Packageindex Classtrees Modulegroups Elementlist Report XML Files
a b B c d e f g i m n o p r S s t V w x

a

$atom_name Variable in Class Science_Chemistry_Atom_PDB
PDB Atom name
$alt_loc Variable in Class Science_Chemistry_Atom_PDB
PDB Atom alternative location
areCoordinates Function in class Science_Chemistry_Coordinates
Checks if the object is an instance of Science_Chemistry_Coordinates
addMolecule Function in class Science_Chemistry_Macromolecule
Adds a Science_Chemistry_Molecule object to the list of molecules in the macromolecule
addAtom Function in class Science_Chemistry_Molecule
Adds a Science_Chemistry_Atom object to the list of atoms in the molecule
$atoms Variable in Class Science_Chemistry_Molecule
Array of atom objects in the molecule

b

$boiling_point Variable in Class Science_Chemistry_Element
Element's boiling point, with comments

B

$BONDCUTOFF Variable in Class Science_Chemistry_Molecule
Distance cutoff for bond estimation

c

$chain_id Variable in Class Science_Chemistry_Atom_PDB
PDB Atom's Residue chain ID
$charge Variable in Class Science_Chemistry_Atom_PDB
PDB Atom electronic charge
$coords Variable in Class Science_Chemistry_Coordinates
Array of tridimensional coordinates: (x, y, z)
calcGeomParams Function in class Science_Chemistry_Residue_PDB
$chain Variable in Class Science_Chemistry_Residue_PDB
PDB Residue chain
calcDistanceMatrix Function in class Science_Chemistry_Molecule
Calculates the atom-atom distance matrix in Angstroms
calcConnectionTable Function in class Science_Chemistry_Molecule
Calculates the connection table for the molecule
$conn_table Variable in Class Science_Chemistry_Molecule
Atom-Atom connection (bond) table
$class Variable in Class Science_Chemistry_PDBFile
PDB macromolecule(s) class
$class Variable in Class Science_Chemistry_PDBParser
PDB macromolecule(s) class

d

distance Function in class Science_Chemistry_Atom
Calculates the cartesian distance from this atom
distance Function in class Science_Chemistry_Coordinates
Castesian distance calculation method
$dist_matrix Variable in Class Science_Chemistry_Molecule
Atom-Atom distance matrix
$date Variable in Class Science_Chemistry_PDBFile
PDB file's date
$date Variable in Class Science_Chemistry_PDBParser
PDB file's date

e

$element Variable in Class Science_Chemistry_Atom
Element symbol
$energy Variable in Class Science_Chemistry_Molecule_XYZ
Energy of the molecule. Optional value in XYZ file format.

f

$family Variable in Class Science_Chemistry_Element
Element's family
$file Variable in Class Science_Chemistry_PDBFile
Full path to PDB file
$file Variable in Class Science_Chemistry_PDBParser
Full path to PDB file

g

getField Function in class Science_Chemistry_Atom_PDB
getElement Function in class Science_Chemistry_Atom
Returns the chemical symbol for the atom
getElement Function in class Science_Chemistry_Periodic_Table
Returns a Science_Chemistry_Element object correspoding to the symbol (case sensitive)
getCoordinates Function in class Science_Chemistry_Atom
Returns the coordinates object for the atom
getCoordinates Function in class Science_Chemistry_Coordinates
Returns the array of coordinates
getMolecules Function in class Science_Chemistry_Macromolecule
Returns an array of Science_Chemistry_Molecule objects
getGeomParams Function in class Science_Chemistry_Residue_PDB
getAtoms Function in class Science_Chemistry_Molecule
Returns an array of Atom objects
getBondCutoff Function in class Science_Chemistry_Molecule
Returns the bond cutoff uses to determine bonds
getDistanceMatrix Function in class Science_Chemistry_Molecule
Returns the atom-atom distance matrix
getConnectionTable Function in class Science_Chemistry_Molecule
Returns an array of connected atoms and their bond distance
getResidueList Function in class Science_Chemistry_PDBParser
Returns an array of residues with a particular name
getElementFamily Function in class Science_Chemistry_Periodic_Table
Returns an array of Science_Chemistry_Element objects belonging to an element family

