SOURSOP 0.2.6__tar.gz

soursop-0.2.6/LICENSE

@@ -0,0 +1,57 @@
+
+GNU LESSER GENERAL PUBLIC LICENSE
+Version 3, 29 June 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+
+Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
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+This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below.
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+The object code form of an Application may incorporate material from a header file that is part of the Library. You may convey such object code under terms of your choice, provided that, if the incorporated material is not limited to numerical parameters, data structure layouts and accessors, or small macros, inline functions and templates (ten or fewer lines in length), you do both of the following:
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+You may convey a Combined Work under terms of your choice that, taken together, effectively do not restrict modification of the portions of the Library contained in the Combined Work and reverse engineering for debugging such modifications, if you also do each of the following:
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soursop-0.2.6/MANIFEST.in

@@ -0,0 +1,8 @@
+include LICENSE
+include MANIFEST.in
+
+graft soursop
+global-exclude *.py[cod] __pycache__ *.so
+
+recursive-include soursop/data *include soursop/_version.py
+include soursop/_version.py

soursop-0.2.6/PKG-INFO

@@ -0,0 +1,103 @@
+Metadata-Version: 2.1
+Name: SOURSOP
+Version: 0.2.6
+Summary: Simulation analysis package for working with disordered proteins
+Author-email: Alex Holehouse <alex.holehouse@wustl.edu>
+License: LGPLv3
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: scipy>=1.5.0
+Requires-Dist: cython
+Requires-Dist: mdtraj>=1.9.5
+Requires-Dist: pandas>=0.23.0
+Requires-Dist: threadpoolctl>=2.2.0
+Requires-Dist: natsort
+Requires-Dist: matplotlib
+Provides-Extra: test
+Requires-Dist: pytest>=6.1.2; extra == "test"
+
+SOURSOP
+==============================
+[![Build Status](https://github.com/jaredl7/soursop/actions/workflows/soursop-ci.yml/badge.svg?branch=master)](https://github.com/jaredl7/soursop/actions)
+[![codecov](https://codecov.io/gh/jaredl7/soursop/branch/master/graph/badge.svg?token=RHGII0235L)](https://codecov.io/gh/jaredl7/soursop)
+[![Documentation Status](https://readthedocs.org/projects/soursop/badge/?version=latest)](https://soursop.readthedocs.io/en/latest/?badge=latest)
+## ABOUT
+SOURSOP is a Python-based simulation analysis package for working with intrinsically disordered and unfolded proteins. It is built on top of [mdtraj](https://mdtraj.org/), and was developed by Jared Lalmansingh and Alex Holehouse. 
+
+The current stable release candidate on PyPI is 0.2.6 (November 2024).
+
+## DOCUMENTATION
+All documentation, including installation information [can be found here](https://soursop.readthedocs.io/). 
+
+## ERRORS, FEATURES, REQUESTS
+If you find a bug, typo, or error [please raise an issue or GitHub](https://github.com/holehouse-lab/soursop/issues).
+
+If you wish to add a new feature, please see our Development information in the docs (especially for adding plugins).
+
+## MISCELLANEOUS
+* As of right now, the continuous integration fails because of a specific mismatch in how an edge-case error is handled between different versions of mdtraj. All other tests are passing and SOURSOP is ready for production. Do not be alarmed by the `failing` status above!
+
+## PUBLICATION
+To read about SOURSOP please see our paper:
+
+Lalmansingh, J. M., Keeley, A. T., Ruff, K. M., Pappu, R. V. & Holehouse, A. S. SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins. J. Chem. Theory Comput. (2023). doi:10.1021/acs.jctc.3c00190
+
+* [Journal link](https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00190)
+* [Paper PDF](https://www.dropbox.com/s/bd5szapvxpn83r6/soursop_jctc.pdf?dl=0)
+
+#### Copyright
+Copyright (c) 2015-2024 under the GNU LESSER GENERAL PUBLIC LICENSE 
+
+# Changelog
+#### Update November 2024 (0.2.6)
+* Major update to SOURSOP. 
+* Explicit support for single-chain one-bead-per-residue trajectory loading that dramatically improves load time (~30x improvement)
+* Officially added the `SSSampling` class and support for PENGUIN (see [Lotthammer & Holehouse, bioRxiv](https://www.biorxiv.org/content/10.1101/2024.11.06.622270v1.abstract)
+* Added support for NH3 and FOR residue types in get_amino_acid_sequence()
