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Add grid-search optimization for rotation and translation, and filter clashing atoms in nanocluster (#43)
* Filter clashing atoms from cluster * Add optimization procedure, clashing filter with tolerance, and logging optimization * Update AtomPacker version * Bump biopython from 1.83.0 to 1.84.0 * Add Paulo as author and change development status to Beta * Update clashing tolerance to 0.0, check if rotations and translations are always inside the cavity, and set angles and translations to be explored in optimizaiton * Fix header description in AtomPacker package * Remove ValueError from cage.centroid * Update UML in README.md * Get radius for single-atom cluster, change logging to save disk usage, and add ValueError for clashing_tolerance * Update testing for AtomPacker.Cage * Add testing for AtomPacker.Cavity * Add testing for AtomPacker pipeline to ensure integration quality * Update dependencies * Update dependencies (pyKVFinder, plotly) * Fix one-atom cluster calculations * Add testing for AtomPacker.Cluster
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‎AtomPacker/__init__.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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the resulting structures.
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"""
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__version__ = "0.2.1"
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__version__ = "0.3.0"
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__name__ = "AtomPacker"
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license = "GNU GPL-3.0 License"
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‎AtomPacker/core/__init__.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/grid/__init__.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/grid/characterize.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/grid/coordinates.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/__init__.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/mmcif/__init__.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/mmcif/file.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/mol2/__init__.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/mol2/file.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/pdb/__init__.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/pdb/file.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/vdw/__init__.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/vdw/file.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/xyz/__init__.py

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# This source code is part of the pyKVFinder package and is distributed
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# This source code is part of the AtomPacker package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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‎AtomPacker/core/io/xyz/file.py

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# This source code is part of the pyKVFinder package and is distributed
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# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
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# information.
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