Science_Chemistry

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Packages:
Science_Chemistry

Classes:

Science_Chemistry_Atom
Science_Chemistry_Atom_PDB
Science_Chemistry_Coordinates
Science_Chemistry_Element
Science_Chemistry_Macromolecule
Science_Chemistry_Macromolecule_PDB
Science_Chemistry_Molecule
Science_Chemistry_Molecule_XYZ
Science_Chemistry_PDBFile
Science_Chemistry_PDBParser
Science_Chemistry_Periodic_Table
Science_Chemistry_Residue_PDB

Files:

Atom.php
Atom_PDB.php
Chemistry.php
Coordinates.php
Element.php
Macromolecule.php
Macromolecule_PDB.php
Molecule.php
Molecule_XYZ.php
PDBFile.php
PDBParser.php
Periodic_Table.php
Residue_PDB.php

Class: Science_Chemistry_PDBParser

Source Location: /Science_Chemistry-1.1.2/Science/Chemistry/PDBParser.php

Class Overview

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

Author(s):

Jesus M. Castagnetto <jmcastagnetto at php.net>

Version:

1.0

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.

Author: Jesus M. Castagnetto <jmcastagnetto@php.net>
Version: 1.0
See: Science_Chemistry_PDBFile
Access: public

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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

See: Science_Chemistry_PDBParser::parseResidues()
Access: public

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

See: Science_Chemistry_PDBParser::parseResidues()

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

See: Science_Chemistry_PDBParser::parseAtom()
See: parseFile()

Parameters:

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

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Documentation generated on Mon, 11 Mar 2019 15:48:16 -0400 by phpDocumentor 1.4.4. PEAR Logo Copyright © PHP Group 2004.