom

equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

equals(Object) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

F

findAtomLinkages(Group, Group, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

Find linkages between two groups within tolerance of bond length, from potential atoms.

findAtomLinkages(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

Find linkages between two groups within tolerance of bond length, from potential atoms.

findLinkage(Group, Group, String, String, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

Find a linkage between two groups within tolerance of bond length.

findNearestAtomLinkage(Group, Group, List<String>, List<String>, boolean, double) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

Find a linkage between two groups within tolerance of bond length, from potential atoms.

fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter

fromXML(String) - Static method in class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter

fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter

fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter

fromXML(Node) - Static method in class org.biojava.nbio.protmod.io.StructureGroupXMLConverter

G

getAminoAcids(Chain) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

Get all amino acids in a chain.

getAtom1() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

getAtom2() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

getAtomDistance(Atom, Atom) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

getAtomLinkages() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

getAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

getAtomName() - Method in class org.biojava.nbio.protmod.structure.StructureAtom

getAtomNames(Group) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

getByCategory(ModificationCategory) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

getByComponent(Component, Component...) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

Get ProteinModifications that involves one or more components.

getById(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

getByKeyword(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationCategory

getByLabel(String) - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType

getByOccurrenceType(ModificationOccurrenceType) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

getByPdbccId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

getByPsimodId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

getByResidId(String) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

getCategory() - Method in interface org.biojava.nbio.protmod.ProteinModification

getCategory() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getChainId() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

getChrLoc() - Method in class org.biojava.nbio.phosphosite.Site

getComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getComponents() - Method in interface org.biojava.nbio.protmod.ModificationCondition

getComponents() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl

}

getCondition() - Method in interface org.biojava.nbio.protmod.ProteinModification

getCondition() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getDescription() - Method in interface org.biojava.nbio.protmod.ProteinModification

getDescription() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getDescription() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

return a description of this compound

getDescription() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

getDistance() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

getFormula() - Method in interface org.biojava.nbio.protmod.ProteinModification

getFormula() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getGeneSymb() - Method in class org.biojava.nbio.phosphosite.Site

getGroup() - Method in class org.biojava.nbio.phosphosite.Site

getGroup() - Method in class org.biojava.nbio.protmod.structure.StructureAtom

getGroups() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

getGroups() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

getGroups(boolean) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

getGroups(boolean) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

getId() - Method in interface org.biojava.nbio.protmod.ProteinModification

getId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getIdentifiedModifiedCompound() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

getIndexOfComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getIndexOfComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getInsCode() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

getKeywords() - Method in interface org.biojava.nbio.protmod.ProteinModification

getKeywords() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getLabelOfAtomOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getLabelOfAtomOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getLinkages() - Method in interface org.biojava.nbio.protmod.ModificationCondition

getLinkages() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl

}

getLocalDir() - Method in class org.biojava.nbio.phosphosite.Dataset

getLocalFiles() - Method in class org.biojava.nbio.phosphosite.Dataset

getModification() - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

getModification() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

getModType() - Method in class org.biojava.nbio.phosphosite.Site

getOccurrenceType() - Method in interface org.biojava.nbio.protmod.ProteinModification

getOccurrenceType() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getOrganism() - Method in class org.biojava.nbio.phosphosite.Site

getPdbccId() - Method in interface org.biojava.nbio.protmod.ProteinModification

getPdbccId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getPdbccIds() - Method in class org.biojava.nbio.protmod.Component

getPdbccName() - Method in interface org.biojava.nbio.protmod.ProteinModification

getPdbccName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getPDBName() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

getPDBNameOfPotentialAtomsOnComponent1() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getPDBNameOfPotentialAtomsOnComponent2() - Method in class org.biojava.nbio.protmod.ModificationLinkage

getPDBResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

getProtein() - Method in class org.biojava.nbio.phosphosite.Site

getPsimodId() - Method in interface org.biojava.nbio.protmod.ProteinModification

getPsimodId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getPsimodName() - Method in interface org.biojava.nbio.protmod.ProteinModification