+* Switched over packaging to use `pyproject.toml` instead of `setup.py` and switched versioning to use v
+
+
+#### Update March 2024 (0.2.5 [patch])
+* Added `return_instantaneous_maps=False` keyword to `get_distance_maps()` function so we can return a [t,n,n] matrix where t = number of frames and n=number of residues for the instantaneous conformer-specific distance maps.
+
+
+#### Update Feb 2024 (0.2.5)
+* Removed periodic correction in SSProtein functions. We could provide periodic boundary condition checks for some but not all functions, and ensuring this flag was possible everywhere is not feasable. With this in mind, we opted to make a design decision to remove the `periodic` flag from the small number of functions that had it, such that there's no risk of a user forgetting and analyzing two distinct properties for a trajectory that requires PBC fixing where one analysis used `periodic=True` whereas another did not have this option. Now, the user must ensure their protein trajectories are corrected ahead of time. Note that we also added support for periodic=True for some of the SSTrajectory analysis functions, because in cases where multiple chains are present reconstructing a non-PBC trajectory becomes much more difficult. As such, intermolecular analysis does provide intrinsic PBC correction, whereas intramolecular analysis does not.
+
+#### Update July 2023
+* Added in `explicit_residue_checking` flag into SSTrajectory constructor, which makes it possible to use a solvated `.gro` file as an input file.
+
+#### Update February 2023
+* Added plugins example
+* Added additional tests and finalized documentation
+
+#### Update July 2022
+For version 0.2.1 we introduce potentially breaking changes into how COM distances are reported. 
+
+##### Details:
+All center-of-mass (COM)-based functions now return distances (as before) and relative positions in x/y/z (this is new) in Angstroms, not nanometers. Previously, the various center-of-mass based functions that returned absolute positions (i.e. 3xn matrices of x/y/z vs frame number) returned them where x/y/z was in units nm. This is fine if you know this, but means if you manually calculate distance between two COM vectors you'd get a distance in nanometers and not Angstroms. This is an unhelpful and unexpected behavior given all other distances are in Angstroms, so we have made the decision to fully update to Angstroms even for vector positions. This DOES NOT break any code internal to soursop, but if you were using COM positions to manually calculate distances these may need to be recalculated.
+
+#### Update April 2022
+For version 0.1.9 the documentation has been extensively extended
+
+#### Update July 2021
+CAMPARITraj is SOURSOP! For the final release we have re-named and re-branded CAMPARITraj as SOURSOP. This change in the name serves two important purposes.
+
+Firstly, CAMPARITraj was borne out of a collection of scripts and code built to work with CAMPARI. However, it has evolved into a stand-alone package for the analysis of all-atom simulations of IDPs and IDRs, and importantly, much of the analysis it performs can also be done in CAMPARI. As such, we felt it was important to decoupled SOURSOP from CAMPARI, both to avoid the implication that CAMPARI cannot perform analyses itself, and to avoid a scenario in which it may appear that this package only works with CAMPARI simulations.
+
+Secondly, there is a long, rich tradition of naming software tools after drinks in the Pappu lab (CAMPARI, ABSINTH, CIDER, LASSI etc.). As such SOURSOP is first-author Jared's Caribbean twist on this theme!
+
+### WARNING
+We are currently and systematically updating all of the CAMPARITraj codebase to SOURSOP. As such, for now, we recommend using a previous version. Note the SOURSOP change breaks all backwards compatibility. Sorry about that.
+
+#### Update December 2020
+Release 0.1.2 includes updated support to ensure CAMPARITraj will continue to work with MDTraj 1.9.5, as well as numerous additional updated.
+
+#### Update May 2019
+This is the *development* repository of CAMPARITraj and SHOULD NOT be used for production. Seriously, it is being modified constantly and with no building requirements during code pushes. If you want a building copy PLEASE contact Alex directly! [last touched June 24th 2019].
+
+#### Acknowledgements
+Project based on the
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.0.

