pygromos.tests.test_files package

Submodules

pygromos.tests.test_files.general_file_functions module

class pygromos.tests.test_files.general_file_functions.general_file_tests(methodName='runTest')[source]

Bases: unittest.case.TestCase

test_copy()[source]
test_deepcopy()[source]
test_equalAfterCopy()[source]
test_equality()[source]
test_pickle()[source]

pygromos.tests.test_files.test_cnf_funcs module

class pygromos.tests.test_files.test_cnf_funcs.test_cnf(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.coord.cnf.Cnf

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/cnf/in_cnf1.cnf'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/cnf_gkw0u6ht'
test_clean_posiResNumsByName()[source]
test_delete_res()[source]
test_parse()[source]
test_visualize()[source]
test_write_out()[source]

pygromos.tests.test_files.test_disres module

class pygromos.tests.test_files.test_disres.test_disres(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.topology.disres.Disres

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/top/disres5.disres'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/top_l_ya9lt2'
test_parsing_test_file()[source]

pygromos.tests.test_files.test_disres_file module

class pygromos.tests.test_files.test_disres_file.test_disres(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.topology.disres.Disres

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/disres/in_disres.dat'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/disres_w0y4_xka'
test_parsing_test_file()[source]

pygromos.tests.test_files.test_gromosSystem module

class pygromos.tests.test_files.test_gromosSystem.test_gromos_system(methodName='runTest')[source]

Bases: unittest.case.TestCase

class_type

alias of pygromos.files.gromos_system.gromos_system.Gromos_System

input_cnf_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/small_system/6J29.cnf'
input_top_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/small_system/6J29.top'
setUp() → None[source]

Hook method for setting up the test fixture before exercising it.

test_construct_empty()[source]
test_construct_files()[source]
test_load()[source]
test_rebase()[source]
test_write()[source]
verbose = True

pygromos.tests.test_files.test_gromosSystem_forcefields module

class pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_2016H66(methodName='runTest')[source]

Bases: pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields

ff = <pygromos.files.forcefield.gromos.gromosff.GromosFF object>
top_residue_list = ['MTL']
class pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_54A7(methodName='runTest')[source]

Bases: pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields

ff = <pygromos.files.forcefield.gromos.gromosff.GromosFF object>
top_residue_list = ['CH3OH']
class pygromos.tests.test_files.test_gromosSystem_forcefields.test_gromos_system_forcefields(methodName='runTest')[source]

Bases: unittest.case.TestCase

ff = <pygromos.files.forcefield.gromos.gromosff.GromosFF object>
file_class

alias of pygromos.files.gromos_system.gromos_system.Gromos_System

smiles = 'CO'
test_construct_empty()[source]
test_construct_top_from_ff()[source]
top_residue_list = ['MTL']
verbose = True

pygromos.tests.test_files.test_imd module

class pygromos.tests.test_files.test_imd.test_imd(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.simulation_parameters.imd.Imd

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/imd/in_REEDS1.imd'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/imd_bh4dpifv'
test_edit_REEDS()[source]
test_parsing_test_file()[source]
test_to_string()[source]
test_write_out()[source]

pygromos.tests.test_files.test_imd_block module

class pygromos.tests.test_files.test_imd_block.test_imd_block(methodName='runTest')[source]

Bases: unittest.case.TestCase

test_some_blocks()[source]

pygromos.tests.test_files.test_mtb module

class pygromos.tests.test_files.test_mtb.test_mtb(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.topology.mtb.Mtb

in_file_path = '/home/mlehner/PyGromosTools/pygromos/data/ff/Gromos2016H66/2016H66.mtb'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/mtb_z1ecz9xp'
test_parsing_test_file()[source]
test_write()[source]
class pygromos.tests.test_files.test_mtb.test_mtb_g54a7(methodName='runTest')[source]

