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.QSiteResults

Bases: schrodinger.application.jaguar.results.JaguarResults

energy_precision = 1e-06

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.qsite.output', 'energy_precision': 1e-06, '_attributes': [<_Attribute: scf_energy>, <_Attribute: external_program_energy>, <_Attribute: gas_phase_energy>, <_Attribute: lmp2_energy>, <_Attribute: solvation_energy>, <_Attribute: solution_phase_energy>, <_Attribute: energy_one_electron>, <_Attribute: energy_two_electron>, <_Attribute: energy_electronic>, <_Attribute: energy_aposteri>, <_Attribute: energy_aposteri0>, <_Attribute: nuclear_repulsion>, <_Attribute: homo>, <_Attribute: homo_alpha>, <_Attribute: homo_beta>, <_Attribute: lumo>, <_Attribute: lumo_alpha>, <_Attribute: lumo_beta>, <_Attribute: zero_point_energy>, <_Attribute: nops_on>, <_Attribute: sm_point>, <_Attribute: sm_iter>, <_Attribute: reaction_coord>, <_Attribute: S_min_eval>, <_Attribute: orbital>, <_Attribute: orbital_alpha>, <_Attribute: orbital_beta>, <_Attribute: zvar>, <_Attribute: thermo>, <_Attribute: dipole_qm>, <_Attribute: dipole_esp>, <_Attribute: dipole_mulliken>, <_Attribute: normal_mode>, <_Attribute: charge_bond_midpoint>, <_Attribute: transition_state_components>, <_Attribute: vetted_ts_vector_index>, <_Attribute: vetted_ts_vector>, <_Attribute: polar_alpha>, <_Attribute: polar_beta>, <_Attribute: polar_gamma>, <_Attribute: et_S_if>, <_Attribute: et_H_ii>, <_Attribute: et_H_if>, <_Attribute: et_T_if>, <_Attribute: min_esp>, <_Attribute: max_esp>, <_Attribute: mean_esp>, <_Attribute: mean_pos_esp>, <_Attribute: mean_neg_esp>, <_Attribute: sig_pos_esp>, <_Attribute: sig_neg_esp>, <_Attribute: sig_tot_esp>, <_Attribute: balance_esp>, <_Attribute: local_pol_esp>, <_Attribute: min_alie>, <_Attribute: max_alie>, <_Attribute: mean_alie>, <_Attribute: mean_pos_alie>, <_Attribute: mean_neg_alie>, <_Attribute: sig_pos_alie>, <_Attribute: sig_neg_alie>, <_Attribute: sig_tot_alie>, <_Attribute: balance_alie>, <_Attribute: local_pol_alie>, <_Attribute: excitation_energies>, <_Attribute: singlet_excitation_energies>, <_Attribute: triplet_excitation_energies>, <_Attribute: oscillator_strengths>, <_Attribute: singlet_oscillator_strengths>, <_Attribute: triplet_oscillator_strengths>, <_Attribute: opt_excited_state_energy_1>, <_Attribute: total_lo_correction>, <_Attribute: spin_splitting_score>, <_Attribute: total_energy>, <_Attribute: total_potential_energy>, <_Attribute: total_kinetic_energy>, <_Attribute: bond_stretch_energy>, <_Attribute: angle_bend_energy>, <_Attribute: torsion_energy>, <_Attribute: lj14_energy>, <_Attribute: electrostatic14_energy>, <_Attribute: lj_energy>, <_Attribute: electrostatic_energy>, <_Attribute: hbond_energy>, <_Attribute: qmmm_electrostatic_energy>, <_Attribute: qmmm_stretch_energy>, <_Attribute: qmmm_bend_energy>, <_Attribute: qmmm_torsion_energy>, <_Attribute: bondchg_repulsion_energy>], '__doc__': None})

__dir__() → list

default dir() implementation

__eq__(other)

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__ = None

__init__()

Create a JaguarResults object.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.qsite.output'

__ne__(other)

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

alie_analysis_precision = 0.01

alpha_polar_precision = 0.001

atom_total

Return the number of atoms in the structure geometry.

balance_alie_precision = 0.001

balance_esp_precision = 0.001

beta_polar_precision = 0.001

diff(other, short_circuit=False, factor=1.0)

Return a set of attributes that differ.