soursop-0.2.6/README.md

@@ -0,0 +1,83 @@
+SOURSOP
+==============================
+[![Build Status](https://github.com/jaredl7/soursop/actions/workflows/soursop-ci.yml/badge.svg?branch=master)](https://github.com/jaredl7/soursop/actions)
+[![codecov](https://codecov.io/gh/jaredl7/soursop/branch/master/graph/badge.svg?token=RHGII0235L)](https://codecov.io/gh/jaredl7/soursop)
+[![Documentation Status](https://readthedocs.org/projects/soursop/badge/?version=latest)](https://soursop.readthedocs.io/en/latest/?badge=latest)
+## ABOUT
+SOURSOP is a Python-based simulation analysis package for working with intrinsically disordered and unfolded proteins. It is built on top of [mdtraj](https://mdtraj.org/), and was developed by Jared Lalmansingh and Alex Holehouse. 
+
+The current stable release candidate on PyPI is 0.2.6 (November 2024).
+
+## DOCUMENTATION
+All documentation, including installation information [can be found here](https://soursop.readthedocs.io/). 
+
+## ERRORS, FEATURES, REQUESTS
+If you find a bug, typo, or error [please raise an issue or GitHub](https://github.com/holehouse-lab/soursop/issues).
+
+If you wish to add a new feature, please see our Development information in the docs (especially for adding plugins).
+
+## MISCELLANEOUS
+* As of right now, the continuous integration fails because of a specific mismatch in how an edge-case error is handled between different versions of mdtraj. All other tests are passing and SOURSOP is ready for production. Do not be alarmed by the `failing` status above!
+
+## PUBLICATION
+To read about SOURSOP please see our paper:
+
+Lalmansingh, J. M., Keeley, A. T., Ruff, K. M., Pappu, R. V. & Holehouse, A. S. SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins. J. Chem. Theory Comput. (2023). doi:10.1021/acs.jctc.3c00190
+
+* [Journal link](https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00190)
+* [Paper PDF](https://www.dropbox.com/s/bd5szapvxpn83r6/soursop_jctc.pdf?dl=0)
+
+#### Copyright
+Copyright (c) 2015-2024 under the GNU LESSER GENERAL PUBLIC LICENSE 
+
+# Changelog
+#### Update November 2024 (0.2.6)
+* Major update to SOURSOP. 
+* Explicit support for single-chain one-bead-per-residue trajectory loading that dramatically improves load time (~30x improvement)
+* Officially added the `SSSampling` class and support for PENGUIN (see [Lotthammer & Holehouse, bioRxiv](https://www.biorxiv.org/content/10.1101/2024.11.06.622270v1.abstract)
+* Added support for NH3 and FOR residue types in get_amino_acid_sequence()
+* Switched over packaging to use `pyproject.toml` instead of `setup.py` and switched versioning to use v
+
+
+#### Update March 2024 (0.2.5 [patch])
+* Added `return_instantaneous_maps=False` keyword to `get_distance_maps()` function so we can return a [t,n,n] matrix where t = number of frames and n=number of residues for the instantaneous conformer-specific distance maps.
+
+
+#### Update Feb 2024 (0.2.5)
+* Removed periodic correction in SSProtein functions. We could provide periodic boundary condition checks for some but not all functions, and ensuring this flag was possible everywhere is not feasable. With this in mind, we opted to make a design decision to remove the `periodic` flag from the small number of functions that had it, such that there's no risk of a user forgetting and analyzing two distinct properties for a trajectory that requires PBC fixing where one analysis used `periodic=True` whereas another did not have this option. Now, the user must ensure their protein trajectories are corrected ahead of time. Note that we also added support for periodic=True for some of the SSTrajectory analysis functions, because in cases where multiple chains are present reconstructing a non-PBC trajectory becomes much more difficult. As such, intermolecular analysis does provide intrinsic PBC correction, whereas intramolecular analysis does not.
