Subsections

8.41 OEResidue

class OEResidue

The OEResidue class in OEChem is used to attach biopolymer information to each OEAtomBase. 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 instances are not shared between different atoms. If the fields of an OEResidue associated with a single atom are updated, only that atom is affected.

8.41.1 operator =

OEResidue& operator = (const OEResidue &res)

The assignment operator may be used to copy all of the fields of an OEResidue.

8.41.2 operator bool

operator bool() const

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

8.41.3 GetAlternateLocation

char GetAlternateLocation() const

Return the alternate location character property of an atom in a residue. The ``alternate location'' property may be set using the OEResidue::SetAlternateLocation method.

8.41.4 GetBFactor

float GetBFactor() const

Return the crystallographic B-factor property of an atom in a residue. The ``b-factor'' property may be set using the OEResidue::SetBFactor method.

8.41.5 GetChainID

char GetChainID() const

Return the chain identifier character property of a residue. The ``chain identifier'' property may be set using the OEResidue::SetChainID method.

8.41.6 GetFragmentNumber

int GetFragmentNumber() const

Return 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::SetFragment number property.

8.41.7 GetInsertCode

char GetInsertCode() const

Return the insertion code character 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.

8.41.8 GetModelNumber

int GetModelNumber() const

Return 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.

8.41.9 GetName

const char *GetName() const

Return the residue name property of a residue. The ``residue name'' property may be set using the OEResidue::SetName method.

8.41.10 GetOccupancy

float GetOccupancy() const

Return the crystallographic ``occupancy'' floating point property of an atom in a residue. The default value is 1.0. The ``occupancy'' property may be set using the OEResidue::SetOccupancy method.

8.41.11 GetResidueNumber

int GetResidueNumber() const

Return the residue number property of a residue. The ``residue number'' property may be set using the OEResidue::SetResidueNumber method.

8.41.12 GetSecondaryStructure

int GetSecondaryStructure() const

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

8.41.13 GetSerialNumber

int GetSerialNumber() const

Return the atom serial number property of an atom in a residue. The ``atom serial number'' property may be set using the OEResidue::SetSerialNumber method.

8.41.14 IsHetAtom

bool IsHetAtom() const

Return the boolean ``hetero atom'' property of an atom in a residue. The ``hetero atom'' property may be set using the OEResidue::SetHetAtom method.

8.41.15 SetAlternateLocation

bool SetAlternateLocation(char alt)

Set the alternate location character 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.

8.41.16 SetBFactor

bool SetBFactor(float temp)

Set 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.

8.41.17 SetChainID

bool SetChainID(char ch)

Set the chain identifier character 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.

8.41.18 SetFragmentNumber

bool SetFragmentNumber(int frag)

Set 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.

8.41.19 SetHetAtom

bool SetHetAtom(bool het)

Set the boolean ``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.

8.41.20 SetInsertCode

bool SetInsertCode(char ins)

Set the insertion code character 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.

8.41.21 SetModelNumber

bool SetModelNumber(char model)

Set 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.

8.41.22 SetName

bool SetName(const std::string name)
bool SetName(const char *name)

Set 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.

8.41.23 SetOccupancy

bool SetOccupancy(float occup)

Set 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.

8.41.24 SetResidueNumber

bool SetResidueNumber(int resno)

Set the residue number property of a residue. The default value is one. The residue number property of a residue may be retrieved using the OEResidue::GetResidueNumber method.

8.41.25 SetSecondaryStructure

bool SetSecondaryStructure(int secstr)

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

8.41.26 SetSerialNumber

bool SetSerialNumber(int serno)

Set 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.

				OEChem - API Manual

				OEChem - API Manual