Science_Chemistry
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Class: Science_Chemistry_PDBParser

Source Location: /Science_Chemistry-1.0.2/Chemistry/PDBParser.php

Class Overview


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


Author(s):

Version:

  • 1.0

Variables

Methods


Inherited Variables

Inherited Methods


Class Details

[line 35]
A self-contained class to parse a PDB file into an array of residues

each containing an array of atoms
Useful when dealing with big PDB files, where using the Science_Chemistry_PDBFile class will generate out of memory errors.



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Class Variables

$pdb =

[line 43]

PDB ID

Type:   string


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Method Detail

Science_Chemistry_PDBParser (Constructor)   [line 96]

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

Constructor for the class, requires a PDB filename

Parameters:

string   $filename   —  PDB filename
boolean   $multi   —  whether to parse all models in a multi-model file
boolean   $meta   —  whether to store the PDB file meta information
boolean   $full   —  whether to store the full set of fields per atom

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getResidueList   [line 247]

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

Returns an array of residues with a particular name from the indicated macromolecule index
  • Return: list of residues with the requested name
  • See: $macromolecules
  • Access: public

Parameters:

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

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parseAtom   [line 211]

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

Parses an atom record into an associative array

Parameters:

string   $atomrec   —  PDB atom record
boolean   $full   —  whether to store the full set of fields per atom
   &$atomname   — 

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parseResidues   [line 168]

void parseResidues( array $records, boolean $full)

Makes the array of residues in the macromolecule

Parameters:

array   $records   — 
boolean   $full   —  whether to store the full set of fields per atom

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