Bases: pygromos.tests.test_files.test_mtb.test_mtb

in_file_path = '/home/mlehner/PyGromosTools/pygromos/data/ff/Gromos54A7/54a7.mtb'
class pygromos.tests.test_files.test_mtb.test_mtb_orga(methodName='runTest')[source]

Bases: pygromos.tests.test_files.test_mtb.test_mtb

in_file_path = '/home/mlehner/PyGromosTools/pygromos/data/ff/Gromos2016H66/2016H66_orga.mtb'
test_CHE_read()[source]
test_all_mtb_solutes_read()[source]

pygromos.tests.test_files.test_ptp module

class pygromos.tests.test_files.test_ptp.test_ptp(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.topology.ptp.Pertubation_topology

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/ptp/eds.ptp'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/ptp_t0kcazzz'
test_IO()[source]
test_add_eds_state()[source]
test_delete_eds_state()[source]
test_eds_gen_all_states_ptp()[source]
test_get_eds_states()[source]
test_new_eds_ptp_from_scratch()[source]
test_remove_eds_atoms()[source]

pygromos.tests.test_files.test_qmmm module

class pygromos.tests.test_files.test_qmmm.test_qmmm(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.qmmm.qmmm.QMMM

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/qmmm/menthol-methanol-dmf.qmmm'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/qmmm_syo04oa8'
test_parsing_test_file()[source]
test_to_string()[source]
test_write_out()[source]
class pygromos.tests.test_files.test_qmmm.test_qmmm_imd(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.simulation_parameters.imd.Imd

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/qmmm/md.imd'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/qmmm_syo04oa8'
test_parsing_test_file()[source]
test_to_string()[source]
test_write_out()[source]

pygromos.tests.test_files.test_repdat module

class pygromos.tests.test_files.test_repdat.test_repdat(methodName='runTest')[source]

Bases: unittest.case.TestCase

class_type

alias of pygromos.files.otherfiles.repdat.Repdat

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/repdat/in_REEDS_repdat2_short.dat'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/repdat_o068y0of'
test_cleaning_concat()[source]
test_get_transitions()[source]
test_parsing_new_file()[source]
test_parsing_test_file()[source]
test_test_transitions()[source]
test_write_out()[source]

pygromos.tests.test_files.test_resnlib module

class pygromos.tests.test_files.test_resnlib.test_resnlib(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.otherfiles.residue_library.residue_library

in_file_path = '/home/mlehner/PyGromosTools/pygromos/data/pdb2g96.lib'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/resnLib_a7039fhi'
test_IO()[source]

pygromos.tests.test_files.test_top module

class pygromos.tests.test_files.test_top.test_top(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.topology.top.Top

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/top/test.top'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/top_o3f9_vmb'
test_parsing_test_file()[source]
class pygromos.tests.test_files.test_top.test_top_simple(methodName='runTest')[source]

Bases: pygromos.tests.test_files.general_file_functions.general_file_tests

class_type

alias of pygromos.files.topology.top.Top

in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/top/simpleTest.top'
root_out = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/top_o3f9_vmb'
test_add_eq_mul()[source]
test_additon()[source]
test_multiplication()[source]
test_parsing_test_file()[source]

pygromos.tests.test_files.test_trajectory module

class pygromos.tests.test_files.test_trajectory.test_trc(methodName='runTest')[source]

