MTK++ Latest version: 0.2.0

Public Attributes
MTKpp::stdAtom Struct Reference

Container for standard atom info. More...

#include <mtkpp/src/Molecule/stdFrag.h>

List of all members.

Public Attributes

std::string identity
 atom name
int index
 internal fragment index
std::string type
 atom type
std::string chain
 chain type
double atmCharge
 atomic charge for MM calculation
int bond12
 index of atom with which its bonded to
double bondLength
 bond length
int bond13
 index of atom with which its forming an angle with bond12
double bondAngle
 angle size
int bond14
 index of atom with which its forming a torsion with bond12 and angle13
double bondTorsion
 torsion size
int atNum
 atomic number
std::string atSymbol
 atomic symbol
int kind
 atom kind definitions

Detailed Description

Container for standard atom info.


Member Data Documentation

std::string MTKpp::stdAtom::type
std::string MTKpp::stdAtom::chain

chain type

  • M => Main chain
  • S => Side, 2 connections
  • E => End, 1 connection
  • B => Branch, 3 connections
  • 3 => 4 connections
  • 4 => 5 connections
  • 5 => 6 connections
  • 6 => 7 connections

Referenced by MTKpp::proProtonate::addHydrogens(), MTKpp::stdFrag::addStdAtom(), MTKpp::connections::bondByLibrary(), MTKpp::stdFrag::getStdAtom(), MTKpp::prepParser::readFragment(), MTKpp::amberParser::Write(), and MTKpp::prepParser::Write().

atomic number

Referenced by MTKpp::stdFrag::generateSimpleFP().

atom kind definitions

  • 0 = Undefined
  • 1 = Hydrogen
  • 2 = Terminal Heavy Atom
  • 3 = Open Chain Heavy Atom
  • 4 = Closed Chain Heavy Atom
  • 5 = Ring Heavy Atom
  • 6 = Aromatic Ring Heavy Atom
  • 7 = Chain Atom (not terminal, Ring or Hydrogen)

Referenced by MTKpp::stdFrag::addStdAtom(), MTKpp::atomTyper::atomTypeByLib(), MTKpp::stdFrag::generateAtomKinds(), MTKpp::stdFrag::generateHeavyAtomKinds(), and MTKpp::prepParser::readFragment().


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

Generated on Fri Dec 23 2011 09:28:57 for MTK++ by Doxygen 1.7.5.1