+
+#### Update July 2023
+* Added in `explicit_residue_checking` flag into SSTrajectory constructor, which makes it possible to use a solvated `.gro` file as an input file.
+
+#### Update February 2023
+* Added plugins example
+* Added additional tests and finalized documentation
+
+#### Update July 2022
+For version 0.2.1 we introduce potentially breaking changes into how COM distances are reported. 
+
+##### Details:
+All center-of-mass (COM)-based functions now return distances (as before) and relative positions in x/y/z (this is new) in Angstroms, not nanometers. Previously, the various center-of-mass based functions that returned absolute positions (i.e. 3xn matrices of x/y/z vs frame number) returned them where x/y/z was in units nm. This is fine if you know this, but means if you manually calculate distance between two COM vectors you'd get a distance in nanometers and not Angstroms. This is an unhelpful and unexpected behavior given all other distances are in Angstroms, so we have made the decision to fully update to Angstroms even for vector positions. This DOES NOT break any code internal to soursop, but if you were using COM positions to manually calculate distances these may need to be recalculated.
+
+#### Update April 2022
+For version 0.1.9 the documentation has been extensively extended
+
+#### Update July 2021
+CAMPARITraj is SOURSOP! For the final release we have re-named and re-branded CAMPARITraj as SOURSOP. This change in the name serves two important purposes.
+
+Firstly, CAMPARITraj was borne out of a collection of scripts and code built to work with CAMPARI. However, it has evolved into a stand-alone package for the analysis of all-atom simulations of IDPs and IDRs, and importantly, much of the analysis it performs can also be done in CAMPARI. As such, we felt it was important to decoupled SOURSOP from CAMPARI, both to avoid the implication that CAMPARI cannot perform analyses itself, and to avoid a scenario in which it may appear that this package only works with CAMPARI simulations.
+
+Secondly, there is a long, rich tradition of naming software tools after drinks in the Pappu lab (CAMPARI, ABSINTH, CIDER, LASSI etc.). As such SOURSOP is first-author Jared's Caribbean twist on this theme!
+
+### WARNING
+We are currently and systematically updating all of the CAMPARITraj codebase to SOURSOP. As such, for now, we recommend using a previous version. Note the SOURSOP change breaks all backwards compatibility. Sorry about that.
+
+#### Update December 2020
+Release 0.1.2 includes updated support to ensure CAMPARITraj will continue to work with MDTraj 1.9.5, as well as numerous additional updated.
+
+#### Update May 2019
+This is the *development* repository of CAMPARITraj and SHOULD NOT be used for production. Seriously, it is being modified constantly and with no building requirements during code pushes. If you want a building copy PLEASE contact Alex directly! [last touched June 24th 2019].
+
+#### Acknowledgements
+Project based on the
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.0.

