Copyright (#68)

* Add copyright notice to source files * Removing title line in the license, adding whitespace between the hashtag and text, removing license from tutorials
pyMBE-dev · Jun 5, 2024 · 2496835 · 2496835
1 parent 55ea6c8
commit 2496835
Show file tree

Hide file tree

Showing 41 changed files with 704 additions and 5 deletions.
diff --git 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 <http://www.gnu.org/licenses/>.
+
 .PHONY: sample
 .PHONY: visual 
 .PHONY: clean

diff --git 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 <http://www.gnu.org/licenses/>.
+
 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
@@ -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 <http://www.gnu.org/licenses/>.
+
 import sys
 import argparse
 import numpy as np

diff --git 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 <http://www.gnu.org/licenses/>.
 
 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
@@ -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 <http://www.gnu.org/licenses/>.
+
 import os
 import argparse
 import sysconfig

diff --git a/maintainer/header_template_license.txt 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 <http://www.gnu.org/licenses/>.
diff --git 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 <http://www.gnu.org/licenses/>.
+
 # Import pyMBE and other libraries
 import pyMBE
 import numpy as np

diff --git 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 <http://www.gnu.org/licenses/>.
+
 import re
 import sys
 import ast

diff --git 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 <http://www.gnu.org/licenses/>.
+
 # 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
@@ -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 <http://www.gnu.org/licenses/>.
+
 import os
 from tqdm import tqdm
 import espressomd

diff --git 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 <http://www.gnu.org/licenses/>.
+
 # 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
@@ -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 <http://www.gnu.org/licenses/>.
+
 #######################################################
 # Loading modules 
 #######################################################

diff --git 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 <http://www.gnu.org/licenses/>.
+
 # Load espresso, pyMBE and other necessary libraries
 import os 
 import espressomd

diff --git 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 <http://www.gnu.org/licenses/>.
+
 # 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
@@ -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 <http://www.gnu.org/licenses/>.
+
 #Load espresso, pyMBE and other necessary libraries
 import os 
 import espressomd

diff --git 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 <http://www.gnu.org/licenses/>.
+
 # 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
@@ -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 <http://www.gnu.org/licenses/>.
+
 # Load python modules
 import os 
 import espressomd

diff --git 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 <http://www.gnu.org/licenses/>.
+
 # Import pyMBE and other libraries
 import pyMBE
 import numpy as np