java.lang.Object
- org.rcsb.cif.model.BaseCategory
- - org.rcsb.cif.model.generated.ChemComp

All Implemented Interfaces:

Category
```
@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class ChemComp
extends BaseCategory
```
Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components.

Field Summary
- Fields inherited from class org.rcsb.cif.model.BaseCategory
  isText, textFields

Constructor Summary

Constructors
Constructor	Description
`ChemComp(String name)`
`ChemComp(String name, int rowCount, Object[] encodedColumns)`
`ChemComp(String name, Map<String,Column> columns)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`StrColumn`	`getFormula()`	The formula for the chemical component.
`FloatColumn`	`getFormulaWeight()`	Formula mass in daltons of the chemical component.
`StrColumn`	`getId()`	The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list.
`StrColumn`	`getModelDetails()`	A description of special aspects of the generation of the coordinates for the model of the component.
`StrColumn`	`getModelErf()`	A pointer to an external reference file from which the atomic description of the component is taken.
`StrColumn`	`getModelSource()`	The source of the coordinates for the model of the component.
`StrColumn`	`getMonNstdClass()`	A description of the class of a nonstandard monomer if the nonstandard monomer represents a modification of a standard monomer.
`StrColumn`	`getMonNstdDetails()`	A description of special details of a nonstandard monomer.
`StrColumn`	`getMonNstdFlag()`	'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'.
`StrColumn`	`getMonNstdParent()`	The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer.
`StrColumn`	`getMonNstdParentCompId()`	The identifier for the parent component of the nonstandard component.
`StrColumn`	`getName()`	The full name of the component.
`IntColumn`	`getNumberAtomsAll()`	The total number of atoms in the component.
`IntColumn`	`getNumberAtomsNh()`	The number of non-hydrogen atoms in the component.
`StrColumn`	`getOneLetterCode()`	For standard polymer components, the one-letter code for the component.
`StrColumn`	`getPdbxAmbiguousFlag()`	A preliminary classification used by PDB to indicate that the chemistry of this component while described as clearly as possible is still ambiguous.
`StrColumn`	`getPdbxCasnum()`	Chemical Abstract Service identifier.
`StrColumn`	`getPdbxClass1()`	Internal classifier used to organize ligand dictionary (broad chemical class).
`StrColumn`	`getPdbxClass2()`	Internal classifier used to organize ligand dictionary (notable chemical features).
`IntColumn`	`getPdbxComponentNo()`	A serial number used by PDB in the FORMUL record.
`StrColumn`	`getPdbxCompType()`	A type classification of this chemical component.
`IntColumn`	`getPdbxFormalCharge()`	The net integer charge assigned to this component.
`StrColumn`	`getPdbxIdealCoordinatesDetails()`	This data item identifies the source of the ideal coordinates in the component definition.
`StrColumn`	`getPdbxIdealCoordinatesMissingFlag()`	This data item identifies if ideal coordinates are missing in this definition.
`StrColumn`	`getPdbxInitialDate()`	Date component was added to database.
`StrColumn`	`getPdbxModelCoordinatesDbCode()`	This data item identifies the PDB database code from which the heavy atom model coordinates were obtained.
`StrColumn`	`getPdbxModelCoordinatesDetails()`	This data item provides additional details about the model coordinates in the component definition.
`StrColumn`	`getPdbxModelCoordinatesMissingFlag()`	This data item identifies if model coordinates are missing in this definition.
`StrColumn`	`getPdbxModificationDetails()`	For nonstandard components a text description of modification of the parent component.
`StrColumn`	`getPdbxModifiedDate()`	Date component was last modified.
`StrColumn`	`getPdbxNscnum()`	NSC identifier for component.
`IntColumn`	`getPdbxNumberSubcomponents()`	The number of subcomponents represented in this component.
`StrColumn`	`getPdbxProcessingSite()`	This data item identifies the deposition site that processed this chemical component defintion.
`StrColumn`	`getPdbxReleaseStatus()`	This data item holds the current release status for the component.
`StrColumn`	`getPdbxReplacedBy()`	Identifies the _chem_comp.id of the component that has replaced this component.
`StrColumn`	`getPdbxReplaces()`	Identifies the _chem_comp.id's of the components which have been replaced by this component.
`StrColumn`	`getPdbxReservedName()`	Previous chemical name used for this component if a name correction has been made.
`StrColumn`	`getPdbxSmiles()`	SMILES code for component.
`StrColumn`	`getPdbxStatus()`	Release status of component
`StrColumn`	`getPdbxSubcomponentList()`	The list of subcomponents contained in this component.
`StrColumn`	`getPdbxSynonyms()`	Synonym list for the component.
`StrColumn`	`getPdbxType()`	A preliminary classification used by PDB.
`IntColumn`	`getPdbxTypeModified()`	Modification flag.
`StrColumn`	`getThreeLetterCode()`	For standard polymer components, the common three-letter code for the component.
`StrColumn`	`getType()`	For standard polymer components, the type of the monomer.

