Package org.helm.notation2.tools

Class WebService

java.lang.Object

org.helm.notation2.tools.WebService

public class WebService
extends Object

WebService class containing all required methods for the web-service

Author:

hecht

Constructor Summary

Constructors

Constructor	Description
WebService()

Method Summary

Modifier and Type	Method	Description
Float	calculateExtinctionCoefficient(String notation)	method to calculate from a non-ambiguous HELM string the extinction coefficient
Double	calculateMolecularWeight(String notation)	method to calculate from a non-ambiguous HELM input the molecular weight
String	convertIntoStandardHELM(String notation)	method to convert the input HELM into a standard HELM
String	convertMolFileSMILESWithAtomMapping(String molfile, List<Attachment> attachments)	method to generate a smiles with atom mapping for a given molfile with the given attachments
String	convertStandardHELMToCanonicalHELM(String notation)	method to convert the input HELM into canonical HELM
String	generateCanSMILESForHELM2(String notation)	method to generate a SMILES representation for a whole HELM2 input
String	generateFasta(String notation)	method to generate FASTA-Formats for all rna and peptide sequences from an HELM input
String	generateHELMFromFastaNucleotide(String notation)	method to generate HELM from a FASTA containing rna/dna sequences
String	generateHELMFromFastaPeptide(String notation)	method to generate HELM from a FASTA containing peptide sequence(s)
byte[]	generateImageForHELMMolecule(String notation)	method to generate a HELM molecule
byte[]	generateImageForMonomer(Monomer monomer, boolean showRgroups)	method to generate an image for a monomer
String	generateJSON(String helm)	method to generate JSON-Output for the HELM
String	generateNaturalAnalogSequencePeptide(String notation)	method to generate the natural analogue sequence for all peptide-sequences from an HELM input
String	generateNaturalAnalogSequenceRNA(String notation)	method to generate the natural analogue sequence for all rna-sequences from an HELM input
String	generateSMILESForHELM2(String notation)	method to generate a SMILES representation for a whole HELM2 input
String	getMolecularFormula(String notation)	method to calculate from a non-ambiguous HELM input the molecular formula
List<String>	getMolecularProperties(String notation)	method to calculate froma non-ambiguous HELM input the molecular properties: molecular formula, molecular weight, exact mass, extinction coefficient
String	readPeptide(String peptide)	method to read a single peptide sequence and generates HELM
String	readRNA(String rna)	method to read a single rna sequence and generates HELM
void	refreshMonomerCache()	method to refresh the monomer cache of the MonomerFactory
void	validateHELM(String helm)	method to validate the input HELM-String
void	validateSyntaxHELM(String helm)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

WebService

public WebService()

Method Details

validateHELM

public void validateHELM(String helm) throws ValidationException, MonomerLoadingException, ChemistryException

method to validate the input HELM-String

Parameters:

helm - input HELM-string

Throws:

ValidationException - if the input HELM is not valid

MonomerLoadingException - if the MonomerFactory can not be refreshed

ChemistryException - if the Chemistry Engine can not be initialized

validateSyntaxHELM

public void validateSyntaxHELM(String helm) throws ChemistryException, ParserException, org.jdom2.JDOMException, IOException, MonomerException

Throws:

ChemistryException

ParserException

org.jdom2.JDOMException

IOException

MonomerException

convertStandardHELMToCanonicalHELM

public String convertStandardHELMToCanonicalHELM(String notation) throws HELM1FormatException, ValidationException, MonomerLoadingException, ChemistryException

method to convert the input HELM into canonical HELM

Parameters:

notation - HELM input

Returns:

canonical HELM

Throws:

HELM1FormatException - if HELM input contains HELM2 features

ValidationException - if the HELM input is not valid

MonomerLoadingException - if the MonomerFactory can not be loaded

ChemistryException - if the Chemistry Engine can not be initialized

convertIntoStandardHELM

public String convertIntoStandardHELM(String notation) throws HELM1FormatException, ValidationException, MonomerLoadingException, org.helm.chemtoolkit.CTKException, ChemistryException

method to convert the input HELM into a standard HELM

Parameters:

notation - HELM input

Returns:

standard HELM

Throws:

HELM1FormatException - if the HELM input contains HELM2 features

ValidationException - if the HELM input is not valid

MonomerLoadingException - if the MonomerFactory can not be loaded

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if the Chemistry Engine can not be initialized

calculateExtinctionCoefficient

public Float calculateExtinctionCoefficient(String notation) throws ExtinctionCoefficientException, ValidationException, MonomerLoadingException, ChemistryException

method to calculate from a non-ambiguous HELM string the extinction coefficient

Parameters:

notation - HELM input

Returns:

extinction coefficient from the HELM input

Throws:

ExtinctionCoefficientException - if the extinction coefficient can not be calculated

