org.helm.notation2

Class Monomer

java.lang.Object

org.helm.notation2.Monomer

All Implemented Interfaces:

Serializable

public class Monomer
extends Object
implements Serializable

This is a data model for Monomer. alternateId is used in polymer notation.

Author:

zhangtianhong

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	ATTACHMENT_LIST_DELIMITER
static String	BACKBONE_MOMONER_TYPE
static String	BRANCH_MOMONER_TYPE
static String	CHEMICAL_POLYMER_TYPE
static String	ID_A
static String	ID_ALA
static String	ID_ARG
static String	ID_ASN
static String	ID_ASP
static String	ID_C
static String	ID_CHEMICAL_STRUCTURE
static String	ID_CYS
static String	ID_dR
static String	ID_G
static String	ID_GLN
static String	ID_GLU
static String	ID_GLY
static String	ID_HIS
static String	ID_ILE
static String	ID_LEU
static String	ID_LYS
static String	ID_MET
static String	ID_P
static String	ID_PHE
static String	ID_PRO
static String	ID_R
static String	ID_SER
static String	ID_T
static String	ID_THR
static String	ID_TRP
static String	ID_TYR
static String	ID_U
static String	ID_VAL
static String	ID_X
static String	NUCLIEC_ACID_POLYMER_TYPE
static String	PEPTIDE_POLYMER_TYPE
static String	STARTING_NAME
static String[]	SUPPORTED_POLYMER_TYPES
static String	UNDEFINED_MOMONER_TYPE

Constructor Summary

Constructors

Constructor and Description
Monomer() constructor
Monomer(String polymerType, String monomerType, String naturalAnalog, String alternateId) Create a new monomer.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	addAttachment(Attachment attachment) Try to add a new attachment to this monomer
boolean	attachmentContains(Monomer monomer)
boolean	attachmentEquals(Monomer monomer)
boolean	containAnyAtom()
static Monomer	fromJSON(String json)
String	getAlternateId()
Attachment	getAttachment(String label) get a specific attachment by passing in a label
List<Attachment>	getAttachmentList()
String	getAttachmentListString()
String	getCanSMILES()
MoleculeProperty	getCapMoleculeInfo(String label) This method returns the MoleculeInfo for the input R group label of this monomer
int	getId()
String	getMolfile()
String	getMonomerType()
String	getName()
String	getNaturalAnalog() get the natural analog of this monomer.
String	getPolymerType()
boolean	isAdHocMonomer()
boolean	isModified() Test if this monomer has been modified.
boolean	isNewMonomer()
boolean	isSameType(Monomer m) Compare this momoner with another one, polymerType, monomerType and naturalAnalog (could be derived) must be the same to return true
void	setAdHocMonomer(boolean adHocMonomer)
void	setAlternateId(String alternateId)
void	setAttachmentList(List<Attachment> attachmentList)
void	setCanSMILES(String canSMILES)
void	setId(int id)
void	setMolfile(String molfile)
void	setMonomerType(String monomerType)
void	setName(String name)
void	setNaturalAnalog(String naturalAnalog)
void	setNewMonomer(boolean newMonomer)
void	setPolymerType(String polymerType)
String	toJSON()

