schrodinger.application.qsite.output module

A class for parsing of QSite output files.

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

class schrodinger.application.qsite.output.QSiteOutput(output=None)

Bases: schrodinger.application.jaguar.output.JaguarOutput

A class to hold output information from a QSite run.

class schrodinger.application.qsite.output.QSiteResults

Bases: schrodinger.application.jaguar.results.JaguarResults

energy_precision = 1e-06

class schrodinger.application.qsite.output.QSiteTextParser(jaguar_output, file_iter=None)

Bases: schrodinger.application.jaguar.textparser.TextParser

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

callback = {'pre': {<_sre.SRE_Pattern object>: <function nfrzmm>, <_sre.SRE_Pattern object at 0x80eb0a0>: <function esp_fit_atoms>, <_sre.SRE_Pattern object at 0x80f00c0>: <function pseudospectral>, <_sre.SRE_Pattern object at 0x7eb7420>: <function coords_frozen1>, <_sre.SRE_Pattern object at 0x88f4ed0>: <function mae>, <_sre.SRE_Pattern object>: <function z_variables>, <_sre.SRE_Pattern object>: <function start_geometry>, <_sre.SRE_Pattern object at 0x80ef430>: <function scan_coordinates>, <_sre.SRE_Pattern object at 0x89746e0>: <function total_lo_correction>, <_sre.SRE_Pattern object at 0x89b6160>: <function point_group>, <_sre.SRE_Pattern object>: <function functional>, <_sre.SRE_Pattern object at 0x765c990>: <function solvation_job>, <_sre.SRE_Pattern object at 0x66d41a0>: <function correlation_type>, <_sre.SRE_Pattern object>: <function point_group_used>, <_sre.SRE_Pattern object at 0x5341210>: <function qst_initial_geometry>, <_sre.SRE_Pattern object at 0x7612a60>: <function mae_in>, <_sre.SRE_Pattern object at 0x579a320>: <function molchg>, <_sre.SRE_Pattern object>: <function ncuts>, <_sre.SRE_Pattern object at 0x634c320>: <function coords_frozen2>, <_sre.SRE_Pattern object at 0x7fe13a0>: <function path_geometry>, <_sre.SRE_Pattern object>: <function symmetrized_geometry>, <_sre.SRE_Pattern object>: <function nddo_atoms>, <_sre.SRE_Pattern object>: <function mol_weight>, <_sre.SRE_Pattern object at 0x66d4420>: <function coords_opt>, <_sre.SRE_Pattern object>: <function custom_functional>, <_sre.SRE_Pattern object at 0x80ee440>: <function spin_splitting_score>, <_sre.SRE_Pattern object>: <function nddo_hcaps>, <_sre.SRE_Pattern object>: <function esp_fit_atoms_and_bonds>, <_sre.SRE_Pattern object at 0x694a500>: <function qst_geometries>, <_sre.SRE_Pattern object at 0x57b8d10>: <function nbasis>, <_sre.SRE_Pattern object at 0x6270520>: <function non_default_print_options>, <_sre.SRE_Pattern object>: <function stoichiometry>, <_sre.SRE_Pattern object>: <function qm_atoms>, <_sre.SRE_Pattern object at 0x73f5dd0>: <function coords_ind>, <_sre.SRE_Pattern object at 0x80eb630>: <function numerical_freqs>, <_sre.SRE_Pattern object at 0x66d3e80>: <function coords_nred>, <_sre.SRE_Pattern object>: <function nhcaps>, <_sre.SRE_Pattern object at 0x4f576b0>: <function qm_atoms>, <_sre.SRE_Pattern object>: <function multip>, <_sre.SRE_Pattern object at 0x665dee0>: <function coords_harmonic>, <_sre.SRE_Pattern object at 0x62b7e80>: <function calc_type>, <_sre.SRE_Pattern object>: <function nconmm>, <_sre.SRE_Pattern object>: <function basis_set>, <_sre.SRE_Pattern object>: <function total_atoms>, <_sre.SRE_Pattern object>: <function jaguar_atoms>}, 'onee': {<_sre.SRE_Pattern object at 0x8105600>: <function s_min_eval>, <_sre.SRE_Pattern object>: <function bondchg_repulsion_energy>, <_sre.SRE_Pattern object at 0x65927f0>: <function canorb>}, 'ch': {<_sre.SRE_Pattern object at 0x80ef800>: <function esp_charges>, <_sre.SRE_Pattern object at 0x828ac80>: <function multipole_esp>, <_sre.SRE_Pattern object at 0x6b6eec0>: <function multipole_mulliken>, <_sre.SRE_Pattern object>: <function fukui_indices>, <_sre.SRE_Pattern object at 0x80efb30>: <function mulliken_charges>, <_sre.SRE_Pattern object at 0x828a940>: <function multipole_qm>}, 'scanner': {<_sre.SRE_Pattern object at 0x7db1e80>: <function end_scan>, <_sre.SRE_Pattern object at 0x6e49790>: <function geometry_scan_step>, <_sre.SRE_Pattern object>: <function start_geometry>}, 'cpolar': {<_sre.SRE_Pattern object>: <function beta_polar>, <_sre.SRE_Pattern object>: <function gamma_polar>, <_sre.SRE_Pattern object>: <function alpha_polar>}, 'scf': {<_sre.SRE_Pattern object>: <function electronic_e>, <_sre.SRE_Pattern object at 0x7c87060>: <function two_e_terms>, <_sre.SRE_Pattern object>: <function aposteri_e>, <_sre.SRE_Pattern object>: <function solvation>, <_sre.SRE_Pattern object>: <function scfe>, <_sre.SRE_Pattern object at 0x8655ee0>: <function nops_on>, <_sre.SRE_Pattern object at 0x7dd5f10>: <function solution_phase>, <_sre.SRE_Pattern object>: <function homo>, <_sre.SRE_Pattern object>: <function gas_phase>, <_sre.SRE_Pattern object at 0x7e921f0>: <function nops_on>, <_sre.SRE_Pattern object>: <function etot>, <_sre.SRE_Pattern object at 0x7636fa0>: <function one_e_terms>, <_sre.SRE_Pattern object>: <function lumo>, <_sre.SRE_Pattern object at 0x73efdc0>: <function orbital_energies>, <_sre.SRE_Pattern object>: <function nucrep1>, <_sre.SRE_Pattern object>: <function nucrep2>}, 'before pre': {<_sre.SRE_Pattern object>: <function jobid>}, 'elden': {<_sre.SRE_Pattern object>: <function esp_analysis>, <_sre.SRE_Pattern object>: <function alie_analysis>, <_sre.SRE_Pattern object>: <function epn>}, 'tdener': {<_sre.SRE_Pattern object at 0x69458c0>: <function reset_tddft_excitation_energies>, <_sre.SRE_Pattern object>: <function tddft_excitation_energies>, <_sre.SRE_Pattern object>: <function tddft_excitation_energies_old>}, 'lmp2': {<_sre.SRE_Pattern object>: <function lmp2>, <_sre.SRE_Pattern object>: <function solvation>, <_sre.SRE_Pattern object>: <function gas_phase>, <_sre.SRE_Pattern object at 0x7dd5f10>: <function solution_phase>}, 'etit': {<_sre.SRE_Pattern object>: <function electron_transfer>}, 'lmp2gdb': {<_sre.SRE_Pattern object at 0x6efa4f0>: <function forces>}, 'freq': {<_sre.SRE_Pattern object at 0x80ea6c0>: <function frequencies_old>, <_sre.SRE_Pattern object at 0x61f73a0>: <function zpe>, <_sre.SRE_Pattern object at 0x828afc0>: <function frequencies>, <_sre.SRE_Pattern object at 0x6265f70>: <function get_vetted_vec_index>}, 'gvblmp2': {<_sre.SRE_Pattern object>: <function rolmp2>, <_sre.SRE_Pattern object>: <function gvblmp2>}, 'impact': {<_sre.SRE_Pattern object>: <function bond_stretch_energy>, <_sre.SRE_Pattern object>: <function nb_cutoff>, <_sre.SRE_Pattern object>: <function ffld>, <_sre.SRE_Pattern object>: <function angle_bend_energy>, <_sre.SRE_Pattern object>: <function torsion_energy>, <_sre.SRE_Pattern object>: <function qmmm_bend_energy>, <_sre.SRE_Pattern object>: <function nb_update>, <_sre.SRE_Pattern object>: <function qmmm_torsion_energy>, <_sre.SRE_Pattern object>: <function lj14_energy>, <_sre.SRE_Pattern object>: <function qmmm_stretch_energy>, <_sre.SRE_Pattern object>: <function total_potential_energy>, <_sre.SRE_Pattern object>: <function electrostatic14_energy>, <_sre.SRE_Pattern object>: <function total_energy>, <_sre.SRE_Pattern object>: <function electrostatic_energy>, <_sre.SRE_Pattern object>: <function qmmm_electrostatic_energy>, <_sre.SRE_Pattern object>: <function hbond_energy>, <_sre.SRE_Pattern object>: <function total_kinetic_energy>, <_sre.SRE_Pattern object>: <function lj_energy>}, 'nmrcphf': {<_sre.SRE_Pattern object>: <function get_nmr>}, None: {<_sre.SRE_Pattern object at 0x63c57c0>: <function fatal_error>, <_sre.SRE_Pattern object>: <function start_of_program>, <_sre.SRE_Pattern object>: <function glibc>, <_sre.SRE_Pattern object>: <function end_time>}, 'sole': {<_sre.SRE_Pattern object at 0x7dd5f10>: <function solution_phase>, <_sre.SRE_Pattern object at 0x6b8a1d0>: <function solvation>}, 'cis': {<_sre.SRE_Pattern object>: <function cis_excitation_energies>}, 'geopt': {<_sre.SRE_Pattern object at 0x80ef010>: <function nofail_geopt>, <_sre.SRE_Pattern object at 0x80eec20>: <function nofail_geopt_restart>, <_sre.SRE_Pattern object>: <function convergence_category>, <_sre.SRE_Pattern object at 0x6896190>: <function tddft_geopt_energy>, <_sre.SRE_Pattern object>: <function geopt_geometry>, <_sre.SRE_Pattern object at 0x8936490>: <function end_geometry>, <_sre.SRE_Pattern object at 0x80ed4a0>: <function stopping_optimization>, <_sre.SRE_Pattern object at 0x7af70c0>: <function nops_on>, <_sre.SRE_Pattern object>: <function z_variables>, <_sre.SRE_Pattern object at 0x8925b30>: <function sm_geometry>, <_sre.SRE_Pattern object at 0x807d290>: <function irc_summary>, <_sre.SRE_Pattern object at 0x80ec590>: <function irc_point>, <_sre.SRE_Pattern object>: <function geopt_stuck2>, <_sre.SRE_Pattern object at 0x6aad7f0>: <function geopt_stuck1>}, 'der1b': {<_sre.SRE_Pattern object at 0x6efa4f0>: <function forces>}, 'tddft_g': {<_sre.SRE_Pattern object at 0x6efa4f0>: <function forces>}, 'nude': {<_sre.SRE_Pattern object at 0x6efa4f0>: <function forces>}, 'lmp2gb': {<_sre.SRE_Pattern object at 0x6efa4f0>: <function forces>}}