Parameters other (JaguarResults)

The instance to compare against.

short_circuit (bool)

If True, return immediately upon finding a difference.

factor (float)

A fudge factor to apply to most comparison precision values. The allowed difference between values is multiplied by factor.

energy

The overall energy for the calculation. For LMP2 calculations this is the LMP2 energy, otherwise it is the SCF energy. If this calculation includes solvation it is the solution phase energy.

esp_analysis_precision = 0.01

esp_balance

esp_local_polarity

espmax

espmean_n

espmean_p

espmin

exc_precision = 0.0006

forces

Convenient access to forces for all atoms as a numpy array.

gamma_polar_precision = 0.1

getAtomTotal()

getStructure(properties=None)

Get a schrodinger.Structure object for a specific geometry.

property_names (list of tuples of (string, object))

A list of properties names and values belonging to the overall job these results are a part of.

lo_precision = 0.01

nucrep_precision = 1e-08

osc_precision = 0.001

rxn_coord_precision = 0.001

sig_n

sig_p

sigtot

spin_splitting_precision = 0.01

ts_component_precision = 0.1

zpe_precision = 0.01

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': {re.compile('net molecular charge:\\s+(-?\\d+)'): <function molchg>, re.compile('multiplicity:\\s+(\\d+)'): <function multip>, re.compile('number of basis functions\\.\\.\\.\\.\\s+(\\d+)'): <function nbasis>, re.compile('Molecular weight:\\s+([0-9.]+)'): <function mol_weight>, re.compile('Stoichiometry:\\s+(\\w+)'): <function stoichiometry>, re.compile('basis set:\\s+(\\S+)'): <function basis_set>, re.compile('Number of optimization coordinates:\\s+(\\d+)'): <function coords_opt>, re.compile('Number of independent coordinates:\\s+(\\d+)'): <function coords_ind>, re.compile('Number of non-redundant coordinates:\\s+(\\d+)'): <function coords_nred>, re.compile('Number of constrained coordinates:\\s+(\\d+)'): <function coords_frozen1>, re.compile('Number of frozen coordinates:\\s+(\\d+)'): <function coords_frozen2>, re.compile('Number of harmonic constraints:\\s+(\\d+)'): <function coords_harmonic>, re.compile('Solvation energy will be computed'): <function solvation_job>, re.compile('Numerical 2nd derivatives will be computed'): <function numerical_freqs>, re.compile('Electrostatic potential fit to point charges on atomic centers'): <function esp_fit_atoms>, re.compile('and bond midpoints'): <function esp_fit_atoms_and_bonds>, re.compile('(Input|new) geometry:'): <function start_geometry>, re.compile('Path geometry: \\(interpolated\\, X\\=.*\\)'): <function path_geometry>, re.compile('Z-variables: (.*)$'): <function z_variables>, re.compile('Maestro file \\(output\\):\\s+(\\S+)'): <function mae>, re.compile('Maestro file \\(input\\):\\s+(\\S+)'): <function mae_in>, re.compile('Molecular Point Group:\\s+(\\w+)'): <function point_group>, re.compile('Point Group used:\\s+(\\w+)'): <function point_group_used>, re.compile('Number of atoms treated by QM:\\s+(\\w+)'): <function qm_atoms>, re.compile('SCF calculation type: ([A-Z/_-]+)'): <function calc_type>, re.compile('Post-SCF correlation type: (\\w+)'): <function correlation_type>, re.compile('DFT=(\\S+)\\s*(\\(.+\\))?'): <function functional>, re.compile('^ *User Defined Functional:'): <function custom_functional>, re.compile('Geometry from &zmat(2|3), &zvar(2|3)'): <function qst_geometries>, re.compile('Symmetrized geometry:'): <function symmetrized_geometry>, re.compile('Initial geometry: \\(interpolated\\)'): <function qst_initial_geometry>, re.compile('Geometry scan coordinates:(?:\\s*\\((angstroms|bohr) and (degrees|radians)\\))?'): <function scan_coordinates>, re.compile('Non-default print settings:'): <function non_default_print_options>, re.compile('Fully analytic SCF calculation: pseudospectral method not used'): <function pseudospectral>, re.compile('Total LO correction:\\s+(\\S+)\\s+kcal/mole'): <function total_lo_correction>, re.compile('Target molecule has a ligand field spin-splitting score of\\s+(\\S+)'): <function spin_splitting_score>, re.compile('^Total number of atoms:\\s+(\\d+)'): <function total_atoms>, re.compile('^Number of atoms passed to Jaguar:\\s+(\\d+)'): <function jaguar_atoms>, re.compile('^Number of atoms treated by