Bases: unittest.case.TestCase

class_name

alias of pygromos.files.trajectory.trc.Trc

help_class = TITLE gch found 22 hydrogen atoms in /home/bschroed/Documents/projects/PyGromosTools_release3/examples/example_files/Tutorial_System/a_build_initial_files/peptide.cnf 0 were within 0.1% of minimum energy bond length 22 were assigned new coordinates based on geometry  >>> Generated with PyGromosTools (riniker group) <<< END POSITION #       1 VAL   H1         1    1.241783665    1.501556791    1.518273147     1 VAL   H2         2    1.221597569    1.373896735    1.618130891     1 VAL   N          3    1.196200000    1.413300000    1.529800000     1 VAL   H3         4    1.097093311    1.426247772    1.526603233     1 VAL   CA         5    1.237300000    1.322400000    1.421900000     1 VAL   CB         6    1.116100000    1.268700000    1.345400000     1 VAL   CG1        7    1.041700000    1.369500000    1.257600000     1 VAL   CG2        8    1.157800000    1.148100000    1.261100000     1 VAL   C          9    1.335700000    1.393300000    1.328600000     1 VAL   O         10    1.447800000    1.344200000    1.316600000     2 TYR   N         11    1.297800000    1.514300000    1.288500000     2 TYR   H         12    1.210575283    1.551469583    1.320284758     2 TYR   CA        13    1.381800000    1.594400000    1.198300000     2 TYR   CB        14    1.320800000    1.731300000    1.167700000     2 TYR   CG        15    1.316700000    1.828700000    1.285500000     2 TYR   CD1       16    1.209300000    1.823700000    1.373600000     2 TYR   HD1       17    1.130290031    1.749796485    1.360307326     2 TYR   CD2       18    1.420400000    1.919600000    1.303000000     2 TYR   HD2       19    1.504990885    1.920076950    1.234260240     2 TYR   CE1       20    1.204100000    1.914300000    1.478900000     2 TYR   HE1       21    1.120330759    1.912712834    1.548622271     2 TYR   CE2       22    1.415700000    2.009900000    1.408600000     2 TYR   HE2       23    1.496221894    2.081795752    1.423707128     2 TYR   CZ        24    1.306500000    2.006900000    1.494600000     2 TYR   OH        25    1.303000000    2.103700000    1.590000000     2 TYR   HH        26    1.385890905    2.159332924    1.584162563     2 TYR   C         27    1.517900000    1.617700000    1.264200000     2 TYR   O         28    1.624900000    1.586100000    1.212400000     3 ARG   N         29    1.514400000    1.657100000    1.391100000     3 ARG   H         30    1.427383863    1.670744779    1.438449888     3 ARG   CA        31    1.642400000    1.680000000    1.459700000     3 ARG   CB        32    1.617000000    1.721100000    1.604800000     3 ARG   CG        33    1.539900000    1.617300000    1.686500000     3 ARG   CD        34    1.608900000    1.606000000    1.822500000     3 ARG   NE        35    1.527400000    1.525500000    1.914700000     3 ARG   HE        36    1.438096810    1.493764282    1.882797265     3 ARG   CZ        37    1.565300000    1.492000000    2.038800000     3 ARG   NH1       38    1.686400000    1.525700000    2.085100000     3 ARG   HH11      39    1.713360963    1.500046328    2.177917001     3 ARG   HH12      40    1.749840898    1.576510923    2.026846223     3 ARG   NH2       41    1.485200000    1.418600000    2.117200000     3 ARG   HH21      42    1.514453755    1.394156276    2.209648484     3 ARG   HH22      43    1.396160354    1.388258647    2.083268543     3 ARG   C         44    1.729900000    1.554500000    1.457100000     3 ARG   O         45    1.845400000    1.559500000    1.415000000     4 LYSH  N         46    1.668200000    1.443600000    1.497000000     4 LYSH  H         47    1.571910359    1.447946461    1.523634813     4 LYSH  CA        48    1.738800000    1.314800000    1.502700000     4 LYSH  CB        49    1.646500000    1.196800000    1.533800000     4 LYSH  CG        50    1.572300000    1.213000000    1.666700000     4 LYSH  CD        51    1.497100000    1.082100000    1.691400000     4 LYSH  CE        52    1.396500000    1.097200000    1.805600000     4 LYSH  NZ        53    1.321000000    0.974500000    1.834700000     4 LYSH  HZ1       54    1.350271838    0.901778367    1.772613579     4 LYSH  HZ2       55    1.223278482    0.991693073    1.822253991     4 LYSH  HZ3       56    1.337909275    0.946523380    1.929206006     4 LYSH  C         57    1.798300000    1.287600000    1.364400000     4 LYSH  O         58    1.917500000    1.258100000    1.359000000     5 GLN   N         59    1.716100000    1.293600000    1.260000000     5 GLN   H         60    1.618525916    1.310613276    1.273778479     5 GLN   CA        61    1.769400000    1.275100000    1.124300000     5 GLN   CB        62    1.656700000    1.300200000    1.023800000     5 GLN   CG        63    1.627000000    1.446800000    0.991700000     5 GLN   CD        64    1.523100000    1.473500000    0.882700000     5 GLN   OE1       65    1.501500000    1.390900000    0.794200000     5 GLN   NE2       66    1.460300000    1.590500000    0.891200000     5 GLN   HE21      67    1.390971831    1.615073255    0.823452231     5 GLN   HE22      68    1.482431587    1.653856690    0.965335839     5 GLN   C         69    1.892900000    1.359900000    1.093300000     5 GLN   O1        70    1.991900000    1.296800000    1.050300000     5 GLN   O2        71    1.885100000    1.482600000    1.116000000 END GENBOX     0     0.000000000    0.000000000    0.000000000     0.000000000    0.000000000    0.000000000     0.000000000    0.000000000    0.000000000     0.000000000    0.000000000    0.000000000 END
in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/trc/in_test.trc'
in_file_path_h5 = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/trc/in_test_trc.h5'
in_file_w_genbox_cnf_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/trc/in_test_genbox.cnf'
in_file_w_genbox_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/trc/in_test_genbox.trc'
outpath = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/trajs_6euj1sgk/out_trc1.h5'
test_constructor_empty()[source]
test_constructor_trc_file_noTop_path()[source]
test_constructor_trc_file_path()[source]
test_constructor_trc_h5_file_path()[source]
test_to_conf()[source]
test_to_trc_file()[source]
test_trc_with_boxes_traj()[source]
test_write()[source]
trc_outpath = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/trajs_6euj1sgk/out_.trc.gz'
class pygromos.tests.test_files.test_trajectory.test_tre(methodName='runTest')[source]