getPsimodName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getRecordAdditionalAttachments() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

getRecordUnidentifiableCompounds() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

getResidId() - Method in interface org.biojava.nbio.protmod.ProteinModification

getResidId() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getResidName() - Method in interface org.biojava.nbio.protmod.ProteinModification

getResidName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getResidue() - Method in class org.biojava.nbio.phosphosite.Site

getResidueNumber() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

getStructureAtom(Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

getStructureAtomLinkage(Atom, boolean, Atom, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

getStructureGroup(Group, boolean) - Static method in class org.biojava.nbio.protmod.structure.StructureUtil

getSystematicName() - Method in interface org.biojava.nbio.protmod.ProteinModification

getSystematicName() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

getUnidentifiableAtomLinkages() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

getUnidentifiableModifiedResidues() - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

getUniprot() - Method in class org.biojava.nbio.phosphosite.Site

H

hashCode() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

hashCode() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

hashCode() - Method in class org.biojava.nbio.protmod.structure.StructureAtom

hashCode() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

hashCode() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

HYPOTHETICAL - org.biojava.nbio.protmod.ModificationOccurrenceType

I

identify(List<Chain>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

Identify all registered modifications in chains.

identify(List<Chain>, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

Identify a set of modifications in a a list of chains.

identify(Chain) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

Identify all registered modifications in a chain.

identify(Chain, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

Identify a set of modifications in a a chains.

identify(Structure) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

Identify all registered modifications in a structure.

identify(Structure, Set<ProteinModification>) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

Identify a set of modifications in a structure.

init() - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

Initialization the static variables and register common modifications.

init(InputStream) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

Initialization the static variables and register common modifications.

isAminoAcid() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

isCrossLink() - Method in enum org.biojava.nbio.protmod.ModificationCategory

isCTerminal() - Method in class org.biojava.nbio.protmod.Component

isNTerminal() - Method in class org.biojava.nbio.protmod.Component

L

label() - Method in enum org.biojava.nbio.protmod.ModificationCategory

label() - Method in enum org.biojava.nbio.protmod.ModificationOccurrenceType

M

main(String[]) - Static method in class org.biojava.nbio.phosphosite.Dataset

METHYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset

ModificationCategory - Enum in org.biojava.nbio.protmod

define modification categories.

ModificationCondition - Interface in org.biojava.nbio.protmod

Conditions of a protein modification, e.g.

ModificationConditionImpl - Class in org.biojava.nbio.protmod

ModificationConditionImpl(List<Component>, List<ModificationLinkage>) - Constructor for class org.biojava.nbio.protmod.ModificationConditionImpl

ModificationLinkage - Class in org.biojava.nbio.protmod

ModificationLinkage(List<Component>, int, int) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage

ModificationLinkage(List<Component>, int, String, int, String) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage

ModificationLinkage(List<Component>, int, List<String>, int, List<String>) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage

ModificationLinkage(List<Component>, int, List<String>, String, int, List<String>, String) - Constructor for class org.biojava.nbio.protmod.ModificationLinkage

ModificationOccurrenceType - Enum in org.biojava.nbio.protmod

ModifiedCompound - Interface in org.biojava.nbio.protmod.structure

Root interface for all modifications in structure.

ModifiedCompoundImpl - Class in org.biojava.nbio.protmod.structure

ModifiedCompoundImpl() - Constructor for class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

ModifiedCompoundImpl(ProteinModification, Collection<StructureAtomLinkage>) - Constructor for class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

ModifiedCompoundImpl(ProteinModification, StructureGroup) - Constructor for class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

Create a ModifiedCompoundImpl that has only one involved component.

