Science_Chemistry
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Class: Science_Chemistry_Atom

Source Location: /Science_Chemistry-1.1.2/Science/Chemistry/Atom.php

Class Overview


Base class representing an Atom


Author(s):

Version:

  • 1.0

Methods


Child classes:

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

Inherited Variables

Inherited Methods


Class Details

[line 32]
Base class representing an Atom


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Method Detail

Science_Chemistry_Atom (Constructor)   [line 65]

object Science_Chemistry_Atom Science_Chemistry_Atom( string $element, [optional $coords = ""])

Constructor for the class, requires the element symbol and an optional array of coordinates

Parameters:

string   $element     chemical symbol
optional   $coords     array $coords array of coordinates (x, y, z)

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distance   [line 119]

float distance( object Science_Chemistry_Atom $atom2)

Calculates the cartesian distance from this atom instance to another
  • Return: distance
  • Access: public

Parameters:

object Science_Chemistry_Atom   $atom2     

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getCoordinates   [line 107]

object Science_Chemistry_Coordinates getCoordinates( )

Returns the coordinates object for the atom
  • See: $xyz;
  • Access: public

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getElement   [line 95]

string getElement( )

Returns the chemical symbol for the atom
  • See: $element;
  • Access: public

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isAtom   [line 134]

boolean isAtom( object Science_Chemistry_Atom $obj)

Checks if the object is an instance of Science_Chemistry_Atom
  • Access: public

Parameters:

object Science_Chemistry_Atom   $obj     

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setCoordinates   [line 82]

boolean setCoordinates( array $coords)

Sets the coordinates for the atom object
  • Access: public

Parameters:

array   $coords     array of coordinates (x, y, z)

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toCML   [line 173]

string toCML( [optional $id = 1])

Returns a CML representation of the Science_Chemistry_Atom object Accepts an optional id
  • Access: public

Parameters:

optional   $id     string $id

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toString   [line 149]

string toString( )

Returns a string representation of the Science_Chemistry_Atom object Alias of toXYZ()

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toXYZ   [line 160]

string toXYZ( )

Returns a XYZ representation of the Science_Chemistry_Atom object

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