pyviblib.io.parsers

Module for parsing files

Classes

AbstractFileParser

abstract base class for the parsers

DaltonOutputParser

Dalton 1.x or 2.0 files

FCHKFileParser

Gaussian Formatted Checkpoint files

VOAVIEWFileParser

VOAVIEW files

MOLDENFileParser

MOLDEN files

XMolXYZFileParser

XMol XYZ files

HESFileParser

cartesian hessian files of DALTON

NumericDataFileParser

files with numeric data only

FittedSpectraFileParser

fitted spectra files of VOAPlot 4.2+

FCMINTFileParser

cartesian hessian files of AcesII

ParserFactory

instantiating parsers

SpectraMixtureFileParser

spectra mixture files (ini-based)

RamanROAExpSpectraFileParser

Raman/ROA experimental files

PyVib2MolFileParser

PyVib2 molecule files

Author:Maxim Fedorovsky

class pyviblib.io.parsers.AbstractFileParser(filename)

Abstract base class for all parsers.

This class defines a set of protected methods which are called in the constructor in the following sequence:

_parse()

initialize some variables (*)

_validate()

validate the read data (*)

The following static method is exported:

get_description()

get the description of a parser (*)

Methods marked with an asterisk must be overridden in subclasses. Their default implementations raise a NotImplementedError.

The following read-only common properties are exposed for all subclasses:

filename

filename argument passed to the contructor

Natoms

number of atoms in the molecule

coords

cartesian coordinates

elements

one-based list of elements

Initializer of the class.

Parameter:filename – file name or file object

static get_description()

Return the description of the parser.

Subclasses must override this static method. Otherwise a NotImplementedError is raised.

class pyviblib.io.parsers.DaltonOutputParser(filename, London_orbitals=True)

Parser for DALTON 1.x or 2.x output files.

The following read-only properties are exposed:

version

DALTON version

NFreq

number of vibrations

L

mass-weighted excursions for the vibrations

Lx

cartesian excursions for the vibrations

freqs

wavenumbers of vibrations in ascending order

lambda_incident

wavelength of the incident light in nm

London_orbitals

whether the London orbitals are to be used

PP

gradients of the polarizability tensor

PM

gradients of the G’ tensor

PQ

gradients of the A tensor (contracted)

A

gradients of the A tensor (non-contracted)

P

gradients of the electric dipole moment (APTs)

M

gradients of the magnetic dipole moment (AATs)

Initializer of the class.

Parameters:

• filename – file name or file object
• London_orbitals – whether the gradients for the London orbitals are to be read from the output

static get_description()

Get the description of the parser.

class pyviblib.io.parsers.FCHKFileParser(filename, g09=False)

Parser for Formatted Checkpoint files of Gaussian.

The following read-only properties are exposed:

hessian

hessian matrix

NBasis

number of basis function

Etotal

total electronic energy in hartree

comment

comment

lambda_incident

wavelength of the incident light

PP

gradients of the polarizability tensor

:attr:` PM`

gradients of the G’ tensor

PQ

gradients of the A tensor (contracted)

A

gradients of the A tensor (non-contracted)

P

gradients of the electric dipole moment (APTs)

M

gradients of the magnetic dipole moment (AATs)

Initializer of the class.

Parameters:

• filename – file name or file object
• g09 – whether the file has been produced with Gaussian09

static get_description()

Get the description of the parser.

class pyviblib.io.parsers.VOAVIEWFileParser(filename)

Parser for VOAVIEW files.

The following read-only properties are exposed:

NFreq

number of vibrations

L

mass-weighted excursions for the vibrations

Lx

cartesian excursions for the vibrations

freqs

wavenumbers of vibrations in ascending order

PP

gradients of the polarizability tensor

PM

gradients of the G’ tensor

PQ

gradients of the A tensor (contracted)

lambda_incident

wavelength of the incident light

The wavelength of the incident light is always 532 nm.

Initializer of the class.

Parameter:filename – file name or file object

static get_description()

Get the description of the parser.

class pyviblib.io.parsers.MOLDENFileParser(filename)

Parser for MOLDEN files.

Currently extracts only the geometry and normal modes of a molecule.

