Element index for package Science_Chemistry

[ a ] [ b ] [ c ] [ d ] [ e ] [ f ] [ g ] [ i ] [ m ] [ n ] [ p ] [ r ] [ s ] [ t ] [ v ] [ w ]

a

addAtom: in file Molecule.php, method Science_Chemistry_Molecule::addAtom()
Adds a Science_Chemistry_Atom object to the list of atoms in the molecule
addMolecule: in file Macromolecule.php, method Science_Chemistry_Macromolecule::addMolecule()
Adds a Science_Chemistry_Molecule object to the list of molecules in the macromolecule
areCoordinates: in file Coordinates.php, method Science_Chemistry_Coordinates::areCoordinates()
Checks if the object is an instance of Science_Chemistry_Coordinates
Atom.php: procedural page Atom.php
Atom_PDB.php: procedural page Atom_PDB.php

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b

$boiling_point: in file Element.php, variable Science_Chemistry_Element::$boiling_point
Element's boiling point, with comments

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c

calcConnectionTable: in file Molecule.php, method Science_Chemistry_Molecule::calcConnectionTable()
Calculates the connection table for the molecule
calcDistanceMatrix: in file Molecule.php, method Science_Chemistry_Molecule::calcDistanceMatrix()
Calculates the atom-atom distance matrix in Angstroms
Coordinates.php: procedural page Coordinates.php
Chemistry.php: procedural page Chemistry.php

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d

distance: in file Coordinates.php, method Science_Chemistry_Coordinates::distance()
Cartesian distance calculation method
distance: in file Atom.php, method Science_Chemistry_Atom::distance()
Calculates the cartesian distance from this atom instance to another

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e

$energy: in file Molecule_XYZ.php, variable Science_Chemistry_Molecule_XYZ::$energy
Energy of the molecule. Optional value in XYZ file format.
Element.php: procedural page Element.php

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f

$family: in file Element.php, variable Science_Chemistry_Element::$family
Element's family

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g

getAtoms: in file Molecule.php, method Science_Chemistry_Molecule::getAtoms()
Returns an array of Atom objects
getBondCutoff: in file Molecule.php, method Science_Chemistry_Molecule::getBondCutoff()
Returns the bond cutoff uses to determine bonds
getConnectionTable: in file Molecule.php, method Science_Chemistry_Molecule::getConnectionTable()
Returns an array of connected atoms and their bond distance e.g. array ( array ($atomobj1, $atomobj2, $distance ), ... )
getCoordinates: in file Atom.php, method Science_Chemistry_Atom::getCoordinates()
Returns the coordinates object for the atom
getCoordinates: in file Coordinates.php, method Science_Chemistry_Coordinates::getCoordinates()
Returns the array of coordinates
getDistanceMatrix: in file Molecule.php, method Science_Chemistry_Molecule::getDistanceMatrix()
Returns the atom-atom distance matrix
getElement: in file Periodic_Table.php, method Science_Chemistry_Periodic_Table::getElement()
Returns a Science_Chemistry_Element object correspoding to the symbol (case sensitive)
getElement: in file Atom.php, method Science_Chemistry_Atom::getElement()
Returns the chemical symbol for the atom
getElementFamily: in file Periodic_Table.php, method Science_Chemistry_Periodic_Table::getElementFamily()
Returns an array of Science_Chemistry_Element objects belonging to an element family
getField: in file Atom_PDB.php, method Science_Chemistry_Atom_PDB::getField()
getMolecules: in file Macromolecule.php, method Science_Chemistry_Macromolecule::getMolecules()
Returns an array of Science_Chemistry_Molecule objects
getResidueList: in file PDBParser.php, method Science_Chemistry_PDBParser::getResidueList()
Returns an array of residues with a particular name from the indicated macromolecule index

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i

initMacromolecule: in file Macromolecule.php, method Science_Chemistry_Macromolecule::initMacromolecule()
Initializes the array of Science_Chemistry_Molecule objects
initMolecule: in file Molecule.php, method Science_Chemistry_Molecule::initMolecule()
Initializes the array of Science_Chemistry_Atom objects
initTable: in file Periodic_Table.php, method Science_Chemistry_Periodic_Table::initTable()
Initializes the Periodic Table array
isAtom: in file Atom.php, method Science_Chemistry_Atom::isAtom()
Checks if the object is an instance of Science_Chemistry_Atom
isElement: in file Element.php, method Science_Chemistry_Element::isElement()
Checks if an object is a Science_Chemistry_Element instance
isMacromolecule: in file Macromolecule.php, method Science_Chemistry_Macromolecule::isMacromolecule()
Checks if the object is an instance of Science_Chemistry_Macromolecule
isMolecule: in file Molecule.php, method Science_Chemistry_Molecule::isMolecule()
Checks if the object is an instance of Science_Chemistry_Molecule

