ChemComp (biojava 5.3.0 API)

java.lang.Object
- org.biojava.nbio.structure.io.mmcif.model.ChemComp

All Implemented Interfaces:

Serializable, Comparable<ChemComp>
```
public class ChemComp
extends Object
implements Serializable, Comparable<ChemComp>
```
A definition for a Chemical Component, as maintained by the wwPDB. For access to all definitions, please download the components.cif.gz file from the wwPDB website.

Author:

Andreas Prlic

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

ChemComp()

Constructors
Constructor and Description
`ChemComp()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compareTo(ChemComp arg0)`
`boolean`	`equals(Object obj)`
`List<ChemCompAtom>`	`getAtoms()`
`List<ChemCompBond>`	`getBonds()`
`List<ChemCompDescriptor>`	`getDescriptors()`
`static ChemComp`	`getEmptyChemComp()` Creates a new instance of the dummy empty ChemComp.
`String`	`getFormula_weight()`
`String`	`getFormula()`
`String`	`getId()`
`String`	`getMon_nstd_flag()`
`String`	`getMon_nstd_parent_comp_id()`
`String`	`getName()`
`String`	`getOne_letter_code()`
`String`	`getPdbx_ambiguous_flag()`
`String`	`getPdbx_formal_charge()`
`String`	`getPdbx_ideal_coordinates_details()`
`String`	`getPdbx_ideal_coordinates_missing_flag()`
`String`	`getPdbx_initial_date()`
`String`	`getPdbx_model_coordinates_db_code()`
`String`	`getPdbx_model_coordinates_details()`
`String`	`getPdbx_model_coordinates_missing_flag()`
`String`	`getPdbx_modified_date()`
`String`	`getPdbx_processing_site()`
`String`	`getPdbx_release_status()`
`String`	`getPdbx_replaced_by()`
`String`	`getPdbx_replaces()`
`String`	`getPdbx_subcomponent_list()`
`String`	`getPdbx_synonyms()`
`String`	`getPdbx_type()`
`PolymerType`	`getPolymerType()`
`ResidueType`	`getResidueType()`
`String`	`getThree_letter_code()`
`String`	`getType()`
`int`	`hashCode()`
`boolean`	`hasParent()`
`boolean`	`isEmpty()` Indicates whether this compound was created with
`boolean`	`isStandard()`
`void`	`setAtoms(List<ChemCompAtom> atoms)`
`void`	`setBonds(List<ChemCompBond> bonds)`
`void`	`setDescriptors(List<ChemCompDescriptor> descriptors)`
`void`	`setFormula_weight(String formula_weight)`
`void`	`setFormula(String formula)`
`void`	`setId(String id)`
`void`	`setMon_nstd_flag(String mon_nstd_flag)`
`void`	`setMon_nstd_parent_comp_id(String mon_nstd_parent_comp_id)`
`void`	`setName(String name)`
`void`	`setOne_letter_code(String one_letter_code)`
`void`	`setPdbx_ambiguous_flag(String pdbx_ambiguous_flag)`
`void`	`setPdbx_formal_charge(String pdbx_formal_charge)`
`void`	`setPdbx_ideal_coordinates_details(String pdbx_ideal_coordinates_details)`
`void`	`setPdbx_ideal_coordinates_missing_flag(String pdbx_ideal_coordinates_missing_flag)`
`void`	`setPdbx_initial_date(String pdbx_initial_date)`
`void`	`setPdbx_model_coordinates_db_code(String pdbx_model_coordinates_db_code)`
`void`	`setPdbx_model_coordinates_details(String pdbx_model_coordinates_details)`
`void`	`setPdbx_model_coordinates_missing_flag(String pdbx_model_coordinates_missing_flag)`
`void`	`setPdbx_modified_date(String pdbx_modified_date)`
`void`	`setPdbx_processing_site(String pdbx_processing_site)`
`void`	`setPdbx_release_status(String pdbx_release_status)`
`void`	`setPdbx_replaced_by(String pdbx_replaced_by)`
`void`	`setPdbx_replaces(String pdbx_replaces)`
`void`	`setPdbx_subcomponent_list(String pdbx_subcomponent_list)`
`void`	`setPdbx_synonyms(String pdbx_synonyms)`
`void`	`setPdbx_type(String pdbx_type)`
`void`	`setPolymerType(PolymerType polymerType)`
`void`	`setResidueType(ResidueType residueType)`
`void`	`setStandard(boolean standard)`
`void`	`setThree_letter_code(String three_letter_code)`
`void`	`setType(String type)`
`String`	`toString()`

