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

__init__()

Create a JaguarResults object.

alie_analysis_precision = 0.01

alpha_polar_precision = 0.001

property 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.

property energy

The overall/final energy for the calculation. Meant to be a simple handle for one to get the energy of a calculation, since there are many different types of energies in JaguarResults. The energy types range from general to method-specific - energy, solution_phase_energy, gas_phase energy, scf_energy, RI-MP2, LMP2, Neural Net (NN), external. More general energy types can be assigned the value of other energy types depending on the calculation.

For instance, a gas-phase HF job has energy = scf_energy. But a gas-phase RI-MP2 job has energy = rimp2_energy, since that is the “final” energy of the calculation. Solution-phase calculations have more layers.

The code that assigns values to the various energy types is split between _getEnergy() and the various functions in textparser.py. For instance see the rimp2_energies, nn_gas/sol_energy fxns.

esp_analysis_precision = 0.01

exc_precision = 0.0006

property 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

spin_splitting_precision = 0.01

tdm_precision = 0.02

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 = {'ssccb': {re.compile('Pair\\s(?P<atom_pair_index>\\d+)\\:\\s+(?P<atom1_name>[a-zA-Z]+\\d+)\\s+\\((?P<atom1_iso>\\d+\\-[a-zA-Z]+)\\s+(?P<atom1_nuc_spin>-?[\\.\\d]+)\\s+(?P<atom1_nuc_dip>-?[\\.\\d]+)\\)\\s+\\<\\-\\-\\>\\s+(): <function ssccb>, re.compile('Summary of total isotropic spin-spin coupling \\(Hz\\)\\:'): <function ssccb_summary>}, 'pre': {re.compile('^\\s*Using up to\\s+(\\d+) threads per process'): <function nthreads>, re.compile('^&gen'): <function gensec>, re.compile('^&atomic'): <function atomicsec>, 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-Za-z0-9/_-]+)'): <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('rotational constants:'): <function rotational_constants>, 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>}, 'scf': {re.compile('^\\s*number of electrons\\.+\\s+(\\d+)'): <function nelectron>, re.compile('^\\s*Sz\\*\\(Sz\\+1\\)[\\s\\.]+(\\S+)'): <function sz2>, re.compile('^\\s*<S\\*\\*2>[\\s\\.]+(\\S+)'): <function s2>, re.compile('^\\s*GVB:\\s+(\\S+)'): <function npair>, 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_off>, re.compile('\\s*No-fail mode: converged with (?P<settings>\\w+) settings'): <function nofail_mode>, 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>, re.compile('The zero point energy \\(ZPE\\):\\s+(\\S+) k(\\w+)/mol'): <function zpe>}, 'read_external_gradient': {re.compile('Energy From External Program \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function external_program_energy>}, 'nn_energy': {re.compile('ANI Gas-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_gas_energy>, re.compile('QRNN Gas-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_gas_energy>, re.compile('GFN2-xTB Gas-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_gas_energy>, re.compile('QRNN Solution-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_sol_energy>, re.compile('GFN2-xTB Solution-Phase Energy \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function nn_sol_energy>, re.compile('ANI Committee Standard Deviation \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function external_program_nn_energy_stddev>, re.compile('QRNN Committee Standard Deviation \\(a\\.u\\.\\)\\s+(-?[\\.\\d]+)'): <function external_program_nn_energy_stddev>}, 'rimp2': {re.compile('RI-MP2 Energies, in hartrees'): <function rimp2_energies>}, 'lmp2': {re.compile('Total LMP2.*\\s+(-?[\\.\\d]+)'): <function mp2>, 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 mp2>, re.compile('Total GVB-LMP2.*\\s+(-?[\\.\\d]+)'): <function gvblmp2>}, 'rolmp2': {re.compile('Total LMP2.*\\s+(-?[\\.\\d]+)'): <function mp2>}, '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('^  gradient maximum:\\s*(\\S+) .  \\(\\s*(\\S+)\\s+\\)'): <function geopt_convcrit>, re.compile('^  energy change:\\s*(\\S+) .  \\(\\s*(\\S+)\\s+\\)'): <function geopt_convcrit>, 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('restarting optimization from step'): <function doubted_geom>, re.compile('[Gg]eometry optimization step\\s+(\\d+)'): <function geopt_step_number>, re.compile('Setting nops=0, recomputing energy'): <function geopt_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>, re.compile('rotational constants:'): <function rotational_constants>}, 'tddft_g': {re.compile('forces \\(hartrees/bohr\\) : (total|numerical)'): <function forces>}, 'rimp2g': {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 Lowdin population analysis'): <function lowdin_charges>, re.compile('Atomic Spin Densities from Lowdin analysis'): <function lowdin_spins>, re.compile('Atomic charges from Mulliken population analysis'): <function mulliken_charges>, re.compile('Atomic Spin Densities from Mulliken analysis'): <function mulliken_spins>, re.compile('Stockholder charges from Hirshfeld partitioning'): <function stockholder_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>}, 'fdpol': {re.compile('polarizability \\(in AU\\) alpha\\(\\s+([0-9.-]+) eV;\\s+([0-9.-]+) eV'): <function alpha_fdpolar>, re.compile('hyperpolarizability \\(in AU\\) beta\\(\\s+([0-9.-]+) eV;'): <function beta_fdpolar>}, 'polar': {re.compile('^  polarizability \\(in AU\\):'): <function alpha_polar>}, '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('NMR Properties for atom\\s+(\\S+)'): <function get_nmr>}, 'cis': {re.compile('CI size ='): <function cis_excitation_energies>}, 'sotdener': {re.compile('Ground State Dipole Moments'): <function initialize_tddft>, re.compile('(.*)Excited State\\s+\\d+:\\s+$'): <function tddft_excitation_properties>}, 'tdener': {re.compile('Ground State Dipole Moments'): <function initialize_tddft>, re.compile('(.*)Excited State\\s+\\d+:\\s+$'): <function tddft_excitation_properties>}, 'stdener': {re.compile('Ground State Dipole Moments'): <function initialize_tddft>, re.compile('(.*)Excited State\\s+\\d+:\\s+$'): <function tddft_excitation_properties>}, 'freq': {re.compile('The zero point energy \\(ZPE\\):\\s+(\\S+) k(\\w+)/mol'): <function zpe>, re.compile('Valid transition vector #\\s+(\\b[0-9]+\\b)'): <function get_vetted_vec_index>, re.compile('normal modes in mass-weighted cartesian coordinates:\\s+(\\d+)'): <function frequencies>, re.compile('normal modes in cartesian coordinates:\\s+(\\d+)'): <function frequencies>, re.compile('normal modes in cartesian coordinates:\\s+$'): <function frequencies_old>, re.compile('\\s*rotational symmetry number:\\s+([0-9]+)'): <function symmetry_number>}, 'before pre': {re.compile('^JobId:\\s+(\\S+)', re.IGNORECASE|re.MULTILINE): <function jobid>}, None: {re.compile('start of program (\\w+)'): <function start_of_program>, re.compile('glibc:\\s+(\\S+)'): <function glibc>, re.compile('\\s+Summary of Natural Population Analysis:'): <function nbo_charges>, re.compile('\\s+Total cpu seconds\\s+user:\\s+(?P<cpu_duration>[\\.\\d]+)\\s+user\\+sys:\\s+(?P<cpu_sys_duration>[\\.\\d]+)'): <function cpu_time>, re.compile('Time\\((?P<routine>\\w+)\\)\\s+user:\\s+(?P<utime>\\d+\\.\\d+)\\s+user\\+sys:\\s+(?P<systime>\\d+\\.\\d+)\\s+wallclock:\\s+(?P<clocktime>\\d+\\.\\d+)'): <function routine_time>, re.compile('Job .+ completed on \\S+ at (\\w.*)$'): <function end_time>, re.compile('ERROR *(\\d+)?: fatal error( -- debug information follows)?'): <function fatal_error>, re.compile('\\s+MEMINIT: failed to allocate *(\\d+)? words of dynamic memory'): <function nbo_mem_failure>}, '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>}}

