Science_Chemistry
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Class: Science_Chemistry_Macromolecule

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

Class Overview


Represents a macromolecule, composed of several Science_Chemistry_Molecule objects


Author(s):

Version:

  • 1.0

Methods


Child classes:

Science_Chemistry_Macromolecule_PDB
Represents a PDB macromolecule, composed of several Science_Chemistry_Residue_PDB objects

Inherited Variables

Inherited Methods


Class Details

[line 35]
Represents a macromolecule, composed of several Science_Chemistry_Molecule objects


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Method Detail

Science_Chemistry_Macromolecule (Constructor)   [line 72]

object Science_Chemistry_Macromolecule Science_Chemistry_Macromolecule( string $name, [optional $molecules = ""])

Constructor for the class, requires a macromolecule name and an optional array of Science_Chemistry_Molecule objects

Parameters:

string   $name     
optional   $molecules     array $molecules

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addMolecule   [line 112]

boolean addMolecule( object Science_Chemistry_Molecule $mol)

Adds a Science_Chemistry_Molecule object to the list of molecules in the macromolecule

Parameters:

object Science_Chemistry_Molecule   $mol     

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getMolecules   [line 129]

array getMolecules( )

Returns an array of Science_Chemistry_Molecule objects
  • See: $molecules
  • Access: public

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initMacromolecule   [line 90]

boolean initMacromolecule( array $molecules)

Initializes the array of Science_Chemistry_Molecule objects

Parameters:

array   $molecules     

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isMacromolecule   [line 140]

boolean isMacromolecule( object Science_Chemistry_Macromolecule $obj)

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

Parameters:


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toCML   [line 186]

string toCML( [optional $title = "macromolecule"], [optional $id = "macromol1"], [ $connect = false])

Returns a CML representation of the molecule Accepts an optional id, and a flag to signal printing of the connection table
  • Access: public

Parameters:

optional   $title     string $id
optional   $id     boolean $connect
   $connect     

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toString   [line 172]

string toString( )

Returns a string representation of the macromolecule as a multiple molecule XYZ-format file Alias of toXYZ()

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toXYZ   [line 156]

string toXYZ( )

Returns a string representation of the macromolecule as a multiple molecule XYZ-format file

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