Methods inherited from class java.lang.Object

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

Field Detail

NUCLIEC_ACID_POLYMER_TYPE

public static final String NUCLIEC_ACID_POLYMER_TYPE

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Constant Field Values

PEPTIDE_POLYMER_TYPE

public static final String PEPTIDE_POLYMER_TYPE

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Constant Field Values

CHEMICAL_POLYMER_TYPE

public static final String CHEMICAL_POLYMER_TYPE

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Constant Field Values

SUPPORTED_POLYMER_TYPES

public static final String[] SUPPORTED_POLYMER_TYPES

BACKBONE_MOMONER_TYPE

public static final String BACKBONE_MOMONER_TYPE

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Constant Field Values

BRANCH_MOMONER_TYPE

public static final String BRANCH_MOMONER_TYPE

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Constant Field Values

UNDEFINED_MOMONER_TYPE

public static final String UNDEFINED_MOMONER_TYPE

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Constant Field Values

STARTING_NAME

public static final String STARTING_NAME

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Constant Field Values

ATTACHMENT_LIST_DELIMITER

public static final String ATTACHMENT_LIST_DELIMITER

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Constant Field Values

ID_A

public static final String ID_A

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Constant Field Values

ID_G

public static final String ID_G

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Constant Field Values

ID_C

public static final String ID_C

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Constant Field Values

ID_U

public static final String ID_U

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Constant Field Values

ID_T

public static final String ID_T

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Constant Field Values

ID_R

public static final String ID_R

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Constant Field Values

ID_dR

public static final String ID_dR

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Constant Field Values

ID_P

public static final String ID_P

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Constant Field Values

ID_X

public static final String ID_X

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Constant Field Values

ID_ALA

public static final String ID_ALA

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Constant Field Values

ID_ARG

public static final String ID_ARG

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Constant Field Values

ID_ASN

public static final String ID_ASN

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Constant Field Values

ID_ASP

public static final String ID_ASP

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Constant Field Values

ID_CYS

public static final String ID_CYS

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Constant Field Values

ID_GLU

public static final String ID_GLU

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Constant Field Values

ID_GLN

public static final String ID_GLN

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Constant Field Values

ID_GLY

public static final String ID_GLY

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Constant Field Values

ID_HIS

public static final String ID_HIS

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Constant Field Values

ID_ILE

public static final String ID_ILE

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Constant Field Values

ID_LEU

public static final String ID_LEU

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Constant Field Values

ID_LYS

public static final String ID_LYS

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Constant Field Values

ID_MET

public static final String ID_MET

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Constant Field Values

ID_PHE

public static final String ID_PHE

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Constant Field Values

ID_PRO

public static final String ID_PRO

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Constant Field Values

ID_SER

public static final String ID_SER

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Constant Field Values

ID_THR

public static final String ID_THR

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Constant Field Values

ID_TRP

public static final String ID_TRP

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Constant Field Values

ID_TYR

public static final String ID_TYR

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Constant Field Values

ID_VAL

public static final String ID_VAL

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Constant Field Values

ID_CHEMICAL_STRUCTURE

public static final String ID_CHEMICAL_STRUCTURE

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Constant Field Values

Constructor Detail

Monomer

public Monomer()

constructor

Monomer

public Monomer(String polymerType,
       String monomerType,
       String naturalAnalog,
       String alternateId)

Create a new monomer.

Parameters:

polymerType - : unique text ID for the monomer, will be used in polymer notation

monomerType - : monomer type, Backbone, Branch, UnDefined

naturalAnalog - : the ID of its closest natural analog

alternateId - : unique text ID for the monomer, will be used in polymer notation

Method Detail

getId

public int getId()

setId

public void setId(int id)

getAlternateId

public String getAlternateId()

setAlternateId

public void setAlternateId(String alternateId)

getNaturalAnalog

public String getNaturalAnalog()

get the natural analog of this monomer. For standard, unmodified monomer, the natural analog should be itself

Returns:

natural analog of the monomer

setNaturalAnalog

public void setNaturalAnalog(String naturalAnalog)

setAdHocMonomer

public void setAdHocMonomer(boolean adHocMonomer)

isAdHocMonomer

public boolean isAdHocMonomer()

getCanSMILES

public String getCanSMILES()

setCanSMILES

public void setCanSMILES(String canSMILES)

getMonomerType

public String getMonomerType()

setMonomerType

public void setMonomerType(String monomerType)

getPolymerType

public String getPolymerType()

setPolymerType

public void setPolymerType(String polymerType)

getAttachmentList

public List<Attachment> getAttachmentList()

setAttachmentList

public void setAttachmentList(List<Attachment> attachmentList)

getMolfile

public String getMolfile()

setMolfile

public void setMolfile(String molfile)

getAttachment

public Attachment getAttachment(String label)

get a specific attachment by passing in a label

Parameters:

label - : unique for each attach point

Returns:

Attachment or null if there is no such attach point

getCapMoleculeInfo

public MoleculeProperty getCapMoleculeInfo(String label)
                                    throws org.helm.chemtoolkit.CTKException,
                                           ChemistryException,
                                           IOException

This method returns the MoleculeInfo for the input R group label of this monomer

Parameters:

label - - R1, R2...

Returns:

MoleculeInfo for the cap group, R group will contribute nothing

Throws:

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

ChemistryException - if chemistry could not be initialized

IOException - if molecule can not be read

addAttachment

public boolean addAttachment(Attachment attachment)

Try to add a new attachment to this monomer

Parameters:

attachment - -- new attachment to be add in

Returns:

true for success and false if there is one such attach point exist

getName

public String getName()

setName

public void setName(String name)

isModified

public boolean isModified()

Test if this monomer has been modified. The length of the alternatedId of an modified monomer should be greater than one.

Returns:

true/false

isSameType

public boolean isSameType(Monomer m)

Compare this momoner with another one, polymerType, monomerType and naturalAnalog (could be derived) must be the same to return true

Parameters:

m - monomer

Returns:

true or false

getAttachmentListString

public String getAttachmentListString()

isNewMonomer

public boolean isNewMonomer()

setNewMonomer

public void setNewMonomer(boolean newMonomer)

attachmentEquals

public boolean attachmentEquals(Monomer monomer)

attachmentContains

public boolean attachmentContains(Monomer monomer)

containAnyAtom

public boolean containAnyAtom()
                       throws IOException,
                              org.helm.chemtoolkit.CTKException,
                              ChemistryException

Throws:

IOException

org.helm.chemtoolkit.CTKException

ChemistryException

fromJSON

public static Monomer fromJSON(String json)

toJSON

public String toJSON()