soursop-0.2.6/SOURSOP.egg-info/PKG-INFO

@@ -0,0 +1,103 @@
+Metadata-Version: 2.1
+Name: SOURSOP
+Version: 0.2.6
+Summary: Simulation analysis package for working with disordered proteins
+Author-email: Alex Holehouse <alex.holehouse@wustl.edu>
+License: LGPLv3
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: scipy>=1.5.0
+Requires-Dist: cython
+Requires-Dist: mdtraj>=1.9.5
+Requires-Dist: pandas>=0.23.0
+Requires-Dist: threadpoolctl>=2.2.0
+Requires-Dist: natsort
+Requires-Dist: matplotlib
+Provides-Extra: test
+Requires-Dist: pytest>=6.1.2; extra == "test"
+
+SOURSOP
+==============================
+[![Build Status](https://github.com/jaredl7/soursop/actions/workflows/soursop-ci.yml/badge.svg?branch=master)](https://github.com/jaredl7/soursop/actions)
+[![codecov](https://codecov.io/gh/jaredl7/soursop/branch/master/graph/badge.svg?token=RHGII0235L)](https://codecov.io/gh/jaredl7/soursop)
+[![Documentation Status](https://readthedocs.org/projects/soursop/badge/?version=latest)](https://soursop.readthedocs.io/en/latest/?badge=latest)
+## ABOUT
+SOURSOP is a Python-based simulation analysis package for working with intrinsically disordered and unfolded proteins. It is built on top of [mdtraj](https://mdtraj.org/), and was developed by Jared Lalmansingh and Alex Holehouse. 
+
+The current stable release candidate on PyPI is 0.2.6 (November 2024).
+
+## DOCUMENTATION
+All documentation, including installation information [can be found here](https://soursop.readthedocs.io/). 
+
+## ERRORS, FEATURES, REQUESTS
+If you find a bug, typo, or error [please raise an issue or GitHub](https://github.com/holehouse-lab/soursop/issues).
+
+If you wish to add a new feature, please see our Development information in the docs (especially for adding plugins).
+
+## MISCELLANEOUS
+* As of right now, the continuous integration fails because of a specific mismatch in how an edge-case error is handled between different versions of mdtraj. All other tests are passing and SOURSOP is ready for production. Do not be alarmed by the `failing` status above!
+
+## PUBLICATION
+To read about SOURSOP please see our paper:
+
+Lalmansingh, J. M., Keeley, A. T., Ruff, K. M., Pappu, R. V. & Holehouse, A. S. SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins. J. Chem. Theory Comput. (2023). doi:10.1021/acs.jctc.3c00190
+
+* [Journal link](https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00190)
+* [Paper PDF](https://www.dropbox.com/s/bd5szapvxpn83r6/soursop_jctc.pdf?dl=0)
+
+#### Copyright
+Copyright (c) 2015-2024 under the GNU LESSER GENERAL PUBLIC LICENSE 
+
+# Changelog
+#### Update November 2024 (0.2.6)
+* Major update to SOURSOP. 
+* Explicit support for single-chain one-bead-per-residue trajectory loading that dramatically improves load time (~30x improvement)
+* Officially added the `SSSampling` class and support for PENGUIN (see [Lotthammer & Holehouse, bioRxiv](https://www.biorxiv.org/content/10.1101/2024.11.06.622270v1.abstract)
+* Added support for NH3 and FOR residue types in get_amino_acid_sequence()
+* Switched over packaging to use `pyproject.toml` instead of `setup.py` and switched versioning to use v
+
+
+#### Update March 2024 (0.2.5 [patch])
+* Added `return_instantaneous_maps=False` keyword to `get_distance_maps()` function so we can return a [t,n,n] matrix where t = number of frames and n=number of residues for the instantaneous conformer-specific distance maps.
+
+
+#### Update Feb 2024 (0.2.5)