Methods inherited from class org.rcsb.cif.model.BaseCategory
getBinaryColumn, getCategoryName, getColumn, getColumnNames, getRowCount, isDefined

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.rcsb.cif.model.Category
columnNames, columns, get

- Constructor Detail
  - ChemComp
```
public ChemComp(String name,
                Map<String,Column> columns)
```
  - ChemComp
```
public ChemComp(String name,
                int rowCount,
                Object[] encodedColumns)
```
  - ChemComp
```
public ChemComp(String name)
```
- Method Detail
  - getFormula
```
public StrColumn getFormula()
```
    The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts.
    
    Returns:
    
    StrColumn
  - getFormulaWeight
```
public FloatColumn getFormulaWeight()
```
    Formula mass in daltons of the chemical component.
    
    Returns:
    
    FloatColumn
  - getId
```
public StrColumn getId()
```
    The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base.
    
    Returns:
    
    StrColumn
  - getModelDetails
```
public StrColumn getModelDetails()
```
    A description of special aspects of the generation of the coordinates for the model of the component.
    
    Returns:
    
    StrColumn
  - getModelErf
```
public StrColumn getModelErf()
```
    A pointer to an external reference file from which the atomic description of the component is taken.
    
    Returns:
    
    StrColumn
  - getModelSource
```
public StrColumn getModelSource()
```
    The source of the coordinates for the model of the component.
    
    Returns:
    
    StrColumn
  - getMonNstdClass
```
public StrColumn getMonNstdClass()
```
    A description of the class of a nonstandard monomer if the nonstandard monomer represents a modification of a standard monomer.
    
    Returns:
    
    StrColumn
  - getMonNstdDetails
```
public StrColumn getMonNstdDetails()
```
    A description of special details of a nonstandard monomer.
    
    Returns:
    
    StrColumn
  - getMonNstdFlag
```
public StrColumn getMonNstdFlag()
```
    'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and _chem_comp.mon_nstd_details data items.
    
    Returns:
    
    StrColumn
  - getMonNstdParent
```
public StrColumn getMonNstdParent()
```
    The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer.
    
    Returns:
    
    StrColumn
  - getMonNstdParentCompId
```
public StrColumn getMonNstdParentCompId()
```
    The identifier for the parent component of the nonstandard component. May be be a comma separated list if this component is derived from multiple components. Items in this indirectly point to _chem_comp.id in the CHEM_COMP category.
    
    Returns:
    
    StrColumn
  - getName
```
public StrColumn getName()
```
    The full name of the component.
    
    Returns:
    
    StrColumn
  - getNumberAtomsAll
```
public IntColumn getNumberAtomsAll()
```
    The total number of atoms in the component.
    
    Returns:
    
    IntColumn
  - getNumberAtomsNh
```
public IntColumn getNumberAtomsNh()
```
    The number of non-hydrogen atoms in the component.
    
