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

Science_Chemistry_Molecule_XYZ

Science_Chemistry_Molecule
   |
  +-- Science_Chemistry_Molecule_XYZ

Base class representing a Molecule from a XYZ format file

 

public class Science_Chemistry_Molecule_XYZ extends Science_Chemistry_Molecule

Base class representing a Molecule from a XYZ format file

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

 

Methods inherited from Science_Chemistry_Molecule

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

Public Method Summary

object Science_Chemistry_Molecule_XYZ

Science_Chemistry_Molecule_XYZ([ string $xyzdata, string $src ])

Constructor for the class, accepts 2 optional parameters:
boolean

parseXYZ(string $xyzdata, string $src)

method that does the parsing of the XYZ data itself
string

toString()

Generates a string representation of the XYZ moleculeWarning: documentation is missing.

Private Method Summary

object Science_Chemistry_Atom

parseAtom(string $line)

Parses an XYZ atom record

Fields inherited from Science_Chemistry_Molecule

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

Public Field Summary

float

$energy

Energy of the molecule. Optional value in XYZ file format.

Public Method Details

Science_Chemistry_Molecule_XYZ

public object Science_Chemistry_Molecule_XYZ Science_Chemistry_Molecule_XYZ( [ string $xyzdata, string $src ] )

  Constructor for the class, accepts 2 optional parameters:
the data and its source. Possible values for $src: "file", "string"

Parameter
string $xyzdata = >>""<<
string $src = >>"file"<<
one of "file" or "string"
Returns object Science_Chemistry_Molecule_XYZ

See Also parseXYZ()

parseXYZ

public boolean parseXYZ( string $xyzdata, string $src )

  method that does the parsing of the XYZ data itself

Parameter
string $xyzdata
string $src
Returns boolean

See Also Science_Chemistry_Molecule_XYZ()

toString

public string toString( )

  Generates a string representation of the XYZ molecule
Overrides parent Science_Chemistry_Molecule::toString() method

Warning: documentation is missing.

Returns string


Private Method Details

parseAtom

private object Science_Chemistry_Atom parseAtom( string $line )

  Parses an XYZ atom record

Parameter
string $line
Returns object Science_Chemistry_Atom

@acess public

See Also parseXYZ()

Public Field Details

$energy

public float $energy

>><<

Energy of the molecule. Optional value in XYZ file format.



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