Add the copyright and license/distribution info to the top of each new file.

wrappers/python/simtk/openmm/app/charmmparameterset.py

@@ -3,9 +3,35 @@ This module contains classes for parsing and processing CHARMM parameter,
 topology, and stream files. It only extracts atom properties from the
 topology files and extracts all parameters from the parameter files
 
+This file is part of the OpenMM molecular simulation toolkit originating from
+Simbios, the NIH National Center for Physics-Based Simulation of Biological
+Structures at Stanford, funded under the NIH Roadmap for Medical Research,
+grant U54 GM072970. See https://simtk.org.  This code was originally part of
+the ParmEd program and was ported for use with OpenMM.
+
+Copyright (c) 2014 the Authors
+
 Author: Jason M. Swails
 Contributors:
-Date: April 5, 2014
+Date: April 18, 2014
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 from simtk.openmm.app.internal.charmm._charmmfile import (
             CharmmFile, CharmmStreamFile)

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -2,9 +2,35 @@
 Provides a Python class for parsing a PSF file and setting up a system
 structure for it within the OpenMM framework.
 
+This file is part of the OpenMM molecular simulation toolkit originating from
+Simbios, the NIH National Center for Physics-Based Simulation of Biological
+Structures at Stanford, funded under the NIH Roadmap for Medical Research,
+grant U54 GM072970. See https://simtk.org.  This code was originally part of
+the ParmEd program and was ported for use with OpenMM.
+
+Copyright (c) 2014 the Authors
+
 Author: Jason M. Swails
 Contributors:
-Date: April 9, 2014
+Date: April 18, 2014
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 from __future__ import division
 

wrappers/python/simtk/openmm/app/internal/charmm/__init__.py

@@ -25,7 +25,8 @@ __all__ = ['psf', 'parameters']
 __authors__ = 'Jason Swails'
 __contributors__ = ''
 __license__ = 'MIT'
-__date__ = 'Apr. 9, 2014'
+__copyright__ = 'Copyright 2014, Jason Swails'
+__date__ = 'Apr. 18, 2014'
 
 
 __private__ = ['topologyobjects', '_charmmfile']

wrappers/python/simtk/openmm/app/internal/charmm/_charmmfile.py

@@ -3,9 +3,35 @@ Provides a class for reading CHARMM-style files. The key component to these
 files is that the ! character is a comment character and everything after ! is
 ignored.
 
+This file is part of the OpenMM molecular simulation toolkit originating from
+Simbios, the NIH National Center for Physics-Based Simulation of Biological
+Structures at Stanford, funded under the NIH Roadmap for Medical Research,
+grant U54 GM072970. See https://simtk.org.  This code was originally part of
+the ParmEd program and was ported for use with OpenMM.
+
+Copyright (c) 2014 the Authors
+
 Author: Jason M. Swails
 Contributors:
-Date: April 9, 2014
+Date: April 18, 2014
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 from simtk.openmm.app.internal.charmm.exceptions import CharmmFileError
 

wrappers/python/simtk/openmm/app/internal/charmm/exceptions.py

@@ -2,9 +2,35 @@
 This package contains exceptions that may be raised by the CHARMM components of
 the OpenMM Application layer
 
+This file is part of the OpenMM molecular simulation toolkit originating from
+Simbios, the NIH National Center for Physics-Based Simulation of Biological
+Structures at Stanford, funded under the NIH Roadmap for Medical Research,
+grant U54 GM072970. See https://simtk.org.  This code was originally part of
+the ParmEd program and was ported for use with OpenMM.
+
+Copyright (c) 2014 the Authors
+
 Author: Jason M. Swails
 Contributors:
-Date: April 9, 2014
+Date: April 18, 2014
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 
 class CharmmError(Exception):

wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py

@@ -2,9 +2,35 @@
 This module contains data structures useful for parsing in CHARMM files and
 constructing chemical structures from those files
 
+This file is part of the OpenMM molecular simulation toolkit originating from
+Simbios, the NIH National Center for Physics-Based Simulation of Biological
+Structures at Stanford, funded under the NIH Roadmap for Medical Research,
+grant U54 GM072970. See https://simtk.org.  This code was originally part of
+the ParmEd program and was ported for use with OpenMM.
+
+Copyright (c) 2014 the Authors
+
 Author: Jason M. Swails
 Contributors:
-Date: April 9, 2014
+Date: April 18, 2014
+
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the "Software"),
+to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense,
+and/or sell copies of the Software, and to permit persons to whom the
+Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
+USE OR OTHER DEALINGS IN THE SOFTWARE.
 """
 from simtk.openmm.app.internal.charmm.exceptions import (
                 SplitResidueWarning, BondError, ResidueError, CmapError,