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

Constructor Detail
- ChemComp
```
public ChemComp()
```

Method Detail

toString
```
public String toString()
```
Overrides:

toString in class Object

hasParent
```
public boolean hasParent()
```

isStandard
```
public boolean isStandard()
```

getId
```
public String getId()
```

setId
```
public void setId(String id)
```

getName
```
public String getName()
```

setName
```
public void setName(String name)
```

getType
```
public String getType()
```

setType
```
public void setType(String type)
```

getResidueType
```
public ResidueType getResidueType()
```

setResidueType

public void setResidueType(ResidueType residueType)

getPolymerType
```
public PolymerType getPolymerType()
```

setPolymerType

public void setPolymerType(PolymerType polymerType)

getPdbx_type
```
public String getPdbx_type()
```

setPdbx_type

public void setPdbx_type(String pdbx_type)

getFormula
```
public String getFormula()
```

setFormula

public void setFormula(String formula)

getMon_nstd_parent_comp_id

public String getMon_nstd_parent_comp_id()

setMon_nstd_parent_comp_id

public void setMon_nstd_parent_comp_id(String mon_nstd_parent_comp_id)

getPdbx_synonyms
```
public String getPdbx_synonyms()
```

setPdbx_synonyms

public void setPdbx_synonyms(String pdbx_synonyms)

getPdbx_formal_charge
```
public String getPdbx_formal_charge()
```

setPdbx_formal_charge

public void setPdbx_formal_charge(String pdbx_formal_charge)

getPdbx_initial_date
```
public String getPdbx_initial_date()
```

setPdbx_initial_date

public void setPdbx_initial_date(String pdbx_initial_date)

getPdbx_modified_date
```
public String getPdbx_modified_date()
```

setPdbx_modified_date

public void setPdbx_modified_date(String pdbx_modified_date)

getPdbx_ambiguous_flag

public String getPdbx_ambiguous_flag()

setPdbx_ambiguous_flag

public void setPdbx_ambiguous_flag(String pdbx_ambiguous_flag)

getPdbx_release_status

public String getPdbx_release_status()

setPdbx_release_status

public void setPdbx_release_status(String pdbx_release_status)

getPdbx_replaced_by
```
public String getPdbx_replaced_by()
```

setPdbx_replaced_by

public void setPdbx_replaced_by(String pdbx_replaced_by)

getPdbx_replaces
```
public String getPdbx_replaces()
```

setPdbx_replaces

public void setPdbx_replaces(String pdbx_replaces)

getFormula_weight
```
public String getFormula_weight()
```

setFormula_weight

public void setFormula_weight(String formula_weight)

getOne_letter_code
```
public String getOne_letter_code()
```

setOne_letter_code

public void setOne_letter_code(String one_letter_code)

getThree_letter_code
```
public String getThree_letter_code()
```

setThree_letter_code

public void setThree_letter_code(String three_letter_code)

getPdbx_model_coordinates_details

public String getPdbx_model_coordinates_details()

setPdbx_model_coordinates_details

public void setPdbx_model_coordinates_details(String pdbx_model_coordinates_details)

getPdbx_model_coordinates_missing_flag

public String getPdbx_model_coordinates_missing_flag()

setPdbx_model_coordinates_missing_flag

public void setPdbx_model_coordinates_missing_flag(String pdbx_model_coordinates_missing_flag)

