OEResidue

class OEResidue

The OEResidue class is used to attach biopolymer information to each OEAtomBase object. This class contains a number of fields specific to processing macromolecules, such as proteins and nucleic acids. Each atom may be annotated with a unique OEResidue, hence OEResidue objects are not shared between different atoms. If the fields of an OEResidue associated with a single atom are updated, only that atom is affected.

Note

See section Biopolymer Residues for a detailed description of the data stored in an OEResidue.

Constructors

OEResidue()

Default constructor.

OEResidue(const OEResidue &rhs)

Copy constructor.

operator=

OEResidue &operator=(const OEResidue &rhs)

Assignment operator that copies the data of the ‘rhs’ OEResidue object into the right-hand side OEResidue object.

operator bool

operator bool() const

Determines whether any field of an OEResidue has a non-default value.

Comparison Operators

bool operator==(const OEResidue &rhs) const
bool operator!=(const OEResidue &rhs) const
bool operator<(const OEResidue &rhs) const
bool operator<=(const OEResidue &rhs) const
bool operator>(const OEResidue &rhs) const
bool operator>=(const OEResidue &rhs) const

The comparison operators compare properties of two OEResidue objects. Two residues are considered equal if all their properties are equal. The <, <=, >, and >= operators consider the residue properties in the following order: model number, chain ID, fragment number, residue number, insertion code, and residue name.

Because of the existence of the < operator, it is possible to sort containers by residue, and also to create std::map containers using OEResidue as a key. The residue sorting order produced by the < operator is the same as that produced by OEPDBOrderAtoms.

GetAlternateLocation

char GetAlternateLocation() const

Returns the ‘alternate location’ property of an atom in a residue. The ‘alternate location’ property may be set using the OEResidue::SetAlternateLocation method.

GetBFactor

float GetBFactor() const

Returns the crystallographic ‘b-factor’ property of an atom in a residue. The ‘b-factor’ property may be set using the OEResidue::SetBFactor method.

GetChainID

char GetChainID() const

Returns the ‘chain identifier’ property of a residue. The ‘chain identifier’ property may be set using the OEResidue::SetChainID method.

GetFragmentNumber

int GetFragmentNumber() const

Returns the ‘fragment number’ property of a residue. Fragment numbers are integer indices that define connected components of a macromolecule. When reading from a PDB file, the first atom is placed in fragment number 1. Each time a TER, END or ENDM record is encountered within a single connection table, the fragment number is incremented. Similarly, when writing a PDB file, a TER record is written between any consecutive pair of atoms with different fragment numbers. The fragment number property may be set using the OEResidue::SetFragmentNumber number property.

GetInsertCode

char GetInsertCode() const

Returns the ‘insertion code’ of a residue. Insertion codes are single character suffixes used to distinguish insertions when using a standardized residue numbering system. By default, this property contains a single space character, ' '. The insertion code property of a residue may be set using the OEResidue::SetInsertCode method.

GetModelNumber

int GetModelNumber() const

Returns the ‘model number’ property of a residue. For NMR or molecular dynamics files, the model number contains the index of the NMR model or dynamics time-step within a file. The ‘model number’ property may be set using the OEResidue::SetModelNumber method.

GetName

const char *GetName() const

Returns the ‘residue name’ property of a residue. The ‘residue name’ property may be set using the OEResidue::SetName method.

GetOccupancy

float GetOccupancy() const

Returns the crystallographic ‘occupancy’ property of an atom in a residue. The default value is 1.0. The ‘occupancy’ property may be set using the OEResidue::SetOccupancy method.

GetResidueNumber

int GetResidueNumber() const

Returns the ‘residue number’ property of a residue. The ‘residue number’ property may be set using the OEResidue::SetResidueNumber method.

GetSecondaryStructure

int GetSecondaryStructure() const

Returns the protein ‘secondary structure’ property of a residue. The default value is zero. The ‘secondary structure’ property of a residue may be set using the OEResidue::SetSecondaryStructure method.