Bases: pygromos.tests.test_files.test_trajectory.traj_standard_tests

class_name

alias of pygromos.files.trajectory.tre.Tre

in_file2_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/tre/in_tre2.tre'
in_file_eds_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/tre/in_eds.tre'
in_file_h5_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/tre/in_tre1.tre.h5'
in_file_lam_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/tre/in_lam.tre'
in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/tre/in_tre1.tre'
outpath: str = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/trajs_6euj1sgk/out_tre1.tre.h5'
test_get_eds()[source]
test_get_lam()[source]
test_get_totals()[source]
class pygromos.tests.test_files.test_trajectory.test_trg(methodName='runTest')[source]

Bases: pygromos.tests.test_files.test_trajectory.traj_standard_tests

class_name

alias of pygromos.files.trajectory.trg.Trg

in_file_h5_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/trg/test.trg.h5'
in_file_path = '/home/mlehner/PyGromosTools/pygromos/tests/in_testfiles/trg/test.trg'
outpath: str = '/home/mlehner/PyGromosTools/pygromos/tests/out_testresults/tmp_test_files_3ji22kzw/trajs_6euj1sgk/out_tre1.tre.h5'
test_get_lambdas()[source]
test_get_precalclam()[source]
test_get_totals()[source]
class pygromos.tests.test_files.test_trajectory.traj_standard_tests(methodName='runTest')[source]

Bases: unittest.case.TestCase

class_name

alias of pygromos.files.trajectory._general_trajectory._General_Trajectory

in_file_h5_path = None
in_file_path = None
outpath: str
setUp() → None[source]

Hook method for setting up the test fixture before exercising it.

test_add()[source]
test_constructor_empty()[source]
test_constructor_trg_file_path()[source]
test_constructor_trg_h5_file_path()[source]
test_write()[source]

Module contents