+* Removed periodic correction in SSProtein functions. We could provide periodic boundary condition checks for some but not all functions, and ensuring this flag was possible everywhere is not feasable. With this in mind, we opted to make a design decision to remove the `periodic` flag from the small number of functions that had it, such that there's no risk of a user forgetting and analyzing two distinct properties for a trajectory that requires PBC fixing where one analysis used `periodic=True` whereas another did not have this option. Now, the user must ensure their protein trajectories are corrected ahead of time. Note that we also added support for periodic=True for some of the SSTrajectory analysis functions, because in cases where multiple chains are present reconstructing a non-PBC trajectory becomes much more difficult. As such, intermolecular analysis does provide intrinsic PBC correction, whereas intramolecular analysis does not.
+
+#### Update July 2023
+* Added in `explicit_residue_checking` flag into SSTrajectory constructor, which makes it possible to use a solvated `.gro` file as an input file.
+
+#### Update February 2023
+* Added plugins example
+* Added additional tests and finalized documentation
+
+#### Update July 2022
+For version 0.2.1 we introduce potentially breaking changes into how COM distances are reported. 
+
+##### Details:
+All center-of-mass (COM)-based functions now return distances (as before) and relative positions in x/y/z (this is new) in Angstroms, not nanometers. Previously, the various center-of-mass based functions that returned absolute positions (i.e. 3xn matrices of x/y/z vs frame number) returned them where x/y/z was in units nm. This is fine if you know this, but means if you manually calculate distance between two COM vectors you'd get a distance in nanometers and not Angstroms. This is an unhelpful and unexpected behavior given all other distances are in Angstroms, so we have made the decision to fully update to Angstroms even for vector positions. This DOES NOT break any code internal to soursop, but if you were using COM positions to manually calculate distances these may need to be recalculated.
+
+#### Update April 2022
+For version 0.1.9 the documentation has been extensively extended
+
+#### Update July 2021
+CAMPARITraj is SOURSOP! For the final release we have re-named and re-branded CAMPARITraj as SOURSOP. This change in the name serves two important purposes.
+
+Firstly, CAMPARITraj was borne out of a collection of scripts and code built to work with CAMPARI. However, it has evolved into a stand-alone package for the analysis of all-atom simulations of IDPs and IDRs, and importantly, much of the analysis it performs can also be done in CAMPARI. As such, we felt it was important to decoupled SOURSOP from CAMPARI, both to avoid the implication that CAMPARI cannot perform analyses itself, and to avoid a scenario in which it may appear that this package only works with CAMPARI simulations.
+
+Secondly, there is a long, rich tradition of naming software tools after drinks in the Pappu lab (CAMPARI, ABSINTH, CIDER, LASSI etc.). As such SOURSOP is first-author Jared's Caribbean twist on this theme!
+
+### WARNING
+We are currently and systematically updating all of the CAMPARITraj codebase to SOURSOP. As such, for now, we recommend using a previous version. Note the SOURSOP change breaks all backwards compatibility. Sorry about that.
+
+#### Update December 2020
+Release 0.1.2 includes updated support to ensure CAMPARITraj will continue to work with MDTraj 1.9.5, as well as numerous additional updated.
+
+#### Update May 2019
+This is the *development* repository of CAMPARITraj and SHOULD NOT be used for production. Seriously, it is being modified constantly and with no building requirements during code pushes. If you want a building copy PLEASE contact Alex directly! [last touched June 24th 2019].
+
+#### Acknowledgements
+Project based on the
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.0.

