├── .gitignore ├── LICENSE ├── README.md ├── docs ├── .buildinfo ├── .nojekyll ├── Makefile ├── build │ ├── doctrees │ │ ├── environment.pickle │ │ ├── index.doctree │ │ └── sections │ │ │ ├── introduction.doctree │ │ │ └── models.doctree │ └── html │ │ ├── .buildinfo │ │ ├── .nojekyll │ │ ├── _modules │ │ ├── core │ │ │ ├── geometry.html │ │ │ ├── models.html │ │ │ └── system.html │ │ ├── index.html │ │ └── reporter │ │ │ └── sbm_reporter.html │ │ ├── _sources │ │ ├── index.rst.txt │ │ └── sections │ │ │ ├── introduction.rst.txt │ │ │ └── models.rst.txt │ │ ├── _static │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── jquery-3.4.1.js │ │ ├── jquery.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── sections │ │ ├── introduction.html │ │ └── models.html ├── index.html └── source │ ├── conf.py │ ├── index.rst │ └── sections │ ├── introduction.rst │ └── models.rst ├── sbmOpenMM ├── __init__.py ├── core │ ├── __init__.py │ ├── geometry.py │ ├── models.py │ └── system.py ├── datasets │ ├── __init__.py │ ├── downloader.py │ └── foxp1_folding.py ├── parameters │ ├── __init__.py │ ├── amber.json │ ├── amber.py │ ├── ca_parameters.py │ └── oplsaa.py └── reporter │ ├── __init__.py │ └── sbm_reporter.py ├── setup.py └── tutorials ├── basic ├── 01-AlphaCarbon │ ├── coarseGrainedSBM.ipynb │ └── inputs │ │ ├── 1YPA_I.pdb │ │ └── 1YPA_I_CA.contacts ├── 02-AllAtom │ ├── allHeavyAtomSBM.ipynb │ └── inputs │ │ ├── 1YPA_I.pdb │ │ └── 1YPA_I_AA.contacts ├── 03-FoldingTemperature │ ├── foldingTemperature.ipynb │ └── inputs │ │ ├── 1YPA_I.pdb │ │ ├── 1YPA_I_CA.contacts │ │ ├── pywham_hc_better_estimate.xml │ │ ├── pywham_hc_rough_estimate.xml │ │ ├── pywham_iterative_01.xml │ │ ├── pywham_iterative_02.xml │ │ ├── pywham_iterative_03.xml │ │ ├── pywham_iterative_04.xml │ │ ├── pywham_iterative_05.xml │ │ ├── pywham_iterative_06.xml │ │ ├── pywham_iterative_07.xml │ │ ├── pywham_iterative_08.xml │ │ ├── pywham_iterative_09.xml │ │ └── pywham_iterative_10.xml ├── 04-FreeEnergySurface │ ├── freeEnergyProfile.ipynb │ └── inputs │ │ ├── 1YPA_I.pdb │ │ ├── 1YPA_I_CA.contacts │ │ ├── pywham_Qf_RMSD_free_energy.xml │ │ ├── pywham_Qf_free_energy.xml │ │ └── pywham_RMSD_free_energy.xml └── 05-MultiBasin │ ├── input │ ├── AK_close.pdb │ ├── AK_close_CA.contacts │ ├── AK_conformationalChange.webm │ ├── AK_open.pdb │ ├── AK_open_CA.contacts │ └── fe_wham.xml │ └── multiBasinModel.ipynb └── folding └── 01-FoxP1_equilibrium_folding ├── 01-Production.ipynb ├── 02-Analysis.ipynb ├── input ├── FoxP_monomer.contacts └── FoxP_monomer.pdb ├── other_notebooks ├── Chapman_Kolmogorov.ipynb ├── getTStrajectory.ipynb └── radiusOfGyration.ipynb └── output ├── radiusOfGyration.npy └── ts_trajectory.dcd /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | eggs/ 16 | .eggs/ 17 | lib/ 18 | lib64/ 19 | parts/ 20 | sdist/ 21 | var/ 22 | wheels/ 23 | pip-wheel-metadata/ 24 | share/python-wheels/ 25 | *.egg-info/ 26 | .installed.cfg 27 | *.egg 28 | MANIFEST 29 | 30 | # PyInstaller 31 | # Usually these files are written by a python script from a template 32 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 33 | *.manifest 34 | *.spec 35 | 36 | # Installer logs 37 | pip-log.txt 38 | pip-delete-this-directory.txt 39 | 40 | # Unit test / coverage reports 41 | htmlcov/ 42 | .tox/ 43 | .nox/ 44 | .coverage 45 | .coverage.* 46 | .cache 47 | nosetests.xml 48 | coverage.xml 49 | *.cover 50 | *.py,cover 51 | .hypothesis/ 52 | .pytest_cache/ 53 | 54 | # Translations 55 | *.mo 56 | *.pot 57 | 58 | # Django stuff: 59 | *.log 60 | local_settings.py 61 | db.sqlite3 62 | db.sqlite3-journal 63 | 64 | # Flask stuff: 65 | instance/ 66 | .webassets-cache 67 | 68 | # Scrapy stuff: 69 | .scrapy 70 | 71 | # Sphinx documentation 72 | docs/_build/ 73 | 74 | # PyBuilder 75 | target/ 76 | 77 | # Jupyter Notebook 78 | .ipynb_checkpoints 79 | 80 | # IPython 81 | profile_default/ 82 | ipython_config.py 83 | 84 | # pyenv 85 | .python-version 86 | 87 | # pipenv 88 | # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. 89 | # However, in case of collaboration, if having platform-specific dependencies or dependencies 90 | # having no cross-platform support, pipenv may install dependencies that don't work, or not 91 | # install all needed dependencies. 92 | #Pipfile.lock 93 | 94 | # PEP 582; used by e.g. github.com/David-OConnor/pyflow 95 | __pypackages__/ 96 | 97 | # Celery stuff 98 | celerybeat-schedule 99 | celerybeat.pid 100 | 101 | # SageMath parsed files 102 | *.sage.py 103 | 104 | # Environments 105 | .env 106 | .venv 107 | env/ 108 | venv/ 109 | ENV/ 110 | env.bak/ 111 | venv.bak/ 112 | 113 | # Spyder project settings 114 | .spyderproject 115 | .spyproject 116 | 117 | # Rope project settings 118 | .ropeproject 119 | 120 | # mkdocs documentation 121 | /site 122 | 123 | # mypy 124 | .mypy_cache/ 125 | .dmypy.json 126 | dmypy.json 127 | 128 | # Pyre type checker 129 | .pyre/ 130 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2019 CompBiochBiophLab 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # SBMOpenMM 2 | 3 | ## Description 4 | 5 | SBMOpenMM is a Python library to run protein structure-based model (SBM) simulations using OpenMM toolkit. The library offers flexibility for creating SBM force fields that can be customised to capture different aspects of protein SBM potential energy exploration. 6 | 7 | Considering an input structure, the library automatizes the creation of forces to specify it as the only minimum configuration in the potential energy function. Bonds, angles and torsions are maintained close to their equilibrium configuration, while native contact interactions are allowed to form and break using regular or modified Lennard-Jones potentials. This allows complete and local protein unfolding, restricting the interactions only to the evolutionarily relevant chemical contacts, to explore more thoroughly the relevant configurational space of protein folding and function. 8 | 9 | Different granularities for the models can be selected as All-heavy-Atom and alpha-carbon representations. These basic models can also be extended to multi-basin potentials employing more than one input configuration. Here, shared native contacts are modeled with special Gaussian functions to allow for more than one equilibrium distance. 10 | 11 | The library offers methods to tailor forcefield parameter for each force term. Combining these basic methods and force implementations, SBMOpenMM offers easy set up of more complex force field definition that can aid in a better exploration of different biophysical phenomena. 12 | 13 | ## Installation 14 | 15 | ### Requirements 16 | 17 | The library was written and tested with python 3.6 and has only two other python dependencies: 18 | 19 | - [openmm>=7.0](http://openmm.org/) 20 | - [numpy>=1.15](https://numpy.org/) 21 | 22 | ### From Source code 23 | 24 | The source code can be obtained from [GitHub]("https://github.com/CompBiochBiophLab/sbm-openmm") or by directly downloading it from the following link: 25 | 26 | [Download SBMOpenMM source code](https://github.com/CompBiochBiophLab/sbm-openmm/archive/master.zip) 27 | 28 | After unziping the source code file and changing to the source directory, execute: 29 | 30 | python setup.py install 31 | 32 | This should build and install SBMOpenMM into your python environment. 33 | 34 | ### Using pip 35 | 36 | Using the correct python 3.6 (or higher) environment, execute: 37 | 38 | pip install SBMOpenMM 39 | 40 | ## Documentation 41 | 42 | Documentation for the SBMOpenMM library functions can be found in the following link: 43 | 44 | [SBMOpenMM Documentation](https://compbiochbiophlab.github.io/sbm-openmm) 45 | 46 | ## Tutorials 47 | 48 | Tutorials are available for learning how to set up SBM simulations using SBMOpenMM. These are shown inside GitHub as executed jupyter notebooks. If you prefer to run them yourself, please go to the "tutorials" folder inside the sbm-openmm package. 49 | 50 | ### Basic tutorials 51 | 52 | [01 - Coarse grained SBM simulations](https://github.com/CompBiochBiophLab/sbm-openmm/blob/master/tutorials/basic/01-AlphaCarbon/coarseGrainedSBM.ipynb) 53 | 54 | [02 - Coarse grained SBM simulations](https://github.com/CompBiochBiophLab/sbm-openmm/blob/master/tutorials/basic/02-AllAtom/allHeavyAtomSBM.ipynb) 55 | 56 | [03 - Estimating the folding temperature](https://github.com/CompBiochBiophLab/sbm-openmm/blob/master/tutorials/basic/03-FoldingTemperature/foldingTemperature.ipynb) 57 | 58 | [04 - Estimating free energy profiles](https://github.com/CompBiochBiophLab/sbm-openmm/blob/master/tutorials/basic/04-FreeEnergySurface/freeEnergyProfile.ipynb) 59 | 60 | [05 - Setting up a multi-basin SBM](https://github.com/CompBiochBiophLab/sbm-openmm/blob/master/tutorials/basic/05-MultiBasin/multiBasinModel.ipynb) 61 | 62 | ### Applied tutorials 63 | 64 | [01 - Protein Folding](https://github.com/CompBiochBiophLab/sbm-openmm/blob/master/tutorials/folding/01-FoxP1_equilibrium_folding/02-Analysis.ipynb) 65 | -------------------------------------------------------------------------------- /docs/.buildinfo: -------------------------------------------------------------------------------- 1 | # Sphinx build info version 1 2 | # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. 3 | config: 0975fc212ac7abe546c5edb878a5312b 4 | tags: 645f666f9bcd5a90fca523b33c5a78b7 5 | -------------------------------------------------------------------------------- /docs/.nojekyll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/docs/.nojekyll -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SPHINXPROJ = sbmOpenMM 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | 22 | github: 23 | @make html 24 | @cp -a build/html/. ../docs 25 | -------------------------------------------------------------------------------- /docs/build/doctrees/environment.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/docs/build/doctrees/environment.pickle -------------------------------------------------------------------------------- /docs/build/doctrees/index.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/docs/build/doctrees/index.doctree -------------------------------------------------------------------------------- /docs/build/doctrees/sections/introduction.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/docs/build/doctrees/sections/introduction.doctree -------------------------------------------------------------------------------- /docs/build/doctrees/sections/models.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/docs/build/doctrees/sections/models.doctree -------------------------------------------------------------------------------- /docs/build/html/.buildinfo: -------------------------------------------------------------------------------- 1 | # Sphinx build info version 1 2 | # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. 3 | config: 1f0175ccf1934841115e635ed342ff3e 4 | tags: 645f666f9bcd5a90fca523b33c5a78b7 5 | -------------------------------------------------------------------------------- /docs/build/html/.nojekyll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/docs/build/html/.nojekyll -------------------------------------------------------------------------------- /docs/build/html/_modules/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | Overview: module code — sbmOpenMM 0.0.1 documentation 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 |
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All modules for which code is available

