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	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 Description

Monomer()
constructor

Monomer(String polymerType, String monomerType, String naturalAnalog, String alternateId)
Create a new monomer.

Method Summary

Modifier and Type	Method	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 Details
- NUCLIEC_ACID_POLYMER_TYPE
  
  public static final String NUCLIEC_ACID_POLYMER_TYPE
  
  See Also:
  
  Constant Field Values
- PEPTIDE_POLYMER_TYPE
  
  public static final String PEPTIDE_POLYMER_TYPE
  
  See Also:
  
  Constant Field Values
- CHEMICAL_POLYMER_TYPE
  
  public static final String CHEMICAL_POLYMER_TYPE
  
  See Also:
  
  Constant Field Values
- SUPPORTED_POLYMER_TYPES
  
  public static final String[] SUPPORTED_POLYMER_TYPES
- BACKBONE_MOMONER_TYPE
  
  public static final String BACKBONE_MOMONER_TYPE
  
  See Also:
  
  Constant Field Values
- BRANCH_MOMONER_TYPE
  
  public static final String BRANCH_MOMONER_TYPE
  
  See Also:
  
  Constant Field Values
- UNDEFINED_MOMONER_TYPE
  
  public static final String UNDEFINED_MOMONER_TYPE
  
  See Also:
  
  Constant Field Values
- STARTING_NAME
  
  public static final String STARTING_NAME
  
  See Also:
  
  Constant Field Values
- ATTACHMENT_LIST_DELIMITER
  
  public static final String ATTACHMENT_LIST_DELIMITER
  
  See Also:
  
  Constant Field Values
- ID_A
  
  public static final String ID_A
  
  See Also:
  
  Constant Field Values
- ID_G
  
  public static final String ID_G
  
  See Also:
  
  Constant Field Values
- ID_C
  
  public static final String ID_C
  
  See Also:
  
  Constant Field Values
- ID_U
  
  public static final String ID_U
  
  See Also:
  
  Constant Field Values
- ID_T
  
  public static final String ID_T
  
  See Also:
  
  Constant Field Values
- ID_R
  
  public static final String ID_R
  
  See Also:
  
  Constant Field Values
- ID_dR
  
  public static final String ID_dR
  
  See Also:
  
  Constant Field Values
- ID_P
  
  public static final String ID_P
  
  See Also:
  
  Constant Field Values
- ID_X
  
  public static final String ID_X
  
  See Also:
  
  Constant Field Values
- ID_ALA
  
  public static final String ID_ALA
  
  See Also:
  
  Constant Field Values
- ID_ARG
  
  public static final String ID_ARG
  
  See Also:
  
  Constant Field Values
- ID_ASN
  
  public static final String ID_ASN
  
  See Also:
  
  Constant Field Values
- ID_ASP
  
  public static final String ID_ASP
  
  See Also:
  
  Constant Field Values
- ID_CYS
  
  public static final String ID_CYS
  
  See Also:
  
  Constant Field Values
- ID_GLU
  
  public static final String ID_GLU
  
  See Also:
  
  Constant Field Values
- ID_GLN
  
  public static final String ID_GLN
  
  See Also:
  
  Constant Field Values
- ID_GLY
  
  public static final String ID_GLY
  
  See Also:
  
  Constant Field Values
- ID_HIS
  
  public static final String ID_HIS
  
  See Also:
  
  Constant Field Values
- ID_ILE
  
  public static final String ID_ILE
  
  See Also:
  
  Constant Field Values
- ID_LEU
  
  public static final String ID_LEU
  
  See Also:
  
  Constant Field Values
- ID_LYS
  
  public static final String ID_LYS
  
  See Also:
  
  Constant Field Values
- ID_MET
  
  public static final String ID_MET
  
  See Also:
  
  Constant Field Values
- ID_PHE
  
  public static final String ID_PHE
  
  See Also:
  
  Constant Field Values
- ID_PRO
  
  public static final String ID_PRO
  
  See Also:
  
  Constant Field Values
- ID_SER
  
  public static final String ID_SER
  
  See Also:
  
  Constant Field Values
- ID_THR
  
  public static final String ID_THR
  
  See Also:
  
  Constant Field Values
- ID_TRP
  
  public static final String ID_TRP
  
  See Also:
  
  Constant Field Values
- ID_TYR
  
  public static final String ID_TYR
  
  See Also:
  
  Constant Field Values
- ID_VAL
  
  public static final String ID_VAL
  
  See Also:
  
  Constant Field Values
- ID_CHEMICAL_STRUCTURE
  
  public static final String ID_CHEMICAL_STRUCTURE
  
  See Also:
  
  Constant Field Values
Constructor Details
- 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 Details
- 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()

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

Class Monomer

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

Constructor Details

Method Details