Science_Chemistry
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Class: Science_Chemistry_Macromolecule_PDB

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

Class Overview

Science_Chemistry_Macromolecule
   |
   --Science_Chemistry_Macromolecule_PDB

Represents a PDB macromolecule, composed of several Science_Chemistry_Residue_PDB objects


Author(s):

Version:

  • 1.0

Methods


Inherited Variables

Inherited Methods

Class: Science_Chemistry_Macromolecule

Science_Chemistry_Macromolecule::Science_Chemistry_Macromolecule()
Constructor for the class, requires a macromolecule name and an optional array of Science_Chemistry_Molecule objects
Science_Chemistry_Macromolecule::addMolecule()
Adds a Science_Chemistry_Molecule object to the list of molecules in the macromolecule
Science_Chemistry_Macromolecule::getMolecules()
Returns an array of Science_Chemistry_Molecule objects
Science_Chemistry_Macromolecule::initMacromolecule()
Initializes the array of Science_Chemistry_Molecule objects
Science_Chemistry_Macromolecule::isMacromolecule()
Checks if the object is an instance of Science_Chemistry_Macromolecule
Science_Chemistry_Macromolecule::toCML()
Returns a CML representation of the molecule Accepts an optional id, and a flag to signal printing of the connection table
Science_Chemistry_Macromolecule::toString()
Returns a string representation of the macromolecule as a multiple molecule XYZ-format file Alias of toXYZ()
Science_Chemistry_Macromolecule::toXYZ()
Returns a string representation of the macromolecule as a multiple molecule XYZ-format file

Class Details

[line 34]
Represents a PDB macromolecule, composed of several Science_Chemistry_Residue_PDB objects


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Method Detail

Science_Chemistry_Macromolecule_PDB (Constructor)   [line 47]

object Science_Chemistry_Macromolecule_PDB Science_Chemistry_Macromolecule_PDB( string $pdb, array $records, [object PDBFile $pdbfile = ""])

Constructor for the class
  • See: parseResidues()
  • See: $pdb
  • Access: public

Parameters:

string   $pdb     PDB ID of the containing file
array   $records     Array of lines comprising the macromolecule
object PDBFile   $pdbfile     reference to the PDB file object

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