QM:\\s+(\\d+)'): <function qm_atoms>, re.compile('^Number of atoms treated by NDDO:\\s+(\\d+)'): <function nddo_atoms>, re.compile('^Number of hydrogen caps:\\s+(\\d+)'): <function nhcaps>, re.compile('^Number of NDDO hydrogen caps:\\s+(\\d+)'): <function nddo_hcaps>, re.compile('^Number of frozen orbital cuts:\\s+(\\d+)'): <function ncuts>, re.compile('^Number of constrained MM atoms:\\s+(\\d+)'): <function nconmm>, re.compile('^Number of frozen MM atoms:\\s+(\\d+)'): <function nfrzmm>}, 'read_external_gradient': {re.compile('Energy From External Program \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function external_program_energy>}, 'scf': {re.compile('(^etot.*$)'): <function etot>, re.compile('SCFE.*\\s+(-?[\\.\\d]+)\\s+hartrees'): <function scfe>, re.compile('\\(B\\)\\s+Nuclear-nuclear\\.+\\s+(-?[\\.\\d]+)'): <function nucrep1>, re.compile('\\(A\\)\\s+Nuclear repulsion\\.+\\s+(-?[\\.\\d]+)'): <function nucrep2>, re.compile('\\(E\\)\\s+Total one-electron terms\\.+\\s+(-?[\\.\\d]+)'): <function one_e_terms>, re.compile('\\(I\\)\\s+Total two-electron terms\\.+\\s+(-?[\\.\\d]+)'): <function two_e_terms>, re.compile('\\(L\\)\\s+Electronic energy\\.+\\s+(-?[\\.\\d]+)'): <function electronic_e>, re.compile('\\(N0\\).*correction\\.+\\s+(-?[\\.\\d]+)'): <function aposteri_e>, re.compile('(Alpha|Beta)? HOMO energy:\\s+(\\S+)'): <function homo>, re.compile('(Alpha|Beta)? LUMO energy:\\s+(\\S+)'): <function lumo>, re.compile('(?P<type>Alpha|Beta)? Orbital energies( \\(hartrees\\))?(?P<label>/symmetry label)?:'): <function orbital_energies>, re.compile('Energy computed with NOPS on.'): <function nops_on>, re.compile('Energy computed with NOPS off.'): <function nops_on>, re.compile('^\\sPCM solvation energy (electrostatic)\\.+\\s*(-?[\\.\\d]+)'): <function solvation>, re.compile('\\(V\\).*Solvation energy\\.+\\s*(-?[\\.\\d]+)'): <function solvation>, re.compile('^\\sSolution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>, re.compile('\\(P\\).*Solution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>, re.compile('^\\sGas phase energy\\.+\\s*(-?[\\.\\d]+)'): <function gas_phase>, re.compile('\\(O\\).*Gas phase energy\\.+\\s*(-?[\\.\\d]+)'): <function gas_phase>}, 'lmp2': {re.compile('Total LMP2.*\\s+(-?[\\.\\d]+)'): <function lmp2>, re.compile('\\(V\\).*Solvation energy\\.+\\s*(-?[\\.\\d]+)'): <function solvation>, re.compile('\\(P\\).*Solution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>, re.compile('\\(O\\).*Gas phase energy\\.+\\s*(-?[\\.\\d]+)'): <function gas_phase>}, 'gvblmp2': {re.compile('Total LMP2.*\\s+(-?[\\.\\d]+)'): <function rolmp2>, re.compile('Total GVB-LMP2.*\\s+(-?[\\.\\d]+)'): <function gvblmp2>}, 'scanner': {re.compile('(Input|new) geometry:'): <function start_geometry>, re.compile('end of geometry scan step'): <function end_scan>, re.compile('Geometry scan step\\s+\\d+\\s*:'): <function geometry_scan_step>}, 'geopt': {re.compile('new geometry:'): <function geopt_geometry>, re.compile('String geometry: \\(iteration=.* point=.*energy=.*\\)'): <function sm_geometry>, re.compile('end of geometry optimization iteration'): <function end_geometry>, re.compile('(stopping optimization: maximum number of iterations reached|Geometry optimization complete)'): <function stopping_optimization>, re.compile('optimization seems to be stuck'): <function geopt_stuck1>, re.compile('Convergence category (\\d+)'): <function convergence_category>, re.compile('IRC point found -\\s+(Forward|Reverse|Downhill)\\s+#\\s+(\\d+)'): <function irc_point>, re.compile('Summary of IRC Reaction Path:'): <function irc_summary>, re.compile('Setting nops=0, recomputing energy'): <function nops_on>, re.compile('to be a stuck geometry'): <function geopt_stuck2>, re.compile('SCF will be redone to get proper energy & wavefunction.'): <function nofail_geopt_restart>, re.compile('Taking the geometry with the lowest energy \\(iteration (\\d+)\\)'): <function nofail_geopt>, re.compile('Z-variables: (.*)$'): <function z_variables>, re.compile('First excited state energy:\\s+(\\S+) hartrees'): <function tddft_geopt_energy>}, 'tddft_g': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'der1b': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'lmp2gb': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'lmp2gdb': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'nude': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'sole': {re.compile('\\(V\\).