The following read-only properties are exposed:

NFreq

number of vibrations

L

mass-weighted excursions for the vibrations

Lx

cartesian excursions for the vibrations

freqs

wavenumbers of vibrations in ascending order

comment

comment

Initializer of the class.

Parameter:filename – file name or file object

static get_description()

Get the description of the parser.

class pyviblib.io.parsers.XMolXYZFileParser(filename)

Parser for XMol XYZ files.

The following read-only property is exposed:

comment

comment

Initializer of the class.

Parameter:filename – file name or file object

static get_description()

Get the description of the parser.

class pyviblib.io.parsers.HESFileParser(hesfile)

Parser for cartesian hessian files of DALTON (*.hes).

The following read-only properties are exposed:

hessian

hessian matrix

Initializer of the class.

Parameter:hesfile – file name

static get_description()

Get the description of the parser.

class pyviblib.io.parsers.NumericDataFileParser(filename, ncols=None)

Parser for files containing only numbers.

The following read-only property is exposed:

data

read data as ndarray

Initializer of the class.

Parameters:

• filename – file name
• ncols – number of columns to be read

class pyviblib.io.parsers.FittedSpectraFileParser(filename)

Parser for fitted spectra files of VOAPlot 4.2+.

This is not a subclass of AbstractFileParser.

The most important columns of fitted spectra files are:

nu raman roa degree_of_circularity

The following read-only properties are exposed:

type

type of the spectrum

molecule_name

the molecule name

data

matrix with all read data

Npoints

number of points read

Initializer of the class.

Parameter:filename – file name

class pyviblib.io.parsers.FCMINTFileParser(filename)

Parser for cartesian hessian files of AcesII (FCMINT).

The following read-only properties are exposed:

Natoms

number of atoms

hessian

hessian

Initializer of the class.

Parameter:filename – file name

class pyviblib.io.parsers.ParserFactory

Instantiating parser objects based on a file’s extension.

The following extensions (case insensitive) are recognized:

• ‘.out’ – Dalton 1.x and 2.0 output files
• ‘.fchk’ ‘.fch’ ‘.fck’ – Gaussian Formatted Checkpoint files
• ‘.dat’ ‘.voa’ – VOAVIEW files
• ‘.mol’ – MOLDEN files
• ‘.xyz’ – XMol XYZ files

The class exports the only static method create_parser().

static create_parser(filename)

Create an appropriate parser.

The extension of the file is analyzed and the approapriate parser object is instantiated and returned.

Parameter:filename – file name

class pyviblib.io.parsers.SpectraMixtureFileParser(filename)

Parser for spectra mixture files (ini-based).

The following read-only properties are exposed:

molecules

list of molecules

composition

composition

Example contents:

[Mixture]
molecules = ('path1', 'path2')
composition = (0.45, 0.55)

Initializer of the class.

Parameter:filename – file name

class pyviblib.io.parsers.RamanROAExpSpectraFileParser(filename)

Parser for Raman/ROA experimental files.

The following read-only properties are exposed:

scattering

scattering as string

laser_power

laser power in mW

total_exposure_time

total exposure time in minutes

X

wavenumbers

raman

raman

roa

roa

degcirc

degree of circularity

filename

file name

Example contents:

laser_power=200,total_exposure_time=60
nu1, raman1, roa1, degcirc1(optional)
.
.
.
nuM, ramanM, roaM, degcircM(optional)

Initializer of the class.

Parameter:filename – file name

class pyviblib.io.parsers.PyVib2MolFileParser(filename)

Parser for PyVib2 molecule files.

The following read-only properties are exposed:

L

mass-weighted excursions for the vibrations

freqs

wavenumbers of vibrations in ascending order

hessian

hessian matrix

lambda_incident

wavelength of the incident light in nm

London_orbitals

whether the London orbitals are to be used

PP

gradients of the polarizability tensor

PM

gradients of the G’ tensor

PQ

gradients of the A tensor (contracted)

A

gradients of the A tensor (non-contracted)

P

gradients of the electric dipole moment (APTs)

M

gradients of the magnetic dipole moment (AATs)

NBasis

number of basis functions

Etotal

total electronic energy in hartree

molecule_id

unique identifier of the molecule

groups

groups associated with the molecule

Initializer of the class.

Parameter:filename – file name or file object

static get_description()

Get the description of the parser.