diff --git a/Makefile b/Makefile index 0092dbc..56d1a05 100644 --- a/Makefile +++ b/Makefile @@ -1,4 +1,22 @@ #!/bin/bash +# +# Copyright (C) 2023-2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + .PHONY: sample .PHONY: visual .PHONY: clean diff --git a/lib/analysis.py b/lib/analysis.py index 9cd119a..d1b380e 100644 --- a/lib/analysis.py +++ b/lib/analysis.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import os import pandas as pd import numpy as np diff --git a/lib/create_cg_from_pdb.py b/lib/create_cg_from_pdb.py index 9c7df7c..c2edb37 100644 --- a/lib/create_cg_from_pdb.py +++ b/lib/create_cg_from_pdb.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import sys import argparse import numpy as np diff --git a/lib/handy_functions.py b/lib/handy_functions.py index a6c4e2e..7d93aff 100644 --- a/lib/handy_functions.py +++ b/lib/handy_functions.py @@ -1,3 +1,20 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . def setup_electrostatic_interactions (units, espresso_system, kT, c_salt=None, solvent_permittivity=78.5, method='p3m', tune_p3m=True, accuracy=1e-3,verbose=True): """ diff --git a/maintainer/configure_venv.py b/maintainer/configure_venv.py index 5719621..b6c9603 100644 --- a/maintainer/configure_venv.py +++ b/maintainer/configure_venv.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2023-2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import os import argparse import sysconfig diff --git a/maintainer/header_template_license.txt b/maintainer/header_template_license.txt new file mode 100644 index 0000000..428cdab --- /dev/null +++ b/maintainer/header_template_license.txt @@ -0,0 +1,17 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . diff --git a/maintainer/standarize_data.py b/maintainer/standarize_data.py index 425a779..c1acfec 100644 --- a/maintainer/standarize_data.py +++ b/maintainer/standarize_data.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2023-2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import pyMBE import numpy as np diff --git a/pyMBE.py b/pyMBE.py index 51e8bcf..9c32e88 100644 --- a/pyMBE.py +++ b/pyMBE.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2023-2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import re import sys import ast diff --git a/samples/Beyer2024/create_paper_data.py b/samples/Beyer2024/create_paper_data.py index 836a0e6..567e054 100644 --- a/samples/Beyer2024/create_paper_data.py +++ b/samples/Beyer2024/create_paper_data.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import pyMBE from lib import analysis diff --git a/samples/Beyer2024/globular_protein.py b/samples/Beyer2024/globular_protein.py index c704b86..11b6c15 100644 --- a/samples/Beyer2024/globular_protein.py +++ b/samples/Beyer2024/globular_protein.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import os from tqdm import tqdm import espressomd diff --git a/samples/Beyer2024/peptide.py b/samples/Beyer2024/peptide.py index de497e8..4ac409e 100644 --- a/samples/Beyer2024/peptide.py +++ b/samples/Beyer2024/peptide.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Load espresso, sugar and other necessary libraries import os import espressomd diff --git a/samples/Beyer2024/weak_polyelectrolyte_dialysis.py b/samples/Beyer2024/weak_polyelectrolyte_dialysis.py index c2e574a..29eea73 100644 --- a/samples/Beyer2024/weak_polyelectrolyte_dialysis.py +++ b/samples/Beyer2024/weak_polyelectrolyte_dialysis.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + ####################################################### # Loading modules ####################################################### diff --git a/samples/branched_polyampholyte.py b/samples/branched_polyampholyte.py index d651ef5..c281a17 100644 --- a/samples/branched_polyampholyte.py +++ b/samples/branched_polyampholyte.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Load espresso, pyMBE and other necessary libraries import os import espressomd diff --git a/samples/peptide.py b/samples/peptide.py index c48e517..6d805c3 100644 --- a/samples/peptide.py +++ b/samples/peptide.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Load espresso, pyMBE and other necessary libraries import os import espressomd diff --git a/samples/peptide_mixture_grxmc_ideal.py b/samples/peptide_mixture_grxmc_ideal.py index 88f95ec..a63981d 100644 --- a/samples/peptide_mixture_grxmc_ideal.py +++ b/samples/peptide_mixture_grxmc_ideal.