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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + +Copyright [yyyy] [name of copyright owner] + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. diff --git a/moldesign/VERSION b/moldesign/VERSION new file mode 100644 index 0000000..81d788b --- /dev/null +++ b/moldesign/VERSION @@ -0,0 +1 @@ +0.4dev \ No newline at end of file diff --git a/moldesign/__init__.py b/moldesign/__init__.py index fe92fae..ad8a660 100644 --- a/moldesign/__init__.py +++ b/moldesign/__init__.py @@ -1,3 +1,17 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + from __future__ import absolute_import import moldesign.__main__ @@ -38,3 +52,10 @@ import warnings as _warnings _np.seterr(all='raise') _warnings.simplefilter('error', _np.ComplexWarning) + +# Other package metadata +__copyright__ = "Copyright 2016 Autodesk Inc." +__license__ = "Apache 2.0" +import os as _os +with open(_os.path.join(PACKAGEPATH, 'VERSION')) as versionfile: + __version__ = versionfile.read().strip() \ No newline at end of file diff --git a/moldesign/__main__.py b/moldesign/__main__.py index ee4866e..29a3f7c 100644 --- a/moldesign/__main__.py +++ b/moldesign/__main__.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """ This file collects the various command line tasks accessed via ``python -m moldesign [command]`` diff --git a/moldesign/atoms.py b/moldesign/atoms.py index 198a109..c4716da 100644 --- a/moldesign/atoms.py +++ b/moldesign/atoms.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import sys import copy import collections diff --git a/moldesign/basemethods.py b/moldesign/basemethods.py index 418690a..3baca74 100644 --- a/moldesign/basemethods.py +++ b/moldesign/basemethods.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """ This module contains abstract base classes for potential models, integrators, and various associated data types (force fields, orbitals, basis sets, etc.). diff --git a/moldesign/biounits.py b/moldesign/biounits.py index ecb1f11..cd50190 100644 --- a/moldesign/biounits.py +++ b/moldesign/biounits.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import moldesign as mdt import moldesign.utils.callsigs import moldesign.utils.classes diff --git a/moldesign/compute.py b/moldesign/compute.py index 66dc255..d84d842 100644 --- a/moldesign/compute.py +++ b/moldesign/compute.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import functools import logging import types diff --git a/moldesign/config.py b/moldesign/config.py index 142db94..e133b44 100644 --- a/moldesign/config.py +++ b/moldesign/config.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import os import sys @@ -39,7 +52,7 @@ def print_configuration(): print 'Image for python commands:', cfg.default_image -def _get_config(): # TODO: refactor, allow runtime changes, move host setup to PyCCC. see BBLL-64 +def _get_config(): # TODO: refactor, allow runtime_ms changes, move host setup to PyCCC. see BBLL-64 # TODO: how to configure workers? (especially ones that don't need to launch any jobs themselves) """Called at import to configure this module""" global cfg, launchcmd, launchpy, config_yaml, _docker_client diff --git a/moldesign/converters.py b/moldesign/converters.py index 80ecd76..e0527e2 100644 --- a/moldesign/converters.py +++ b/moldesign/converters.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import os import cStringIO as StringIO import cPickle as pkl diff --git a/moldesign/data.py b/moldesign/data.py index f33b5e0..15c364c 100644 --- a/moldesign/data.py +++ b/moldesign/data.