ModifiedCompoundXMLConverter - Class in org.biojava.nbio.protmod.io

ModifiedCompoundXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter

N

NATURAL - org.biojava.nbio.protmod.ModificationOccurrenceType

newline - Static variable in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

O

of(String) - Static method in class org.biojava.nbio.protmod.Component

Get a Component that does not have to occur at terminals.

of(String, boolean, boolean) - Static method in class org.biojava.nbio.protmod.Component

Get or create a Component.

of(Set<String>) - Static method in class org.biojava.nbio.protmod.Component

Get a Component that does not have to occur at terminals.

of(Set<String>, boolean, boolean) - Static method in class org.biojava.nbio.protmod.Component

Get or create a Component.

org.biojava.nbio.phosphosite - package org.biojava.nbio.phosphosite

org.biojava.nbio.protmod - package org.biojava.nbio.protmod

org.biojava.nbio.protmod.io - package org.biojava.nbio.protmod.io

org.biojava.nbio.protmod.structure - package org.biojava.nbio.protmod.structure

P

parseSites(File) - Static method in class org.biojava.nbio.phosphosite.Site

PHOSPHORYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset

ProteinModification - Interface in org.biojava.nbio.protmod

This interface defines information about a specific protein modification.

ProteinModificationIdentifier - Class in org.biojava.nbio.protmod.structure

Identify attachment modification in a 3-D structure.

ProteinModificationIdentifier() - Constructor for class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

ProteinModificationImpl - Class in org.biojava.nbio.protmod

This class contains information about a specific protein modification.

ProteinModificationImpl.Builder - Class in org.biojava.nbio.protmod

Uses Builder pattern to build a ProteinModification.

ProteinModificationRegistry - Class in org.biojava.nbio.protmod

This class serves as a instance registry by maintaining a pool of ProteinModification instances.

ProteinModificationRegistry() - Constructor for class org.biojava.nbio.protmod.ProteinModificationRegistry

ProteinModificationXmlReader - Class in org.biojava.nbio.protmod.io

R

register(ProteinModification) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

Register a new ProteinModification.

registerProteinModificationFromXml(InputStream) - Static method in class org.biojava.nbio.protmod.io.ProteinModificationXmlReader

Read protein modifications from XML file and register them.

REGULATORY - Static variable in class org.biojava.nbio.phosphosite.Dataset

S

setAtomLinkages(Set<StructureAtomLinkage>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

Set atom linkages

setAtomLinkages(Set<StructureAtomLinkage>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

setbondLengthTolerance(double) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

setCategory(ModificationCategory) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

setChainId(String) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setChrLoc(String) - Method in class org.biojava.nbio.phosphosite.Site

setCondition(ModificationCondition) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

setDescription(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

setDescription(String) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

setDescription(String) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

setFormula(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the residue formula.

setGeneSymb(String) - Method in class org.biojava.nbio.phosphosite.Site

setGroup(String) - Method in class org.biojava.nbio.phosphosite.Site

setGroups(Set<StructureGroup>) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

setGroups(Set<StructureGroup>) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

setInsCode(Character) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setIsAminoAcid(boolean) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setModification(ProteinModification) - Method in interface org.biojava.nbio.protmod.structure.ModifiedCompound

setModification(ProteinModification) - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

setModType(String) - Method in class org.biojava.nbio.phosphosite.Site

setOccurrenceType(ModificationOccurrenceType) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

setOrganism(String) - Method in class org.biojava.nbio.phosphosite.Site

setPdbccId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the Protein Data Bank Chemical Component ID.

setPdbccName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the Protein Data Bank Chemical Component name.

setPDBName(String) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setPDBResidueNumber(ResidueNumber) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setProtein(String) - Method in class org.biojava.nbio.phosphosite.Site

setPsimodId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the PSI-MOD ID.

setPsimodName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the PSI-MOD name.

setRecordAdditionalAttachments(boolean) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

setRecordUnidentifiableCompounds(boolean) - Method in class org.biojava.nbio.protmod.structure.ProteinModificationIdentifier

setResidId(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the RESID ID.

setResidName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the RESID name.

setResidue(String) - Method in class org.biojava.nbio.phosphosite.Site

setResidueNumber(int) - Method in class org.biojava.nbio.protmod.structure.StructureGroup

setSystematicName(String) - Method in class org.biojava.nbio.protmod.ProteinModificationImpl.Builder

Set the systematic name.

setUniprot(String) - Method in class org.biojava.nbio.phosphosite.Site

Site - Class in org.biojava.nbio.phosphosite

Created by ap3 on 31/10/2014.

