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

Science_Chemistry_Residue_PDB

Science_Chemistry_Molecule
   |
  +-- Science_Chemistry_Residue_PDB

Represents a PDB residue

 

public class Science_Chemistry_Residue_PDB extends Science_Chemistry_Molecule

Represents a PDB residue

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

 

Methods inherited from Science_Chemistry_Molecule

science_chemistry_molecule, initmolecule, addatom, getatoms, ismolecule, tostring, tocml, setbondcutoff, getbondcutoff, calcdistancematrix, printdistancematrix, getdistancematrix, calcconnectiontable, printconnectiontable, getconnectiontable

Public Method Summary

object Science_Chemistry_Residue_PDB

Science_Chemistry_Residue_PDB(string $pdb, array $atomrec_arr, [ string $macromol ])

Constructor for the class

Private Method Summary

void

calcGeomParams()

Warning: documentation is missing.
void

getGeomParams( $param)

Warning: documentation is missing.

Fields inherited from Science_Chemistry_Molecule

$name, $num_atoms, $atoms, $dist_matrix, $conn_table, $bondcutoff

Public Field Summary

boolean

$VALID

If the PDB residue object has been initialized
object Science_Chemistry_Macromolecule_PDB

$macromol

Reference to the protein

Private Field Summary

integer

$seq_num

PDB Residue sequence number
string

$chain

PDB Residue chain
string

$id

PDB Residue ID
string

$pdb

PDB ID for the protein that contains

Public Method Details

Science_Chemistry_Residue_PDB

public object Science_Chemistry_Residue_PDB Science_Chemistry_Residue_PDB( string $pdb, array $atomrec_arr, [ string $macromol ] )

  Constructor for the class

Parameter
string $pdb
PDB if of the protein/nucleic acid/etc.
array $atomrec_arr
Array of PDB atom record lines
string $macromol = >>""<<
reference to the containing macromolecule
Returns object Science_Chemistry_Residue_PDB


Private Method Details

calcGeomParams

private void calcGeomParams( )

 

Warning: documentation is missing.

Returns void


getGeomParams

private void getGeomParams( $param )

 

Warning: documentation is missing.

Parameter
$param
Warning: documentation is missing.
Returns void


Public Field Details

$VALID

public boolean $VALID

>>false<<

If the PDB residue object has been initialized


$macromol

public object Science_Chemistry_Macromolecule_PDB $macromol

>><<

Reference to the protein
to which this residue belongs


Private Field Details

$seq_num

private integer $seq_num

>><<

PDB Residue sequence number


$chain

private string $chain

>><<

PDB Residue chain


$id

private string $id

>><<

PDB Residue ID
$id = "$name:$seq_num:$chain"


$pdb

private string $pdb

>><<

PDB ID for the protein that contains
this residue



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