PDB Package

PDBAminoAcid

Base Classes:

Public Base Classes:

None

Member Functions:

Constructor:

PDBAminoAcid(int id, char *name, char *code, char letter, int group,

int natoms, RNScalar hydrophobicity, const RNRgb& color);

Properties:

int ID(void) const;

const char *Name(void) const;

const char *Code(void) const;

char Letter(void) const;

int Group(void) const;

RNScalar Hydrophobicity(void) const;

const RNRgb& Color(void) const;

RNBoolean IsMarked(void) const;

RNScalar Value(void) const;

void *Data(void) const;

Properties for each atom of amino acid:

int NAtoms(void) const;

const char *AtomName(int k) const;

PDBElement *AtomElement(int k) const;

RNScalar AtomCharge(int k) const;

Manipulation functions:

void SetData(void *data);

void SetValue(RNScalar value);

void SetMark(void);

void UnsetMark(void);

Data fields:

int id;

char name[16];

char code[4];

char letter;

int group;

int natoms;

RNScalar hydrophobicity;

RNRgb color;

RNMark mark;

RNScalar value;

void *data;

PDBAtom

Base Classes:

Public Base Classes:

None

Member Functions:

Constructor:

PDBAtom(PDBModel *model, PDBChain *chain, PDBResidue *residue, PDBElement *element,

int serial, const char *atom_name, int altLoc, RNScalar x, RNScalar y, RNScalar z,

RNScalar occupancy, RNScalar tempFactor, RNScalar charge, RNBoolean hetatm = FALSE);

~PDBAtom(void);

Properties:

int ID(void) const;

int Serial(void) const;

const char *Name(void) const;

const R3Point& Position(void) const;

RNScalar Occupancy(void) const;

RNScalar TempFactor(void) const;

RNScalar Charge(void) const;

int AlternateLocation(void) const;

RNScalar Radius(void) const;

RNScalar Hydrophobicity(void) const;

const RNRgb& Color(void) const;

R3Box BBox(void) const;

RNBoolean IsHetAtom(void) const;

RNBoolean IsBackbone(void) const;

RNBoolean IsBonded(PDBAtom *atom);

RNBoolean IsBonded(PDBResidue *residue);

RNBoolean IsMarked(void) const;

RNScalar Value(void) const;

void *Data(void) const;

Bond access functions:

int NBonds(void) const;

PDBBond *Bond(int k) const;

Other access functions:

PDBElement *Element(void) const;

PDBResidue *Residue(void) const;

PDBAminoAcid *AminoAcid(void) const;

PDBChain *Chain(void) const;

PDBModel *Model(void) const;

PDBFile *File(void) const;

Manipulation functions:

void Transform(const R3Affine& affine);

void SetPosition(const R3Point& position);

void SetName(const char *name);

void SetData(void *data);

void SetValue(RNScalar value);

void SetMark(void);

void UnsetMark(void);

Straight from PDB file:

int serial;

char name[8];

int altLoc;

R3Point position;

RNScalar occupancy;

RNScalar tempFactor;

RNScalar charge;

RNBoolean hetatm;

Other data fields:

int id;

PDBResidue *residue;

PDBElement *element;

RNArray bonds;

RNScalar accessible_surface_area;

int aminoacid_atom_type;

RNMark mark;

User-definable data fields:

RNScalar value;

void *data;

PDBBond

Base Classes:

Public Base Classes:

None

Member Functions:

Constructor:

PDBBond(PDBAtom *atom1, PDBAtom *atom2, PDBBondType type = PDB_UNKNOWN_BOND);

~PDBBond(void);

Properties:

int ID(void) const;

PDBBondType Type(void) const;

RNLength Length(void) const;

const RNRgb& Color(void) const;

RNBoolean IsMarked(void) const;

RNScalar Value(void) const;

void *Data(void) const;

Atom access functions:

int NAtoms(void) const;

PDBAtom *Atom(int k) const;

PDBAtom *OtherAtom(PDBAtom *atom) const;

Manipulation functions:

void SetData(void *data);

void SetValue(RNScalar value);

void SetMark(void);

void UnsetMark(void);

Data fields:

PDBAtom *atoms[2];

PDBBondType type;

RNMark mark;

RNScalar value;

void *data;

int id;

PDBChain

Base Classes:

Public Base Classes:

None

Member Functions:

Constructor:

PDBChain(PDBModel *model, const char *name);