Site() - Constructor for class org.biojava.nbio.phosphosite.Site

StructureAtom - Class in org.biojava.nbio.protmod.structure

Everything that is needed to uniquely describe a atom.

StructureAtom(StructureGroup, String) - Constructor for class org.biojava.nbio.protmod.structure.StructureAtom

StructureAtomLinkage - Class in org.biojava.nbio.protmod.structure

StructureAtomLinkage(StructureAtom, StructureAtom, double) - Constructor for class org.biojava.nbio.protmod.structure.StructureAtomLinkage

StructureAtomXMLConverter - Class in org.biojava.nbio.protmod.io

StructureAtomXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.StructureAtomXMLConverter

StructureGroup - Class in org.biojava.nbio.protmod.structure

Information of a group (residue or ligand) involved in a modification.

StructureGroup() - Constructor for class org.biojava.nbio.protmod.structure.StructureGroup

StructureGroup(ResidueNumber, String, boolean) - Constructor for class org.biojava.nbio.protmod.structure.StructureGroup

StructureGroupXMLConverter - Class in org.biojava.nbio.protmod.io

StructureGroupXMLConverter() - Constructor for class org.biojava.nbio.protmod.io.StructureGroupXMLConverter

StructureUtil - Class in org.biojava.nbio.protmod.structure

SUMOYLATION - Static variable in class org.biojava.nbio.phosphosite.Dataset

T

toString() - Method in class org.biojava.nbio.phosphosite.Site

toString() - Method in class org.biojava.nbio.protmod.Component

toString() - Method in enum org.biojava.nbio.protmod.ModificationCategory

toString() - Method in class org.biojava.nbio.protmod.ModificationConditionImpl

toString() - Method in class org.biojava.nbio.protmod.ModificationLinkage

toString() - Method in enum org.biojava.nbio.protmod.ModificationOccurrenceType

toString() - Method in class org.biojava.nbio.protmod.ProteinModificationImpl

toString() - Method in class org.biojava.nbio.protmod.structure.ModifiedCompoundImpl

toString() - Method in class org.biojava.nbio.protmod.structure.StructureAtom

toString() - Method in class org.biojava.nbio.protmod.structure.StructureAtomLinkage

toString() - Method in class org.biojava.nbio.protmod.structure.StructureGroup

toXML(Component) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter

toXML(Component, PrettyXMLWriter) - Static method in class org.biojava.nbio.protmod.io.ComponentXMLConverter

toXML(ModifiedCompound) - Static method in class org.biojava.nbio.protmod.io.ModifiedCompoundXMLConverter

toXML(StructureAtom) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter

toXML(StructureAtom, PrettyXMLWriter) - Static method in class org.biojava.nbio.protmod.io.StructureAtomXMLConverter

toXML(StructureGroup, PrettyXMLWriter) - Static method in class org.biojava.nbio.protmod.io.StructureGroupXMLConverter

U

UBIQUITINATION - Static variable in class org.biojava.nbio.phosphosite.Dataset

UNDEFINED - org.biojava.nbio.protmod.ModificationCategory

unregister(ProteinModification) - Static method in class org.biojava.nbio.protmod.ProteinModificationRegistry

Remove a modification from registry.

V

valueOf(String) - Static method in enum org.biojava.nbio.protmod.ModificationCategory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biojava.nbio.protmod.ModificationCategory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.protmod.ModificationOccurrenceType

Returns an array containing the constants of this enum type, in the order they are declared.

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