*Solvation energy\\.+\\s*(-?[\\.\\d]+).*\\(P-O\\)'): <function solvation>, re.compile('\\(P\\).*Solution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>}, 'onee': {re.compile('number of canonical orbitals\\.\\.\\.\\.\\.\\s+(\\d+)'): <function canorb>, re.compile('smallest eigenvalue of S:\\s+(\\S+)'): <function s_min_eval>, re.compile('^ bond-charge repulsion energy\\.+\\s+(\\S+) '): <function bondchg_repulsion_energy>}, 'ch': {re.compile('Atomic charges from electrostatic potential'): <function esp_charges>, re.compile('Atomic charges from Mulliken population analysis'): <function mulliken_charges>, re.compile('Moments from quantum mechanical wavefunction'): <function multipole_qm>, re.compile('Moments from electrostatic potential charges'): <function multipole_esp>, re.compile('Moments from Mulliken charges'): <function multipole_mulliken>, re.compile('Atomic Fukui indices'): <function fukui_indices>}, 'etit': {re.compile('^ Reading '): <function electron_transfer>}, 'cpolar': {re.compile('^ polarizability \\(in AU\\):'): <function alpha_polar>, re.compile('^ first hyperpolarizability \\(in AU\\):'): <function beta_polar>, re.compile('^ second hyperpolarizability \\(in AU\\):'): <function gamma_polar>}, 'elden': {re.compile('^ Electrostatic Potential at the Nuclei'): <function epn>, re.compile('^ Analysis of ESP on isodensity surface:'): <function esp_analysis>, re.compile('^ Analysis of ALIE on isodensity surface:'): <function alie_analysis>}, 'nmrcphf': {re.compile('solving first-order CPHF'): <function get_nmr>}, 'cis': {re.compile('CI size ='): <function cis_excitation_energies>}, 'tdener': {re.compile('Ground State Dipole Moments'): <function reset_tddft_excitation_energies>, re.compile('(.*)Excited State\\s+\\d+:\\s+$'): <function tddft_excitation_energies>, re.compile('(.*)Excited State\\s+\\d+:\\s+(\\S+) eV'): <function tddft_excitation_energies_old>}, 'freq': {re.compile('The zero point energy \\(ZPE\\):\\s+(\\S+) kcal/mol'): <function zpe>, re.compile('Valid transition vector #\\s+(\\b[0-9]+\\b)'): <function get_vetted_vec_index>, re.compile('normal modes in cartesian coordinates:\\s+(\\d+)'): <function frequencies>, re.compile('normal modes in cartesian coordinates:\\s+$'): <function frequencies_old>}, 'before pre': {re.compile('^JobId:\\s+(\\S+)', re.IGNORECASE|re.MULTILINE): <function jobid>}, None: {re.compile('start of program (\\w+)'): <function start_of_program>, re.compile('glibc:\\s+(\\S+)'): <function glibc>, re.compile('Job \\S+ completed on \\S+ at (\\w.*)$'): <function end_time>, re.compile('ERROR *(\\d+)?: fatal error( -- debug information follows)?'): <function fatal_error>}, 'impact': {re.compile(' calling (\\S+)\\s+atomtyping'): <function ffld>, re.compile('^ Cutoff radius:\\s+(\\S+)'): <function nb_cutoff>, re.compile('^ Update frequency: every\\s+(\\d+) '): <function nb_update>, re.compile('^ Total Energy of the system\\.+\\s+(\\S+) '): <function total_energy>, re.compile('^ Total Potential Energy\\.+\\s+(\\S+) '): <function total_potential_energy>, re.compile('^ Total Kinetic Energy\\.+\\s+(\\S+) '): <function total_kinetic_energy>, re.compile('^ Bond Stretch Energy\\.+\\s+(\\S+) '): <function bond_stretch_energy>, re.compile('^ Angle Bending Energy\\.+\\s+(\\S+) '): <function angle_bend_energy>, re.compile('^ Torsion Angle Energy\\.+\\s+(\\S+) '): <function torsion_energy>, re.compile('^ 1,4 Lennard Jones Energy\\.+\\s+(\\S+) '): <function lj14_energy>, re.compile('^ 1,4 Electrostatic Energy\\.+\\s+(\\S+) '): <function electrostatic14_energy>, re.compile('^ Lennard Jones Energy\\.+\\s+(\\S+) '): <function lj_energy>, re.compile('^ Electrostatic Energy\\.+\\s+(\\S+) '): <function electrostatic_energy>, re.compile('^ H-bond Energy\\.+\\s+(\\S+) '): <function hbond_energy>, re.compile('^ QM/MM Electrostatic Energy\\.+\\s+(\\S+) '): <function qmmm_electrostatic_energy>, re.compile('^ QM/MM Stretch Energy\\.+\\s+(\\S+) '): <function qmmm_stretch_energy>, re.compile('^ QM/MM Bend Energy\\.+\\s+(\\S+) '): <function qmmm_bend_energy>, re.compile('^ QM/MM Torsion Energy\\.+\\s+(\\S+) '): <function qmmm_torsion_energy>}}