getPdbx_ideal_coordinates_details

public String getPdbx_ideal_coordinates_details()

setPdbx_ideal_coordinates_details

public void setPdbx_ideal_coordinates_details(String pdbx_ideal_coordinates_details)

getPdbx_ideal_coordinates_missing_flag

public String getPdbx_ideal_coordinates_missing_flag()

setPdbx_ideal_coordinates_missing_flag

public void setPdbx_ideal_coordinates_missing_flag(String pdbx_ideal_coordinates_missing_flag)

getPdbx_model_coordinates_db_code

public String getPdbx_model_coordinates_db_code()

setPdbx_model_coordinates_db_code

public void setPdbx_model_coordinates_db_code(String pdbx_model_coordinates_db_code)

getPdbx_subcomponent_list

public String getPdbx_subcomponent_list()

setPdbx_subcomponent_list

public void setPdbx_subcomponent_list(String pdbx_subcomponent_list)

getPdbx_processing_site

public String getPdbx_processing_site()

setPdbx_processing_site

public void setPdbx_processing_site(String pdbx_processing_site)

setStandard

public void setStandard(boolean standard)

getMon_nstd_flag
```
public String getMon_nstd_flag()
```

setMon_nstd_flag

public void setMon_nstd_flag(String mon_nstd_flag)

getDescriptors

public List<ChemCompDescriptor> getDescriptors()

setDescriptors

public void setDescriptors(List<ChemCompDescriptor> descriptors)

getBonds
```
public List<ChemCompBond> getBonds()
```

setBonds

public void setBonds(List<ChemCompBond> bonds)

getAtoms
```
public List<ChemCompAtom> getAtoms()
```

setAtoms

public void setAtoms(List<ChemCompAtom> atoms)

compareTo
```
public int compareTo(ChemComp arg0)
```
Specified by:

compareTo in interface Comparable<ChemComp>

hashCode
```
public int hashCode()
```
Overrides:

hashCode in class Object

equals
```
public boolean equals(Object obj)
```
Overrides:

equals in class Object

getEmptyChemComp
```
public static ChemComp getEmptyChemComp()
```
Creates a new instance of the dummy empty ChemComp.

Returns:

isEmpty
```
public boolean isEmpty()
```
Indicates whether this compound was created with

Returns:

Class ChemComp

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ChemComp

Method Detail

toString

hasParent

isStandard

getId

setId

getName

setName

getType

setType

getResidueType

setResidueType

getPolymerType

setPolymerType

getPdbx_type

setPdbx_type

getFormula

setFormula

getMon_nstd_parent_comp_id

setMon_nstd_parent_comp_id

getPdbx_synonyms

setPdbx_synonyms

getPdbx_formal_charge

setPdbx_formal_charge

getPdbx_initial_date

setPdbx_initial_date

getPdbx_modified_date

setPdbx_modified_date

getPdbx_ambiguous_flag

setPdbx_ambiguous_flag

getPdbx_release_status

setPdbx_release_status

getPdbx_replaced_by

setPdbx_replaced_by

getPdbx_replaces

setPdbx_replaces

getFormula_weight

setFormula_weight

getOne_letter_code

setOne_letter_code

getThree_letter_code

setThree_letter_code

getPdbx_model_coordinates_details

setPdbx_model_coordinates_details

getPdbx_model_coordinates_missing_flag

setPdbx_model_coordinates_missing_flag

getPdbx_ideal_coordinates_details

setPdbx_ideal_coordinates_details

getPdbx_ideal_coordinates_missing_flag

setPdbx_ideal_coordinates_missing_flag

getPdbx_model_coordinates_db_code

setPdbx_model_coordinates_db_code

getPdbx_subcomponent_list

setPdbx_subcomponent_list

getPdbx_processing_site

setPdbx_processing_site

setStandard

getMon_nstd_flag

setMon_nstd_flag

getDescriptors

setDescriptors

getBonds

setBonds

getAtoms

setAtoms

compareTo

hashCode

equals

getEmptyChemComp

isEmpty