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m

$macromol: in file Residue_PDB.php, variable Science_Chemistry_Residue_PDB::$macromol
Reference to the protein to which this residue belongs
$melting_point: in file Element.php, variable Science_Chemistry_Element::$melting_point
Element's melting point, with comments
Macromolecule.php: procedural page Macromolecule.php
Macromolecule_PDB.php: procedural page Macromolecule_PDB.php
Molecule.php: procedural page Molecule.php
Molecule_XYZ.php: procedural page Molecule_XYZ.php

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n

$name: in file Element.php, variable Science_Chemistry_Element::$name
Element's name
$name: in file Molecule.php, variable Science_Chemistry_Molecule::$name
Molecule name
$number: in file Element.php, variable Science_Chemistry_Element::$number
Element's atomic number
$num_atoms: in file Molecule.php, variable Science_Chemistry_Molecule::$num_atoms
Number of atoms in the molecule

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p

$parent_residue: in file Atom_PDB.php, variable Science_Chemistry_Atom_PDB::$parent_residue
Reference to the containing Residue object
$periodic_table: in file Periodic_Table.php, variable Science_Chemistry_Periodic_Table::$periodic_table
The associative array containing the chemical elements
parseAtom: in file PDBParser.php, method Science_Chemistry_PDBParser::parseAtom()
Parses an atom record into an associative array
parseAtom: in file Molecule_XYZ.php, method Science_Chemistry_Molecule_XYZ::parseAtom()
Parses an XYZ atom record
parseResidues: in file PDBParser.php, method Science_Chemistry_PDBParser::parseResidues()
Makes the array of residues in the macromolecule
parseXYZ: in file Molecule_XYZ.php, method Science_Chemistry_Molecule_XYZ::parseXYZ()
method that does the parsing of the XYZ data itself
printConnectionTable: in file Molecule.php, method Science_Chemistry_Molecule::printConnectionTable()
Prints the molecule's connection table
printDistanceMatrix: in file Molecule.php, method Science_Chemistry_Molecule::printDistanceMatrix()
Prints the atom-atom distance matrix
PDBFile.php: procedural page PDBFile.php
PDBParser.php: procedural page PDBParser.php
Periodic_Table.php: procedural page Periodic_Table.php