__init__(jaguar_output, file_iter=None)

Parameters

file_iter (iterator returning lines of Jaguar output file)

jaguar_output (JaguarOutput instance)

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 .+ 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.

Raises

• StopIteration – In cases of unexpected file termination

• JaguarParseError – For parsing errors

class schrodinger.application.qsite.output.QSiteOutput(output: Optional[str] = None, partial_ok: bool = False, timing_thresh: Optional[Dict[str, float]] = None)

Bases: schrodinger.application.jaguar.output.JaguarOutput

A class to hold output information from a QSite run.

OK = 1

PARSING_EXCEPTIONS = (<class 'OSError'>, <class 'schrodinger.application.jaguar.textparser.JaguarParseError'>, <class 'StopIteration'>)

SPLAT = 2

UNKNOWN = 0

__init__(output: Optional[str] = None, partial_ok: bool = False, timing_thresh: Optional[Dict[str, float]] = None)

Initialize from an output filename or output name.

Parameters

• output – The name of the Jaguar output file to read. Can be the .out or .out.gz name or a file with the same basename as the desired .out/.out.gz file.

• partial_ok – Do not raise an exception if parsing fails partway through the file. Instead, process what has been read and store the parsing error in the parsing_error attribute. The resulting JaguarOutput object may be in an incomplete state.

• timing_thresh – Precision thresholds for comparing timings of specified routines.

Exceptions:

Raises

• 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.

• StopIteration – Raised in some cases if the file ends unexpectedly If this is raised, the state of the resulting object is not guaranteed to be useful.

attach_atom_dict_to_structures(structures: List[schrodinger.structure._structure.Structure])

Takes a list of structures and labels them with atomic properties that have previously been parsed from the output into the atomicsec_dict

A handler function is defined to attach an entry into the atomic section onto the relevant atom property, casting from string to the required data type. This should be expanded as needed to carry further properties through.

This assumes the structure atom names correspond to the input &atom section, raises JaguarRuntimeError otherwise.

NOTE: The atomic properties will be attached to every atom in every structure that matches the name pattern in the &atomic section table(s)

Parameters

structures – List of structure objects to which atomic section properties should be attached.

diff(other, factor: float = 1.0, short_circuit: bool = 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.

property duration: Optional[datetime.timedelta]

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

getStructure() → schrodinger.structure._structure.Structure

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

getStructures() → List[schrodinger.structure._structure.Structure]

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.

property irc_step

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

mol_weight_precision = 0.01

property path_structures: List[schrodinger.structure._structure.Structure]

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

property restart: str

Return the restart name for this output object.

rmsd_precision = 0.0001

property scan_step

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

write(filename: Optional[str] = None, mimic_backend: bool = False, add_title: bool = False, add_entry: bool = 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).

Parameters

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

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

• add_entry – If mimic_backend, then an empty entry name will be replaced with the output file’s jobname.

writeGrd(filename: str)

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)