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File: /home/jesus/devel/php/pear/Science/Chemistry/Atom_PDB.php
Chemical classes - Science_Chemistry

Science_Chemistry_Atom_PDB

Science_Chemistry_Atom
   |
  +-- Science_Chemistry_Atom_PDB

Represents a PDB atom record

 

public class Science_Chemistry_Atom_PDB extends Science_Chemistry_Atom

Represents a PDB atom record
and contains a reference to the PDB residue to which it belongs

AuthorsJesus M. Castagnetto <jmcastagnetto@php.net>
Version1.0
 

Methods inherited from Science_Chemistry_Atom
science_chemistry_atom, setcoordinates, getelement, getcoordinates, distance, isatom, tostring, tocml

Public Method Summary
void

Science_Chemistry_Atom_PDB( $atomrec, string $residue)

Warning: documentation is missing.

Private Method Summary
void

getField( $field)

Warning: documentation is missing.

Fields inherited from Science_Chemistry_Atom
$element, $xyz

Public Field Summary
boolean

$VALID

If the atom object has been initialized
object Residue_PDB

$parent_residue

Reference to the containing Residue object

Private Field Summary
string

$rec_name

PDB Atom record type, one of ATOM or HETATM
integer

$ser_num

PDB Atom serial number
string

$atom_name

PDB Atom name
string

$alt_loc

PDB Atom alternative location
string

$res_name

PDB Atom's Residue name
string

$chain_id

PDB Atom's Residue chain ID
string

$res_seq_num

PDB Atom's Residue sequential numnber
string

$ins_code

PDB Atom insert code
float

$occupancy

PDB Atom occupancy
float

$temp_factor

PDB Atom temperature factor
string

$segment_id

PDB Atom segment identifier
float

$charge

PDB Atom electronic charge

Public Method Details

Science_Chemistry_Atom_PDB

public void Science_Chemistry_Atom_PDB( $atomrec, string $residue )
 

Warning: documentation is missing.

Parameter
$atomrec
Warning: documentation is missing.
string $residue
Warning: documentation is missing.
Returns void

Private Method Details

getField

private void getField( $field )
 

Warning: documentation is missing.

Parameter
$field
Warning: documentation is missing.
Returns void

Public Field Details

$VALID

public boolean $VALID

>>false<<

If the atom object has been initialized

$parent_residue

public object Residue_PDB $parent_residue

>><<

Reference to the containing Residue object

Private Field Details

$rec_name

private string $rec_name

>><<

PDB Atom record type, one of ATOM or HETATM

See Also getField()

$ser_num

private integer $ser_num

>><<

PDB Atom serial number

See Also getField()

$atom_name

private string $atom_name

>><<

PDB Atom name

See Also getField()

$alt_loc

private string $alt_loc

>><<

PDB Atom alternative location

See Also getField()

$res_name

private string $res_name

>><<

PDB Atom's Residue name

See Also getField()

$chain_id

private string $chain_id

>><<

PDB Atom's Residue chain ID

See Also getField()

$res_seq_num

private string $res_seq_num

>><<

PDB Atom's Residue sequential numnber

See Also getField()

$ins_code

private string $ins_code

>><<

PDB Atom insert code

See Also getField()

$occupancy

private float $occupancy

>><<

PDB Atom occupancy

See Also getField()

$temp_factor

private float $temp_factor

>><<

PDB Atom temperature factor

See Also getField()

$segment_id

private string $segment_id

>><<

PDB Atom segment identifier

See Also getField()

$charge

private float $charge

>><<

PDB Atom electronic charge

See Also getField()
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