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import json import os diff --git a/moldesign/dockerfiles/DockerMake-dev.yml b/moldesign/dockerfiles/DockerMake-dev.yml index 72b9d83..960f05a 100644 --- a/moldesign/dockerfiles/DockerMake-dev.yml +++ b/moldesign/dockerfiles/DockerMake-dev.yml @@ -4,7 +4,7 @@ _SOURCES_: moldesign_base: requires: - mdt_python_base - build_directory: ~/mycode/Buckyball_repo + build_directory: ~/mycode/molecular-design-toolkit build: | ADD requirements.txt /opt/mdtreqs.txt RUN pip install -r /opt/mdtreqs.txt @@ -13,7 +13,7 @@ moldesign_base: pyccc: requires: - mdt_python_base - build_directory: ~/mycode/bioplatform_repo + build_directory: ~/mycode/py-cloud-compute-cannon build: | ADD requirements.txt /opt/pycccreqs.txt RUN pip install -r /opt/pycccreqs.txt @@ -24,7 +24,7 @@ nbmolviz: requires: - mdt_python_base - notebook - build_directory: ~/mycode/Py3DMol_Package + build_directory: ~/mycode/notebook-molecular-visualization build: | ADD requirements.txt /opt/nbmvreqs.txt RUN pip install -r /opt/nbmvreqs.txt diff --git a/moldesign/excited_dynamics/__init__.py b/moldesign/excited_dynamics/__init__.py index f933956..7d0691f 100644 --- a/moldesign/excited_dynamics/__init__.py +++ b/moldesign/excited_dynamics/__init__.py @@ -1 +1,14 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. __author__ = 'aaronvirshup' diff --git a/moldesign/excited_dynamics/aims_basis.py b/moldesign/excited_dynamics/aims_basis.py index eced5e6..7ca70a2 100644 --- a/moldesign/excited_dynamics/aims_basis.py +++ b/moldesign/excited_dynamics/aims_basis.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from moldesign.excited_dynamics import wavepackets from moldesign.base import propagators from moldesign.units import * diff --git a/moldesign/excited_dynamics/nonadiabatic.py b/moldesign/excited_dynamics/nonadiabatic.py index ccc654b..10cd1aa 100644 --- a/moldesign/excited_dynamics/nonadiabatic.py +++ b/moldesign/excited_dynamics/nonadiabatic.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """This module contains mixins that are required for a variety of nonadiabatic calculations.""" from moldesign.base.geometry import MultiStateGeometry diff --git a/moldesign/excited_dynamics/surface_hopping.py b/moldesign/excited_dynamics/surface_hopping.py index f8c2a43..7b6257b 100644 --- a/moldesign/excited_dynamics/surface_hopping.py +++ b/moldesign/excited_dynamics/surface_hopping.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from moldesign.base.geometry import MultiStateGeometry,MDGeometry from moldesign.units import * diff --git a/moldesign/excited_dynamics/tully_problems.py b/moldesign/excited_dynamics/tully_problems.py index e12a302..ac09f67 100644 --- a/moldesign/excited_dynamics/tully_problems.py +++ b/moldesign/excited_dynamics/tully_problems.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from types import FunctionType import numpy as np diff --git a/moldesign/excited_dynamics/wavepackets.py b/moldesign/excited_dynamics/wavepackets.py index b1f519f..492eeef 100644 --- a/moldesign/excited_dynamics/wavepackets.py +++ b/moldesign/excited_dynamics/wavepackets.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import copy import unittest diff --git a/moldesign/forcefield.py b/moldesign/forcefield.py index 3a11181..55669e2 100644 --- a/moldesign/forcefield.py +++ b/moldesign/forcefield.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import math import numpy as np import moldesign as mdt diff --git a/moldesign/geometry.py b/moldesign/geometry.py index 2510f54..97bc81b 100644 --- a/moldesign/geometry.py +++ b/moldesign/geometry.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import numpy as np import math diff --git a/moldesign/helpers.py b/moldesign/helpers.py index 6920aa2..f2ed04a 100644 --- a/moldesign/helpers.py +++ b/moldesign/helpers.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import collections import moldesign as mdt diff --git a/moldesign/integrators.py b/moldesign/integrators.py index e03cb98..9822ca9 100644 --- a/moldesign/integrators.py +++ b/moldesign/integrators.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from moldesign.trajectory import Trajectory from moldesign import units as u diff --git a/moldesign/interfaces/__init__.py b/moldesign/interfaces/__init__.py index 5b18c5a..4ee942f 100644 --- a/moldesign/interfaces/__init__.py +++ b/moldesign/interfaces/__init__.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from __future__ import absolute_import from moldesign.interfaces import openmm, ambertools, pyscf_interface, nbo_interface diff --git a/moldesign/interfaces/ambertools.py b/moldesign/interfaces/ambertools.py index 2d1c606..ce38eeb 100644 --- a/moldesign/interfaces/ambertools.py +++ b/moldesign/interfaces/ambertools.