soursop-0.2.6/SOURSOP.egg-info/SOURCES.txt

@@ -0,0 +1,103 @@
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+setup.cfg
+SOURSOP.egg-info/PKG-INFO
+SOURSOP.egg-info/SOURCES.txt
+SOURSOP.egg-info/dependency_links.txt
+SOURSOP.egg-info/not-zip-safe
+SOURSOP.egg-info/requires.txt
+SOURSOP.egg-info/top_level.txt
+soursop/__init__.py
+soursop/_internal_data.py
+soursop/_version.py
+soursop/configs.py
+soursop/soursop.py
+soursop/ssdata.py
+soursop/ssexceptions.py
+soursop/ssio.py
+soursop/ssmutualinformation.py
+soursop/ssnmr.py
+soursop/sspolymer.py
+soursop/sspre.py
+soursop/ssprotein.py
+soursop/sssampling.py
+soursop/sstools.py
+soursop/sstrajectory.py
+soursop/ssutils.py
+soursop/.ipynb_checkpoints/Untitled-checkpoint.ipynb
+soursop/data/SASA_SUMMARY.csv
+soursop/data/bbseg2.dat
+soursop/data/phi_excluded_volume_tripeptides.pickle
+soursop/data/psi_excluded_volume_tripeptides.pickle
+soursop/data/test_data/all_residues.pdb
+soursop/data/test_data/all_residues.xtc
+soursop/data/test_data/ctl9.pdb
+soursop/data/test_data/ctl9.xtc
+soursop/data/test_data/gs6.dcd
+soursop/data/test_data/gs6.pdb
+soursop/data/test_data/gs6.xtc
+soursop/data/test_data/gs6_distance_map_mean.npy
+soursop/data/test_data/gs6_distance_map_std.npy
+soursop/data/test_data/gs6_invalid_r1.pdb
+soursop/data/test_data/ntl9.dcd
+soursop/data/test_data/ntl9.pdb
+soursop/data/test_data/ntl9.xtc
+soursop/data/test_data/ntl9_distance_map_mean.npy
+soursop/data/test_data/ntl9_distance_map_std.npy
+soursop/data/test_data/.ipynb_checkpoints/Untitled-checkpoint.ipynb
+soursop/data/test_data/cap_tests/ACD_start_1.pdb
+soursop/data/test_data/cap_tests/ACD_start_10.pdb
+soursop/data/test_data/cap_tests/ACE_NH2.pdb
+soursop/data/test_data/cap_tests/ACE_NME.pdb
+soursop/data/test_data/cap_tests/ACE_NME_multichain.pdb
+soursop/data/test_data/cap_tests/ACE_NME_start_at_5.pdb
+soursop/data/test_data/cap_tests/ACE_UCAP.pdb
+soursop/data/test_data/cap_tests/FOR_NH2.pdb
+soursop/data/test_data/cap_tests/FOR_NME.pdb
+soursop/data/test_data/cap_tests/FOR_UCAP.pdb
+soursop/data/test_data/cap_tests/UCAP_NH2.pdb
+soursop/data/test_data/cap_tests/UCAP_NME.pdb
+soursop/data/test_data/cap_tests/UCAP_UCAP.pdb
+soursop/data/test_data/cap_tests/__START.pdb
+soursop/data/test_data/gromacs1chain/top.pdb
+soursop/data/test_data/gromacs1chain/traj.xtc
+soursop/data/test_data/gromacs2chains/top.pdb
+soursop/data/test_data/gromacs2chains/traj.xtc
+soursop/data/test_data/pre_data/PRE_109_unweighted.csv
+soursop/data/test_data/pre_data/PRE_119_unweighted.csv
+soursop/data/test_data/pre_data/PRE_149_unweighted.csv
+soursop/data/test_data/pre_data/PRE_61_unweighted.csv
+soursop/data/test_data/pre_data/PRE_74_unweighted.csv
+soursop/data/test_data/pre_data/PRE_96_unweighted.csv
+soursop/data/test_data/sampling_quality/EV/1/__START.pdb
+soursop/data/test_data/sampling_quality/EV/1/__traj.xtc
+soursop/data/test_data/sampling_quality/EV/2/__START.pdb
+soursop/data/test_data/sampling_quality/EV/2/__traj.xtc
+soursop/data/test_data/sampling_quality/EV/3/__START.pdb
+soursop/data/test_data/sampling_quality/EV/3/__traj.xtc
+soursop/data/test_data/sampling_quality/WT/1/__START.pdb
+soursop/data/test_data/sampling_quality/WT/1/__traj.xtc
+soursop/data/test_data/sampling_quality/WT/2/__START.pdb
+soursop/data/test_data/sampling_quality/WT/2/__traj.xtc
+soursop/data/test_data/sampling_quality/WT/3/__START.pdb
+soursop/data/test_data/sampling_quality/WT/3/__traj.xtc
+soursop/plugins/__init__.py
+soursop/plugins/sparrow_plugin/__init__.py
+soursop/tests/__init__.py
+soursop/tests/conftest.py
+soursop/tests/test_caps.py
+soursop/tests/test_numbering.py
+soursop/tests/test_scratchpad.ipynb
+soursop/tests/test_soursop.py
+soursop/tests/test_ssmutual_information.py
+soursop/tests/test_ssnmr.py
+soursop/tests/test_ssnmr_extended.py
+soursop/tests/test_sspre.py
+soursop/tests/test_ssproteins.py
+soursop/tests/test_sssampling.py
+soursop/tests/test_sstrajectory.py
+soursop/tests/test_ssutils.py
+soursop/tests/.ipynb_checkpoints/test_scratchpad-checkpoint.ipynb
+soursop/tests/.ipynb_checkpoints/test_ssproteins-checkpoint.py