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62 | ©2019, "Martin Floor, Kengjie Li". 63 | 64 | | 65 | Powered by Sphinx 2.3.1 66 | & Alabaster 0.7.12 67 | 68 |
69 | 70 | 71 | 72 | 73 | 74 | -------------------------------------------------------------------------------- /docs/build/html/_modules/reporter/sbm_reporter.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | reporter.sbm_reporter — sbmOpenMM 0.0.1 documentation 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 |
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Source code for reporter.sbm_reporter

 35 | #!/usr/bin/env python
 36 | # coding: utf-8
 37 | 
 38 | # In[1]:
 39 | 
 40 | 
 41 | from simtk.openmm.app.statedatareporter import StateDataReporter
 42 | from simtk import unit
 43 | from sbmOpenMM.core import system
 44 | 
 45 | 
 46 | # In[ ]:
 47 | 
 48 | 
 49 | 
[docs]class sbmReporter(StateDataReporter):
 50 |     """
 51 |     A special case of the StateDataReporter class that outputs information about a simulation, 
 52 |     such as energy and temperature, etc. to a file. This special reporter outputs the sbmOpenMM 
 53 |     force group energies inside the sbmOpenMM system object.
 54 |     
 55 |     It is used in the same way as the OpenMM StateDataReporter class, but it takes as additional
 56 |     input an instance of the sbmOpenMM object with the option 'sbmObject'.
 57 |     """
 58 |     
 59 |     def __init__(self, file, reportInterval, sbmObject=None, **kwargs):
 60 |         """
 61 |         Initialises the SBM OpenMM system class.
 62 |         
 63 |         Parameters
 64 |         ----------
 65 |         reportInterval : int
 66 |             The interval (in time steps) at which to write frames
 67 |         sbmObject : sbmOpenMM.system
 68 |             The sbmOpenMM system instance to read force groups from.
 69 |         **kwargs : openMM StateDataReporter arguments
 70 |             
 71 |         Returns
 72 |         -------
 73 |         initialized StateDataReporter class.
 74 |         
 75 |         """
 76 |         super(sbmReporter, self).__init__(file, reportInterval, **kwargs)
 77 |         self._sbmObject = sbmObject
 78 |         
 79 |     def _constructHeaders(self):
 80 |         """
 81 |         Build headers for the StateDataReporter class. It builds the headers
 82 |         for the force groups contained in the sbmOpenMM system instance. 
 83 |         
 84 |         Parameters
 85 |         ----------
 86 |         None
 87 |             
 88 |         Returns
 89 |         -------
 90 |         headers : list
 91 |             List with strings representing the headers to be written to the report file.
 92 |         """
 93 |         
 94 |         headers = super()._constructHeaders()
 95 |         if isinstance(self._sbmObject, system):
 96 |             for i,n in enumerate(self._sbmObject.forceGroups):
 97 |                  headers.append(n+' (kJ/mol)')
 98 |                     
 99 |         return headers
100 |     
101 |     def _constructReportValues(self, simulation, state):
102 |         """
103 |         Calculates the energies for the force groups in the sbmOpenMM system instance.
104 |         
105 |         Parameters
106 |         ----------
107 |         None
108 |             
109 |         Returns
110 |         -------
111 |         values : list
112 |             List with floats representing the values to be written to the report file.
113 |         """
114 |         
115 |         values = super()._constructReportValues(simulation, state)
116 |         
117 |         if isinstance(self._sbmObject, system):
118 |             for i,n in enumerate(self._sbmObject.forceGroups):
119 |                 values.append(simulation.context.getState(getEnergy=True, groups={i}).getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole))
120 |         
121 |         return values