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import numpy as np import cgi import collections diff --git a/moldesign/interfaces/biopython_interface.py b/moldesign/interfaces/biopython_interface.py index 8fca49c..5ff3ef2 100644 --- a/moldesign/interfaces/biopython_interface.py +++ b/moldesign/interfaces/biopython_interface.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import string import collections diff --git a/moldesign/interfaces/nbo_interface.py b/moldesign/interfaces/nbo_interface.py index 658f51e..0567b20 100644 --- a/moldesign/interfaces/nbo_interface.py +++ b/moldesign/interfaces/nbo_interface.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import numpy as np import moldesign.logs diff --git a/moldesign/interfaces/openbabel.py b/moldesign/interfaces/openbabel.py index 7ada5d6..3a5c7d8 100644 --- a/moldesign/interfaces/openbabel.py +++ b/moldesign/interfaces/openbabel.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from __future__ import absolute_import import os import string diff --git a/moldesign/interfaces/openmm.py b/moldesign/interfaces/openmm.py index 550a526..6ce21d5 100644 --- a/moldesign/interfaces/openmm.py +++ b/moldesign/interfaces/openmm.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import tempfile import itertools from cStringIO import StringIO diff --git a/moldesign/interfaces/opsin_interface.py b/moldesign/interfaces/opsin_interface.py index 5bed96c..8d6586a 100644 --- a/moldesign/interfaces/opsin_interface.py +++ b/moldesign/interfaces/opsin_interface.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import moldesign as mdt import moldesign.logs from moldesign import utils diff --git a/moldesign/interfaces/pdbfixer_interface.py b/moldesign/interfaces/pdbfixer_interface.py index 3b88318..5cf77a5 100644 --- a/moldesign/interfaces/pdbfixer_interface.py +++ b/moldesign/interfaces/pdbfixer_interface.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. try: import pdbfixer as pf diff --git a/moldesign/interfaces/pyscf_interface.py b/moldesign/interfaces/pyscf_interface.py index e5eb401..949f841 100644 --- a/moldesign/interfaces/pyscf_interface.py +++ b/moldesign/interfaces/pyscf_interface.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import warnings from cStringIO import StringIO import sys diff --git a/moldesign/interfaces/qmmm.py b/moldesign/interfaces/qmmm.py index 918b420..93af2c4 100644 --- a/moldesign/interfaces/qmmm.py +++ b/moldesign/interfaces/qmmm.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import moldesign as mdt from moldesign import basemethods import moldesign.units as u diff --git a/moldesign/interfaces/symmol_interface.py b/moldesign/interfaces/symmol_interface.py index 7a27a4c..bc2bf22 100644 --- a/moldesign/interfaces/symmol_interface.py +++ b/moldesign/interfaces/symmol_interface.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import re import fortranformat as ff diff --git a/moldesign/keywords.py b/moldesign/keywords.py index f2f3ac8..a2cd119 100644 --- a/moldesign/keywords.py +++ b/moldesign/keywords.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """ This is where we store lists of keywords that should be consistent across moldesign. diff --git a/moldesign/logs.py b/moldesign/logs.py index cd6eb65..6a63b7c 100644 --- a/moldesign/logs.py +++ b/moldesign/logs.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from collections import OrderedDict import logging import ipywidgets as ipy diff --git a/moldesign/minimizers.py b/moldesign/minimizers.py index b562c24..e14ae4b 100644 --- a/moldesign/minimizers.py +++ b/moldesign/minimizers.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import sys import numpy as np diff --git a/moldesign/models.py b/moldesign/models.py index c3af446..defbf93 100644 --- a/moldesign/models.py +++ b/moldesign/models.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """ This module mostly contains potential energy classes for users to import. TODO: look into http://molmod.github.io/ diff --git a/moldesign/molecule.py b/moldesign/molecule.py index 5fb3aee..c01b165 100644 --- a/moldesign/molecule.py +++ b/moldesign/molecule.