    Returns:
    
    IntColumn
  - getOneLetterCode
```
public StrColumn getOneLetterCode()
```
    For standard polymer components, the one-letter code for the component. For non-standard polymer components, the one-letter code for parent component if this exists; otherwise, the one-letter code should be given as 'X'. Components that derived from multiple parents components are described by a sequence of one-letter-codes.
    
    Returns:
    
    StrColumn
  - getThreeLetterCode
```
public StrColumn getThreeLetterCode()
```
    For standard polymer components, the common three-letter code for the component. Non-standard polymer components and non-polymer components are also assigned three-letter-codes. For ambiguous polymer components three-letter code should be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'. Ambiguous non-polymer components are assigned the code 'UNL'.
    
    Returns:
    
    StrColumn
  - getType
```
public StrColumn getType()
```
    For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap.
    
    Returns:
    
    StrColumn
  - getPdbxSynonyms
```
public StrColumn getPdbxSynonyms()
```
    Synonym list for the component.
    
    Returns:
    
    StrColumn
  - getPdbxModificationDetails
```
public StrColumn getPdbxModificationDetails()
```
    For nonstandard components a text description of modification of the parent component.
    
    Returns:
    
    StrColumn
  - getPdbxComponentNo
```
public IntColumn getPdbxComponentNo()
```
    A serial number used by PDB in the FORMUL record.
    
    Returns:
    
    IntColumn
  - getPdbxType
```
public StrColumn getPdbxType()
```
    A preliminary classification used by PDB.
    
    Returns:
    
    StrColumn
  - getPdbxAmbiguousFlag
```
public StrColumn getPdbxAmbiguousFlag()
```
    A preliminary classification used by PDB to indicate that the chemistry of this component while described as clearly as possible is still ambiguous. Software tools may not be able to process this component definition.
    
    Returns:
    
    StrColumn
  - getPdbxReplacedBy
```
public StrColumn getPdbxReplacedBy()
```
    Identifies the _chem_comp.id of the component that has replaced this component.
    
    Returns:
    
    StrColumn
  - getPdbxReplaces
```
public StrColumn getPdbxReplaces()
```
    Identifies the _chem_comp.id's of the components which have been replaced by this component. Multiple id codes should be separated by commas.
    
    Returns:
    
    StrColumn
  - getPdbxFormalCharge
```
public IntColumn getPdbxFormalCharge()
```
    The net integer charge assigned to this component. This is the formal charge assignment normally found in chemical diagrams.
    
    Returns:
    
    IntColumn
  - getPdbxSubcomponentList
```
public StrColumn getPdbxSubcomponentList()
```
    The list of subcomponents contained in this component.
    
    Returns:
    
    StrColumn
  - getPdbxModelCoordinatesDetails
```
public StrColumn getPdbxModelCoordinatesDetails()
```
    This data item provides additional details about the model coordinates in the component definition.
    
    Returns:
    
    StrColumn
  - getPdbxModelCoordinatesDbCode
```
public StrColumn getPdbxModelCoordinatesDbCode()
```
    This data item identifies the PDB database code from which the heavy atom model coordinates were obtained.
    
    Returns:
    
    StrColumn
  - getPdbxIdealCoordinatesDetails
```
public StrColumn getPdbxIdealCoordinatesDetails()
```
    This data item identifies the source of the ideal coordinates in the component definition.
    
    Returns:
    
    StrColumn
  - getPdbxIdealCoordinatesMissingFlag
```
public StrColumn getPdbxIdealCoordinatesMissingFlag()
```
    This data item identifies if ideal coordinates are missing in this definition.
    
    Returns:
    
    StrColumn
  - getPdbxModelCoordinatesMissingFlag
```
public StrColumn getPdbxModelCoordinatesMissingFlag()
```
    This data item identifies if model coordinates are missing in this definition.
    
