BALL  1.4.79
Classes
Molecular Datastructures

Classes

class  BALL::Atom::BondIteratorTraits
 
class  BALL::Atom
 
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 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.

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.

Enumerator
NUMBER_OF_PROPERTIES 

Definition at line 32 of file fragment.h.

Enumerator
NUMBER_OF_PROPERTIES 

Definition at line 40 of file nucleicAcid.h.

Enumerator
NUMBER_OF_PROPERTIES 

Definition at line 41 of file protein.h.

The number of predefined properties for AtomContainer.

Enumerator
NUMBER_OF_PROPERTIES 

Definition at line 42 of file atomContainer.h.

Properties

Enumerator
IS_SOLVENT 
NUMBER_OF_PROPERTIES 

Definition at line 42 of file molecule.h.

Enumerator
NUMBER_OF_PROPERTIES 

Definition at line 43 of file chain.h.

Enumerator
PROPERTY__5_PRIME 
PROPERTY__3_PRIME 
PROPERTY__NUCLEOTIDE 
NUMBER_OF_PROPERTIES 

Definition at line 47 of file nucleotide.h.

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.

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.

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.

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.