ValidationException - if the HELM input is not valid

MonomerLoadingException - if the MonomerFactory can not be refreshed

ChemistryException - if the Chemistry Engine can not be initialized

generateFasta

public String generateFasta(String notation) throws FastaFormatException, ValidationException, MonomerLoadingException, ChemistryException

method to generate FASTA-Formats for all rna and peptide sequences from an HELM input

Parameters:

notation - HELM input

Returns:

FASTA containing all rna and peptide sequences

Throws:

ValidationException - if the HELM input is not valid

FastaFormatException - if the FASTA-sequences can not be built

MonomerLoadingException - if the MonomerFactory can not be loaded

ChemistryException - if the Chemistry Engine can not be initialized

generateHELMFromFastaNucleotide

public String generateHELMFromFastaNucleotide(String notation) throws FastaFormatException, org.helm.notation2.parser.exceptionparser.NotationException, ChemistryException, MonomerLoadingException, NucleotideLoadingException

method to generate HELM from a FASTA containing rna/dna sequences

Parameters:

notation - FASTA containing rna/dna sequences

Returns:

HELM

Throws:

FastaFormatException - if the input is not valid

org.helm.notation2.parser.exceptionparser.NotationException - if notation is not valid

ChemistryException - if chemistry engine can not be initialized

MonomerLoadingException - if monomers can not be loaded

NucleotideLoadingException - if nucleotides can not be loaded

generateHELMFromFastaPeptide

public String generateHELMFromFastaPeptide(String notation) throws FastaFormatException, MonomerLoadingException, ChemistryException

method to generate HELM from a FASTA containing peptide sequence(s)

Parameters:

notation - FASTA containing peptide sequence(s)

Returns:

HELM

Throws:

FastaFormatException - if the FASTA input is not valid

MonomerLoadingException - if the MonomerFactory can not be loaded

ChemistryException - if chemistry engine can not be initialized

calculateMolecularWeight

public Double calculateMolecularWeight(String notation) throws MonomerLoadingException, BuilderMoleculeException, org.helm.chemtoolkit.CTKException, ValidationException, ChemistryException

method to calculate from a non-ambiguous HELM input the molecular weight

Parameters:

notation - HELM input

Returns:

moleuclar weight from the HELM input

Throws:

MonomerLoadingException - if the MonomerFactory can not be refreshed

ValidationException - if the HELM input is not valid

BuilderMoleculeException - if the molecule for the calculation can not be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if the Chemistry Engine can not be initialized

getMolecularFormula

public String getMolecularFormula(String notation) throws BuilderMoleculeException, org.helm.chemtoolkit.CTKException, ValidationException, MonomerLoadingException, ChemistryException

method to calculate from a non-ambiguous HELM input the molecular formula

Parameters:

notation - HELM input

Returns:

molecular formula from the HELM input

Throws:

ValidationException - if the HELM input is not valid

BuilderMoleculeException - if the molecule for the calculation can not be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

MonomerLoadingException - if the MonomerFactory can not be refreshed

ChemistryException - if the Chemistry Engine can not be initialized

getMolecularProperties

public List<String> getMolecularProperties(String notation) throws BuilderMoleculeException, org.helm.chemtoolkit.CTKException, ExtinctionCoefficientException, ValidationException, MonomerLoadingException, ChemistryException

method to calculate froma non-ambiguous HELM input the molecular properties: molecular formula, molecular weight, exact mass, extinction coefficient

Parameters:

notation - given HELM

Returns:

List<String> containing the molecule properties

Throws:

BuilderMoleculeException - if the molecule can't be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ExtinctionCoefficientException - if extinction coefficient can not be calculated

ValidationException - if notation is not valid

MonomerLoadingException - if monomers can not be loaded

ChemistryException - if the Chemistry Engine can not be initialized

readPeptide

public String readPeptide(String peptide) throws FastaFormatException, org.helm.notation2.parser.exceptionparser.NotationException, ChemistryException

method to read a single peptide sequence and generates HELM

Parameters:

peptide - peptide sequence

Returns:

HELM

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if the notation object can not be built

FastaFormatException - if the peptide sequence is not in the right format

ChemistryException - if chemistry engine can not be initialized

readRNA

public String readRNA(String rna) throws org.helm.notation2.parser.exceptionparser.NotationException, FastaFormatException, ChemistryException, NucleotideLoadingException

method to read a single rna sequence and generates HELM

Parameters:

rna - rna sequence

Returns:

HELM

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if the notation object can not be built

FastaFormatException - if the rna-sequence is not in the right format HELM

ChemistryException - if chemistry engine can not be initialized

NucleotideLoadingException - if nucleotides can not be loaded

generateImageForHELMMolecule

public byte[] generateImageForHELMMolecule(String notation) throws BuilderMoleculeException, org.helm.chemtoolkit.CTKException, IOException, ValidationException, ChemistryException

method to generate a HELM molecule

Parameters:

notation - HELM string

Returns:

generated molecule image in byte[]