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153 | 154 | 155 | 156 | 157 | 158 | -------------------------------------------------------------------------------- /docs/build/html/_sources/index.rst.txt: -------------------------------------------------------------------------------- 1 | .. sbmOpenMM documentation master file, created by 2 | sphinx-quickstart on Tue Nov 12 10:07:34 2019. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | .. toctree:: 7 | :caption: Contents 8 | :maxdepth: 3 9 | 10 | sbmOpenMM Documentation 11 | ####################### 12 | 13 | Introduction 14 | ************ 15 | 16 | .. include:: sections/introduction.rst 17 | 18 | SBM Models 19 | ********** 20 | 21 | .. include:: sections/models.rst 22 | 23 | Core classes 24 | ============ 25 | 26 | sbmOpenMM.geometry 27 | ------------------ 28 | 29 | .. automodule:: core 30 | :members: geometry 31 | 32 | sbmOpenMM.models 33 | ---------------- 34 | 35 | .. automodule:: core 36 | :noindex: 37 | :members: models 38 | 39 | sbmOpenMM.system 40 | ---------------- 41 | 42 | .. automodule:: core 43 | :noindex: 44 | :members: system 45 | 46 | Reporter class 47 | ============== 48 | 49 | sbmOpenMM.sbmReporter 50 | --------------------- 51 | 52 | .. automodule:: reporter 53 | :members: sbmReporter 54 | 55 | -------------------------------------------------------------------------------- /docs/build/html/_sources/sections/introduction.rst.txt: -------------------------------------------------------------------------------- 1 | Structure Based Models (SBMs) are representations of protein systems based on simplifications made over classical Molecular Dynamics (MD) force fields. Their are based on the energy landscape theory of protein folding and the principle of minimal frustration. The models maintain protein structures by focusing on chemical contacts formed at the native protein configuration, ignoring other non-native contacts. This allows for simpler force field definitions which capture essential protein dynamics at a much lower computational expense than traditional MD simulations. 2 | 3 | sbmOpenMM is a Python library that offers flexibility to set up SBMs using the MD framework of OpenMM toolkit. It automates the creation of openmm.system classes that contain the necessary force field parameters to run molecular dynamics simulations using a protein structure and a contact map as the only necessary inputs. 4 | 5 | sbmOpenMM is divided in three main classes: 6 | 7 | 1. geometry 8 | 2. models 9 | 3. system 10 | 11 | The first class, geometry, contains methods to calculate the geometrical parameters from the input structures. These parameters are used to define the input conformation as the global minimum configuration in the potential energy function. The second class, models, allows to easily set up predefined SBM models, that encompass coarse grained, all atom and multi basin potentials. The third class, system, is the main class that holds all the methods to define, modify and create SBMs to be simulated with OpenMM. 12 | 13 | The library is open-source and offers flexibility to create custom SBMs or to modify the predefined topology based models included in it. 14 | -------------------------------------------------------------------------------- /docs/build/html/_sources/sections/models.rst.txt: -------------------------------------------------------------------------------- 1 | The models class of sbmOpenMM contains three methods for automatic setting up predefined SBM potentials. It works by initializing a system class with the necessary force field parameters, derived from the input files, to set up one of the possible models which are detailed next: 2 | 3 | Coarse grained, alpha-carbon (CA), model 4 | ++++++++++++++++++++++++++++++++++++++++ 5 | 6 | The coarse grained method represents the protein system as beads centered at the alpha carbons of each residue in the protein. It uses harmonic potentials to hold the covalent connectivity and geometry of the beads. Torsional geometries are modeled with a periodic torsion potential. Native contacts are represented through the use of Lennard-Jones potentials that allow to form and break non-bonded interactions, permitting complete and local unfolding of the structures. 7 | 8 | To create a CA model, call: 9 | 10 | sbmOpenMM.models.getCAModel(pdb_file, contacts_file) 11 | 12 | Here, pdb_file is the path to the PDB format structure of the protein and contacts_file is the path to the contact file containing only the CA atoms of the system. This last file should be numbered considering the CA atoms consecutively. 13 | 14 | The force field equations are: 15 | 16 | .. math:: 17 | H_A = \sum_{bonds}V_{bond}+\sum_{angles}V_{angle}+\sum_{torsions}V_{torsion}+\sum_{contacts}V_{LJ_{12-10}}+\sum_{non-contacts}V_{LJ_{12}} 18 | 19 | .. math:: 20 | V_{bond} = \frac{k_b}{2}(r-r_0)^2 21 | 22 | .. math:: 23 | V_{angle} = \frac{k_a}{2}(\theta-\theta_0)^2 24 | 25 | .. math:: 26 | V_{torsion} = k_t(1-cos(\phi-\phi_0))+\frac{1}{2}(1-cos(3(\phi-\phi_0)))) 27 | 28 | .. math:: 29 | V_{LJ_{12-10}} = \epsilon_{c}(5(\frac{\sigma_{ij}}{r})^{12}-6(\frac{\sigma_{ij}}{r})^{10}) 30 | 31 | .. math:: 32 | V_{LJ_{12}} = \epsilon_{nc}(\frac{\sigma_{nc}}{r})^{12} 33 | 34 | 35 | Here the default values are :math:`k_b=20000\ kJ/(mol \cdot nm^2)`, :math:`k_a=40\ kJ/(mol \cdot rad^2)`, :math:`k_t=1.0\ kJ/mol`, :math:`\epsilon_{c}=1.0\ kJ/mol`, :math:`\epsilon_{nc}=1.0\ kJ/mol` and :math:`\sigma_{nc}=0.4\ nm`. The geometric parameters are set to the calculated structural values in the input structure, with :math:`r_0` the equilibrium bond distance in nanometers, :math:`\theta_0` the equilibrium angle length in radians, :math:`\phi_0` the equilibrium torsional angle in radians and :math:`\sigma_{ij}` the equilibrium contact distance in nanometers. The variable :math:`r` represents, accordingly, the current bond or (non)contact distance in nanometers, :math:`\theta` the current angle length in radians and :math:`\phi` the current torsional angle in radians. 36 | 37 | It is possible to use a :math:`V_{LJ_{12-10-6}}` potential for the native contact interactions, defined as: 38 | 39 | .. math:: 40 | V_{LJ_{12-10-6}} = \epsilon_{c}(13(\frac{\sigma_{ij}}{r})^{12}-18(\frac{\sigma_{ij}}{r})^{10}+4(\frac{\sigma_{ij}}{r})^{6}) 41 | 42 | This potential gives a small energy barrier for contact formation/breaking that emulates a "desolvation effect". To use this potential as the native contact energy function, instead of the :math:`V_{LJ_{12-10}}` potential, give the option contact_force ='12-10-6' to the sbmOpenMM.models.getCAModel() method. 43 | 44 | Note that even if the units for the force constants are given in real physical units (e.g. :math:`kJ/mol`), this is just to match the variables used by OpenMM. The models are not parametrized to equate this real physical values and comparison with experiments will require further adjustment to the energy unit system. 45 | 46 | All-heavy-atoms (AA) model 47 | ++++++++++++++++++++++++++ 48 | 49 | The all-atom model represents the protein system with all its heavy atoms (i.e. excluding hydrogens). It uses harmonic potentials to hold the covalent connectivity, geometry and chirality of the protein residues. Periodic torsional potentials are used to maintain dihedral geometries of backbones and side chains. Native contacts are represented through the use of Lennard-Jones potentials that allow to form and break non-bonded interactions, permitting complete and local unfolding of the structures. 50 | 51 | The method to create an AA model is: 52 | 53 | sbmOpenMM.models.getAllAtomModel(pdb_file, contacts_file) 54 | 55 | Here, pdb_file is the path to the PDB format structure of the protein and contacts_file is the path to the contact file containing only the non-hydorgen atoms of the protein system. 56 | 57 | The force field equations are: 58 | 59 | .. math:: 60 | H_A = \sum_{bonds}V_{bond}+\sum_{angles}V_{angle}+\sum_{torsions}V_{torsion}+\sum_{impropers}V_{improper}+\sum_{planars}V_{planar}+\sum_{contacts}V_{LJ_{12-10}}+\sum_{non-contacts}V_{LJ_{12}} 61 | 62 | .. math:: 63 | V_{bond} = \frac{k_b}{2}(r-r_0)^2 64 | 65 | .. math:: 66 | V_{angle} = \frac{k_a}{2}(\theta-\theta_0)^2 67 | 68 | .. math:: 69 | V_{torsion} = k_t(1-cos(\phi-\phi_0))+\frac{1}{2}(1-cos(3(\phi-\phi_0)))) 70 | 71 | .. math:: 72 | V_{improper} = \frac{k_i}{2}(\chi-\chi_{0})^2 73 | 74 | .. math:: 75 | V_{planar} = \frac{k_p}{2}(\chi-\chi_{0})^2 76 | 77 | .. math:: 78 | V_{LJ_{12-10}} = \epsilon_{c}(5(\frac{\sigma_{ij}}{r})^{12}-6(\frac{\sigma_{ij}}{r})^{10}) 79 | 80 | .. math:: 81 | V_{LJ_{12}} = \epsilon_{nc}(\frac{\sigma_{nc}}{r})^{12} 82 | 83 | Here the default values are :math:`k_b=10000\ kJ/(mol \cdot nm^2)`, :math:`k_a=80\ kJ/(mol \cdot rad^2)`, :math:`k_i=10.0\ kJ/(mol \cdot rad^2)`, :math:`k_p=20.0\ kJ/(mol \cdot rad^2)`, :math:`\epsilon_{nc}=0.1\ kJ/mol` and :math:`\sigma_{nc}=0.25\ nm`. The values of the torsional :math:`k_t` and native energy constant :math:`\epsilon_{c}` are assigned by the following equations: 84 | 85 | .. math:: 86 | k_t=N_{atoms}/3N_{torsions}\ (kJ/mol) 87 | .. math:: 88 | k_c=2N_{atoms}/3N_{contacts}\ (kJ/mol) 89 | 90 | 91 | Where :math:`N_{atoms}` is the total number of atoms in the system, :math:`N_{torsions}` is the total number of proper torsions assigned by the forcefield and :math:`N_{contacts}` is the number of native contacts in the contact file definition. Additionally, the torsional energy constant :math:`k_t` is further divided by classifying the torsions into backbone and sidechain groups. The assignment is carried out as: 92 | 93 | .. math:: 94 | k_{t}^{bb}=2k_t/3 95 | .. math:: 96 | k_{t}^{sc}=k_t/3 97 | 98 | Here, :math:`k_{t}^{bb}` and :math:`k_{t}^{sc}` are the torsional energy constant for backbone and sidechain torsion groups, respectively. This grouping of torsions into backbone and side chains is the default behaviour of the sbmOpenMM.models.getAllAtomModel() method. It can be disabled by given the option group_by_bb_and_sc=False. 99 | 100 | The geometric parameters are set to the calculated structural values in the input structure, with :math:`r_0` the equilibrium bond distance in nanometers, :math:`\theta_0` the equilibrium angle length in radians, :math:`\phi_0` the equilibrium torsional angle in radians, :math:`\chi_0` the equilibrium improper or planar equilibrium angle in radians and :math:`\sigma_{ij}` the equilibrium contact distance in nanometers. The variable :math:`r` represents, accordingly, the current bond or (non)contact distance in nanometers, :math:`\theta` the current angle length in radians, :math:`\phi` the current proper torsional angle in radians and :math:`\chi` the equilibrium improper or planar torsional angles in radians. 101 | 102 | Note that even if the units for the force constants are given in real physical units (e.g. :math:`kJ/mol`), this is just to match the variables used by OpenMM. The models are not parametrized to equate this real physical values and comparison with experiments will require further adjustment to the energy unit system. 103 | 104 | Multi basin model 105 | +++++++++++++++++ 106 | 107 | The multi basin model automates the creation of a dual basin native contact potential. It receives as input two sbmOpenMM system classes, either CA or AA models, containing two different definitions of native contacts. One of the configurations is defined as the main model and the other is considered as the alternate model. All forcefield and topology parameters, different than the native contacts, are passed from the main configuration into the multi basin model. Then, the contacts are compared between the input configurations to define the sets of common and unique contacts. Common contacts with equilibrium length distances that differ more than a threshold are defined as dual basin and are assigned a special non-bonded Gaussian potential. The rest of the contacts are treated as single minima and are modeled with a Lennard-Jones (default) or a single basin Gaussian potential. 108 | 109 | The multi basin Gaussian potential is defined as: 110 | 111 | .. math:: 112 | V_{Multi-basin} = \epsilon_{C}((1+(\frac{r_{ex}}{r})^{12})\prod_{minima}G(r,r_{0}^{\alpha})-1) 113 | .. math:: 114 | G(r,r_{0}^{\alpha}) = 1-exp(\frac{-(r-r_{0}^{\alpha})^2}{2\sigma^2}) 115 | 116 | .. math:: 117 | \sigma^{2} = \frac{(r_{0}^{\alpha})^2}{50ln(2)} 118 | 119 | Here, :math:`\epsilon_{C}` is the native contact energy constant inherited from the main configuration, :math:`r_{ex}` is the contact excluded volume radius, :math:`r_{0}^{\alpha}` is the equilibrium distance for the :math:`alpha`-th configuration and :math:`r` is the current contact distance. :math:`\sigma` is a parameter that modulates the well amplitude of the :math:`V_{Multi-basin}` energy function. The single and double basin gaussian potential are distinguished by the number of :math:`r_{0}^{\alpha}` parameters given. 120 | 121 | The Lennard Jones contact potential is inherited accordingly from the CA or AA models used to build the multi basin SBM. 122 | 123 | The method to create a multi basin model is: 124 | 125 | sbmOpenMM.models.getMultiBasinModel(main_model, alternate_configuration=alternate_model) 126 | 127 | Here, main_model and alternate_model are initialized sbmOpenMM system classes containing full force field parameter definitions. 128 | -------------------------------------------------------------------------------- /docs/build/html/_static/custom.css: -------------------------------------------------------------------------------- 1 | /* This file intentionally left blank. */ 2 | -------------------------------------------------------------------------------- /docs/build/html/_static/doctools.js: -------------------------------------------------------------------------------- 1 | /* 2 | * doctools.js 3 | * ~~~~~~~~~~~ 4 | * 5 | * Sphinx JavaScript utilities for all documentation. 6 | * 7 | * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS. 8 | * :license: BSD, see LICENSE for details. 9 | * 10 | */ 11 | 12 | /** 13 | * select a different prefix for underscore 14 | */ 15 | $u = _.noConflict(); 16 | 17 | /** 18 | * make the code below compatible with browsers without 19 | * an installed firebug like debugger 20 | if (!window.console || !console.firebug) { 21 | var names = ["log", "debug", "info", "warn", "error", "assert", "dir", 22 | "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace", 23 | "profile", "profileEnd"]; 24 | window.console = {}; 25 | for (var i = 0; i < names.length; ++i) 26 | window.console[names[i]] = function() {}; 27 | } 28 | */ 29 | 30 | /** 31 | * small helper function to urldecode strings 32 | */ 33 | jQuery.urldecode = function(x) { 34 | return decodeURIComponent(x).replace(/\+/g, ' '); 35 | }; 36 | 37 | /** 38 | * small helper function to urlencode strings 39 | */ 40 | jQuery.urlencode = encodeURIComponent; 41 | 42 | /** 43 | * This function returns the parsed url parameters of the 44 | * current request. 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29 |
30 |
31 | 32 | 33 |
34 | 35 | 36 |