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import string import numpy as np diff --git a/moldesign/orbitals.py b/moldesign/orbitals.py index 924c570..2b47538 100644 --- a/moldesign/orbitals.py +++ b/moldesign/orbitals.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. # NEW FEATURE: less nesting, more referencing import collections import ipywidgets as ipy diff --git a/moldesign/plotting.py b/moldesign/plotting.py index 6e02033..aa2a2fc 100644 --- a/moldesign/plotting.py +++ b/moldesign/plotting.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from copy import deepcopy from moldesign.units import * diff --git a/moldesign/static/apply_copyright.sh b/moldesign/static/apply_copyright.sh new file mode 100644 index 0000000..6d2723d --- /dev/null +++ b/moldesign/static/apply_copyright.sh @@ -0,0 +1,21 @@ +#!/bin/bash + +for file in `grep -L "Copyright 2016 Autodesk Inc." *.py`; do + mv $file{.bak} + cat > $file <> $file +done diff --git a/moldesign/static/generate_residue_bonds.py b/moldesign/static/generate_residue_bonds.py old mode 100755 new mode 100644 index b4fa133..6b31e8e --- a/moldesign/static/generate_residue_bonds.py +++ b/moldesign/static/generate_residue_bonds.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. #!/usr/bin/env python """ Script to generate connection tables from the official PDB definitions diff --git a/moldesign/symmetry.py b/moldesign/symmetry.py index da2f651..b0f593c 100644 --- a/moldesign/symmetry.py +++ b/moldesign/symmetry.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import collections import numpy as np import scipy.spatial.distance diff --git a/moldesign/tools.py b/moldesign/tools.py index 5299f37..a30d341 100644 --- a/moldesign/tools.py +++ b/moldesign/tools.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import moldesign as mdt import moldesign.units as u diff --git a/moldesign/trajectory.py b/moldesign/trajectory.py index 20e1059..48cd556 100644 --- a/moldesign/trajectory.py +++ b/moldesign/trajectory.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import os from cStringIO import StringIO from collections import OrderedDict diff --git a/moldesign/ui.py b/moldesign/ui.py index 20054b6..67d6b16 100644 --- a/moldesign/ui.py +++ b/moldesign/ui.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. # TODO: catch and log event exceptions import collections diff --git a/moldesign/units.py b/moldesign/units.py index 975810c..7ba7a1f 100644 --- a/moldesign/units.py +++ b/moldesign/units.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. """ Set up physical constants and unit systems """ diff --git a/moldesign/utils/__init__.py b/moldesign/utils/__init__.py index 06e2b49..0108c47 100644 --- a/moldesign/utils/__init__.py +++ b/moldesign/utils/__init__.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. from .callsigs import * from .classes import * from .databases import * diff --git a/moldesign/utils/callsigs.py b/moldesign/utils/callsigs.py index 2ba545a..2bd0edd 100644 --- a/moldesign/utils/callsigs.py +++ b/moldesign/utils/callsigs.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import functools from functools import wraps diff --git a/moldesign/utils/classes.py b/moldesign/utils/classes.py index 8aaa416..c844298 100644 --- a/moldesign/utils/classes.py +++ b/moldesign/utils/classes.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. class Categorizer(dict): """ Create a dict of lists from an iterable, with dict keys given by keyfn diff --git a/moldesign/utils/databases.py b/moldesign/utils/databases.py index 8c5e1d9..7c963b8 100644 --- a/moldesign/utils/databases.py +++ b/moldesign/utils/databases.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import os import dumbdbm import json diff --git a/moldesign/viewer.py b/moldesign/viewer.py index 0a82f58..d1c5eda 100644 --- a/moldesign/viewer.py +++ b/moldesign/viewer.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import collections import sys from itertools import product diff --git a/setup.py b/setup.py index b2978e5..073678f 100644 --- a/setup.py +++ b/setup.py @@ -1,3 +1,16 @@ +# Copyright 2016 Autodesk Inc. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. import os import sys from os.path import relpath, join