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + #Load espresso, pyMBE and other necessary libraries import os import espressomd diff --git a/samples/plot_HH.py b/samples/plot_HH.py index f3757ed..2cfd830 100644 --- a/samples/plot_HH.py +++ b/samples/plot_HH.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Plots the charge of a peptide with a given sequence using either a custom or reference set of pKa values import numpy as np diff --git a/samples/salt_solution_gcmc.py b/samples/salt_solution_gcmc.py index 42c8b57..e692123 100644 --- a/samples/salt_solution_gcmc.py +++ b/samples/salt_solution_gcmc.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Load python modules import os import espressomd diff --git a/testsuite/bond_tests.py b/testsuite/bond_tests.py index fdd196d..64b6ff3 100644 --- a/testsuite/bond_tests.py +++ b/testsuite/bond_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import pyMBE import numpy as np diff --git a/testsuite/calculate_net_charge_unit_test.py b/testsuite/calculate_net_charge_unit_test.py index e1677c1..2ef714e 100644 --- a/testsuite/calculate_net_charge_unit_test.py +++ b/testsuite/calculate_net_charge_unit_test.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import numpy as np import espressomd # Create an instance of pyMBE library diff --git a/testsuite/cph_ideal_tests.py b/testsuite/cph_ideal_tests.py index 5e3d888..910a778 100644 --- a/testsuite/cph_ideal_tests.py +++ b/testsuite/cph_ideal_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import pyMBE import sys diff --git a/testsuite/create_molecule_position_test.py b/testsuite/create_molecule_position_test.py index 733962e..808f337 100644 --- a/testsuite/create_molecule_position_test.py +++ b/testsuite/create_molecule_position_test.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import numpy as np import espressomd # Create an instance of pyMBE library diff --git a/testsuite/define_and_create_molecules_unit_tests.py b/testsuite/define_and_create_molecules_unit_tests.py index d0788ab..a52e9a4 100644 --- a/testsuite/define_and_create_molecules_unit_tests.py +++ b/testsuite/define_and_create_molecules_unit_tests.py @@ -1,3 +1,20 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . # Import pyMBE and other libraries import pyMBE @@ -410,4 +427,4 @@ np.testing.assert_equal(actual=len(espresso_system.part.all()), desired=starting_number_of_particles, verbose=True) -print("*** Unit test passed ***") \ No newline at end of file +print("*** Unit test passed ***") diff --git a/testsuite/gcmc_tests.py b/testsuite/gcmc_tests.py index 1878780..1cee373 100644 --- a/testsuite/gcmc_tests.py +++ b/testsuite/gcmc_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import sys import tempfile diff --git a/testsuite/generate_perpendicular_vectors_test.py b/testsuite/generate_perpendicular_vectors_test.py index f837a23..7153ee3 100644 --- a/testsuite/generate_perpendicular_vectors_test.py +++ b/testsuite/generate_perpendicular_vectors_test.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import numpy as np import pyMBE from itertools import combinations diff --git a/testsuite/globular_protein_tests.py b/testsuite/globular_protein_tests.py index ed43d4d..c2394d4 100644 --- a/testsuite/globular_protein_tests.py +++ b/testsuite/globular_protein_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import pyMBE from lib import analysis diff --git a/testsuite/globular_protein_unit_tests.py b/testsuite/globular_protein_unit_tests.py index 7a28f57..b44ae32 100644 --- a/testsuite/globular_protein_unit_tests.py +++ b/testsuite/globular_protein_unit_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import numpy as np # Create an instance of pyMBE library import pyMBE diff --git a/testsuite/grxmc_ideal_tests.py b/testsuite/grxmc_ideal_tests.py index 8265d8b..86d1538 100644 --- a/testsuite/grxmc_ideal_tests.py +++ b/testsuite/grxmc_ideal_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import pyMBE import sys diff --git a/testsuite/henderson_hasselbalch_tests.py b/testsuite/henderson_hasselbalch_tests.py index de36f6b..02ff629 100644 --- a/testsuite/henderson_hasselbalch_tests.py +++ b/testsuite/henderson_hasselbalch_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import numpy as np import pyMBE pmb = pyMBE.pymbe_library(SEED=42) diff --git a/testsuite/lj_tests.py b/testsuite/lj_tests.py index 42aaa2b..11b4dad 100644 --- a/testsuite/lj_tests.py +++ b/testsuite/lj_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import pyMBE import numpy as np diff --git a/testsuite/parameter_test.py b/testsuite/parameter_test.py index 2cc7734..1b16e16 100644 --- a/testsuite/parameter_test.py +++ b/testsuite/parameter_test.