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a b B c d e f g i m n o p r S s t V w x | |||||||
a |
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$atom_name |
Variable in Class Science_Chemistry_Atom_PDB PDB Atom name |
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$alt_loc |
Variable in Class Science_Chemistry_Atom_PDB PDB Atom alternative location |
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areCoordinates |
Function in class Science_Chemistry_Coordinates Checks if the object is an instance of Science_Chemistry_Coordinates |
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addMolecule |
Function in class Science_Chemistry_Macromolecule Adds a Science_Chemistry_Molecule object to the list of molecules in the macromolecule |
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addAtom |
Function in class Science_Chemistry_Molecule Adds a Science_Chemistry_Atom object to the list of atoms in the molecule |
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$atoms |
Variable in Class Science_Chemistry_Molecule Array of atom objects in the molecule |
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b |
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$boiling_point |
Variable in Class Science_Chemistry_Element Element's boiling point, with comments |
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B |
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$BONDCUTOFF |
Variable in Class Science_Chemistry_Molecule Distance cutoff for bond estimation |
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c |
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$chain_id |
Variable in Class Science_Chemistry_Atom_PDB PDB Atom's Residue chain ID |
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$charge |
Variable in Class Science_Chemistry_Atom_PDB PDB Atom electronic charge |
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$coords |
Variable in Class Science_Chemistry_Coordinates Array of tridimensional coordinates: (x, y, z) |
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calcGeomParams |
Function in class Science_Chemistry_Residue_PDB |
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$chain |
Variable in Class Science_Chemistry_Residue_PDB PDB Residue chain |
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calcDistanceMatrix |
Function in class Science_Chemistry_Molecule Calculates the atom-atom distance matrix in Angstroms |
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calcConnectionTable |
Function in class Science_Chemistry_Molecule Calculates the connection table for the molecule |
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$conn_table |
Variable in Class Science_Chemistry_Molecule Atom-Atom connection (bond) table |
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$class |
Variable in Class Science_Chemistry_PDBFile PDB macromolecule(s) class |
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$class |
Variable in Class Science_Chemistry_PDBParser PDB macromolecule(s) class |
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d |
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distance |
Function in class Science_Chemistry_Atom Calculates the cartesian distance from this atom |
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distance |
Function in class Science_Chemistry_Coordinates Castesian distance calculation method |
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$dist_matrix |
Variable in Class Science_Chemistry_Molecule Atom-Atom distance matrix |
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$date |
Variable in Class Science_Chemistry_PDBFile PDB file's date |
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$date |
Variable in Class Science_Chemistry_PDBParser PDB file's date |
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e |
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$element |
Variable in Class Science_Chemistry_Atom Element symbol |
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$energy |
Variable in Class Science_Chemistry_Molecule_XYZ Energy of the molecule. Optional value in XYZ file format. |
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f |
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$family |
Variable in Class Science_Chemistry_Element Element's family |
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$file |
Variable in Class Science_Chemistry_PDBFile Full path to PDB file |
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$file |
Variable in Class Science_Chemistry_PDBParser Full path to PDB file |
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g |
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getField |
Function in class Science_Chemistry_Atom_PDB |
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getElement |
Function in class Science_Chemistry_Atom Returns the chemical symbol for the atom |
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getElement |
Function in class Science_Chemistry_Periodic_Table Returns a Science_Chemistry_Element object correspoding to the symbol (case sensitive) |
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getCoordinates |
Function in class Science_Chemistry_Atom Returns the coordinates object for the atom |
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getCoordinates |
Function in class Science_Chemistry_Coordinates Returns the array of coordinates |
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getMolecules |
Function in class Science_Chemistry_Macromolecule Returns an array of Science_Chemistry_Molecule objects |
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getGeomParams |
Function in class Science_Chemistry_Residue_PDB |
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getAtoms |
Function in class Science_Chemistry_Molecule Returns an array of Atom objects |
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getBondCutoff |
Function in class Science_Chemistry_Molecule Returns the bond cutoff uses to determine bonds |
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getDistanceMatrix |
Function in class Science_Chemistry_Molecule Returns the atom-atom distance matrix |
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getConnectionTable |
Function in class Science_Chemistry_Molecule Returns an array of connected atoms and their bond distance |
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getResidueList |
Function in class Science_Chemistry_PDBParser Returns an array of residues with a particular name |
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getElementFamily |
Function in class Science_Chemistry_Periodic_Table Returns an array of Science_Chemistry_Element objects belonging to an element family |
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i |
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$ins_code |
Variable in Class Science_Chemistry_Atom_PDB PDB Atom insert code |
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isAtom |
Function in class Science_Chemistry_Atom Checks if the object is an instance of Science_Chemistry_Atom |
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isElement |
Function in class Science_Chemistry_Element Checks if an object is a Science_Chemistry_Element instance |
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initMacromolecule |
Function in class Science_Chemistry_Macromolecule Initializes the array of Science_Chemistry_Molecule objects |
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isMacromolecule |
Function in class Science_Chemistry_Macromolecule Checks if the object is an instance of Science_Chemistry_Macromolecule |
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$id |
Variable in Class Science_Chemistry_Residue_PDB PDB Residue ID |
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initMolecule |
Function in class Science_Chemistry_Molecule Initializes the array of Science_Chemistry_Atom objects |
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isMolecule |
Function in class Science_Chemistry_Molecule Checks if the object is an instance of Science_Chemistry_Molecule |
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initTable |
Function in class Science_Chemistry_Periodic_Table Initializes the Periodic Table array |
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m |
|||||||
$melting_point |
Variable in Class Science_Chemistry_Element Element's melting point, with comments |
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$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 |
||||||
$macromolecules |
Variable in Class Science_Chemistry_PDBFile Array of macromolecular objects |
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$macromolecules |
Variable in Class Science_Chemistry_PDBParser Array of macromolecules |
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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 |
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o |
|||||||
$occupancy |
Variable in Class Science_Chemistry_Atom_PDB PDB Atom occupancy |
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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 |
||||||
$pdb |
Variable in Class Science_Chemistry_PDBFile PDB ID |
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$pdb |
Variable in Class Science_Chemistry_PDBParser PDB ID |
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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 |
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$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 |
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S |
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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 |
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Science_Chemistry_Atom |
Class Science_Chemistry_Atom. Base class representing an Atom |
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Science_Chemistry_Atom |
Function in class Science_Chemistry_Atom Constructor for the class, requires the element symbol |
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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 |
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Science_Chemistry_Element |
Class Science_Chemistry_Element. Utility class that defines a chemical element object |
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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 |
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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: |
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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 |
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Science_Chemistry_PDBFile |
Function in class Science_Chemistry_PDBFile Constructor for the class, requires a PDB filename |
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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 |
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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 |
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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 |
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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 |
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|
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PHPDoc 1.0beta |