~PDBChain(void);

Property functions:

int ID(void) const;

const char *Name(void) const;

const R3Box& BBox(void) const;

R3Point Centroid(void) const;

RNLength Radius(void) const;

const RNRgb& Color(void) const;

RNBoolean IsMarked(void) const;

RNScalar Value(void) const;

void *Data(void) const;

Atom access functions:

int NAtoms(void) const;

PDBAtom *Atom(int k) const;

Residue access functions:

int NResidues(void) const;

PDBResidue *Residue(int k) const;

Other access functions:

PDBModel *Model(void) const;

PDBFile *File(void) const;

Bond access functions:

int NBonds(void) const;

PDBBond *Bond(int k) const;

Search access functions:

PDBAtom *FindAtom(const char *str) const;

PDBResidue *FindResidue(const char *str) const;

PDBResidue *FindResidue(const char *residue_name, int residue_sequence, int residue_insertion_code) const;

PDBStructureType FindAny(const char *str, PDBResidue **residue = NULL,

PDBAtom **atom = NULL, PDBStructureType maxlevel = PDB_ATOM) const;

Manipulation functions:

void Transform(const R3Affine& affine);

PDBResidue *InsertCopy(PDBResidue *residue);

void SetName(const char *name);

void SetData(void *data);

void SetValue(RNScalar value);

void SetMark(void);

void UnsetMark(void);

Data fields:

int id;

char name[4];

R3Box bbox;

PDBModel *model;

RNArray atoms;

RNArray residues;

RNArray bonds;

RNMark mark;

RNScalar value;

void *data;

PDBElement

Base Classes:

Public Base Classes:

None

Member Functions:

Constructor:

PDBElement(int id, const char *name, int atomic_number, RNScalar atomic_weight,

RNLength covalent_radius, RNLength van_der_waals_radius, RNLength united_atom_radius,

RNScalar electronegativity, RNScalar charge, const RNRgb& color);

Properties:

int ID(void) const;

const char *Name(void) const;

int AtomicNumber(void) const;

RNScalar AtomicWeight(void) const;

RNLength Radius(void) const;

RNScalar Electronegativity(void) const;

RNScalar Charge(void) const;

const RNRgb& Color(void) const;

RNBoolean IsMarked(void) const;

RNScalar Value(void) const;

void *Data(void) const;

Manipulation functions:

void SetData(void *data);

void SetValue(RNScalar value);

void SetMark(void);

void UnsetMark(void);

Data fields:

int id;

char name[4];

int atomic_number;

RNScalar atomic_weight;

RNLength covalent_radius;

RNLength van_der_waals_radius;

RNLength united_atom_radius;

RNScalar electronegativity;

RNScalar charge;

RNRgb color;

RNMark mark;

RNScalar value;

void *data;

PDBFile

Base Classes:

Public Base Classes:

None

Member Functions:

Constructor:

PDBFile(const char *name = NULL);

~PDBFile(void);

Property functions:

int ID(void) const;

const char *Name(void) const;

const R3Box BBox(void) const;

R3Point Centroid(void) const;

RNLength Radius(void) const;

const RNRgb& Color(void) const;

RNBoolean IsMarked(void) const;

RNScalar Value(void) const;

void *Data(void) const;

Model access functions:

int NModels(void) const;

PDBModel *Model(int k) const;

Search access functions:

PDBAtom *FindAtom(const char *str) const;

PDBResidue *FindResidue(const char *str) const;

PDBChain *FindChain(const char *str) const;

PDBModel *FindModel(const char *str) const;

PDBStructureType FindAny(const char *str,

PDBModel **model = NULL, PDBChain **chain = NULL,

PDBResidue **residue = NULL, PDBAtom **atom = NULL,

PDBStructureType maxlevel = PDB_ATOM) const;

Manipulation functions:

void Transform(const R3Affine& affine);

PDBModel *InsertCopy(PDBModel *model);

void SetName(const char *name);

void SetData(void *data);

void SetValue(RNScalar value);

void SetMark(void);

void UnsetMark(void);

I/O functions:

int ReadFile(const char *filename);

int WriteFile(const char *filename) const;

int Read(FILE *fp = NULL);

int Write(FILE *fp = NULL) const;

More I/O functions:

int ReadASAFile(char *filename);

int ReadGrowFile(char *filename);

int ReadConsurfFiles(char *hssp_basename);

int ReadHsspFiles(char *hssp_basename);

int ReadJsdFiles(char *hssp_basename);