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.qsite.output', '__doc__': '\n\n A subclass of the Jaguar output text parser that adds QSite specific\n parsing.\n\n ', 'callback': {'pre': {re.compile('net molecular charge:\\s+(-?\\d+)'): <function molchg>, re.compile('multiplicity:\\s+(\\d+)'): <function multip>, re.compile('number of basis functions\\.\\.\\.\\.\\s+(\\d+)'): <function nbasis>, re.compile('Molecular weight:\\s+([0-9.]+)'): <function mol_weight>, re.compile('Stoichiometry:\\s+(\\w+)'): <function stoichiometry>, re.compile('basis set:\\s+(\\S+)'): <function basis_set>, re.compile('Number of optimization coordinates:\\s+(\\d+)'): <function coords_opt>, re.compile('Number of independent coordinates:\\s+(\\d+)'): <function coords_ind>, re.compile('Number of non-redundant coordinates:\\s+(\\d+)'): <function coords_nred>, re.compile('Number of constrained coordinates:\\s+(\\d+)'): <function coords_frozen1>, re.compile('Number of frozen coordinates:\\s+(\\d+)'): <function coords_frozen2>, re.compile('Number of harmonic constraints:\\s+(\\d+)'): <function coords_harmonic>, re.compile('Solvation energy will be computed'): <function solvation_job>, re.compile('Numerical 2nd derivatives will be computed'): <function numerical_freqs>, re.compile('Electrostatic potential fit to point charges on atomic centers'): <function esp_fit_atoms>, re.compile('and bond midpoints'): <function esp_fit_atoms_and_bonds>, re.compile('(Input|new) geometry:'): <function start_geometry>, re.compile('Path geometry: \\(interpolated\\, X\\=.*\\)'): <function path_geometry>, re.compile('Z-variables: (.*)$'): <function z_variables>, re.compile('Maestro file \\(output\\):\\s+(\\S+)'): <function mae>, re.compile('Maestro file \\(input\\):\\s+(\\S+)'): <function mae_in>, re.compile('Molecular Point Group:\\s+(\\w+)'): <function point_group>, re.compile('Point Group used:\\s+(\\w+)'): <function point_group_used>, re.compile('Number of atoms treated by QM:\\s+(\\w+)'): <function qm_atoms>, re.compile('SCF calculation type: ([A-Z/_-]+)'): <function calc_type>, re.compile('Post-SCF correlation type: (\\w+)'): <function correlation_type>, re.compile('DFT=(\\S+)\\s*(\\(.+\\))?'): <function functional>, re.compile('^ *User Defined Functional:'): <function custom_functional>, re.compile('Geometry from &zmat(2|3), &zvar(2|3)'): <function qst_geometries>, re.compile('Symmetrized geometry:'): <function symmetrized_geometry>, re.compile('Initial geometry: \\(interpolated\\)'): <function qst_initial_geometry>, re.compile('Geometry scan coordinates:(?:\\s*\\((angstroms|bohr) and (degrees|radians)\\))?'): <function scan_coordinates>, re.compile('Non-default print settings:'): <function non_default_print_options>, re.compile('Fully analytic SCF calculation: pseudospectral method not used'): <function pseudospectral>, re.compile('Total LO correction:\\s+(\\S+)\\s+kcal/mole'): <function total_lo_correction>, re.compile('Target molecule has a ligand field spin-splitting score of\\s+(\\S+)'): <function spin_splitting_score>, re.compile('^Total number of atoms:\\s+(\\d+)'): <function total_atoms>, re.compile('^Number of atoms passed to Jaguar:\\s+(\\d+)'): <function jaguar_atoms>, re.compile('^Number of atoms treated by QM:\\s+(\\d+)'): <function qm_atoms>, re.compile('^Number of atoms treated by NDDO:\\s+(\\d+)'): <function nddo_atoms>, re.compile('^Number of hydrogen caps:\\s+(\\d+)'): <function nhcaps>, re.compile('^Number of NDDO hydrogen caps:\\s+(\\d+)'): <function nddo_hcaps>, re.compile('^Number of frozen orbital cuts:\\s+(\\d+)'): <function ncuts>, re.compile('^Number of constrained MM atoms:\\s+(\\d+)'): <function nconmm>, re.compile('^Number of frozen MM atoms:\\s+(\\d+)'): <function nfrzmm>}, 'read_external_gradient': {re.compile('Energy From External Program \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function external_program_energy>}, 'scf': {re.compile('(^etot.*$)'): <function etot>, re.compile('SCFE.