Package schrodinger :: Package application :: Package qsite :: Module output

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Module output

A class for parsing of QSite output files.

This module provides a class QSiteOutput that holds the information from a QSite run.

Classes

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QSiteResults
A class for holding results for a specific geometry.

QSiteTextParser
A subclass of the Jaguar output text parser that adds QSite specific parsing.

QSiteOutput
A class to hold output information from a QSite run.

Functions

[hide private]

callback(prog, regexp=None, debug=False)
A decorator based on the Jaguar output callback decorator, but that adds the callbacks to the QSiteTextParser instead.

ffld(tp, qo, m, it)

nb_cutoff(tp, qo, m, it)

nb_update(tp, qo, m, it)

total_energy(tp, qo, m, it)

total_potential_energy(tp, qo, m, it)

total_kinetic_energy(tp, qo, m, it)

bond_stretch_energy(tp, qo, m, it)

angle_bend_energy(tp, qo, m, it)

torsion_energy(tp, qo, m, it)

lj14_energy(tp, qo, m, it)

electrostatic14_energy(tp, qo, m, it)

lj_energy(tp, qo, m, it)

electrostatic_energy(tp, qo, m, it)

hbond_energy(tp, qo, m, it)

qmmm_electrostatic_energy(tp, qo, m, it)

qmmm_stretch_energy(tp, qo, m, it)

qmmm_bend_energy(tp, qo, m, it)

qmmm_torsion_energy(tp, qo, m, it)

total_atoms(tp, qo, m, it)

jaguar_atoms(tp, qo, m, it)

qm_atoms(tp, qo, m, it)

nddo_atoms(tp, qo, m, it)

nhcaps(tp, qo, m, it)

nddo_hcaps(tp, qo, m, it)

ncuts(tp, qo, m, it)

nconmm(tp, qo, m, it)

nfrzmm(tp, qo, m, it)

bondchg_repulsion_energy(tp, qo, m, it)

Variables

[hide private]

__package__ = 'schrodinger.application.qsite'

Function Details

[hide private]

ffld(tp, qo, m, it)

Decorators:

@callback("impact", r" calling (\S+)\s+atomtyping")

nb_cutoff(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Cutoff radius:\s+(\S+)")

nb_update(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Update frequency: every\s+(\d+) ")

total_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Total Energy of the system\.+\s+(\S+) ")

total_potential_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Total Potential Energy\.+\s+(\S+) ")

total_kinetic_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Total Kinetic Energy\.+\s+(\S+) ")

bond_stretch_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Bond Stretch Energy\.+\s+(\S+) ")

angle_bend_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Angle Bending Energy\.+\s+(\S+) ")

torsion_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Torsion Angle Energy\.+\s+(\S+) ")

lj14_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ 1,4 Lennard Jones Energy\.+\s+(\S+) ")

electrostatic14_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ 1,4 Electrostatic Energy\.+\s+(\S+) ")

lj_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Lennard Jones Energy\.+\s+(\S+) ")

electrostatic_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ Electrostatic Energy\.+\s+(\S+) ")

hbond_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ H-bond Energy\.+\s+(\S+) ")

qmmm_electrostatic_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ QM/MM Electrostatic Energy\.+\s+(\S+) ")

qmmm_stretch_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ QM/MM Stretch Energy\.+\s+(\S+) ")

qmmm_bend_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ QM/MM Bend Energy\.+\s+(\S+) ")

qmmm_torsion_energy(tp, qo, m, it)

Decorators:

@callback("impact", r"^ QM/MM Torsion Energy\.+\s+(\S+) ")

total_atoms(tp, qo, m, it)

Decorators:

@callback("pre", r"^Total number of atoms:\s+(\d+)")

jaguar_atoms(tp, qo, m, it)

Decorators:

@callback("pre", r"^Number of atoms passed to Jaguar:\s+(\d+)")

qm_atoms(tp, qo, m, it)

Decorators:

@callback("pre", r"^Number of atoms treated by QM:\s+(\d+)")

nddo_atoms(tp, qo, m, it)

Decorators:

@callback("pre", r"^Number of atoms treated by NDDO:\s+(\d+)")

nhcaps(tp, qo, m, it)

Decorators:

@callback("pre", r"^Number of hydrogen caps:\s+(\d+)")

nddo_hcaps(tp, qo, m, it)

Decorators:

@callback("pre", r"^Number of NDDO hydrogen caps:\s+(\d+)")

ncuts(tp, qo, m, it)

Decorators:

@callback("pre", r"^Number of frozen orbital cuts:\s+(\d+)")

nconmm(tp, qo, m, it)

Decorators:

@callback("pre", r"^Number of constrained MM atoms:\s+(\d+)")

nfrzmm(tp, qo, m, it)

Decorators:

@callback("pre", r"^Number of frozen MM atoms:\s+(\d+)")

bondchg_repulsion_energy(tp, qo, m, it)

Decorators:

@callback("onee", r"^ bond-charge repulsion energy\.+\s+(\S+) ")