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):

Jesus M. Castagnetto <jmcastagnetto at php.net>

Version:

Variables

Methods

Science_Chemistry_Residue_PDB

Inherited Variables

Class: Science_Chemistry_Molecule

Science_Chemistry_Molecule::$name
Science_Chemistry_Molecule::$num_atoms

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

Author: Jesus M. Castagnetto <jmcastagnetto@php.net>
Version: 1.0
Access: public

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Class Variables

$macromol =

[line 86]

Reference to the protein to which this residue belongs

Access: public

Type:

object Science_Chemistry_Macromolecule_PDB

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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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