GetSerialNumber

int GetSerialNumber() const

Returns the ‘atom serial number’ property of an atom in a residue. The ‘atom serial number’ property may be set using the OEResidue::SetSerialNumber method.

IsHetAtom

bool IsHetAtom() const

Returns the ‘hetero atom’ property of an atom in a residue. The ‘hetero atom’ property may be set using the OEResidue::SetHetAtom method.

Note

A ‘hetero atom’ is distinguished from a ‘standard atom’ in a PDB file by using the record type HETATM rather than ATOM.

SetAlternateLocation

bool SetAlternateLocation(char v)

Sets the ‘alternate location’ property of an atom in a residue. The default value is a space character. The ‘alternate location’ property of an atom in a residue may be retrieved using the OEResidue::GetAlternateLocation method.

SetBFactor

bool SetBFactor(float v)

Sets the crystallographic ‘b-factor’ property of an atom in a residue. The default value is 0.0. The ‘b-factor’ property of an atom in a residue may be retrieved using the OEResidue::GetBFactor method.

SetChainID

bool SetChainID(char v)

Sets the ‘chain identifier’ property of a residue. The default value is a space character. The ‘chain identifier’ property of a residue may be retrieved using the OEResidue::GetChainID method.

SetFragmentNumber

bool SetFragmentNumber(int v)

Sets the fragment number property of a residue. Fragment numbers are integer indices that define the connected components of a macromolecule. When reading from a PDB file, the first atom is placed in fragment number 1. Each time a TER, END or ENDM record is encountered within a single connection table, the fragment number is incremented. Similarly, when writing a PDB file, a TER record is written between any consecutive pair of atoms with different fragment numbers. The default value is zero. The ‘fragment number’ property of a residue may be retrieved using the OEResidue::GetFragmentNumber method.

SetHetAtom

bool SetHetAtom(bool v)

Set the ‘hetero atom’ property of an atom in a residue. The default value is false. The ‘hetero atom’ property of an atom in a residue may be retrieved using the OEResidue::IsHetAtom method.

SetInsertCode

bool SetInsertCode(char v)

Sets the ‘insertion code’ of a residue. Insertion codes are single character suffices used to distinguish insertions when using a standardized residue numbering system. By default, this property contains a single space character ' '. The ‘insertion code’ property of a residue may be retrieved using the OEResidue::GetInsertCode method.

SetModelNumber

bool SetModelNumber(int v)

Sets the model number property of a residue. For NMR or molecular dynamics files, the model number contains the index of the NMR model or dynamics time-step within a file. The default value is zero. The ‘model number’ property of a residue may be retrieved using the OEResidue::GetModelNumber method.

SetName

bool SetName(const char *v)
bool SetName(const std::string &v)

Sets the ‘residue name’ property of a residue. The default value is MOL. The ‘residue name’ property of a residue may be retrieved using the OEResidue::GetName method.

SetOccupancy

bool SetOccupancy(float v)

Sets the crystallographic ‘occupancy’ property of an atom in a residue. The default value is 1.0. The ‘occupancy’ property of an atom in a molecule may be retrieved using the OEResidue::GetOccupancy method.

SetResidueNumber

bool SetResidueNumber(int v)

Sets the ‘residue number’ property of a residue. The default value is 1. The ‘residue number’ property of a residue may be retrieved using the OEResidue::GetResidueNumber method.

SetSecondaryStructure

bool SetSecondaryStructure(int v)

Sets the protein ‘secondary structure’ property of a residue. The default value is zero. The ‘secondary structure’ property of a residue may be retrieved using the OEResidue::GetSecondaryStructure method.

SetSerialNumber

bool SetSerialNumber(int v)

Sets the ‘atom serial number’ property of an atom in a residue. The default value is zero. The ‘atom serial number’ property may be retrieved using the OEResidue::GetSerialNumber method.