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 at 0x63ea020>: <function solvation_job>, <_sre.SRE_Pattern object>: <function functional>, <_sre.SRE_Pattern object>: <function custom_functional>, <_sre.SRE_Pattern object at 0x7266050>: <function spin_splitting_score>, <_sre.SRE_Pattern object at 0x714a060>: <function total_lo_correction>, <_sre.SRE_Pattern object>: <function multip>, <_sre.SRE_Pattern object at 0x54840a0>: <function numerical_freqs>, <_sre.SRE_Pattern object at 0x498a8f0>: <function coords_ind>, <_sre.SRE_Pattern object>: <function z_variables>, <_sre.SRE_Pattern object>: <function qm_atoms>, <_sre.SRE_Pattern object at 0x5484950>: <function coords_nred>, <_sre.SRE_Pattern object at 0x4b01180>: <function coords_harmonic>, <_sre.SRE_Pattern object>: <function jaguar_atoms>, <_sre.SRE_Pattern object at 0x52ee1a0>: <function qst_geometries>, <_sre.SRE_Pattern object at 0x69ae9d0>: <function non_default_print_options>, <_sre.SRE_Pattern object>: <function stoichiometry>, <_sre.SRE_Pattern object>: <function ncuts>, <_sre.SRE_Pattern object>: <function nddo_atoms>, <_sre.SRE_Pattern object>: <function point_group_used>, <_sre.SRE_Pattern object at 0x70b5260>: <function mae_in>, <_sre.SRE_Pattern object>: <function nddo_hcaps>, <_sre.SRE_Pattern object>: <function symmetrized_geometry>, <_sre.SRE_Pattern object at 0x7264b60>: <function scan_coordinates>, <_sre.SRE_Pattern object>: <function nfrzmm>, <_sre.SRE_Pattern object>: <function start_geometry>, <_sre.SRE_Pattern object>: <function nconmm>, <_sre.SRE_Pattern object at 0x725dc20>: <function calc_type>, <_sre.SRE_Pattern object at 0x71af470>: <function correlation_type>, <_sre.SRE_Pattern object at 0x5131cc0>: <function coords_frozen1>, <_sre.SRE_Pattern object at 0x6f914e0>: <function molchg>, <_sre.SRE_Pattern object>: <function esp_fit_atoms_and_bonds>, <_sre.SRE_Pattern object at 0x50d5d00>: <function nbasis>, <_sre.SRE_Pattern object at 0x63f9d20>: <function path_geometry>, <_sre.SRE_Pattern object at 0x55410f0>: <function coords_frozen2>, <_sre.SRE_Pattern object>: <function mol_weight>, <_sre.SRE_Pattern object at 0x5484640>: <function coords_opt>, <_sre.SRE_Pattern object at 0x71b1660>: <function point_group>, <_sre.SRE_Pattern object>: <function total_atoms>, <_sre.SRE_Pattern object>: <function nhcaps>, <_sre.SRE_Pattern object at 0x4d56eb0>: <function qst_initial_geometry>, <_sre.SRE_Pattern object at 0x725dec0>: <function esp_fit_atoms>, <_sre.SRE_Pattern object at 0x53a6520>: <function qm_atoms>, <_sre.SRE_Pattern object at 0x7260f50>: <function pseudospectral>, <_sre.SRE_Pattern object>: <function basis_set>, <_sre.SRE_Pattern object at 0x64037c0>: <function mae>}, 'onee': {<_sre.SRE_Pattern object at 0x6c242b0>: <function s_min_eval>, <_sre.SRE_Pattern object at 0x48e09b0>: <function canorb>, <_sre.SRE_Pattern object>: <function bondchg_repulsion_energy>}, 'ch': {<_sre.SRE_Pattern object at 0x7265650>: <function mulliken_charges>, <_sre.SRE_Pattern object at 0x7265d10>: <function multipole_esp>, <_sre.SRE_Pattern object>: <function fukui_indices>, <_sre.SRE_Pattern object at 0x7265380>: <function multipole_mulliken>, <_sre.SRE_Pattern object at 0x72613b0>: <function esp_charges>, <_sre.SRE_Pattern object at 0x72659d0>: <function multipole_qm>}, 'scanner': {<_sre.SRE_Pattern object>: <function start_geometry>, <_sre.SRE_Pattern object at 0x5acfcb0>: <function end_scan>, <_sre.SRE_Pattern object at 0x63f0ec0>: <function geometry_scan_step>}, 'cpolar': {<_sre.SRE_Pattern object>: <function beta_polar>, <_sre.SRE_Pattern object>: <function alpha_polar>, <_sre.SRE_Pattern object>: <function gamma_polar>}, 'scf': {<_sre.SRE_Pattern object>: <function electronic_e>, <_sre.SRE_Pattern object>: <function nucrep2>, <_sre.SRE_Pattern object at 0x61db020>: <function nops_on>, <_sre.SRE_Pattern object>: <function nucrep1>, <_sre.SRE_Pattern object>: <function gas_phase>, <_sre.SRE_Pattern object at 0x3db34b0>: <function two_e_terms>, <_sre.SRE_Pattern object at 0x4b48220>: <function solution_phase>, <_sre.SRE_Pattern object>: <function solvation>, <_sre.SRE_Pattern object>: <function lumo>, <_sre.SRE_Pattern object at 0x4c26030>: <function