Molecular Datastructures

Classes
class	BALL::Atom
class	BALL::Atom::BondIteratorTraits
class	BALL::AtomContainer
class	BALL::Chain
class	BALL::Fragment
class	BALL::Molecule
class	BALL::NucleicAcid
class	BALL::Nucleotide
class	BALL::PDBAtom
class	BALL::Protein
class	BALL::Residue
class	BALL::System

Enumerations
enum	{ BALL::Atom::UNKNOWN_TYPE = -1, BALL::Atom::ANY_TYPE = 0, BALL::Atom::MAX_NUMBER_OF_BONDS = 12 }
enum	BALL::Atom::Property { BALL::Atom::NUMBER_OF_PROPERTIES = 0 }
enum	BALL::Atom::FullNameType {   BALL::Atom::NO_VARIANT_EXTENSIONS, BALL::Atom::ADD_VARIANT_EXTENSIONS, BALL::Atom::ADD_RESIDUE_ID, BALL::Atom::ADD_VARIANT_EXTENSIONS_AND_ID,   BALL::Atom::ADD_CHAIN_RESIDUE_ID, BALL::Atom::ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID }

Enums
enum	BALL::AtomContainer::Property { BALL::AtomContainer::NUMBER_OF_PROPERTIES = 0 }
	The number of predefined properties for AtomContainer. More...

Enums
enum	BALL::Chain::Property { BALL::Chain::NUMBER_OF_PROPERTIES = AtomContainer::NUMBER_OF_PROPERTIES }

Enums
enum	BALL::Fragment::Property { BALL::Fragment::NUMBER_OF_PROPERTIES = AtomContainer::NUMBER_OF_PROPERTIES }

Enums
enum	BALL::Molecule::Property { BALL::Molecule::IS_SOLVENT = AtomContainer::NUMBER_OF_PROPERTIES, BALL::Molecule::NUMBER_OF_PROPERTIES }

Enums
enum	BALL::NucleicAcid::Property { BALL::NucleicAcid::NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES }

Enums
enum	BALL::Nucleotide::Property { BALL::Nucleotide::PROPERTY__5_PRIME = Residue::NUMBER_OF_PROPERTIES + 1, BALL::Nucleotide::PROPERTY__3_PRIME, BALL::Nucleotide::PROPERTY__NUCLEOTIDE, BALL::Nucleotide::NUMBER_OF_PROPERTIES }

Enums
enum	BALL::PDBAtom::RemotenessIndicator {   BALL::PDBAtom::REMOTENESS_INDICATOR__UNKNOWN = BALL_PDBATOM_DEFAULT_REMOTENESS_INDICATOR, BALL::PDBAtom::REMOTENESS_INDICATOR__ALPHA = 'A', BALL::PDBAtom::REMOTENESS_INDICATOR__alpha = 'a', BALL::PDBAtom::REMOTENESS_INDICATOR__BETA = 'B',   BALL::PDBAtom::REMOTENESS_INDICATOR__beta = 'b', BALL::PDBAtom::REMOTENESS_INDICATOR__GAMMA = 'G', BALL::PDBAtom::REMOTENESS_INDICATOR__gamma = 'g', BALL::PDBAtom::REMOTENESS_INDICATOR__DELTA = 'D',   BALL::PDBAtom::REMOTENESS_INDICATOR__delta = 'd', BALL::PDBAtom::REMOTENESS_INDICATOR__EPSILON = 'E', BALL::PDBAtom::REMOTENESS_INDICATOR__epsilon = 'e', BALL::PDBAtom::REMOTENESS_INDICATOR__ZETA = 'Z',   BALL::PDBAtom::REMOTENESS_INDICATOR__zeta = 'z', BALL::PDBAtom::REMOTENESS_INDICATOR__ETA = 'H', BALL::PDBAtom::REMOTENESS_INDICATOR__eta = 'h', BALL::PDBAtom::NUMBER_OF_REMOTENESS_INDICATORS }
enum	BALL::PDBAtom::Property { BALL::PDBAtom::PROPERTY__HETATM = Atom::NUMBER_OF_PROPERTIES + 1, BALL::PDBAtom::NUMBER_OF_PROPERTIES }

Enums
enum	BALL::Protein::Property { BALL::Protein::NUMBER_OF_PROPERTIES = Molecule::NUMBER_OF_PROPERTIES }

Enums
enum	BALL::Residue::Property {   BALL::Residue::PROPERTY__NON_STANDARD = Fragment::NUMBER_OF_PROPERTIES + 1, BALL::Residue::PROPERTY__AMINO_ACID, BALL::Residue::PROPERTY__WATER, BALL::Residue::PROPERTY__HAS_SSBOND,   BALL::Residue::PROPERTY__C_TERMINAL, BALL::Residue::PROPERTY__N_TERMINAL, BALL::Residue::PROPERTY__CYCLIC, BALL::Residue::NUMBER_OF_PROPERTIES }
enum	BALL::Residue::FullNameType { BALL::Residue::NO_VARIANT_EXTENSIONS, BALL::Residue::ADD_VARIANT_EXTENSIONS, BALL::Residue::ADD_RESIDUE_ID, BALL::Residue::ADD_VARIANT_EXTENSIONS_AND_ID }

Detailed Description

Enumeration Type Documentation

anonymous enum

Unnamed enumeration of all non-categorized constants.