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r

Residue_PDB.php: procedural page Residue_PDB.php

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s

$symbol: in file Element.php, variable Science_Chemistry_Element::$symbol
Element's symbol, one or two characters, case sensitive
Science_Chemistry_Atom: in file Atom.php, class Science_Chemistry_Atom
Base class representing an Atom
Science_Chemistry_Atom: in file Atom.php, method Science_Chemistry_Atom::Science_Chemistry_Atom()
Constructor for the class, requires the element symbol and an optional array of coordinates
Science_Chemistry_Atom_PDB: in file Atom_PDB.php, method Science_Chemistry_Atom_PDB::Science_Chemistry_Atom_PDB()
Science_Chemistry_Atom_PDB: in file Atom_PDB.php, class Science_Chemistry_Atom_PDB
Represents a PDB atom record and contains a reference to the PDB residue to which it belongs
Science_Chemistry_Coordinates: in file Coordinates.php, method Science_Chemistry_Coordinates::Science_Chemistry_Coordinates()
Constructor for the class, returns null if parameter is not an array with 3 entries
Science_Chemistry_Coordinates: in file Coordinates.php, class Science_Chemistry_Coordinates
Utility class for defining 3D coordinates and its associated distance() method
Science_Chemistry_Element: in file Element.php, method Science_Chemistry_Element::Science_Chemistry_Element()
Constructor for the class
Science_Chemistry_Element: in file Element.php, class Science_Chemistry_Element
Utility class that defines a chemical element object
Science_Chemistry_Macromolecule: in file Macromolecule.php, class Science_Chemistry_Macromolecule
Represents a macromolecule, composed of several Science_Chemistry_Molecule objects
Science_Chemistry_Macromolecule: in file Macromolecule.php, method 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_PDB: in file Macromolecule_PDB.php, method Science_Chemistry_Macromolecule_PDB::Science_Chemistry_Macromolecule_PDB()
Constructor for the class
Science_Chemistry_Macromolecule_PDB: in file Macromolecule_PDB.php, class Science_Chemistry_Macromolecule_PDB
Represents a PDB macromolecule, composed of several Science_Chemistry_Residue_PDB objects
Science_Chemistry_Molecule: in file Molecule.php, method 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: in file Molecule.php, class Science_Chemistry_Molecule
Base class representing a Molecule
Science_Chemistry_Molecule_XYZ: in file Molecule_XYZ.php, class Science_Chemistry_Molecule_XYZ
Base class representing a Molecule from a XYZ format file
Science_Chemistry_Molecule_XYZ: in file Molecule_XYZ.php, method Science_Chemistry_Molecule_XYZ::Science_Chemistry_Molecule_XYZ()
Constructor for the class, accepts 2 optional parameters: the data and its source. Possible values for $src: "file", "string"
Science_Chemistry_PDBFile: in file PDBFile.php, class Science_Chemistry_PDBFile
Represents a PDB file, composed of one or more Science_Chemistry_Macromolecule_PDB objects
Science_Chemistry_PDBFile: in file PDBFile.php, method Science_Chemistry_PDBFile::Science_Chemistry_PDBFile()
Constructor for the class, requires a PDB filename
Science_Chemistry_PDBParser: in file PDBParser.php, method Science_Chemistry_PDBParser::Science_Chemistry_PDBParser()
Constructor for the class, requires a PDB filename
Science_Chemistry_PDBParser: in file PDBParser.php, class Science_Chemistry_PDBParser
A self-contained class to parse a PDB file into an array of residues
Science_Chemistry_Periodic_Table: in file Periodic_Table.php, class Science_Chemistry_Periodic_Table
Utility class that defines a Periodic Table of elements
Science_Chemistry_Residue_PDB: in file Residue_PDB.php, method Science_Chemistry_Residue_PDB::Science_Chemistry_Residue_PDB()
Constructor for the class
Science_Chemistry_Residue_PDB: in file Residue_PDB.php, class Science_Chemistry_Residue_PDB
Represents a PDB residue
SCIENCE_CHEMISTRY_VERSION: in file Chemistry.php, constant SCIENCE_CHEMISTRY_VERSION
Package version constant
setBondCutoff: in file Molecule.php, method Science_Chemistry_Molecule::setBondCutoff()
Sets the distance cutoff for bond determination
setCoordinates: in file Atom.php, method Science_Chemistry_Atom::setCoordinates()
Sets the coordinates for the atom object

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t

toCML: in file Macromolecule.php, method 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
toCML: in file Atom.php, method Science_Chemistry_Atom::toCML()
Returns a CML representation of the Science_Chemistry_Atom object Accepts an optional id
toCML: in file Molecule.php, method 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
toCML: in file Coordinates.php, method Science_Chemistry_Coordinates::toCML()
Returns a CML representation of the coordinates
toCML: in file PDBFile.php, method Science_Chemistry_PDBFile::toCML()
Returns a CML representation of the PDB file TODO
toString: in file Molecule_XYZ.php, method Science_Chemistry_Molecule_XYZ::toString()
Generates a string representation of the XYZ molecule Overrides parent Science_Chemistry_Molecule::toString() method
toString: in file Molecule.php, method Science_Chemistry_Molecule::toString()
Returns a string representation of the molecule as a XYZ-format file Alias of toXYZ()
toString: in file Macromolecule.php, method Science_Chemistry_Macromolecule::toString()
Returns a string representation of the macromolecule as a multiple molecule XYZ-format file Alias of toXYZ()
toString: in file Atom.php, method Science_Chemistry_Atom::toString()
Returns a string representation of the Science_Chemistry_Atom object Alias of toXYZ()
toString: in file Coordinates.php, method Science_Chemistry_Coordinates::toString()
Returns a string representation of the coordinates: x y z
toXYZ: in file Atom.php, method Science_Chemistry_Atom::toXYZ()
Returns a XYZ representation of the Science_Chemistry_Atom object
toXYZ: in file Molecule.php, method Science_Chemistry_Molecule::toXYZ()
Returns a string representation of the molecule as a XYZ-format file
toXYZ: in file Macromolecule.php, method Science_Chemistry_Macromolecule::toXYZ()
Returns a string representation of the macromolecule as a multiple molecule XYZ-format file

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v

$VALID: in file Residue_PDB.php, variable Science_Chemistry_Residue_PDB::$VALID
If the PDB residue object has been initialized
$VALID: in file Atom_PDB.php, variable Science_Chemistry_Atom_PDB::$VALID
If the atom object has been initialized

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w

$weight: in file Element.php, variable Science_Chemistry_Element::$weight
Element's atomic weight in a.m.u (atomic mass units)

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