ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.

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ProtoMol::PDB::PDBAtom Struct Reference

#include <PDB.h>

List of all members.

Public Types
enum	Start {   S_RECORD_NAME = 0,   S_SERIAL = 6,   S_ATOM_NAME = 12,   S_ALT_LOC = 16,   S_RES_NAME = 17,   S_CHAIN_ID = 21,   S_RES_SEQ = 22,   S_I_CODE = 26,   S_X = 30,   S_Y = 38,   S_Z = 46,   S_OCCUP = 54,   S_TEMP = 60,   S_FOOT_NOTE = 67,   S_SEG_ID = 72,   S_ELEMENT_SYMBOL = 76,   S_CHARGE = 78 }
enum	Length {   L_RECORD_NAME = 6,   L_SERIAL = 5,   L_ATOM_NAME = 4,   L_ALT_LOC = 1,   L_RES_NAME = 4,   L_CHAIN_ID = 1,   L_RES_SEQ = 4,   L_I_CODE = 1,   L_X = 8,   L_Y = 8,   L_Z = 8,   L_OCCUP = 6,   L_TEMP = 6,   L_FOOT_NOTE = 3,   L_SEG_ID = 4,   L_ELEMENT_SYMBOL = 2,   L_CHARGE = 2 }
Public Member Functions
	PDBAtom ()
	PDBAtom (std::string elementType, int elementNum, std::string elementName, std::string altLoc, std::string residueName, std::string chainID, int residueNum, std::string insertionCode, Real occupancy, Real tempFactor, int footnote, std::string segID, std::string symbol, std::string charge, int hvyAtomGrpsize)
Public Attributes
std::string	elementType
int	elementNum
std::string	elementName
std::string	altLoc
std::string	residueName
std::string	chainID
int	residueNum
std::string	insertionCode
Real	occupancy
Real	tempFactor
int	footnote
std::string	segID
std::string	symbol
std::string	charge
int	hvyAtomGrpsize
Friends
Report::MyStreamer &	operator<< (Report::MyStreamer &OS, const PDBAtom &p)

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Detailed Description

This class holds data for a basic PDB element; excluding the coordinates (x,y,z), stored separately.

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Member Enumeration Documentation

enum ProtoMol::PDB::PDBAtom::Length

Record element length. Enumeration values: L_RECORD_NAME  L_SERIAL  L_ATOM_NAME  L_ALT_LOC  L_RES_NAME  L_CHAIN_ID  L_RES_SEQ  L_I_CODE  L_X  L_Y  L_Z  L_OCCUP  L_TEMP  L_FOOT_NOTE  L_SEG_ID  L_ELEMENT_SYMBOL  L_CHARGE

enum ProtoMol::PDB::PDBAtom::Start

Record element start positions. Enumeration values: S_RECORD_NAME  S_SERIAL  S_ATOM_NAME  S_ALT_LOC  S_RES_NAME  S_CHAIN_ID  S_RES_SEQ  S_I_CODE  S_X  S_Y  S_Z  S_OCCUP  S_TEMP  S_FOOT_NOTE  S_SEG_ID  S_ELEMENT_SYMBOL  S_CHARGE

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Constructor & Destructor Documentation

ProtoMol::PDB::PDBAtom::PDBAtom (   )

ProtoMol::PDB::PDBAtom::PDBAtom (  std::string  elementType, int  elementNum, std::string  elementName, std::string  altLoc, std::string  residueName, std::string  chainID, int  residueNum, std::string  insertionCode, Real  occupancy, Real  tempFactor, int  footnote, std::string  segID, std::string  symbol, std::string  charge, int  hvyAtomGrpsize )

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Friends And Related Function Documentation

Report::MyStreamer& operator<< (  Report::MyStreamer &  OS, const PDBAtom &  p )  [friend]

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Member Data Documentation

std::string ProtoMol::PDB::PDBAtom::altLoc

alternate_location

std::string ProtoMol::PDB::PDBAtom::chainID

chain_id

std::string ProtoMol::PDB::PDBAtom::charge

charge

std::string ProtoMol::PDB::PDBAtom::elementName

atom_name

int ProtoMol::PDB::PDBAtom::elementNum

serial_size

std::string ProtoMol::PDB::PDBAtom::elementType

record_name

int ProtoMol::PDB::PDBAtom::footnote

footnote number

int ProtoMol::PDB::PDBAtom::hvyAtomGrpsize

??? throw in zeros

std::string ProtoMol::PDB::PDBAtom::insertionCode

insertion_code

Real ProtoMol::PDB::PDBAtom::occupancy

occupancy

std::string ProtoMol::PDB::PDBAtom::residueName

residue_name

int ProtoMol::PDB::PDBAtom::residueNum

residue_sequence

std::string ProtoMol::PDB::PDBAtom::segID

seg_id

std::string ProtoMol::PDB::PDBAtom::symbol

element_symbol

Real ProtoMol::PDB::PDBAtom::tempFactor

temp_factor

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The documentation for this struct was generated from the following files:

• PDB.h
• PDB.cpp

Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.