i

$ins_code Variable in Class Science_Chemistry_Atom_PDB
PDB Atom insert code
isAtom Function in class Science_Chemistry_Atom
Checks if the object is an instance of Science_Chemistry_Atom
isElement Function in class Science_Chemistry_Element
Checks if an object is a Science_Chemistry_Element instance
initMacromolecule Function in class Science_Chemistry_Macromolecule
Initializes the array of Science_Chemistry_Molecule objects
isMacromolecule Function in class Science_Chemistry_Macromolecule
Checks if the object is an instance of Science_Chemistry_Macromolecule
$id Variable in Class Science_Chemistry_Residue_PDB
PDB Residue ID
initMolecule Function in class Science_Chemistry_Molecule
Initializes the array of Science_Chemistry_Atom objects
isMolecule Function in class Science_Chemistry_Molecule
Checks if the object is an instance of Science_Chemistry_Molecule
initTable Function in class Science_Chemistry_Periodic_Table
Initializes the Periodic Table array

m

$melting_point Variable in Class Science_Chemistry_Element
Element's melting point, with comments
$molecules Variable in Class Science_Chemistry_Macromolecule
Array of molecular objects
$macromol Variable in Class Science_Chemistry_Residue_PDB
Reference to the protein
$meta Variable in Class Science_Chemistry_PDBFile
Array of meta records
$macromolecules Variable in Class Science_Chemistry_PDBFile
Array of macromolecular objects
$macromolecules Variable in Class Science_Chemistry_PDBParser
Array of macromolecules

n

$name Variable in Class Science_Chemistry_Element
Element's name
$name Variable in Class Science_Chemistry_Macromolecule
Macromolecule's name
$name Variable in Class Science_Chemistry_Molecule
Molecule name
$number Variable in Class Science_Chemistry_Element
Element's atomic number
$num_molecules Variable in Class Science_Chemistry_Macromolecule
Number of molecules/subunits
$num_atoms Variable in Class Science_Chemistry_Molecule
Number of atoms in the molecule
$num_macromolecules Variable in Class Science_Chemistry_PDBFile
Number of molecules/subunits
$num_macromolecules Variable in Class Science_Chemistry_PDBParser
Number of macromolecules

o

$occupancy Variable in Class Science_Chemistry_Atom_PDB
PDB Atom occupancy

p

$parent_residue Variable in Class Science_Chemistry_Atom_PDB
Reference to the containing Residue object
parseResidues Function in class Science_Chemistry_Macromolecule_PDB
Makes the array of residues in the macromolecule
parseResidues Function in class Science_Chemistry_PDBParser
Makes the array of residues in the macromolecule
parseXYZ Function in class Science_Chemistry_Molecule_XYZ
method that does the parsing of the XYZ data itself
parseAtom Function in class Science_Chemistry_Molecule_XYZ
Parses an XYZ atom record
parseAtom Function in class Science_Chemistry_PDBParser
Parses an atom record into an associative array
$pdb Variable in Class Science_Chemistry_Residue_PDB
PDB ID for the protein that contains
$pdb Variable in Class Science_Chemistry_PDBFile
PDB ID
$pdb Variable in Class Science_Chemistry_PDBParser
PDB ID
printDistanceMatrix Function in class Science_Chemistry_Molecule
Prints the atom-atom distance matrix
printConnectionTable Function in class Science_Chemistry_Molecule
Prints the molecule's connection table
parseFile Function in class Science_Chemistry_PDBFile
Makes the arrays of all present PDB record types
$periodic_table Variable in Class Science_Chemistry_Periodic_Table
The associative array containing the chemical elements

r

$rec_name Variable in Class Science_Chemistry_Atom_PDB
PDB Atom record type, one of ATOM or HETATM
$res_name Variable in Class Science_Chemistry_Atom_PDB
PDB Atom's Residue name
$res_seq_num Variable in Class Science_Chemistry_Atom_PDB
PDB Atom's Residue sequential numnber