*\\s+(-?[\\.\\d]+)\\s+hartrees'): <function scfe>, re.compile('\\(B\\)\\s+Nuclear-nuclear\\.+\\s+(-?[\\.\\d]+)'): <function nucrep1>, re.compile('\\(A\\)\\s+Nuclear repulsion\\.+\\s+(-?[\\.\\d]+)'): <function nucrep2>, re.compile('\\(E\\)\\s+Total one-electron terms\\.+\\s+(-?[\\.\\d]+)'): <function one_e_terms>, re.compile('\\(I\\)\\s+Total two-electron terms\\.+\\s+(-?[\\.\\d]+)'): <function two_e_terms>, re.compile('\\(L\\)\\s+Electronic energy\\.+\\s+(-?[\\.\\d]+)'): <function electronic_e>, re.compile('\\(N0\\).*correction\\.+\\s+(-?[\\.\\d]+)'): <function aposteri_e>, re.compile('(Alpha|Beta)? HOMO energy:\\s+(\\S+)'): <function homo>, re.compile('(Alpha|Beta)? LUMO energy:\\s+(\\S+)'): <function lumo>, re.compile('(?P<type>Alpha|Beta)? Orbital energies( \\(hartrees\\))?(?P<label>/symmetry label)?:'): <function orbital_energies>, re.compile('Energy computed with NOPS on.'): <function nops_on>, re.compile('Energy computed with NOPS off.'): <function nops_on>, re.compile('^\\sPCM solvation energy (electrostatic)\\.+\\s*(-?[\\.\\d]+)'): <function solvation>, re.compile('\\(V\\).*Solvation energy\\.+\\s*(-?[\\.\\d]+)'): <function solvation>, re.compile('^\\sSolution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>, re.compile('\\(P\\).*Solution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>, re.compile('^\\sGas phase energy\\.+\\s*(-?[\\.\\d]+)'): <function gas_phase>, re.compile('\\(O\\).*Gas phase energy\\.+\\s*(-?[\\.\\d]+)'): <function gas_phase>}, 'lmp2': {re.compile('Total LMP2.*\\s+(-?[\\.\\d]+)'): <function lmp2>, re.compile('\\(V\\).*Solvation energy\\.+\\s*(-?[\\.\\d]+)'): <function solvation>, re.compile('\\(P\\).*Solution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>, re.compile('\\(O\\).*Gas phase energy\\.+\\s*(-?[\\.\\d]+)'): <function gas_phase>}, 'gvblmp2': {re.compile('Total LMP2.*\\s+(-?[\\.\\d]+)'): <function rolmp2>, re.compile('Total GVB-LMP2.*\\s+(-?[\\.\\d]+)'): <function gvblmp2>}, 'scanner': {re.compile('(Input|new) geometry:'): <function start_geometry>, re.compile('end of geometry scan step'): <function end_scan>, re.compile('Geometry scan step\\s+\\d+\\s*:'): <function geometry_scan_step>}, 'geopt': {re.compile('new geometry:'): <function geopt_geometry>, re.compile('String geometry: \\(iteration=.* point=.*energy=.*\\)'): <function sm_geometry>, re.compile('end of geometry optimization iteration'): <function end_geometry>, re.compile('(stopping optimization: maximum number of iterations reached|Geometry optimization complete)'): <function stopping_optimization>, re.compile('optimization seems to be stuck'): <function geopt_stuck1>, re.compile('Convergence category (\\d+)'): <function convergence_category>, re.compile('IRC point found -\\s+(Forward|Reverse|Downhill)\\s+#\\s+(\\d+)'): <function irc_point>, re.compile('Summary of IRC Reaction Path:'): <function irc_summary>, re.compile('Setting nops=0, recomputing energy'): <function nops_on>, re.compile('to be a stuck geometry'): <function geopt_stuck2>, re.compile('SCF will be redone to get proper energy & wavefunction.'): <function nofail_geopt_restart>, re.compile('Taking the geometry with the lowest energy \\(iteration (\\d+)\\)'): <function nofail_geopt>, re.compile('Z-variables: (.*)$'): <function z_variables>, re.compile('First excited state energy:\\s+(\\S+) hartrees'): <function tddft_geopt_energy>}, 'tddft_g': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'der1b': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'lmp2gb': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'lmp2gdb': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'nude': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'sole': {re.compile('\\(V\\).*Solvation energy\\.+\\s*(-?[\\.\\d]+).*\\(P-O\\)'): <function solvation>, re.compile('\\(P\\).*Solution phase energy\\.+\\s*(-?[\\.\\d]+)'): <function solution_phase>}, 'onee': {re.compile('number of canonical orbitals\\.\\.\\.\\.\\.