???:

void CreateBonds(PDBResidue *ligand, RNLength max_gap = 1);

PDBFile *CopyBiomolecule(void);

int IsBiomolecule(void) const;

Data fields:

int id;

char name[128];

RNArray headers;

RNArray trailers;

RNArray models;

RNMark mark;

RNScalar value;

void *data;

PDBModel

Base Classes:

Public Base Classes:

None

Member Functions:

Constructor:

PDBModel(PDBFile *file, const char *name = NULL);

~PDBModel(void);

Property functions:

int ID(void) const;

const char *Name(void) const;

const R3Box& BBox(void) const;

R3Point Centroid(void) const;

RNLength Radius(void) const;

const RNRgb& Color(void) const;

RNBoolean IsMarked(void) const;

RNScalar Value(void) const;

void *Data(void) const;

Atom access functions:

int NAtoms(void) const;

PDBAtom *Atom(int k) const;

Residue access functions:

int NResidues(void) const;

PDBResidue *Residue(int k) const;

Chain access functions:

int NChains(void) const;

PDBChain *Chain(int k) const;

File access functions:

PDBFile *File(void) const;

Bond access functions:

int NBonds(void) const;

PDBBond *Bond(int k) const;

Search access functions:

PDBAtom *FindAtom(const char *str) const;

PDBResidue *FindResidue(const char *str) const;

PDBChain *FindChain(const char *str) const;

PDBStructureType FindAny(const char *str,

PDBChain **chain = NULL, PDBResidue **residue = NULL,

PDBAtom **atom = NULL, PDBStructureType maxlevel = PDB_ATOM) const;

Manipulation functions:

void Transform(const R3Affine& affine);

PDBChain *InsertCopy(PDBChain *chain);

void SetName(const char *name);

void SetData(void *data);

void SetValue(RNScalar value);

void SetMark(void);

void UnsetMark(void);

Data fields:

int id;

char name[32];

R3Box bbox;

RNArray atoms;

RNArray residues;

RNArray chains;

RNArray bonds;

PDBFile *file;

RNMark mark;

RNScalar value;

void *data;

PDBResidue

Base Classes:

Public Base Classes:

None

Member Functions:

Constructor:

PDBResidue(PDBModel *model, PDBChain *chain, const char *name, int sequence, int insertion_code);

~PDBResidue(void);

Property functions:

int ID(void) const;

const char *Name(void) const;

int Sequence(void) const;

int InsertionCode(void) const;

const RNRgb& Color(void) const;

const R3Box& BBox(void) const;

R3Point Centroid(void) const;

RNLength Radius(void) const;

RNBoolean HasHetAtoms(void) const;

RNBoolean IsBonded(PDBAtom *atom);

RNBoolean IsBonded(PDBResidue *residue);

RNBoolean IsMarked(void) const;

RNScalar Value(void) const;

void *Data(void) const;

Atom access functions:

int NAtoms(void) const;

PDBAtom *Atom(int k) const;

Bond access functions:

int NBonds(void) const;

PDBBond *Bond(int k) const;

Other access functions:

PDBAminoAcid *AminoAcid(void) const;

PDBChain *Chain(void) const;

PDBModel *Model(void) const;

PDBFile *File(void) const;

Search access functions:

PDBAtom *FindAtom(const char *str) const;

PDBAtom *FindAtom(const char *atom_name, int atom_serial, int altLoc = 0) const;

int FindAtoms(char **atom_names, PDBAtom **atom_ptrs, int natoms);

PDBStructureType FindAny(const char *str, PDBAtom **atom = NULL, PDBStructureType maxlevel = PDB_ATOM) const;

Manipulation functions:

void Transform(const R3Affine& affine);

PDBAtom *InsertCopy(PDBAtom *atom);

void SetName(const char *name);

void SetData(void *data);

void SetValue(RNScalar value);

void SetMark(void);

void UnsetMark(void);

Other stuff:

int ConstructCoordinateSystem(R3CoordSystem& cs, int coordinate_system_type = 0);

Data fields:

int id;

char name[4];

int sequence;

int insertion_code;

R3Box bbox;

PDBChain *chain;

PDBAminoAcid *aminoacid;

RNArray atoms;

RNArray bonds;

RNScalar conservation;

RNMark mark;

RNScalar value;

void *data;