S

Science_Chemistry_Atom_PDB Class Science_Chemistry_Atom_PDB.
Represents a PDB atom record
Science_Chemistry_Atom_PDB Function in class Science_Chemistry_Atom_PDB
Science_Chemistry_Atom Class Science_Chemistry_Atom.
Base class representing an Atom
Science_Chemistry_Atom Function in class Science_Chemistry_Atom
Constructor for the class, requires the element symbol
Science_Chemistry_Coordinates Class Science_Chemistry_Coordinates.
Utility class for defining 3D coordinates and
Science_Chemistry_Coordinates Function in class Science_Chemistry_Coordinates
Constructor for the class, returns null if parameter is
Science_Chemistry_Element Class Science_Chemistry_Element.
Utility class that defines a chemical element object
Science_Chemistry_Element Function in class Science_Chemistry_Element
Constructor for the class
Science_Chemistry_Macromolecule_PDB Class Science_Chemistry_Macromolecule_PDB.
Represents a PDB macromolecule, composed of several
Science_Chemistry_Macromolecule_PDB Function in class Science_Chemistry_Macromolecule_PDB
Constructor for the class
Science_Chemistry_Macromolecule Class Science_Chemistry_Macromolecule.
Represents a macromolecule, composed of several
Science_Chemistry_Macromolecule Function in class Science_Chemistry_Macromolecule
Constructor for the class, requires a macromolecule name
Science_Chemistry_Molecule_XYZ Class Science_Chemistry_Molecule_XYZ.
Base class representing a Molecule from a XYZ format file
Science_Chemistry_Molecule_XYZ Function in class Science_Chemistry_Molecule_XYZ
Constructor for the class, accepts 2 optional parameters:
Science_Chemistry_Residue_PDB Class Science_Chemistry_Residue_PDB.
Represents a PDB residue
Science_Chemistry_Residue_PDB Function in class Science_Chemistry_Residue_PDB
Constructor for the class
Science_Chemistry_Molecule Class Science_Chemistry_Molecule.
Base class representing a Molecule
Science_Chemistry_Molecule Function in class Science_Chemistry_Molecule
Constructor for the class, requires a molecule name
Science_Chemistry_PDBFile Class Science_Chemistry_PDBFile.
Represents a PDB file, composed of one or more Science_Chemistry_Macromolecule_PDB objects
Science_Chemistry_PDBFile Function in class Science_Chemistry_PDBFile
Constructor for the class, requires a PDB filename
Science_Chemistry_PDBParser Class Science_Chemistry_PDBParser.
A self-contained class to parse a PDB file into an array of residues
Science_Chemistry_PDBParser Function in class Science_Chemistry_PDBParser
Constructor for the class, requires a PDB filename
Science_Chemistry_Periodic_Table Class Science_Chemistry_Periodic_Table.
Utility class that defines a Periodic Table of elements
Science_Chemistry Package

s

$ser_num Variable in Class Science_Chemistry_Atom_PDB
PDB Atom serial number
$segment_id Variable in Class Science_Chemistry_Atom_PDB
PDB Atom segment identifier
setCoordinates Function in class Science_Chemistry_Atom
Sets the coordinates for the atom object
$symbol Variable in Class Science_Chemistry_Element
Element's symbol, one or two characters, case sensitive
$seq_num Variable in Class Science_Chemistry_Residue_PDB
PDB Residue sequence number
setBondCutoff Function in class Science_Chemistry_Molecule
Sets the distance cutoff for bond determination

t

$temp_factor Variable in Class Science_Chemistry_Atom_PDB
PDB Atom temperature factor
toString Function in class Science_Chemistry_Atom
Returns a string representation of the Science_Chemistry_Atom object
toString Function in class Science_Chemistry_Coordinates
Returns a string representation of the coordinates: x y z
toString Function in class Science_Chemistry_Macromolecule
Returns a string representation of the macromolecule
toString Function in class Science_Chemistry_Molecule_XYZ
Generates a string representation of the XYZ molecule
toString Function in class Science_Chemistry_Molecule
Returns a string representation of the molecule
toCML Function in class Science_Chemistry_Atom
Returns a CML representation of the Science_Chemistry_Atom object
toCML Function in class Science_Chemistry_Coordinates
Returns a CML representation of the coordinates
toCML Function in class Science_Chemistry_Macromolecule
Returns a CML representation of the molecule
toCML Function in class Science_Chemistry_Molecule
Returns a CML representation of the molecule
toCML Function in class Science_Chemistry_PDBFile
Returns a CML representation of the PDB file

V

$VALID Variable in Class Science_Chemistry_Atom_PDB
If the atom object has been initialized
$VALID Variable in Class Science_Chemistry_Residue_PDB
If the PDB residue object has been initialized

w

$weight Variable in Class Science_Chemistry_Element
Element's atomic weight in a.m.u (atomic mass units)

x

$xyz Variable in Class Science_Chemistry_Atom
Science_Chemistry_Coordinates object
Packageindex Classtrees Modulegroups Elementlist Report XML Files
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