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import pathlib import pyMBE import pandas as pd @@ -110,4 +128,4 @@ path_to_interactions=pmb.get_resource("testsuite/test_parameters/test_non_valid_bond.json") input_parameters={"filename":path_to_interactions} np.testing.assert_raises(ValueError, pmb.load_interaction_parameters, **input_parameters) -print("*** Test passed ***") \ No newline at end of file +print("*** Test passed ***") diff --git a/testsuite/peptide_tests.py b/testsuite/peptide_tests.py index 11b35f8..6fe98d9 100644 --- a/testsuite/peptide_tests.py +++ b/testsuite/peptide_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import sys import tempfile diff --git a/testsuite/read-write-df_test.py b/testsuite/read-write-df_test.py index 8ae7ebd..2ce154c 100644 --- a/testsuite/read-write-df_test.py +++ b/testsuite/read-write-df_test.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import re import ast import tempfile diff --git a/testsuite/seed_test.py b/testsuite/seed_test.py index 9f6f0d8..f36c768 100644 --- a/testsuite/seed_test.py +++ b/testsuite/seed_test.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import numpy as np import espressomd import pyMBE diff --git a/testsuite/serialization_test.py b/testsuite/serialization_test.py index eea3ad2..5f5960f 100644 --- a/testsuite/serialization_test.py +++ b/testsuite/serialization_test.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import io import json import contextlib diff --git a/testsuite/set_particle_acidity_test.py b/testsuite/set_particle_acidity_test.py index 9c5623f..4a70200 100644 --- a/testsuite/set_particle_acidity_test.py +++ b/testsuite/set_particle_acidity_test.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import numpy as np import pyMBE diff --git a/testsuite/setup_salt_ions_unit_tests.py b/testsuite/setup_salt_ions_unit_tests.py index b14e968..efcbccd 100644 --- a/testsuite/setup_salt_ions_unit_tests.py +++ b/testsuite/setup_salt_ions_unit_tests.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import numpy as np import espressomd # Create an instance of pyMBE library @@ -261,4 +279,4 @@ def test_counterions(molecule_name, cation_name, anion_name, espresso_system, ex espresso_system.setup_type_map(type_map.values()) np.testing.assert_equal(espresso_system.number_of_particles(type_map["Na"]),0) np.testing.assert_equal(espresso_system.number_of_particles(type_map["Cl"]),0) -print("*** Unit test passed ***") \ No newline at end of file +print("*** Unit test passed ***") diff --git a/testsuite/weak_polyelectrolyte_dialysis_test.py b/testsuite/weak_polyelectrolyte_dialysis_test.py index c770cc3..563b3ae 100644 --- a/testsuite/weak_polyelectrolyte_dialysis_test.py +++ b/testsuite/weak_polyelectrolyte_dialysis_test.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + # Import pyMBE and other libraries import pyMBE from lib import analysis diff --git a/tutorials/pyMBE_tutorial.ipynb b/tutorials/pyMBE_tutorial.ipynb index b12d7b3..31daaa4 100644 --- a/tutorials/pyMBE_tutorial.ipynb +++ b/tutorials/pyMBE_tutorial.ipynb @@ -1202,7 +1202,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.8.10" }, "vscode": { "interpreter": { diff --git a/tutorials/solution_tutorial.ipynb b/tutorials/solution_tutorial.ipynb index 07095be..7b33cd7 100644 --- a/tutorials/solution_tutorial.ipynb +++ b/tutorials/solution_tutorial.ipynb @@ -244,7 +244,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.8.10" }, "vscode": { "interpreter": { diff --git a/visualization/create_vmd_script.py b/visualization/create_vmd_script.py index 44e8fc3..51d4dab 100644 --- a/visualization/create_vmd_script.py +++ b/visualization/create_vmd_script.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import glob import re import argparse diff --git a/visualization/vmd-traj.py b/visualization/vmd-traj.py index 57869fe..fec54f7 100644 --- a/visualization/vmd-traj.py +++ b/visualization/vmd-traj.py @@ -1,3 +1,21 @@ +# +# Copyright (C) 2024 pyMBE-dev team +# +# This file is part of pyMBE. +# +# pyMBE is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# pyMBE is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see . + import os import math import re