Index

37 | 38 |
39 | A 40 | | B 41 | | C 42 | | G 43 | | P 44 | | R 45 | | S 46 | | T 47 | 48 |
49 |

A

50 | 51 | 55 |
56 | 57 |

B

58 | 59 | 63 |
64 | 65 |

C

66 | 67 | 71 |
72 | 73 |

G

74 | 75 | 79 |
80 | 81 |

P

82 | 83 | 87 |
88 | 89 |

R

90 | 91 | 95 |
96 | 97 |

S

98 | 99 | 103 |
104 | 105 |

T

106 | 107 | 111 |
112 | 113 | 114 | 115 |
116 | 117 |
118 |
119 | 133 |
134 |
135 |
136 | ©2019, "Martin Floor, Kengjie Li". 137 | 138 | | 139 | Powered by Sphinx 2.3.1 140 | & Alabaster 0.7.12 141 | 142 |
143 | 144 | 145 | 146 | 147 | 148 | -------------------------------------------------------------------------------- /docs/build/html/objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/docs/build/html/objects.inv -------------------------------------------------------------------------------- /docs/build/html/py-modindex.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | Python Module Index — sbmOpenMM 0.0.1 documentation 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 29 | 30 | 31 | 32 | 33 | 34 |
35 |
36 |
37 | 38 | 39 |
40 | 41 | 42 |

Python Module Index

43 | 44 |
45 | c | 46 | r 47 |
48 | 49 | 50 | 51 | 53 | 54 | 55 | 58 | 59 | 61 | 62 | 63 | 66 |
 
52 | c
56 | core 57 |
 
60 | r
64 | reporter 65 |
67 | 68 | 69 |
70 | 71 |
72 |
73 | 87 |
88 |
89 |
90 | ©2019, "Martin Floor, Kengjie Li". 91 | 92 | | 93 | Powered by Sphinx 2.3.1 94 | & Alabaster 0.7.12 95 | 96 |
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81 | 82 | 83 | 84 | 85 | 86 | -------------------------------------------------------------------------------- /docs/build/html/searchindex.js: -------------------------------------------------------------------------------- 1 | Search.setIndex({docnames:["index","sections/introduction","sections/models"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.viewcode":1,sphinx:56},filenames:["index.rst","sections/introduction.rst","sections/models.rst"],objects:{"":{core:[0,0,0,"-"],reporter:[0,0,0,"-"]},"core.geometry":{angle:[0,2,1,""],bond:[0,2,1,""],position2Array:[0,2,1,""],torsion:[0,2,1,""]},core:{geometry:[0,1,1,""]},reporter:{sbmReporter:[0,1,1,""]}},objnames:{"0":["py","module","Python module"],"1":["py","class","Python class"],"2":["py","method","Python 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Documentation","<no title>","Coarse grained, alpha-carbon (CA), model"],titleterms:{"class":0,all:[0,2],alpha:[0,2],atom:[0,2],basin:[0,2],carbon:[0,2],coars:[0,2],core:0,document:0,geometri:0,grain:[0,2],heavi:[0,2],introduct:0,model:[0,2],multi:[0,2],report:0,sbm:0,sbmopenmm:0,sbmreport:0,system:0}}) -------------------------------------------------------------------------------- /docs/build/html/sections/introduction.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | <no title> — sbmOpenMM 0.0.1 documentation 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 |
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Structure Based Models (SBMs) are representations of protein systems based on simplifications made over classical Molecular Dynamics (MD) force fields. Their are based on the energy landscape theory of protein folding and the principle of minimal frustration. The models maintain protein structures by focusing on chemical contacts formed at the native protein configuration, ignoring other non-native contacts. This allows for simpler force field definitions which capture essential protein dynamics at a much lower computational expense than traditional MD simulations.

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sbmOpenMM is a Python library that offers flexibility to set up SBMs using the MD framework of OpenMM toolkit. It automates the creation of openmm.system classes that contain the necessary force field parameters to run molecular dynamics simulations using a protein structure and a contact map as the only necessary inputs.

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sbmOpenMM is divided in three main classes:

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  1. geometry

    2. 39 |

  2. models

    3. 40 |

  3. system

    4. 41 |
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The first class, geometry, contains methods to calculate the geometrical parameters from the input structures. These parameters are used to define the input conformation as the global minimum configuration in the potential energy function. The second class, models, allows to easily set up predefined SBM models, that encompass coarse grained, all atom and multi basin potentials. The third class, system, is the main class that holds all the methods to define, modify and create SBMs to be simulated with OpenMM.

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The library is open-source and offers flexibility to create custom SBMs or to modify the predefined topology based models included in it.