    Returns:
    
    StrColumn
  - getPdbxInitialDate
```
public StrColumn getPdbxInitialDate()
```
    Date component was added to database.
    
    Returns:
    
    StrColumn
  - getPdbxModifiedDate
```
public StrColumn getPdbxModifiedDate()
```
    Date component was last modified.
    
    Returns:
    
    StrColumn
  - getPdbxReleaseStatus
```
public StrColumn getPdbxReleaseStatus()
```
    This data item holds the current release status for the component.
    
    Returns:
    
    StrColumn
  - getPdbxProcessingSite
```
public StrColumn getPdbxProcessingSite()
```
    This data item identifies the deposition site that processed this chemical component defintion.
    
    Returns:
    
    StrColumn
  - getPdbxNumberSubcomponents
```
public IntColumn getPdbxNumberSubcomponents()
```
    The number of subcomponents represented in this component.
    
    Returns:
    
    IntColumn
  - getPdbxClass1
```
public StrColumn getPdbxClass1()
```
    Internal classifier used to organize ligand dictionary (broad chemical class).
    
    Returns:
    
    StrColumn
  - getPdbxClass2
```
public StrColumn getPdbxClass2()
```
    Internal classifier used to organize ligand dictionary (notable chemical features).
    
    Returns:
    
    StrColumn
  - getPdbxCompType
```
public StrColumn getPdbxCompType()
```
    A type classification of this chemical component.
    
    Returns:
    
    StrColumn
  - getPdbxReservedName
```
public StrColumn getPdbxReservedName()
```
    Previous chemical name used for this component if a name correction has been made.
    
    Returns:
    
    StrColumn
  - getPdbxStatus
```
public StrColumn getPdbxStatus()
```
    Release status of component
    
    Returns:
    
    StrColumn
  - getPdbxTypeModified
```
public IntColumn getPdbxTypeModified()
```
    Modification flag.
    
    Returns:
    
    IntColumn
  - getPdbxCasnum
```
public StrColumn getPdbxCasnum()
```
    Chemical Abstract Service identifier.
    
    Returns:
    
    StrColumn
  - getPdbxSmiles
```
public StrColumn getPdbxSmiles()
```
    SMILES code for component.
    
    Returns:
    
    StrColumn
  - getPdbxNscnum
```
public StrColumn getPdbxNscnum()
```
    NSC identifier for component.
    
    Returns:
    
    StrColumn

Class ChemComp

Field Summary

Fields inherited from class org.rcsb.cif.model.BaseCategory

Constructor Summary

Method Summary

Methods inherited from class org.rcsb.cif.model.BaseCategory

Methods inherited from class java.lang.Object

Methods inherited from interface org.rcsb.cif.model.Category

Constructor Detail

ChemComp

ChemComp

ChemComp

Method Detail

getFormula

getFormulaWeight

getId

getModelDetails

getModelErf

getModelSource

getMonNstdClass

getMonNstdDetails

getMonNstdFlag

getMonNstdParent

getMonNstdParentCompId

getName

getNumberAtomsAll

getNumberAtomsNh

getOneLetterCode

getThreeLetterCode

getType

getPdbxSynonyms

getPdbxModificationDetails

getPdbxComponentNo

getPdbxType

getPdbxAmbiguousFlag

getPdbxReplacedBy

getPdbxReplaces

getPdbxFormalCharge

getPdbxSubcomponentList

getPdbxModelCoordinatesDetails

getPdbxModelCoordinatesDbCode

getPdbxIdealCoordinatesDetails

getPdbxIdealCoordinatesMissingFlag

getPdbxModelCoordinatesMissingFlag

getPdbxInitialDate

getPdbxModifiedDate

getPdbxReleaseStatus

getPdbxProcessingSite

getPdbxNumberSubcomponents

getPdbxClass1

getPdbxClass2

getPdbxCompType

getPdbxReservedName

getPdbxStatus

getPdbxTypeModified

getPdbxCasnum

getPdbxSmiles

getPdbxNscnum