Science_Chemistry
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Class: Science_Chemistry_Residue_PDB

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

Class Overview

Science_Chemistry_Molecule
   |
   --Science_Chemistry_Residue_PDB

Represents a PDB residue


Author(s):

Version:

  • 1.0

Variables

Methods


Inherited Variables

Inherited Methods

Class: Science_Chemistry_Molecule

Science_Chemistry_Molecule::Science_Chemistry_Molecule()
Constructor for the class, requires a molecule name and an optional array of Science_Chemistry_Atom objects
Science_Chemistry_Molecule::addAtom()
Adds a Science_Chemistry_Atom object to the list of atoms in the molecule
Science_Chemistry_Molecule::calcConnectionTable()
Calculates the connection table for the molecule
Science_Chemistry_Molecule::calcDistanceMatrix()
Calculates the atom-atom distance matrix in Angstroms
Science_Chemistry_Molecule::getAtoms()
Returns an array of Atom objects
Science_Chemistry_Molecule::getBondCutoff()
Returns the bond cutoff uses to determine bonds
Science_Chemistry_Molecule::getConnectionTable()
Returns an array of connected atoms and their bond distance e.g. array ( array ($atomobj1, $atomobj2, $distance ), ... )
Science_Chemistry_Molecule::getDistanceMatrix()
Returns the atom-atom distance matrix
Science_Chemistry_Molecule::initMolecule()
Initializes the array of Science_Chemistry_Atom objects
Science_Chemistry_Molecule::isMolecule()
Checks if the object is an instance of Science_Chemistry_Molecule
Science_Chemistry_Molecule::printConnectionTable()
Prints the molecule's connection table
Science_Chemistry_Molecule::printDistanceMatrix()
Prints the atom-atom distance matrix
Science_Chemistry_Molecule::setBondCutoff()
Sets the distance cutoff for bond determination
Science_Chemistry_Molecule::toCML()
Returns a CML representation of the molecule Accepts an optional id, and a flag to signal printing of the connection table
Science_Chemistry_Molecule::toString()
Returns a string representation of the molecule as a XYZ-format file Alias of toXYZ()
Science_Chemistry_Molecule::toXYZ()
Returns a string representation of the molecule as a XYZ-format file

Class Details

[line 34]
Represents a PDB residue


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Class Variables

$macromol =

[line 86]

Reference to the protein to which this residue belongs
  • Access: public



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$VALID =  false

[line 76]

If the PDB residue object has been initialized
  • Access: public

Type:   boolean


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Method Detail

Science_Chemistry_Residue_PDB (Constructor)   [line 97]

object Science_Chemistry_Residue_PDB Science_Chemistry_Residue_PDB( string $pdb, array $atomrec_arr, [object Science_Chemistry_Macromolecule_PDB $macromol = ""])

Constructor for the class
  • Access: public

Parameters:

string   $pdb     PDB if of the protein/nucleic acid/etc.
array   $atomrec_arr     Array of PDB atom record lines
object Science_Chemistry_Macromolecule_PDB   $macromol     reference to the containing macromolecule

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