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67 | ©2019, "Martin Floor, Kengjie Li". 68 | 69 | | 70 | Powered by Sphinx 2.3.1 71 | & Alabaster 0.7.12 72 | 73 | | 74 | Page source 76 |
77 | 78 | 79 | 80 | 81 | 82 | -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # 3 | # Configuration file for the Sphinx documentation builder. 4 | # 5 | # This file does only contain a selection of the most common options. For a 6 | # full list see the documentation: 7 | # http://www.sphinx-doc.org/en/master/config 8 | 9 | # -- Path setup -------------------------------------------------------------- 10 | 11 | # If extensions (or modules to document with autodoc) are in another directory, 12 | # add these directories to sys.path here. If the directory is relative to the 13 | # documentation root, use os.path.abspath to make it absolute, like shown here. 14 | # 15 | 16 | from sphinx.ext.autosummary import Autosummary 17 | from sphinx.ext.autosummary import get_documenter 18 | from docutils.parsers.rst import directives 19 | from sphinx.util.inspect import safe_getattr 20 | import re 21 | import os 22 | import sys 23 | 24 | sys.path.insert(0, os.path.abspath('../../sbmOpenMM')) 25 | sys.setrecursionlimit(1500) 26 | 27 | # -- Project information ----------------------------------------------------- 28 | 29 | project = 'sbmOpenMM' 30 | copyright = '2019, "Martin Floor, Kengjie Li"' 31 | author = '"Martin Floor, Kengjie Li"' 32 | 33 | # The short X.Y version 34 | version = '' 35 | # The full version, including alpha/beta/rc tags 36 | release = '0.0.1' 37 | 38 | 39 | # -- General configuration --------------------------------------------------- 40 | 41 | # If your documentation needs a minimal Sphinx version, state it here. 42 | # 43 | # needs_sphinx = '1.0' 44 | 45 | # Add any Sphinx extension module names here, as strings. They can be 46 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 47 | # ones. 48 | extensions = [ 49 | 'sphinx.ext.autodoc', 50 | 'sphinx.ext.autosummary', 51 | 'sphinx.ext.intersphinx', 52 | 'sphinx.ext.ifconfig', 53 | 'sphinx.ext.viewcode', 54 | 'sphinx.ext.githubpages', 55 | 'numpydoc' 56 | ] 57 | 58 | # Add any paths that contain templates here, relative to this directory. 59 | templates_path = ['_templates'] 60 | 61 | # The suffix(es) of source filenames. 62 | # You can specify multiple suffix as a list of string: 63 | # 64 | # source_suffix = ['.rst', '.md'] 65 | source_suffix = '.rst' 66 | 67 | # The master toctree document. 68 | master_doc = 'index' 69 | 70 | # The language for content autogenerated by Sphinx. Refer to documentation 71 | # for a list of supported languages. 72 | # 73 | # This is also used if you do content translation via gettext catalogs. 74 | # Usually you set "language" from the command line for these cases. 75 | language = None 76 | 77 | # List of patterns, relative to source directory, that match files and 78 | # directories to ignore when looking for source files. 79 | # This pattern also affects html_static_path and html_extra_path . 80 | exclude_patterns = [] 81 | 82 | # The name of the Pygments (syntax highlighting) style to use. 83 | pygments_style = 'sphinx' 84 | 85 | # If true, the current module name will be prepended to all description unit titles. 86 | add_module_names = False 87 | 88 | # -- Options for HTML output ------------------------------------------------- 89 | 90 | # The theme to use for HTML and HTML Help pages. See the documentation for 91 | # a list of builtin themes. 92 | # 93 | html_theme = 'alabaster' 94 | 95 | # Theme options are theme-specific and customize the look and feel of a theme 96 | # further. For a list of options available for each theme, see the 97 | # documentation. 98 | # 99 | # html_theme_options = {} 100 | 101 | # Add any paths that contain custom static files (such as style sheets) here, 102 | # relative to this directory. They are copied after the builtin static files, 103 | # so a file named "default.css" will overwrite the builtin "default.css". 104 | html_static_path = [] 105 | 106 | # Custom sidebar templates, must be a dictionary that maps document names 107 | # to template names. 108 | # 109 | # The default sidebars (for documents that don't match any pattern) are 110 | # defined by theme itself. Builtin themes are using these templates by 111 | # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', 112 | # 'searchbox.html']``. 113 | # 114 | html_sidebars = { 115 | '**': ['localtoc.html', 'searchbox.html'], 116 | } 117 | 118 | 119 | # -- Options for HTMLHelp output --------------------------------------------- 120 | 121 | # Output file base name for HTML help builder. 122 | htmlhelp_basename = 'sbmOpenMMdoc' 123 | 124 | 125 | # -- Options for LaTeX output ------------------------------------------------ 126 | 127 | latex_elements = { 128 | # The paper size ('letterpaper' or 'a4paper'). 129 | # 130 | # 'papersize': 'letterpaper', 131 | 132 | # The font size ('10pt', '11pt' or '12pt'). 133 | # 134 | # 'pointsize': '10pt', 135 | 136 | # Additional stuff for the LaTeX preamble. 137 | # 138 | # 'preamble': '', 139 | 140 | # Latex figure (float) alignment 141 | # 142 | # 'figure_align': 'htbp', 143 | } 144 | 145 | # Grouping the document tree into LaTeX files. List of tuples 146 | # (source start file, target name, title, 147 | # author, documentclass [howto, manual, or own class]). 148 | latex_documents = [ 149 | (master_doc, 'sbmOpenMM.tex', 'sbmOpenMM Documentation', 150 | '"Martin Floor, Kengjie Li"', 'manual'), 151 | ] 152 | 153 | 154 | # -- Options for manual page output ------------------------------------------ 155 | 156 | # One entry per manual page. List of tuples 157 | # (source start file, name, description, authors, manual section). 158 | man_pages = [ 159 | (master_doc, 'sbmopenmm', 'sbmOpenMM Documentation', 160 | [author], 1) 161 | ] 162 | 163 | 164 | # -- Options for Texinfo output ---------------------------------------------- 165 | 166 | # Grouping the document tree into Texinfo files. List of tuples 167 | # (source start file, target name, title, author, 168 | # dir menu entry, description, category) 169 | texinfo_documents = [ 170 | (master_doc, 'sbmOpenMM', 'sbmOpenMM Documentation', 171 | author, 'sbmOpenMM', 'Python library to run structure based model (SBM) simulations using the OpenMM toolkit.', 172 | 'Miscellaneous'), 173 | ] 174 | 175 | 176 | # -- Options for Epub output ------------------------------------------------- 177 | 178 | # Bibliographic Dublin Core info. 179 | epub_title = project 180 | epub_author = author 181 | epub_publisher = author 182 | epub_copyright = copyright 183 | 184 | # The unique identifier of the text. This can be a ISBN number 185 | # or the project homepage. 186 | # 187 | # epub_identifier = '' 188 | 189 | # A unique identification for the text. 190 | # 191 | # epub_uid = '' 192 | 193 | # A list of files that should not be packed into the epub file. 194 | epub_exclude_files = ['search.html'] 195 | 196 | 197 | # -- Extension configuration ------------------------------------------------- 198 | 199 | # -- Options for intersphinx extension --------------------------------------- 200 | 201 | # Example configuration for intersphinx: refer to the Python standard library. 202 | intersphinx_mapping = {'https://docs.python.org/': None} 203 | 204 | class AutoAutoSummary(Autosummary): 205 | 206 | option_spec = { 207 | 'methods': directives.unchanged, 208 | 'attributes': directives.unchanged 209 | } 210 | 211 | required_arguments = 1 212 | 213 | @staticmethod 214 | def get_members(obj, typ, include_public=None): 215 | if not include_public: 216 | include_public = [] 217 | items = [] 218 | for name in dir(obj): 219 | try: 220 | documenter = get_documenter(safe_getattr(obj, name), obj) 221 | except AttributeError: 222 | continue 223 | if documenter.objtype == typ: 224 | items.append(name) 225 | public = [x for x in items if x in include_public or not x.startswith('_')] 226 | return public, items 227 | 228 | def run(self): 229 | clazz = str(self.arguments[0]) 230 | try: 231 | (module_name, class_name) = clazz.rsplit('.', 1) 232 | m = __import__(module_name, globals(), locals(), [class_name]) 233 | c = getattr(m, class_name) 234 | if 'methods' in self.options: 235 | _, methods = self.get_members(c, 'method', ['__init__']) 236 | 237 | self.content = ["~%s.%s" % (clazz, method) for method in methods if not method.startswith('_')] 238 | if 'attributes' in self.options: 239 | _, attribs = self.get_members(c, 'attribute') 240 | self.content = ["~%s.%s" % (clazz, attrib) for attrib in attribs if not attrib.startswith('_')] 241 | finally: 242 | return super(AutoAutoSummary, self).run() 243 | 244 | def setup(app): 245 | app.add_directive('autoautosummary', AutoAutoSummary) 246 | -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- 1 | .. sbmOpenMM documentation master file, created by 2 | sphinx-quickstart on Tue Nov 12 10:07:34 2019. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | .. toctree:: 7 | :caption: Contents 8 | :maxdepth: 3 9 | 10 | sbmOpenMM Documentation 11 | ####################### 12 | 13 | Introduction 14 | ************ 15 | 16 | .. include:: sections/introduction.rst 17 | 18 | SBM Models 19 | ********** 20 | 21 | .. include:: sections/models.rst 22 | 23 | Core classes 24 | ============ 25 | 26 | sbmOpenMM.geometry 27 | ------------------ 28 | 29 | .. automodule:: core 30 | :members: geometry 31 | 32 | sbmOpenMM.models 33 | ---------------- 34 | 35 | .. automodule:: core 36 | :noindex: 37 | :members: models 38 | 39 | sbmOpenMM.system 40 | ---------------- 41 | 42 | .. automodule:: core 43 | :noindex: 44 | :members: system 45 | 46 | Reporter class 47 | ============== 48 | 49 | sbmOpenMM.sbmReporter 50 | --------------------- 51 | 52 | .. automodule:: reporter 53 | :members: sbmReporter 54 | 55 | -------------------------------------------------------------------------------- /docs/source/sections/introduction.rst: -------------------------------------------------------------------------------- 1 | Structure Based Models (SBMs) are representations of protein systems based on simplifications made over classical Molecular Dynamics (MD) force fields. Their are based on the energy landscape theory of protein folding and the principle of minimal frustration. The models maintain protein structures by focusing on chemical contacts formed at the native protein configuration, ignoring other non-native contacts. This allows for simpler force field definitions which capture essential protein dynamics at a much lower computational expense than traditional MD simulations. 2 | 3 | sbmOpenMM is a Python library that offers flexibility to set up SBMs using the MD framework of OpenMM toolkit. It automates the creation of openmm.system classes that contain the necessary force field parameters to run molecular dynamics simulations using a protein structure and a contact map as the only necessary inputs. 4 | 5 | sbmOpenMM is divided in three main classes: 6 | 7 | 1. geometry 8 | 2. models 9 | 3. system 10 | 11 | The first class, geometry, contains methods to calculate the geometrical parameters from the input structures. These parameters are used to define the input conformation as the global minimum configuration in the potential energy function. The second class, models, allows to easily set up predefined SBM models, that encompass coarse grained, all atom and multi basin potentials. The third class, system, is the main class that holds all the methods to define, modify and create SBMs to be simulated with OpenMM. 