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Chemical classes - Science_Chemistry

Science_Chemistry_PDBParser

Science_Chemistry_PDBParser

A self-contained class to parse a PDB file into an array of residues

 

public class Science_Chemistry_PDBParser

A self-contained class to parse a PDB file into an array of residues
each containing an array of atoms<br>Useful when dealing with big PDB files, where using the Science_Chemistry_PDBFileclass will generate out of memory errors.

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

 

Public Method Summary

object PDBParser

Science_Chemistry_PDBParser(string $filename, [ boolean $multi, boolean $meta, boolean $full ])

Constructor for the class, requires a PDB filename
array

getResidueList(integer $macromol, string $resname)

Returns an array of residues with a particular name

Private Method Summary

void

parseResidues(array $records, boolean $full)

Makes the array of residues in the macromolecule
void

parseAtom(string $atomrec, boolean $full, &$atomname)

Parses an atom record into an associative array

Private Field Summary

string

$pdb

PDB ID
string

$file

Full path to PDB file
unknown

$date

PDB file's date
string

$class

PDB macromolecule(s) class
array

$macromolecules

Array of macromolecules
int

$num_macromolecules

Number of macromolecules

Public Method Details

Science_Chemistry_PDBParser

public object PDBParser Science_Chemistry_PDBParser( string $filename, [ boolean $multi, boolean $meta, boolean $full ] )

  Constructor for the class, requires a PDB filename

Parameter
string $filename
PDB filename
boolean $multi = >>false<<
whether to parse all models in a multi-model file
boolean $meta = >>false<<
whether to store the PDB file meta information
boolean $full = >>false<<
whether to store the full set of fields per atom
Returns object PDBParser

See Also parseResidues()

getResidueList

public array getResidueList( integer $macromol, string $resname )

  Returns an array of residues with a particular name
from the indicated macromolecule index

Parameter
integer $macromol
Index of the macromolecule in the $macromolecules array
string $resname
Residue name, e.g. HIS, CYS, etc.
Returns array

list of residues with the requested name

See Also $macromolecules

Private Method Details

parseResidues

private void parseResidues( array $records, boolean $full )

  Makes the array of residues in the macromolecule

Parameter
array $records
boolean $full
whether to store the full set of fields per atom
Returns void

See Also parseAtom()

parseAtom

private void parseAtom( string $atomrec, boolean $full, &$atomname )

  Parses an atom record into an associative array

Parameter
string $atomrec
PDB atom record
boolean $full
whether to store the full set of fields per atom
&$atomname
Warning: documentation is missing.
Returns void

See Also parseResidues()

Private Field Details

$pdb

private string $pdb

>><<

PDB ID


$file

private string $file

>><<

Full path to PDB file


$date

private unknown $date

>><<

PDB file's date


$class

private string $class

>><<

PDB macromolecule(s) class


$macromolecules

private array $macromolecules

>><<

Array of macromolecules


$num_macromolecules

private int $num_macromolecules

>><<

Number of macromolecules



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