Enumerator
UNKNOWN_TYPE	Unknown atom type. The type assigned for default-constructed atoms.
ANY_TYPE	Any atom type. Used as a wild card in the context of forcefields mainly
MAX_NUMBER_OF_BONDS	Maximum number of bonds of an atom.

Definition at line 111 of file atom.h.

enum BALL::Residue::FullNameType

Enum used to describe the kind of name constructed by getFullName .

Enumerator
NO_VARIANT_EXTENSIONS	This returns the unmodified residue name only.
ADD_VARIANT_EXTENSIONS	Add the residue variant extensions (e.g. '-C' for C-terminal residues)
ADD_RESIDUE_ID
ADD_VARIANT_EXTENSIONS_AND_ID

Definition at line 76 of file residue.h.

enum BALL::Atom::FullNameType

The type of name used for getFullName.

See also

getFullName

Enumerator
NO_VARIANT_EXTENSIONS
ADD_VARIANT_EXTENSIONS
ADD_RESIDUE_ID
ADD_VARIANT_EXTENSIONS_AND_ID
ADD_CHAIN_RESIDUE_ID
ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID

Definition at line 138 of file atom.h.

enum BALL::Fragment::Property

Enumerator
NUMBER_OF_PROPERTIES

Definition at line 32 of file fragment.h.

enum BALL::NucleicAcid::Property

Enumerator
NUMBER_OF_PROPERTIES

Definition at line 40 of file nucleicAcid.h.

enum BALL::Protein::Property

Enumerator
NUMBER_OF_PROPERTIES

Definition at line 41 of file protein.h.

enum BALL::AtomContainer::Property

The number of predefined properties for AtomContainer.

Enumerator
NUMBER_OF_PROPERTIES

Definition at line 42 of file atomContainer.h.

enum BALL::Molecule::Property

Properties

Enumerator
IS_SOLVENT
NUMBER_OF_PROPERTIES

Definition at line 42 of file molecule.h.

enum BALL::Chain::Property

Enumerator
NUMBER_OF_PROPERTIES

Definition at line 43 of file chain.h.

enum BALL::Nucleotide::Property

Enumerator
PROPERTY__5_PRIME
PROPERTY__3_PRIME
PROPERTY__NUCLEOTIDE
NUMBER_OF_PROPERTIES

Definition at line 47 of file nucleotide.h.

enum BALL::Residue::Property

Enumerator
PROPERTY__NON_STANDARD
PROPERTY__AMINO_ACID
PROPERTY__WATER
PROPERTY__HAS_SSBOND
PROPERTY__C_TERMINAL
PROPERTY__N_TERMINAL
PROPERTY__CYCLIC	Property for cyclic peptides. This property is set by the build bonds processor, if an atom of the first and an atom of the last residue in a chain share a bond.
NUMBER_OF_PROPERTIES

Definition at line 48 of file residue.h.

enum BALL::PDBAtom::Property

Properties of the PDBAtom.

Enumerator
PROPERTY__HETATM	Property which indicates whether the current atom is a HETATM.
NUMBER_OF_PROPERTIES	The number of properties in PDBAtom.

Definition at line 76 of file PDBAtom.h.

enum BALL::Atom::Property

Predefined properties. Enumeration of all properties that are used by the BALL kernel.

Enumerator
NUMBER_OF_PROPERTIES

Definition at line 130 of file atom.h.

enum BALL::PDBAtom::RemotenessIndicator

Possible values for the PDB remoteness indicator

Enumerator
REMOTENESS_INDICATOR__UNKNOWN
REMOTENESS_INDICATOR__ALPHA
REMOTENESS_INDICATOR__alpha
REMOTENESS_INDICATOR__BETA
REMOTENESS_INDICATOR__beta
REMOTENESS_INDICATOR__GAMMA
REMOTENESS_INDICATOR__gamma
REMOTENESS_INDICATOR__DELTA
REMOTENESS_INDICATOR__delta
REMOTENESS_INDICATOR__EPSILON
REMOTENESS_INDICATOR__epsilon
REMOTENESS_INDICATOR__ZETA
REMOTENESS_INDICATOR__zeta
REMOTENESS_INDICATOR__ETA
REMOTENESS_INDICATOR__eta
NUMBER_OF_REMOTENESS_INDICATORS

Definition at line 53 of file PDBAtom.h.