soursop-0.2.6/SOURSOP.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

soursop-0.2.6/SOURSOP.egg-info/not-zip-safe

@@ -0,0 +1 @@
+

soursop-0.2.6/SOURSOP.egg-info/requires.txt

@@ -0,0 +1,11 @@
+numpy>=1.20.0
+scipy>=1.5.0
+cython
+mdtraj>=1.9.5
+pandas>=0.23.0
+threadpoolctl>=2.2.0
+natsort
+matplotlib
+
+[test]
+pytest>=6.1.2

soursop-0.2.6/SOURSOP.egg-info/top_level.txt

@@ -0,0 +1 @@
+soursop

soursop-0.2.6/pyproject.toml

@@ -0,0 +1,68 @@
+[build-system]
+
+# delete cython/numpy if not needed
+requires = ["setuptools>=61", "versioningit~=2.0", "numpy", ]
+build-backend = "setuptools.build_meta"
+
+
+# define project info
+[project]
+name = "SOURSOP"
+dynamic = ["version"]
+description = "Simulation analysis package for working with disordered proteins"
+authors = [
+    {name = "Alex Holehouse", email = "alex.holehouse@wustl.edu"}
+]
+license = {text = "LGPLv3"}
+readme = "README.md"  
+requires-python = ">=3.7"
+
+# add in as needed  
+dependencies = [      
+        "numpy>=1.20.0",
+        "scipy>=1.5.0",
+        "cython",
+        "mdtraj>=1.9.5",
+        "pandas>=0.23.0",
+        "threadpoolctl>=2.2.0",
+        "natsort",
+        "matplotlib",
+]
+
+[project.optional-dependencies]
+test = [
+  "pytest>=6.1.2",
+]
+
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true 
+
+[tool.setuptools.packages.find]
+namespaces = true
+where = ["."]
+include = ["soursop", "soursop*"]  # Discover all sub-packages inside the main package
+
+[tool.setuptools.package-data]
+soursop = [
+    "py.typed"
+]
+
+[tool.versioningit]
+default-version = "1+unknown"
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.versioningit.vcs]
+# The method key:
+method = "git"  # <- The method name
+# Parameters to pass to the method:
+match = ["*"]
+default-tag = "1.0.0"
+
+[tool.versioningit.write]
+file = "soursop/_version.py"

soursop-0.2.6/setup.cfg

@@ -0,0 +1,20 @@
+[coverage:run]
+omit = 
+	*/tests/*
+	metapredict/_version.py
+
+[yapf]
+COLUMN_LIMIT = 119
+INDENT_WIDTH = 4
+USE_TABS = False
+
+[flake8]
+max-line-length = 119
+
+[aliases]
+test = pytest
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

soursop-0.2.6/soursop/.ipynb_checkpoints/Untitled-checkpoint.ipynb

@@ -0,0 +1,6 @@
+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

soursop-0.2.6/soursop/__init__.py

@@ -0,0 +1,33 @@
+##     _____  ____  _    _ _____   _____  ____  _____  
+##   / ____|/ __ \| |  | |  __ \ / ____|/ __ \|  __ \ 
+##  | (___ | |  | | |  | | |__) | (___ | |  | | |__) |
+##   \___ \| |  | | |  | |  _  / \___ \| |  | |  ___/ 
+##   ____) | |__| | |__| | | \ \ ____) | |__| | |     
+##  |_____/ \____/ \____/|_|  \_\_____/ \____/|_|     
+
+## Alex Holehouse (Pappu Lab and Holehouse Lab) and Jared Lalmansing (Pappu lab)
+## Simulation analysis package
+## Copyright 2014 - 2022
+##
+
+import os
+
+# Add imports here
+from soursop import *
+
+# Generate _version.py if missing and in the Read the Docs environment
+if os.getenv("READTHEDOCS") == "True" and not os.path.isfile('../soursop/_version.py'):   
+    import versioningit            
+    __version__ = versioningit.get_version('../')
+else:
+    from soursop._version import __version__
+
+# code that allows access to the data directory
+_ROOT = os.path.abspath(os.path.dirname(__file__))
+def get_data(path):
+    return os.path.join(_ROOT, 'data', path)
+
+
+def get_version():
+    return "%s - %s" % (str(__version__), str(__git_revision__))
+