orbital_energies>, <_sre.SRE_Pattern object>: <function homo>, <_sre.SRE_Pattern object at 0x7081b60>: <function nops_on>, <_sre.SRE_Pattern object>: <function etot>, <_sre.SRE_Pattern object>: <function aposteri_e>, <_sre.SRE_Pattern object at 0x54843c0>: <function one_e_terms>, <_sre.SRE_Pattern object>: <function scfe>}, 'before pre': {<_sre.SRE_Pattern object>: <function jobid>}, 'elden': {<_sre.SRE_Pattern object>: <function esp_analysis>, <_sre.SRE_Pattern object>: <function epn>, <_sre.SRE_Pattern object>: <function alie_analysis>}, 'tdener': {<_sre.SRE_Pattern object>: <function tddft_excitation_energies>, <_sre.SRE_Pattern object>: <function tddft_excitation_energies_old>, <_sre.SRE_Pattern object at 0x69a24f0>: <function reset_tddft_excitation_energies>}, 'lmp2': {<_sre.SRE_Pattern object>: <function gas_phase>, <_sre.SRE_Pattern object>: <function lmp2>, <_sre.SRE_Pattern object at 0x4b48220>: <function solution_phase>, <_sre.SRE_Pattern object>: <function solvation>}, 'etit': {<_sre.SRE_Pattern object>: <function electron_transfer>}, 'lmp2gdb': {<_sre.SRE_Pattern object at 0x4b56650>: <function forces>}, 'freq': {<_sre.SRE_Pattern object at 0x7264f30>: <function frequencies>, <_sre.SRE_Pattern object at 0x51ef4d0>: <function zpe>, <_sre.SRE_Pattern object at 0x7266650>: <function frequencies_old>, <_sre.SRE_Pattern object at 0x71101d0>: <function get_vetted_vec_index>}, 'gvblmp2': {<_sre.SRE_Pattern object>: <function gvblmp2>, <_sre.SRE_Pattern object>: <function rolmp2>}, 'impact': {<_sre.SRE_Pattern object>: <function qmmm_bend_energy>, <_sre.SRE_Pattern object>: <function torsion_energy>, <_sre.SRE_Pattern object>: <function nb_cutoff>, <_sre.SRE_Pattern object>: <function total_kinetic_energy>, <_sre.SRE_Pattern object>: <function hbond_energy>, <_sre.SRE_Pattern object>: <function nb_update>, <_sre.SRE_Pattern object>: <function lj14_energy>, <_sre.SRE_Pattern object>: <function qmmm_electrostatic_energy>, <_sre.SRE_Pattern object>: <function angle_bend_energy>, <_sre.SRE_Pattern object>: <function qmmm_stretch_energy>, <_sre.SRE_Pattern object>: <function total_energy>, <_sre.SRE_Pattern object>: <function electrostatic14_energy>, <_sre.SRE_Pattern object>: <function electrostatic_energy>, <_sre.SRE_Pattern object>: <function bond_stretch_energy>, <_sre.SRE_Pattern object>: <function total_potential_energy>, <_sre.SRE_Pattern object>: <function lj_energy>, <_sre.SRE_Pattern object>: <function qmmm_torsion_energy>, <_sre.SRE_Pattern object>: <function ffld>}, 'nmrcphf': {<_sre.SRE_Pattern object>: <function get_nmr>}, None: {<_sre.SRE_Pattern object>: <function start_of_program>, <_sre.SRE_Pattern object>: <function glibc>, <_sre.SRE_Pattern object at 0x71494d0>: <function fatal_error>, <_sre.SRE_Pattern object>: <function end_time>}, 'sole': {<_sre.SRE_Pattern object at 0x5424120>: <function solvation>, <_sre.SRE_Pattern object at 0x4b48220>: <function solution_phase>}, 'cis': {<_sre.SRE_Pattern object>: <function cis_excitation_energies>}, 'geopt': {<_sre.SRE_Pattern object>: <function z_variables>, <_sre.SRE_Pattern object>: <function convergence_category>, <_sre.SRE_Pattern object at 0x725fc70>: <function irc_point>, <_sre.SRE_Pattern object at 0x56ce4a0>: <function geopt_stuck1>, <_sre.SRE_Pattern object at 0x4b10470>: <function nops_on>, <_sre.SRE_Pattern object at 0x4aa0cf0>: <function end_geometry>, <_sre.SRE_Pattern object at 0x7261730>: <function nofail_geopt>, <_sre.SRE_Pattern object at 0x725e320>: <function nofail_geopt_restart>, <_sre.SRE_Pattern object at 0x5209730>: <function irc_summary>, <_sre.SRE_Pattern object>: <function geopt_geometry>, <_sre.SRE_Pattern object at 0x69c7370>: <function tddft_geopt_energy>, <_sre.SRE_Pattern object>: <function geopt_stuck2>, <_sre.SRE_Pattern object at 0x725ffb0>: <function stopping_optimization>, <_sre.SRE_Pattern object at 0x582e8f0>: <function sm_geometry>}, 'der1b': {<_sre.SRE_Pattern object at 0x4b56650>: <function forces>}, 'tddft_g': {<_sre.SRE_Pattern object at 0x4b56650>: <function forces>}, 'nude': {<_sre.SRE_Pattern object at 0x4b56650>: <function forces>}, 'lmp2gb': {<_sre.SRE_Pattern object at 0x4b56650>: <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)