schrodinger.application.qsite.output.angle_bend_energy(tp, qo, m, it)

schrodinger.application.qsite.output.bond_stretch_energy(tp, qo, m, it)

schrodinger.application.qsite.output.bondchg_repulsion_energy(tp, qo, m, it)

schrodinger.application.qsite.output.callback(prog, regexp=None, debug=False)

A decorator based on the Jaguar output callback decorator, but that adds the callbacks to the QSiteTextParser instead.

schrodinger.application.qsite.output.electrostatic14_energy(tp, qo, m, it)

schrodinger.application.qsite.output.electrostatic_energy(tp, qo, m, it)

schrodinger.application.qsite.output.ffld(tp, qo, m, it)

schrodinger.application.qsite.output.hbond_energy(tp, qo, m, it)

schrodinger.application.qsite.output.jaguar_atoms(tp, qo, m, it)

schrodinger.application.qsite.output.lj14_energy(tp, qo, m, it)

schrodinger.application.qsite.output.lj_energy(tp, qo, m, it)

schrodinger.application.qsite.output.nb_cutoff(tp, qo, m, it)

schrodinger.application.qsite.output.nb_update(tp, qo, m, it)

schrodinger.application.qsite.output.nconmm(tp, qo, m, it)

schrodinger.application.qsite.output.ncuts(tp, qo, m, it)

schrodinger.application.qsite.output.nddo_atoms(tp, qo, m, it)

schrodinger.application.qsite.output.nddo_hcaps(tp, qo, m, it)

schrodinger.application.qsite.output.nfrzmm(tp, qo, m, it)

schrodinger.application.qsite.output.nhcaps(tp, qo, m, it)

schrodinger.application.qsite.output.qm_atoms(tp, qo, m, it)

schrodinger.application.qsite.output.qmmm_bend_energy(tp, qo, m, it)

schrodinger.application.qsite.output.qmmm_electrostatic_energy(tp, qo, m, it)

schrodinger.application.qsite.output.qmmm_stretch_energy(tp, qo, m, it)

schrodinger.application.qsite.output.qmmm_torsion_energy(tp, qo, m, it)

schrodinger.application.qsite.output.torsion_energy(tp, qo, m, it)

schrodinger.application.qsite.output.total_atoms(tp, qo, m, it)

schrodinger.application.qsite.output.total_energy(tp, qo, m, it)

schrodinger.application.qsite.output.total_kinetic_energy(tp, qo, m, it)

schrodinger.application.qsite.output.total_potential_energy(tp, qo, m, it)