\\s+(\\d+)'): <function canorb>, re.compile('smallest eigenvalue of S:\\s+(\\S+)'): <function s_min_eval>, re.compile('^ bond-charge repulsion energy\\.+\\s+(\\S+) '): <function bondchg_repulsion_energy>}, 'ch': {re.compile('Atomic charges from electrostatic potential'): <function esp_charges>, re.compile('Atomic charges from Mulliken population analysis'): <function mulliken_charges>, re.compile('Moments from quantum mechanical wavefunction'): <function multipole_qm>, re.compile('Moments from electrostatic potential charges'): <function multipole_esp>, re.compile('Moments from Mulliken charges'): <function multipole_mulliken>, re.compile('Atomic Fukui indices'): <function fukui_indices>}, 'etit': {re.compile('^ Reading '): <function electron_transfer>}, 'cpolar': {re.compile('^ polarizability \\(in AU\\):'): <function alpha_polar>, re.compile('^ first hyperpolarizability \\(in AU\\):'): <function beta_polar>, re.compile('^ second hyperpolarizability \\(in AU\\):'): <function gamma_polar>}, 'elden': {re.compile('^ Electrostatic Potential at the Nuclei'): <function epn>, re.compile('^ Analysis of ESP on isodensity surface:'): <function esp_analysis>, re.compile('^ Analysis of ALIE on isodensity surface:'): <function alie_analysis>}, 'nmrcphf': {re.compile('solving first-order CPHF'): <function get_nmr>}, 'cis': {re.compile('CI size ='): <function cis_excitation_energies>}, 'tdener': {re.compile('Ground State Dipole Moments'): <function reset_tddft_excitation_energies>, re.compile('(.*)Excited State\\s+\\d+:\\s+$'): <function tddft_excitation_energies>, re.compile('(.*)Excited State\\s+\\d+:\\s+(\\S+) eV'): <function tddft_excitation_energies_old>}, 'freq': {re.compile('The zero point energy \\(ZPE\\):\\s+(\\S+) kcal/mol'): <function zpe>, re.compile('Valid transition vector #\\s+(\\b[0-9]+\\b)'): <function get_vetted_vec_index>, re.compile('normal modes in cartesian coordinates:\\s+(\\d+)'): <function frequencies>, re.compile('normal modes in cartesian coordinates:\\s+$'): <function frequencies_old>}, 'before pre': {re.compile('^JobId:\\s+(\\S+)', re.IGNORECASE|re.MULTILINE): <function jobid>}, None: {re.compile('start of program (\\w+)'): <function start_of_program>, re.compile('glibc:\\s+(\\S+)'): <function glibc>, re.compile('Job \\S+ completed on \\S+ at (\\w.*)$'): <function end_time>, re.compile('ERROR *(\\d+)?: fatal error( -- debug information follows)?'): <function fatal_error>}, 'impact': {re.compile(' calling (\\S+)\\s+atomtyping'): <function ffld>, re.compile('^ Cutoff radius:\\s+(\\S+)'): <function nb_cutoff>, re.compile('^ Update frequency: every\\s+(\\d+) '): <function nb_update>, re.compile('^ Total Energy of the system\\.+\\s+(\\S+) '): <function total_energy>, re.compile('^ Total Potential Energy\\.+\\s+(\\S+) '): <function total_potential_energy>, re.compile('^ Total Kinetic Energy\\.+\\s+(\\S+) '): <function total_kinetic_energy>, re.compile('^ Bond Stretch Energy\\.+\\s+(\\S+) '): <function bond_stretch_energy>, re.compile('^ Angle Bending Energy\\.+\\s+(\\S+) '): <function angle_bend_energy>, re.compile('^ Torsion Angle Energy\\.+\\s+(\\S+) '): <function torsion_energy>, re.compile('^ 1,4 Lennard Jones Energy\\.+\\s+(\\S+) '): <function lj14_energy>, re.compile('^ 1,4 Electrostatic Energy\\.+\\s+(\\S+) '): <function electrostatic14_energy>, re.compile('^ Lennard Jones Energy\\.+\\s+(\\S+) '): <function lj_energy>, re.compile('^ Electrostatic Energy\\.+\\s+(\\S+) '): <function electrostatic_energy>, re.compile('^ H-bond Energy\\.+\\s+(\\S+) '): <function hbond_energy>, re.compile('^ QM/MM Electrostatic Energy\\.+\\s+(\\S+) '): <function qmmm_electrostatic_energy>, re.compile('^ QM/MM Stretch Energy\\.+\\s+(\\S+) '): <function qmmm_stretch_energy>, re.compile('^ QM/MM Bend Energy\\.+\\s+(\\S+) '): <function qmmm_bend_energy>, re.compile('^ QM/MM Torsion Energy\\.+\\s+(\\S+) '): <function qmmm_torsion_energy>}}})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(jaguar_output, file_iter=None)

