Science_Chemistry
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Class: Science_Chemistry_Atom_PDB

Source Location: /Science_Chemistry-1.0.2/Chemistry/Atom_PDB.php

Class Overview

Science_Chemistry_Atom
   |
   --Science_Chemistry_Atom_PDB

Represents a PDB atom record and contains a reference to the PDB residue to which it belongs


Author(s):

Version:

  • 1.0

Variables

Methods


Inherited Variables

Inherited Methods

Class: Science_Chemistry_Atom

Science_Chemistry_Atom::Science_Chemistry_Atom()
Constructor for the class, requires the element symbol and an optional array of coordinates
Science_Chemistry_Atom::distance()
Calculates the cartesian distance from this atom instance to another
Science_Chemistry_Atom::getCoordinates()
Returns the coordinates object for the atom
Science_Chemistry_Atom::getElement()
Returns the chemical symbol for the atom
Science_Chemistry_Atom::isAtom()
Checks if the object is an instance of Science_Chemistry_Atom
Science_Chemistry_Atom::setCoordinates()
Sets the coordinates for the atom object
Science_Chemistry_Atom::toCML()
Returns a CML representation of the Science_Chemistry_Atom object Accepts an optional id
Science_Chemistry_Atom::toString()
Returns a string representation of the Science_Chemistry_Atom object

Class Details

[line 33]
Represents a PDB atom record and contains a reference to the PDB residue to which it belongs


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Class Variables

$parent_residue =

[line 158]

Reference to the containing Residue object
  • Access: public

Type:   object Residue_PDB


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$ser_num =

[line 51]

PDB Atom serial number

Type:   integer


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$VALID =  false

[line 150]

If the atom object has been initialized
  • See: initAtom()
  • Access: public

Type:   boolean


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Method Detail

Science_Chemistry_Atom_PDB (Constructor)   [line 161]

Science_Chemistry_Atom_PDB Science_Chemistry_Atom_PDB( $atomrec, [ $residue = ""])


Parameters:

   $atomrec   — 
   $residue   — 

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getField   [line 188]

void getField( $field)


Parameters:

   $field   — 

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