Throws:

ValidationException - if the HELM string is not valid

BuilderMoleculeException - if the molecule can't be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

IOException - if the image can not be produced

ChemistryException - if the Chemistry Engine can not be initialized

generateImageForMonomer

public byte[] generateImageForMonomer(Monomer monomer, boolean showRgroups) throws BuilderMoleculeException, org.helm.chemtoolkit.CTKException, ChemistryException

method to generate an image for a monomer

Parameters:

monomer - Monomer Input

showRgroups - wheter to show the r groups in the image

Returns:

generated molecule image in byte[]

Throws:

BuilderMoleculeException - if the molecule can not be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if the Chemistry Engine can not be initialized

generateJSON

public String generateJSON(String helm) throws ValidationException, MonomerLoadingException, ChemistryException, com.fasterxml.jackson.core.JsonProcessingException

method to generate JSON-Output for the HELM

Parameters:

helm - HELM input

Returns:

HELM as JSON-objects

Throws:

ValidationException - if the HELM input is not valid

MonomerLoadingException - if the MonomerFactory can not be refreshed

ChemistryException - if the Chemistry Engine can not be initialized

com.fasterxml.jackson.core.JsonProcessingException - if json can not be produced

refreshMonomerCache

public void refreshMonomerCache() throws MonomerLoadingException, ChemistryException

method to refresh the monomer cache of the MonomerFactory

Throws:

MonomerLoadingException - if the MonomerFactory can not be loaded

ChemistryException - if chemistry engine can not be initialized

generateNaturalAnalogSequencePeptide

public String generateNaturalAnalogSequencePeptide(String notation) throws HELM2HandledException, ValidationException, MonomerLoadingException, PeptideUtilsException, org.helm.notation2.parser.exceptionparser.NotationException, ChemistryException

method to generate the natural analogue sequence for all peptide-sequences from an HELM input

Parameters:

notation - input HELM

Returns:

natural analogue peptide sequences, divided by white spaces

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if the input complex notation contains non-peptide polymer(s)

HELM2HandledException - if the HELM input contains HELM2 features

ValidationException - if the input HELM is not valid

MonomerLoadingException - if the MonomerFactory can not be refreshed

PeptideUtilsException - if the polymer is not a peptide

org.helm.notation2.parser.exceptionparser.NotationException - if notation is not valid

ChemistryException - if the Chemistry Engine can not be initialized

generateNaturalAnalogSequenceRNA

public String generateNaturalAnalogSequenceRNA(String notation) throws org.helm.notation2.parser.exceptionparser.NotationException, HELM2HandledException, ValidationException, MonomerLoadingException, ChemistryException

method to generate the natural analogue sequence for all rna-sequences from an HELM input

Parameters:

notation - HELM input

Returns:

natural analogue rna sequences, divided by white spaces

Throws:

org.helm.notation2.parser.exceptionparser.NotationException - if the input complex notation contains non-nucleid acid polymer(s)

HELM2HandledException - if HELM input contains HELM2 features

ValidationException - if the HELM input is not valid

MonomerLoadingException - if the MonomerFactory can not be refreshed

ChemistryException - if the Chemistry Engine can not be initialized

generateSMILESForHELM2

public String generateSMILESForHELM2(String notation) throws BuilderMoleculeException, org.helm.chemtoolkit.CTKException, ChemistryException, ValidationException, MonomerLoadingException

method to generate a SMILES representation for a whole HELM2 input

Parameters:

notation - given helm notation

Returns:

generated smiles for the given helm notation

Throws:

BuilderMoleculeException - if the molecule can't be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if chemistry engine can not be initialized

ValidationException - if notation is not valid

MonomerLoadingException - if monomers can not be loaded

generateCanSMILESForHELM2

public String generateCanSMILESForHELM2(String notation) throws BuilderMoleculeException, org.helm.chemtoolkit.CTKException, ChemistryException, ValidationException, MonomerLoadingException, NotationException

method to generate a SMILES representation for a whole HELM2 input

Parameters:

notation - given helm notation

Returns:

generated canonical smiles for the given notation

Throws:

BuilderMoleculeException - if the molecule can't be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if chemistry engine can not be initialized

ValidationException - if notation is not valid

MonomerLoadingException - if monomers can not be loaded

NotationException - if notation is not valid

convertMolFileSMILESWithAtomMapping

public String convertMolFileSMILESWithAtomMapping(String molfile, List<Attachment> attachments) throws org.helm.chemtoolkit.CTKException, ChemistryException

method to generate a smiles with atom mapping for a given molfile with the given attachments

Parameters:

molfile - given molfile

attachments - given attachments

Returns:

smiles with atom mapping

Throws:

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if the chemistry engine can not be initialized