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Index of all elements

[ 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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