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