12 | 13 | The library is open-source and offers flexibility to create custom SBMs or to modify the predefined topology based models included in it. 14 | -------------------------------------------------------------------------------- /docs/source/sections/models.rst: -------------------------------------------------------------------------------- 1 | The models class of sbmOpenMM contains three methods for automatic setting up predefined SBM potentials. It works by initializing a system class with the necessary force field parameters, derived from the input files, to set up one of the possible models which are detailed next: 2 | 3 | Coarse grained, alpha-carbon (CA), model 4 | ++++++++++++++++++++++++++++++++++++++++ 5 | 6 | The coarse grained method represents the protein system as beads centered at the alpha carbons of each residue in the protein. It uses harmonic potentials to hold the covalent connectivity and geometry of the beads. Torsional geometries are modeled with a periodic torsion potential. Native contacts are represented through the use of Lennard-Jones potentials that allow to form and break non-bonded interactions, permitting complete and local unfolding of the structures. 7 | 8 | To create a CA model, call: 9 | 10 | sbmOpenMM.models.getCAModel(pdb_file, contacts_file) 11 | 12 | Here, pdb_file is the path to the PDB format structure of the protein and contacts_file is the path to the contact file containing only the CA atoms of the system. This last file should be numbered considering the CA atoms consecutively. 13 | 14 | The force field equations are: 15 | 16 | .. math:: 17 | H_A = \sum_{bonds}V_{bond}+\sum_{angles}V_{angle}+\sum_{torsions}V_{torsion}+\sum_{contacts}V_{LJ_{12-10}}+\sum_{non-contacts}V_{LJ_{12}} 18 | 19 | .. math:: 20 | V_{bond} = \frac{k_b}{2}(r-r_0)^2 21 | 22 | .. math:: 23 | V_{angle} = \frac{k_a}{2}(\theta-\theta_0)^2 24 | 25 | .. math:: 26 | V_{torsion} = k_t(1-cos(\phi-\phi_0))+\frac{1}{2}(1-cos(3(\phi-\phi_0)))) 27 | 28 | .. math:: 29 | V_{LJ_{12-10}} = \epsilon_{c}(5(\frac{\sigma_{ij}}{r})^{12}-6(\frac{\sigma_{ij}}{r})^{10}) 30 | 31 | .. math:: 32 | V_{LJ_{12}} = \epsilon_{nc}(\frac{\sigma_{nc}}{r})^{12} 33 | 34 | 35 | Here the default values are :math:`k_b=20000\ kJ/(mol \cdot nm^2)`, :math:`k_a=40\ kJ/(mol \cdot rad^2)`, :math:`k_t=1.0\ kJ/mol`, :math:`\epsilon_{c}=1.0\ kJ/mol`, :math:`\epsilon_{nc}=1.0\ kJ/mol` and :math:`\sigma_{nc}=0.4\ nm`. The geometric parameters are set to the calculated structural values in the input structure, with :math:`r_0` the equilibrium bond distance in nanometers, :math:`\theta_0` the equilibrium angle length in radians, :math:`\phi_0` the equilibrium torsional angle in radians and :math:`\sigma_{ij}` the equilibrium contact distance in nanometers. The variable :math:`r` represents, accordingly, the current bond or (non)contact distance in nanometers, :math:`\theta` the current angle length in radians and :math:`\phi` the current torsional angle in radians. 36 | 37 | It is possible to use a :math:`V_{LJ_{12-10-6}}` potential for the native contact interactions, defined as: 38 | 39 | .. math:: 40 | V_{LJ_{12-10-6}} = \epsilon_{c}(13(\frac{\sigma_{ij}}{r})^{12}-18(\frac{\sigma_{ij}}{r})^{10}+4(\frac{\sigma_{ij}}{r})^{6}) 41 | 42 | This potential gives a small energy barrier for contact formation/breaking that emulates a "desolvation effect". To use this potential as the native contact energy function, instead of the :math:`V_{LJ_{12-10}}` potential, give the option contact_force ='12-10-6' to the sbmOpenMM.models.getCAModel() method. 43 | 44 | Note that even if the units for the force constants are given in real physical units (e.g. :math:`kJ/mol`), this is just to match the variables used by OpenMM. The models are not parametrized to equate this real physical values and comparison with experiments will require further adjustment to the energy unit system. 45 | 46 | All-heavy-atoms (AA) model 47 | ++++++++++++++++++++++++++ 48 | 49 | The all-atom model represents the protein system with all its heavy atoms (i.e. excluding hydrogens). It uses harmonic potentials to hold the covalent connectivity, geometry and chirality of the protein residues. Periodic torsional potentials are used to maintain dihedral geometries of backbones and side chains. Native contacts are represented through the use of Lennard-Jones potentials that allow to form and break non-bonded interactions, permitting complete and local unfolding of the structures. 50 | 51 | The method to create an AA model is: 52 | 53 | sbmOpenMM.models.getAllAtomModel(pdb_file, contacts_file) 54 | 55 | Here, pdb_file is the path to the PDB format structure of the protein and contacts_file is the path to the contact file containing only the non-hydorgen atoms of the protein system. 56 | 57 | The force field equations are: 58 | 59 | .. math:: 60 | H_A = \sum_{bonds}V_{bond}+\sum_{angles}V_{angle}+\sum_{torsions}V_{torsion}+\sum_{impropers}V_{improper}+\sum_{planars}V_{planar}+\sum_{contacts}V_{LJ_{12-10}}+\sum_{non-contacts}V_{LJ_{12}} 61 | 62 | .. math:: 63 | V_{bond} = \frac{k_b}{2}(r-r_0)^2 64 | 65 | .. math:: 66 | V_{angle} = \frac{k_a}{2}(\theta-\theta_0)^2 67 | 68 | .. math:: 69 | V_{torsion} = k_t(1-cos(\phi-\phi_0))+\frac{1}{2}(1-cos(3(\phi-\phi_0)))) 70 | 71 | .. math:: 72 | V_{improper} = \frac{k_i}{2}(\chi-\chi_{0})^2 73 | 74 | .. math:: 75 | V_{planar} = \frac{k_p}{2}(\chi-\chi_{0})^2 76 | 77 | .. math:: 78 | V_{LJ_{12-10}} = \epsilon_{c}(5(\frac{\sigma_{ij}}{r})^{12}-6(\frac{\sigma_{ij}}{r})^{10}) 79 | 80 | .. math:: 81 | V_{LJ_{12}} = \epsilon_{nc}(\frac{\sigma_{nc}}{r})^{12} 82 | 83 | Here the default values are :math:`k_b=10000\ kJ/(mol \cdot nm^2)`, :math:`k_a=80\ kJ/(mol \cdot rad^2)`, :math:`k_i=10.0\ kJ/(mol \cdot rad^2)`, :math:`k_p=20.0\ kJ/(mol \cdot rad^2)`, :math:`\epsilon_{nc}=0.1\ kJ/mol` and :math:`\sigma_{nc}=0.25\ nm`. The values of the torsional :math:`k_t` and native energy constant :math:`\epsilon_{c}` are assigned by the following equations: 84 | 85 | .. math:: 86 | k_t=N_{atoms}/3N_{torsions}\ (kJ/mol) 87 | .. math:: 88 | k_c=2N_{atoms}/3N_{contacts}\ (kJ/mol) 89 | 90 | 91 | Where :math:`N_{atoms}` is the total number of atoms in the system, :math:`N_{torsions}` is the total number of proper torsions assigned by the forcefield and :math:`N_{contacts}` is the number of native contacts in the contact file definition. Additionally, the torsional energy constant :math:`k_t` is further divided by classifying the torsions into backbone and sidechain groups. The assignment is carried out as: 92 | 93 | .. math:: 94 | k_{t}^{bb}=2k_t/3 95 | .. math:: 96 | k_{t}^{sc}=k_t/3 97 | 98 | Here, :math:`k_{t}^{bb}` and :math:`k_{t}^{sc}` are the torsional energy constant for backbone and sidechain torsion groups, respectively. This grouping of torsions into backbone and side chains is the default behaviour of the sbmOpenMM.models.getAllAtomModel() method. It can be disabled by given the option group_by_bb_and_sc=False. 99 | 100 | The geometric parameters are set to the calculated structural values in the input structure, with :math:`r_0` the equilibrium bond distance in nanometers, :math:`\theta_0` the equilibrium angle length in radians, :math:`\phi_0` the equilibrium torsional angle in radians, :math:`\chi_0` the equilibrium improper or planar equilibrium angle in radians and :math:`\sigma_{ij}` the equilibrium contact distance in nanometers. The variable :math:`r` represents, accordingly, the current bond or (non)contact distance in nanometers, :math:`\theta` the current angle length in radians, :math:`\phi` the current proper torsional angle in radians and :math:`\chi` the equilibrium improper or planar torsional angles in radians. 101 | 102 | Note that even if the units for the force constants are given in real physical units (e.g. :math:`kJ/mol`), this is just to match the variables used by OpenMM. The models are not parametrized to equate this real physical values and comparison with experiments will require further adjustment to the energy unit system. 103 | 104 | Multi basin model 105 | +++++++++++++++++ 106 | 107 | The multi basin model automates the creation of a dual basin native contact potential. It receives as input two sbmOpenMM system classes, either CA or AA models, containing two different definitions of native contacts. One of the configurations is defined as the main model and the other is considered as the alternate model. All forcefield and topology parameters, different than the native contacts, are passed from the main configuration into the multi basin model. Then, the contacts are compared between the input configurations to define the sets of common and unique contacts. Common contacts with equilibrium length distances that differ more than a threshold are defined as dual basin and are assigned a special non-bonded Gaussian potential. The rest of the contacts are treated as single minima and are modeled with a Lennard-Jones (default) or a single basin Gaussian potential. 108 | 109 | The multi basin Gaussian potential is defined as: 110 | 111 | .. math:: 112 | V_{Multi-basin} = \epsilon_{C}((1+(\frac{r_{ex}}{r})^{12})\prod_{minima}G(r,r_{0}^{\alpha})-1) 113 | .. math:: 114 | G(r,r_{0}^{\alpha}) = 1-exp(\frac{-(r-r_{0}^{\alpha})^2}{2\sigma^2}) 115 | 116 | .. math:: 117 | \sigma^{2} = \frac{(r_{0}^{\alpha})^2}{50ln(2)} 118 | 119 | Here, :math:`\epsilon_{C}` is the native contact energy constant inherited from the main configuration, :math:`r_{ex}` is the contact excluded volume radius, :math:`r_{0}^{\alpha}` is the equilibrium distance for the :math:`alpha`-th configuration and :math:`r` is the current contact distance. :math:`\sigma` is a parameter that modulates the well amplitude of the :math:`V_{Multi-basin}` energy function. The single and double basin gaussian potential are distinguished by the number of :math:`r_{0}^{\alpha}` parameters given. 120 | 121 | The Lennard Jones contact potential is inherited accordingly from the CA or AA models used to build the multi basin SBM. 122 | 123 | The method to create a multi basin model is: 124 | 125 | sbmOpenMM.models.getMultiBasinModel(main_model, alternate_configuration=alternate_model) 126 | 127 | Here, main_model and alternate_model are initialized sbmOpenMM system classes containing full force field parameter definitions. 128 | -------------------------------------------------------------------------------- /sbmOpenMM/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Python library to run structure based model (SBM) simulations using the OpenMM toolkit 3 | 4 | 5 | sbmOpenMM is a Python library to run protein structure-based model (SBM) simulations using OpenMM toolkit. The library offers flexibility for creating SBM force fields that can be customised to capture different aspects of protein SBM potential energy exploration. 6 | 7 | Considering an input structure, the library automatizes the creation of forces to specify it as the only minimum configuration in the potential energy function. Bonds, angles and torsions are maintained close to their equilibrium configuration, while native contact interactions are allowed to form and break using regular or modified Lennard-Jones potentials. This allows complete and local protein unfolding, restricting the interactions only to the evolutionarily relevant chemical contacts, to explore more thoroughly the relevant configurational space of protein folding and function. 8 | 9 | Different granularities for the models can be selected as All-heavy-Atom and alpha-carbon representations. These basic models can also be extended to multi-basin potentials employing more than one input configuration. Here, shared native contacts are modeled with special Gaussian functions to allow for more than one equilibrium distance. 10 | 11 | The library offers methods to tailor forcefield parameter for each force term. Combining these basic methods and force implementations, sbmOpenMM offers easy set up of more complex force field definition that can aid in a better exploration of different biophysical phenomena. 