org.helm.notation2.tools

Class MonomerParser

java.lang.Object

org.helm.notation2.tools.MonomerParser

public class MonomerParser
extends Object

MonomerParser

Author:

hecht

Field Summary

Fields

Modifier and Type	Field and Description
static String	ATTACHEMENT_ELEMENT
static String	ATTACHEMENT_ID_ELEMENT
static String	ATTACHEMENT_LABEL_ELEMENT
static String	ATTACHEMENTS_ELEMENT
static String	ATTACHEMENTS_LIST_ELEMENT
static String	CAP_GROUP_NAME_ELEMENT
static String	CAP_GROUP_SMILES_ELEMENT
static String	MONOMER_ELEMENT
static String	MONOMER_ID_ELEMENT
static String	MONOMER_MOL_FILE_ELEMENT
static String	MONOMER_NAME_ELEMENT
static String	MONOMER_SMILES_ELEMENT
static String	MONOMER_TYPE_ELEMENT
static String	NATURAL_ANALOG_ELEMENT
static String	POLYMER_TYPE_ELEMENT
protected static String	SMILES_EXTENSION_SEPARATOR_REGEX

Constructor Summary

Constructors

Constructor and Description
MonomerParser()

Method Summary

Methods

Modifier and Type	Method and Description
static void	fillAttachmentInfo(Attachment att)
static org.jdom2.Element	getAttachementElement(Attachment att) This method converts Attachment to ATTACHMENT XML element
static Attachment	getAttachment(org.jdom2.Element attachment) Convert ATTACHMENT element to Attachment object
static Monomer	getMonomer(org.jdom2.Element monomer) Convert monomer element to Monomer object
static Monomer	getMonomer(String monomerXMLString)
static org.jdom2.Element	getMonomerElement(Monomer monomer) This method converts Monomer to MONOMER XML element
static List<Monomer>	getMonomerList(String monomerXMLString)
static boolean	validateAttachement(Attachment attachment) This method validates Attachment by the following rules Attachment must have unique ID cap group SMILES must be valid cap group SMILES must contain one R group R group in SMILES must match R group label
static void	validateAttachmentLabel(String label) This method checks if attachment label is in the format of R#, where # is a number
static boolean	validateMonomer(Monomer monomer) This methods checks the validity of the monomer based on the following rules monomer cannot be null polymer type cannot be null and must be one of the defined polymer type monomer type cannot be null and must be one of the defined monomer type for a given polymer type Monomer ID cannot be null structure cannot be null for non-chemical type monomer structure SMILES must be valid attachment labels on monomer must be unique Attachment number on SMILES must match attachment List size Each attachment in attachment list must be valid (call validateAttachment()) Attachment labels on monomer must match atachment label on attachment list For non-chemical type monomers, modified monomer (ID length greater than 1) must have natural analog All monomers must have at least one attachment

Methods inherited from class java.lang.Object

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

Field Detail

MONOMER_ELEMENT

public static final String MONOMER_ELEMENT

See Also:

Constant Field Values

MONOMER_ID_ELEMENT

public static final String MONOMER_ID_ELEMENT

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Constant Field Values

MONOMER_SMILES_ELEMENT

public static final String MONOMER_SMILES_ELEMENT

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Constant Field Values

MONOMER_MOL_FILE_ELEMENT

public static final String MONOMER_MOL_FILE_ELEMENT

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Constant Field Values

MONOMER_TYPE_ELEMENT

public static final String MONOMER_TYPE_ELEMENT

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Constant Field Values

POLYMER_TYPE_ELEMENT

public static final String POLYMER_TYPE_ELEMENT

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Constant Field Values

NATURAL_ANALOG_ELEMENT

public static final String NATURAL_ANALOG_ELEMENT

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Constant Field Values

MONOMER_NAME_ELEMENT

public static final String MONOMER_NAME_ELEMENT

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Constant Field Values

ATTACHEMENTS_LIST_ELEMENT

public static final String ATTACHEMENTS_LIST_ELEMENT

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Constant Field Values

ATTACHEMENTS_ELEMENT

public static final String ATTACHEMENTS_ELEMENT

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Constant Field Values

ATTACHEMENT_ELEMENT

public static final String ATTACHEMENT_ELEMENT

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Constant Field Values

ATTACHEMENT_ID_ELEMENT

public static final String ATTACHEMENT_ID_ELEMENT

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Constant Field Values

ATTACHEMENT_LABEL_ELEMENT

public static final String ATTACHEMENT_LABEL_ELEMENT

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Constant Field Values

CAP_GROUP_NAME_ELEMENT

public static final String CAP_GROUP_NAME_ELEMENT

See Also:

Constant Field Values

CAP_GROUP_SMILES_ELEMENT

public static final String CAP_GROUP_SMILES_ELEMENT

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Constant Field Values

SMILES_EXTENSION_SEPARATOR_REGEX

protected static final String SMILES_EXTENSION_SEPARATOR_REGEX

See Also:

Constant Field Values

Constructor Detail

MonomerParser

public MonomerParser()

Method Detail

getAttachment

public static Attachment getAttachment(org.jdom2.Element attachment)

Convert ATTACHMENT element to Attachment object

Parameters:

attachment - element

Returns:

Attachment

getAttachementElement

public static org.jdom2.Element getAttachementElement(Attachment att)

This method converts Attachment to ATTACHMENT XML element

Parameters:

att - -- Attachment

Returns:

Element

validateAttachement

public static boolean validateAttachement(Attachment attachment)
                                   throws MonomerException,
                                          IOException,
                                          ChemistryException

This method validates Attachment by the following rules Attachment must have unique ID cap group SMILES must be valid cap group SMILES must contain one R group R group in SMILES must match R group label

Parameters:

attachment - given attachment

Returns:

true or false

Throws:

MonomerException - if attachment is not valid

IOException - IO error

ChemistryException - if chemistry engine can not be initialized

getMonomer

public static Monomer getMonomer(org.jdom2.Element monomer)
                          throws MonomerException

Convert monomer element to Monomer object

Parameters:

monomer - element

Returns:

Monomer

Throws:

MonomerException - if element is not a valid monomer

getMonomerElement

public static org.jdom2.Element getMonomerElement(Monomer monomer)
                                           throws MonomerException

This method converts Monomer to MONOMER XML element

Parameters:

monomer - given monomer

Returns:

Element

Throws:

MonomerException - if monomer is not valid

getMonomerList

public static List<Monomer> getMonomerList(String monomerXMLString)
                                    throws org.jdom2.JDOMException,
                                           IOException,
                                           MonomerException,
                                           org.helm.chemtoolkit.CTKException,
                                           ChemistryException

Throws:

org.jdom2.JDOMException

IOException

MonomerException

org.helm.chemtoolkit.CTKException

ChemistryException

getMonomer

public static Monomer getMonomer(String monomerXMLString)
                          throws org.jdom2.JDOMException,
                                 IOException,
                                 MonomerException

Throws:

org.jdom2.JDOMException

IOException

MonomerException

validateMonomer

public static boolean validateMonomer(Monomer monomer)
                               throws MonomerException,
                                      IOException,
                                      org.helm.chemtoolkit.CTKException,
                                      ChemistryException

This methods checks the validity of the monomer based on the following rules monomer cannot be null polymer type cannot be null and must be one of the defined polymer type monomer type cannot be null and must be one of the defined monomer type for a given polymer type Monomer ID cannot be null structure cannot be null for non-chemical type monomer structure SMILES must be valid attachment labels on monomer must be unique Attachment number on SMILES must match attachment List size Each attachment in attachment list must be valid (call validateAttachment()) Attachment labels on monomer must match atachment label on attachment list For non-chemical type monomers, modified monomer (ID length greater than 1) must have natural analog All monomers must have at least one attachment

Parameters:

monomer - given monomer

Returns:

true or false

Throws:

MonomerException - if monomer is not valid

IOException - IO error

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

ChemistryException - if chemistry engine can not be initialized

validateAttachmentLabel

public static void validateAttachmentLabel(String label)
                                    throws MonomerException

This method checks if attachment label is in the format of R#, where # is a number

Parameters:

label - attachment label

Throws:

MonomerException - if label is not valid

fillAttachmentInfo

public static void fillAttachmentInfo(Attachment att)
                               throws MonomerException,
                                      IOException,
                                      org.jdom2.JDOMException,
                                      ChemistryException,
                                      org.helm.chemtoolkit.CTKException

Throws:

MonomerException

IOException

org.jdom2.JDOMException

ChemistryException

org.helm.chemtoolkit.CTKException