diff --git a/docs/topic_guides/data_structures.rst b/docs/topic_guides/data_structures.rst index fdd3305..403d3e7 100644 --- a/docs/topic_guides/data_structures.rst +++ b/docs/topic_guides/data_structures.rst @@ -17,5 +17,3 @@ Fit a Dihedral .. automodule:: mosdef_dihedral_fit.dihedral_fit.fit_dihedral_with_gomc :members: fit_dihedral_with_gomc - - diff --git a/mosdef_dihedral_fit/tests/files/gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_zeroed.inp b/mosdef_dihedral_fit/tests/files/gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_zeroed.inp index 050b317..e791c11 100644 --- a/mosdef_dihedral_fit/tests/files/gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_zeroed.inp +++ b/mosdef_dihedral_fit/tests/files/gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_zeroed.inp @@ -57,7 +57,7 @@ DIHEDRALS * CHARMM ! Boltzmann = 0.0019872041 kcal / (mol * K) ! ! type_1 type_2 type_3 type_4 Kchi n delta ! extended_type_1 extended_type_2 extended_type_3 extended_type_4 -HC CT CT HC 0.5 0 90.0 ! TMP_opls_140 TMP_opls_135 TMP_opls_135 TMP_opls_140 +HC CT CT HC 0.5 0 90.0 ! TMP_opls_140 TMP_opls_135 TMP_opls_135 TMP_opls_140 ! The input dihedral to periodic dihedral conversion error is OK [error <= 10^(-10)] ! Maximum( |(input dihedral calc)-(periodic dihedral calc)| ) = 3.608224830031759e-16 diff --git a/mosdef_dihedral_fit/tests/test_fit_dihedral_with_gomc.py b/mosdef_dihedral_fit/tests/test_fit_dihedral_with_gomc.py index 5e54df3..54a2c89 100644 --- a/mosdef_dihedral_fit/tests/test_fit_dihedral_with_gomc.py +++ b/mosdef_dihedral_fit/tests/test_fit_dihedral_with_gomc.py @@ -661,7 +661,7 @@ def test_gaussian_log_file_fit_oplsaa_fit_ethane_HC_CT_CT_HC_with_2_log_files( ) == mdf_math.round_to_sig_figs( correct_line_values[i][j], number_sig_i ) - + def test_gaussian_log_file_fit_oplsaa_protonated_fragment_CT_CT_C_OH_in_COOH( self, ): @@ -5025,7 +5025,7 @@ def test_r_squared_rtol_not_a_float(self): r_squared_rtol=2, opls_force_k0_zero=True, ) - + def test_error_r_squared_min_and_r_squared_rtol_need_adjusted( self, ): @@ -5085,7 +5085,7 @@ def test_error_r_squared_min_and_r_squared_rtol_need_adjusted( r_squared_min=0.99, r_squared_rtol=0.0000002, ) - + def test_warning_r_squared_min_and_r_squared_rtol_need_adjusted( self, ): @@ -5136,7 +5136,7 @@ def test_warning_r_squared_min_and_r_squared_rtol_need_adjusted( r_squared_min=0.98, r_squared_rtol=0.015, ) - + def test_gaussian_log_file_fit_oplsaa_protonated_fragment_CT_CT_C_OH_in_COOH_in_mie_form( self, ): @@ -5803,7 +5803,7 @@ def test_gaussian_log_file_fit_oplsaa_protonated_fragment_CT_CT_C_OH_in_COOH_in_ atol=0.02, rtol=0.08, ) - + def test_gaussian_style_files_fit_amber_aa_fit_CT_CT_CT_CT_in_butane_files( self, ): @@ -5970,7 +5970,15 @@ def test_gaussian_style_files_fit_amber_aa_fit_CT_CT_CT_CT_in_butane_files( [str("1"), 0, 0.4721804016, 0, 0, 0, -1.38239818695], [str("2"), 0, 0, 0.575010099536, 0, 0, -0.546636504029], [str("3"), 0, 0, 0, 0.685865110811, 0, 0.538213945525], - [str("4"), 0.549332597925, 0, 0, 0, -0.274666298962, -1.1033603631], + [ + str("4"), + 0.549332597925, + 0, + 0, + 