12 | 13 | sbmOpenMM is divided in three main classes: 14 | 15 | 1. geometry 16 | 17 | 2. models 18 | 19 | 3. system 20 | 21 | The first class, geometry, contains methods to calculate the geometrical parameters from the input structures. These parameters are used to define the input conformation as the global minimum configuration in the potential energy function. The second class, models, allows to easily set up predefined SBM models, that encompass coarse grained, all atom and multi basin potentials. The third class, system, is the main class that holds all the methods to define, modify and create SBMs to be simulated with OpenMM. 22 | 23 | The library is open-source and offers flexibility to create custom SBMs or to modify the predefined topology based models included in it. 24 | """ 25 | 26 | from .core import geometry 27 | from .core import system 28 | from .core import models 29 | 30 | from .reporter import sbmReporter 31 | from .parameters import oplsaa 32 | from .parameters import amber 33 | from .parameters import ca_parameters 34 | 35 | from . import datasets 36 | -------------------------------------------------------------------------------- /sbmOpenMM/core/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | core package of the sbmOpenMM package that contains the main sbmOpenMM classes. 3 | 4 | The sbmOpenMM.core package contains the three sbmOpenMM main classes: 5 | 6 | 1. geometry 7 | 8 | 2. models 9 | 10 | 3. system 11 | 12 | The first class, geometry, contains methods to calculate the geometrical parameters from the input structures. These parameters are used to define the input conformation as the global minimum configuration in the potential energy function. The second class, models, allows to easily set up predefined SBM models, that encompass coarse grained, all atom and multi basin potentials. The third class, system, is the main class that holds all the methods to define, modify and create SBMs to be simulated with OpenMM. 13 | 14 | """ 15 | 16 | from .geometry import geometry 17 | from .models import models 18 | from .system import system 19 | -------------------------------------------------------------------------------- /sbmOpenMM/core/geometry.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # coding: utf-8 3 | 4 | # In[ ]: 5 | 6 | 7 | from simtk import unit 8 | import numpy as np 9 | 10 | class geometry: 11 | """ 12 | A class to hold methods for calculating geometrical values 13 | given sets of atom coordinates. 14 | """ 15 | 16 | def position2Array(position, output_unit): 17 | """Converts an OpenMM position object quantity into a numpy array. 18 | 19 | Parameters 20 | ---------- 21 | position : simtk.unit.quantity.Quantity 22 | Array containing quantity objects [e.g. (x,y,z) array returned 23 | from positions]. 24 | output_unit : simtk.unit.unit.Unit 25 | Unit in which to return the items of the array. 26 | 27 | Returns 28 | ------- 29 | numpy.ndarray 30 | A numpy array containing the quantity values converted to floats. 31 | """ 32 | 33 | return np.array([c.value_in_unit(output_unit) for c in position]) 34 | 35 | def bond(coord1, coord2): 36 | """Calculate the distance length between two (x,y,z) quantity coordinates. 37 | 38 | Parameters 39 | ---------- 40 | coord1 : simtk.unit.quantity.Quantity array 41 | Vector for the first coordinate. 42 | coord2 : simtk.unit.quantity.Quantity array 43 | Vector for the second coordinate. 44 | 45 | Returns 46 | ------- 47 | simtk.unit.quantity.Quantity 48 | Quantity (value and unit) of the distance length in nanometers. 49 | """ 50 | 51 | coord1 = geometry.position2Array(coord1, unit.nanometer) 52 | 53 | coord2 = geometry.position2Array(coord2, unit.nanometer) 54 | 55 | bond_length = np.linalg.norm(coord2 - coord1) 56 | 57 | return bond_length * unit.nanometer 58 | 59 | def angle(coord1, coord2, coord3): 60 | """Calculate the angle length between three (x,y,z) quantity coordinates. 61 | 62 | Parameters 63 | ---------- 64 | coord1 : simtk.unit.quantity.Quantity array 65 | Vector for the first coordinate. 66 | coord2 : simtk.unit.quantity.Quantity array 67 | Vector for the second coordinate. 68 | coord3 : simtk.unit.quantity.Quantity array 69 | Vector for the third coordinate. 70 | 71 | Returns 72 | ------- 73 | simtk.unit.quantity.Quantity 74 | Quantity (value and unit) of the angle length in radians. 75 | """ 76 | 77 | coord1 = geometry.position2Array(coord1, unit.nanometer) 78 | coord2 = geometry.position2Array(coord2, unit.nanometer) 79 | coord3 = geometry.position2Array(coord3, unit.nanometer) 80 | 81 | v1 = coord1 - coord2 82 | v2 = coord3 - coord2 83 | cos_theta = np.dot(v1, v2)/(np.linalg.norm(v1)*np.linalg.norm(v2)) 84 | angle = np.arccos(np.clip(cos_theta, -1, 1)) 85 | 86 | return angle * unit.radian 87 | 88 | def torsion(coord1, coord2, coord3, coord4): 89 | """Calculate the torsion angle length between four (x,y,z) quantity 90 | coordinates. 91 | 92 | Parameters 93 | ---------- 94 | coord1 : simtk.unit.quantity.Quantity array 95 | Vector for the first coordinate. 96 | coord2 : simtk.unit.quantity.Quantity array 97 | Vector for the second coordinate. 98 | coord3 : simtk.unit.quantity.Quantity array 99 | Vector for the third coordinate. 100 | coord4 : simtk.unit.quantity.Quantity array 101 | Vector for the fourth coordinate. 102 | 103 | Returns 104 | ------- 105 | simtk.unit.quantity.Quantity 106 | Quantity (value and unit) of the torsion length in radians. 107 | """ 108 | 109 | coord1 = geometry.position2Array(coord1, unit.nanometer) 110 | coord2 = geometry.position2Array(coord2, unit.nanometer) 111 | coord3 = geometry.position2Array(coord3, unit.nanometer) 112 | coord4 = geometry.position2Array(coord4, unit.nanometer) 113 | 114 | v1 = coord2 - coord1 115 | v2 = coord3 - coord2 116 | v3 = coord4 - coord3 117 | 118 | c1 = np.cross(v2, v3) 119 | c2 = np.cross(v1, v2) 120 | 121 | p1 = (v1 * c1).sum(-1) 122 | p1 *= (v2 * v2).sum(-1) ** 0.5 123 | p2 = (c1 * c2).sum(-1) 124 | 125 | return np.arctan2(p1, p2) * unit.radian 126 | 127 | -------------------------------------------------------------------------------- /sbmOpenMM/datasets/__init__.py: -------------------------------------------------------------------------------- 1 | from . import foxp1_folding 2 | -------------------------------------------------------------------------------- /sbmOpenMM/datasets/downloader.py: -------------------------------------------------------------------------------- 1 | import requests 2 | from tqdm import tqdm 3 | 4 | def get_file_from_url(url, filename): 5 | 6 | r = requests.get(url, stream=True) 7 | 8 | file_size = int(r.headers.get('content-length', 0)) 9 | initial_pos = 0 10 | 11 | with open(filename, 'wb') as f: 12 | with tqdm(total=file_size, unit='B', 13 | unit_scale=True, unit_divisor=1024, 14 | desc=filename, initial=initial_pos, 15 | ascii=True, miniters=1) as pbar: 16 | for chunk in r.iter_content(32 * 1024): 17 | f.write(chunk) 18 | pbar.update(len(chunk)) 19 | -------------------------------------------------------------------------------- /sbmOpenMM/datasets/foxp1_folding.py: -------------------------------------------------------------------------------- 1 | import os 2 | import shutil 3 | from .downloader import get_file_from_url 4 | 5 | def download_dataset(output_dir, dcd_only=False, data_only=False, overwrite=False): 6 | """ 7 | Download the dataset in the specified location. 8 | 9 | Parameters 10 | ========== 11 | output_dir : str 12 | Path to the output directory where to store the files. 13 | dcd_only : bool 14 | Get only DCD trajectories files? 15 | data_only : bool 16 | Get only energy DATA files? 17 | overwrite : bool 18 | Delete and replace all dataset files? 19 | """ 20 | 21 | dcd = True 22 | data = True 23 | if dcd_only: 24 | if data_only: 25 | raise ValueError('Only one option must be given (dcd_only of data_only?)') 26 | data = False 27 | dcd = True 28 | 29 | if data_only: 30 | if dcd_only: 31 | raise ValueError('Only one option must be given (dcd_only of data_only?)') 32 | data = True 33 | dcd = False 34 | 35 | # Create output directory if it does not exists 36 | if os.path.exists(output_dir): 37 | if overwrite: 38 | shutil.rmtree(output_dir) 39 | os.mkdir(output_dir) 40 | else: 41 | os.mkdir(output_dir) 42 | 43 | if data: 44 | data_paths = pathsToDATAfiles() 45 | for p in data_paths: 46 | get_file_from_url(data_paths[p], output_dir+'/'+p) 47 | 48 | if dcd: 49 | dcd_paths = pathsToDCDfiles() 50 | for p in dcd_paths: 51 | get_file_from_url(dcd_paths[p], output_dir+'/'+p) 52 | 53 | def pathsToDCDfiles(): 54 | """ 55 | Method to contain paths to DCD files in the dataset 56 | """ 57 | doi = 'https://dataverse.csuc.cat/api/access/datafile/:persistentId?persistentId=doi:10.34810/data31/' 58 | # Get DCD files permanent links 59 | dcd_suffix = '_trajectory.dcd' 60 | dcd_paths = { '01':'32','02':'33','03':'37','04':'36','05':'35','06':'39', 61 | '07':'38','08':'40','09':'41','10':'42','11':'43','12':'44', 62 | '13':'45','14':'60','15':'46'} 63 | return {p+dcd_suffix:doi+dcd_paths[p] for p in dcd_paths} 64 | 65 | def pathsToDATAfiles(): 66 | """ 67 | Method to contain paths to DATA files in the dataset 68 | """ 69 | doi = 'https://dataverse.csuc.cat/api/access/datafile/:persistentId?persistentId=doi:10.34810/data31/' 70 | # Get DATA energy files permanent links 71 | data_suffix = '_energies.data' 72 | data_paths = { '01':'24','02':'16','03':'6','04':'18','05':'3','06':'11', 73 | '07':'28','08':'20','09':'4','10':'7','11':'26','12':'1', 74 | '13':'8','14':'14','15':'23'} 75 | return {p+data_suffix:doi+data_paths[p] for p in data_paths} 76 | -------------------------------------------------------------------------------- /sbmOpenMM/parameters/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/sbmOpenMM/parameters/__init__.py -------------------------------------------------------------------------------- /sbmOpenMM/parameters/ca_parameters.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # coding: utf-8 3 | 4 | aa_masses = {'ALA': 71.0, 'ARG': 157.0, 'ASN': 114.0, 5 | 'ASP': 114.0, 'CYS': 103.0, 'GLU': 128.0, 6 | 'GLN': 128.0, 'GLY': 57.0, 'HIS': 138.0, 7 | 'ILE': 113.0, 'LEU': 113.0, 'LYS': 128.0, 8 | 'MET': 131.0, 'PHE': 147.0, 'PRO': 97.0, 9 | 'SER': 87.0, 'THR': 101.0, 'TRP': 186.0, 10 | 'TYR': 163.0, 'VAL': 99.0} 11 | 12 | aa_radii = {'ALA': 0.335, 'ARG': 0.395, 'ASN': 0.365, 13 | 'ASP': 0.350, 'CYS': 0.370, 'GLU': 0.365, 14 | 'GLN': 0.390, 'GLY': 0.315, 'HIS': 0.400, 15 | 'ILE': 0.450, 'LEU': 0.460, 'LYS': 0.365, 16 | 'MET': 0.450, 'PHE': 0.460, 'PRO': 0.370, 17 | 'SER': 0.330, 'THR': 0.360, 'TRP': 0.470, 18 | 'TYR': 0.450, 'VAL': 0.400} 19 | 20 | -------------------------------------------------------------------------------- /sbmOpenMM/reporter/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | reporter package of the sbmOpenMM package that contains the sbmReporter class. 3 | 4 | The sbmOpenMM.reproter package contains the sbmReporter class. 5 | 6 | sbmReporter is a special class of the OpenMM StateDataReporter class, that additionally 7 | accepts a sbmobject to print the SBM forcefield energies. 8 | """ 9 | 10 | from .sbm_reporter import sbmReporter 11 | from .sbm_reporter import readOpenMMReporterFile 12 | -------------------------------------------------------------------------------- /sbmOpenMM/reporter/sbm_reporter.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # coding: utf-8 3 | 4 | from simtk.openmm.app import statedatareporter 5 | StateDataReporter = statedatareporter.StateDataReporter 6 | from simtk import unit 7 | from sbmOpenMM.core import system 8 | 9 | class sbmReporter(StateDataReporter): 10 | """ 11 | A special case of the StateDataReporter class that outputs information about a simulation, 12 | such as energy and temperature, etc. to a file. This special reporter outputs the sbmOpenMM 13 | force group energies inside the sbmOpenMM system object. 14 | 15 | It is used in the same way as the OpenMM StateDataReporter class, but it takes as additional 16 | input an instance of the sbmOpenMM object with the option 'sbmObject'. 17 | """ 18 | 19 | def __init__(self, file, reportInterval, sbmObject=None, **kwargs): 20 | """ 21 | Initialises the SBM OpenMM system class. 