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