0, + -0.274666298962, + -1.1033603631, + ], [ str("1_3"), 0, @@ -6014,7 +6022,7 @@ def test_gaussian_style_files_fit_amber_aa_fit_CT_CT_CT_CT_in_butane_files( 0.239549950189, 0.57212115096, 0, - 0.749172728898 , + 0.749172728898, ], [ str("1_2_3_4"), @@ -6051,7 +6059,7 @@ def test_gaussian_style_files_fit_amber_aa_fit_CT_CT_CT_CT_in_butane_files( atol=0.02, rtol=0.08, ) - + # check the periodic dihedral file with open("periodic_dihedral_k_constants_fit_energy.txt", "r") as fp: number_sig_i = 4 @@ -6471,12 +6479,12 @@ def test_gaussian_style_files_fit_amber_aa_fit_CT_CT_CT_CT_in_butane_files( atol=0.02, rtol=0.08, ) - + def test_gaussian_style_files_fit_amber_aa_all_unique_fit_CT_CT_CT_CT_in_butane_files( self, ): fit_dihedral_with_gomc( - ['CT1', 'CT0', 'CT0', 'CT1'], + ["CT1", "CT0", "CT0", "CT1"], self.get_fn( "gaussian_style_output_files/CT_CT_CT_CT/input/starting_coords/butane_aa.mol2" ), @@ -6638,7 +6646,15 @@ def test_gaussian_style_files_fit_amber_aa_all_unique_fit_CT_CT_CT_CT_in_butane_ [str("1"), 0, 0.4721804016, 0, 0, 0, -1.38239818695], [str("2"), 0, 0, 0.575010099536, 0, 0, -0.546636504029], [str("3"), 0, 0, 0, 0.685865110811, 0, 0.538213945525], - [str("4"), 0.549332597925, 0, 0, 0, -0.274666298962, -1.1033603631], + [ + str("4"), + 0.549332597925, + 0, + 0, + 0, + -0.274666298962, + -1.1033603631, + ], [ str("1_3"), 0, @@ -6682,7 +6698,7 @@ def test_gaussian_style_files_fit_amber_aa_all_unique_fit_CT_CT_CT_CT_in_butane_ 0.239549950189, 0.57212115096, 0, - 0.749172728898 , + 0.749172728898, ], [ str("1_2_3_4"), @@ -6719,7 +6735,7 @@ def test_gaussian_style_files_fit_amber_aa_all_unique_fit_CT_CT_CT_CT_in_butane_ atol=0.02, rtol=0.08, ) - + # check the periodic dihedral file with open("periodic_dihedral_k_constants_fit_energy.txt", "r") as fp: number_sig_i = 4 @@ -7350,7 +7366,7 @@ def test_gaussian_style_files_fit_amber_aa_fit_CT_CT_CT_CT_force_k0_to_True_in_b 0.239549950189, 0.57212115096, 0, - 0.749172728898 , + 0.749172728898, ], [ str("1_2_3_4"), @@ -7388,7 +7404,7 @@ def test_gaussian_style_files_fit_amber_aa_fit_CT_CT_CT_CT_force_k0_to_True_in_b atol=0.02, rtol=0.08, ) - + # check the periodic dihedral file with open("periodic_dihedral_k_constants_fit_energy.txt", "r") as fp: number_sig_i = 4 @@ -7664,7 +7680,7 @@ def test_gaussian_style_files_fit_amber_aa_fit_CT_CT_CT_CT_force_k0_to_True_in_b atol=0.02, rtol=0.08, ) - + # check the RB torsion file with open("RB_torsion_k_constants_fit_energy.txt", "r") as fp: number_sig_i = 4 @@ -7808,7 +7824,7 @@ def test_gaussian_style_files_fit_amber_aa_fit_CT_CT_CT_CT_force_k0_to_True_in_b atol=0.02, rtol=0.08, ) - + def test_gaussian_style_files_fit_trappe_ua_fit_CT_CT_CT_CT_in_butane_files( self, ): @@ -8476,7 +8492,6 @@ def test_gaussian_style_files_fit_trappe_ua_fit_CT_CT_CT_CT_in_butane_files( atol=0.02, rtol=0.08, ) - def test_gaussian_style_files_fit_mia_ua_fit_CT_CT_CT_CT_in_butane_files( self, @@ -9145,7 +9160,7 @@ def test_gaussian_style_files_fit_mia_ua_fit_CT_CT_CT_CT_in_butane_files( atol=0.02, rtol=0.08, ) - + def test_gaussian_style_files_fit_exp6_fit_CT_CT_CT_CT_in_butane_files( self, ):