Parameters

file_iter (iterator returning lines of Jaguar output file)

jaguar_output (JaguarOutput instance)

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.qsite.output'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

endGeopt(jo)

Clean up at the end of a geopt step.

Adds the current results to the geopt list and creates a new current results object if appropriate.

endIRC(direction)

Set state indicating the end of an IRC step and its direction.

direction (str)

Must be ‘Forward’ or ‘Reverse’.

endScan(jo)

Clean up at the end of a scan step.

Adds the current results to the scan list and creates a new current results object. Or, if this a relaxed scan, archives the geopt steps to the scan list and creates an empty geopt_step list.

first_line_re = re.compile('^Job \\S+ started on (\\S+) at (\\w.*)$')

parse(jaguar_output=None)

Parse the provided file iterator.

Return a JaguarOutput instance populated with properties parsed from the output file.

Parameters

jaguar_output (JaguarOutput instance)

If jaguar_output is provided, that instance will be populated with the properties parsed from the output file. Otherwise, the object provided to the TextParser constructor will be used.

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

Bases: schrodinger.application.jaguar.output.JaguarOutput

A class to hold output information from a QSite run.

OK = 1

SPLAT = 2

UNKNOWN = 0

__class__

alias of builtins.type

__del__()

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.qsite.output', '__doc__': '\n\n A class to hold output information from a QSite run.\n\n ', '_results_class': <class 'schrodinger.application.qsite.output.QSiteResults'>, '_text_parser_class': <class 'schrodinger.application.qsite.output.QSiteTextParser'>, '_attributes': [<_Attribute: _sm_n_points>, <_Attribute: basis>, <_Attribute: canonical_orbitals>, <_Attribute: charge>, <_Attribute: coords_frozen>, <_Attribute: coords_harmonic>, <_Attribute: coords_ind>, <_Attribute: coords_nred>, <_Attribute: coords_opt>, <_Attribute: functional>, <_Attribute: method>, <_Attribute: mol_weight>, <_Attribute: multiplicity>, <_Attribute: nbasis>, <_Attribute: path_structures>, <_Attribute: point_group>, <_Attribute: point_group_used>, <_Attribute: qm_atoms>, <_Attribute: scan_coords>, <_Attribute: stoichiometry>, <_Attribute: ts_component_descriptions>, <_Attribute: job_id>, <_Attribute: opts>, <_Attribute: host>, <_Attribute: mae_out>, <_Attribute: mae_in>, <_Attribute: status>, <_Attribute: fatal_error>, <_Attribute: fatal_errorno>, <_Attribute: glibc>, <_Attribute: lastexe>, <_Attribute: start_time>, <_Attribute: end_time>, <_Attribute: sm_geopt_step>, <_Attribute: sm_n_steps>, <_Attribute: geopt_step>, <_Attribute: gas_phase_geopt_step>, <_Attribute: solution_phase_geopt_step>, <_Attribute: scan_geopt_step>, <_Attribute: irc_geopt_step>, <_Attribute: input_geometry>, <_Attribute: input_geometry2>, <_Attribute: input_geometry3>, <_Attribute: symmetrized>, <_Attribute: geopt_stuck>, <_Attribute: convergence_category>, <_Attribute: ffld>, <_Attribute: nb_cutoff>, <_Attribute: nb_update>, <_Attribute: total_atoms>, <_Attribute: jaguar_atoms>, <_Attribute: qm_atoms>, <_Attribute: nddo_atoms>, <_Attribute: nhcaps>, <_Attribute: nddo_hcaps>, <_Attribute: ncuts>, <_Attribute: nconmm>, <_Attribute: nfrzmm>]})

__dir__() → list

default dir() implementation

__eq__(other)

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(attr)

Fall back to the last_results object for attribute access.

If an attribute isn’t present, try getting it from the last_results attribute.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__ = None

__init__(output=None)

Initialize from an output filename or output name.

Exceptions:

IOError

Raised if output file cannot be found.

JaguarParseError

Raised if the output file can’t be parsed. If this is raised, the state of the resulting object is not guaranteed to be useful.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.qsite.output'

__ne__(other)

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

buildDerivedAttributes()

diff(other, factor=1.0, short_circuit=False)

Return a list of all differing attributes.

Each item is a tuple of (property name, self value, other value).

Note that the property names are not necessarily usable in getattr; some may be properties of atoms, such as “atom[1].forces”.

Parameters

other (JaguarOutput)

The JaguarOutput instance to compare against.

factor (float)

A constant factor to multiply all float comparison tolerances by.

short_circuit (boolean)

If true, will return immediately upon finding a difference. The values in the tuple will both be None in this case.

duration

Return the duration of the job as a datetime.timedelta object.

getDuration()

getIrcStep()

getScanStep()

getStructure()

Return a structure object for the last geometry in the file.

getStructures()

Get Structure objects for the geometries in the output file.

If this job is a geometry optimization, it will contain geometries for all steps. If it’s a scan, it will contain the geometries for each scan point (but only the end geometries if it’s a relaxed scan).

Return a list of Structure objects.

irc_step

Return a list of final IRC geometries for each IRC step.

mol_weight_precision = 0.01

path_structures

List of structures along path for IRC or RSM jobs, empty list otherwise

restart

Return the restart name for this output object.

rmsd_precision = 0.0001

scan_step

Return a list of final scan geometries for each scan step.

write(filename=None, mimic_backend=False, add_title=False, add_entry=False)

Write a maestro file for the structure in the output file.

Note that this method overwrites any file with the same pathname.

If this job is a geometry optimization, it will contain geometries for all steps. If it’s a scan, it will contain the geometries for each scan point (but only the end geometries if it’s a relaxed scan).

filename (str)

The filename to write to; if not specified, defaults to the restart name with the ‘.mae’ suffix.

mimic_backend (bool)

If false, all geometry optimization structures will be written. If true, the geometry optimization structures will be written as in regular jobs; by default, only the last geometry will be used, but if ip472 is greater than 1, all geometries will be included.

add_title (bool)

If true, then an empty title will be replaced with the output file’s jobname.

add_entry (bool)

If the entry name is empty or starts with ‘Scratch’ it will be replaced with the output file’s jobname.

writeGrd(filename)

Write a .grd file for 1D or 2D visualization of scans in maestro to file ‘filename’.

If the job is not a scan job, this will raise a RuntimeError.

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.ffld(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.total_energy(tp, qo, m, it)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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