22 | 23 | Parameters 24 | ---------- 25 | reportInterval : int 26 | The interval (in time steps) at which to write frames 27 | sbmObject : sbmOpenMM.system 28 | The sbmOpenMM system instance to read force groups from. 29 | **kwargs : openMM StateDataReporter arguments 30 | 31 | Returns 32 | ------- 33 | initialized StateDataReporter class. 34 | 35 | """ 36 | super(sbmReporter, self).__init__(file, reportInterval, **kwargs) 37 | self._sbmObject = sbmObject 38 | 39 | def _constructHeaders(self): 40 | """ 41 | Build headers for the StateDataReporter class. It builds the headers 42 | for the force groups contained in the sbmOpenMM system instance. 43 | 44 | Parameters 45 | ---------- 46 | None 47 | 48 | Returns 49 | ------- 50 | headers : list 51 | List with strings representing the headers to be written to the report file. 52 | """ 53 | 54 | headers = super()._constructHeaders() 55 | if isinstance(self._sbmObject, system): 56 | for i,n in enumerate(self._sbmObject.forceGroups): 57 | headers.append(n+' (kJ/mol)') 58 | 59 | return headers 60 | 61 | def _constructReportValues(self, simulation, state): 62 | """ 63 | Calculates the energies for the force groups in the sbmOpenMM system instance. 64 | 65 | Parameters 66 | ---------- 67 | None 68 | 69 | Returns 70 | ------- 71 | values : list 72 | List with floats representing the values to be written to the report file. 73 | """ 74 | 75 | values = super()._constructReportValues(simulation, state) 76 | 77 | if isinstance(self._sbmObject, system): 78 | for i,n in enumerate(self._sbmObject.forceGroups): 79 | values.append(simulation.context.getState(getEnergy=True, groups={i}).getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole)) 80 | 81 | return values 82 | 83 | def readOpenMMReporterFile(reporter_file): 84 | """ 85 | Creates a dictionary containing all the entries in the reported data reporter_file 86 | 87 | Parameters 88 | ---------- 89 | reporter_file : str 90 | Path to the reporter output file 91 | 92 | """ 93 | with open(reporter_file, 'r') as ef: 94 | lines = ef.readlines() 95 | data = {} 96 | for r in lines[0].split(','): 97 | data[r.replace('#','').replace('"','').strip()] = [] 98 | for i,r in enumerate(data): 99 | for line in lines[1:]: 100 | data[r].append(float(line.strip().split(',')[i])) 101 | return data 102 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | import setuptools 2 | 3 | with open("README.md", "r") as fh: 4 | long_description = fh.read() 5 | 6 | setuptools.setup( 7 | name="sbmOpenMM", 8 | version="1.0.0", 9 | author="Martin Floor, Kengjie Li", 10 | author_email="martinfloor@gmail.com", 11 | description="An OpenMM package for simulating protein Structure Based Models.", 12 | long_description=long_description, 13 | long_description_content_type="text/markdown", 14 | url="https://github.com/CompBiochBiophLab/sbm-openmm", 15 | packages=setuptools.find_packages(), 16 | classifiers=[ 17 | "Programming Language :: Python :: 3", 18 | "License :: OSI Approved :: MIT License", 19 | "Operating System :: OS Independent", 20 | ], 21 | python_requires='>=3.6', 22 | install_requires=[ 23 | 'numpy>=1.15', 24 | ], 25 | ) 26 | -------------------------------------------------------------------------------- /tutorials/basic/01-AlphaCarbon/inputs/1YPA_I_CA.contacts: -------------------------------------------------------------------------------- 1 | 1 1 1 63 2 | 1 1 1 24 3 | 1 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11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | heatCapacityData/135.data 21 | 22 | 23 | 24 | V 25 | 26 | heatCapacityData/136.data 27 | 28 | 29 | 30 | V 31 | 32 | heatCapacityData/137.data 33 | 34 | 35 | 36 | V 37 | 38 | heatCapacityData/138.data 39 | 40 | 41 | 42 | V 43 | 44 | heatCapacityData/139.data 45 | 46 | 47 | 48 | V 49 | 50 | heatCapacityData/140.data 51 | 52 | 53 | 54 | V 55 | 56 | heatCapacityData/141.data 57 | 58 | 59 | 60 | V 61 | 62 | heatCapacityData/142.data 63 | 64 | 65 | 66 | V 67 | 68 | heatCapacityData/143.data 69 | 70 | 71 | 72 | V 73 | 74 | heatCapacityData/144.data 75 | 76 | 77 | 78 | V 79 | 80 | heatCapacityData/145.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_hc_rough_estimate.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | heatCapacityData/100_rough.data 21 | 22 | 23 | 24 | V 25 | 26 | heatCapacityData/105_rough.data 27 | 28 | 29 | 30 | V 31 | 32 | heatCapacityData/110_rough.data 33 | 34 | 35 | 36 | V 37 | 38 | heatCapacityData/115_rough.data 39 | 40 | 41 | 42 | V 43 | 44 | heatCapacityData/120_rough.data 45 | 46 | 47 | 48 | V 49 | 50 | heatCapacityData/125_rough.data 51 | 52 | 53 | 54 | V 55 | 56 | heatCapacityData/130_rough.data 57 | 58 | 59 | 60 | V 61 | 62 | heatCapacityData/135_rough.data 63 | 64 | 65 | 66 | V 67 | 68 | heatCapacityData/140_rough.data 69 | 70 | 71 | 72 | V 73 | 74 | heatCapacityData/145_rough.data 75 | 76 | 77 | 78 | V 79 | 80 | heatCapacityData/150_rough.data 81 | 82 | 83 | 84 | V 85 | 86 | heatCapacityData/155_rough.data 87 | 88 | 89 | 90 | V 91 | 92 | heatCapacityData/160_rough.data 93 | 94 | 95 | 96 | V 97 | 98 | heatCapacityData/165_rough.data 99 | 100 | 101 | 102 | V 103 | 104 | heatCapacityData/170_rough.data 105 | 106 | 107 | 108 | V 109 | 110 | heatCapacityData/175_rough.data 111 | 112 | 113 | 114 | V 115 | 116 | heatCapacityData/180_rough.data 117 | 118 | 119 | 120 | V 121 | 122 | heatCapacityData/185_rough.data 123 | 124 | 125 | 126 | V 127 | 128 | heatCapacityData/190_rough.data 129 | 130 | 131 | 132 | V 133 | 134 | heatCapacityData/195_rough.data 135 | 136 | 137 | 138 | V 139 | 140 | heatCapacityData/200_rough.data 141 | 142 | 143 | 144 | 145 | 146 | V 147 | 100,105,110,115,120,125,130,135,140,145,150,155,160,165,170,175,180,185,190,195,200 148 | 149 | 150 | 151 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_01.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_01.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_01.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_01.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_01.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_01.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_01.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_01.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_01.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_01.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_01.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_01.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_02.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_02.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_02.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_02.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_02.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_02.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_02.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_02.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_02.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_02.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_02.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_02.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_03.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_03.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_03.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_03.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_03.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_03.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_03.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_03.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_03.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_03.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_03.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_03.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_04.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_04.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_04.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_04.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_04.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_04.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_04.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_04.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_04.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_04.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_04.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_04.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_05.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_05.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_05.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_05.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_05.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_05.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_05.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_05.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_05.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_05.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_05.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_05.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_06.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_06.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_06.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_06.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_06.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_06.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_06.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_06.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_06.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_06.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_06.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_06.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_07.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_07.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_07.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_07.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_07.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_07.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_07.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_07.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_07.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_07.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_07.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_07.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_08.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_08.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_08.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_08.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_08.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_08.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_08.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_08.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_08.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_08.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_08.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_08.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_09.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_09.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_09.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_09.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_09.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_09.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_09.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_09.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_09.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_09.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_09.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_09.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/03-FoldingTemperature/inputs/pywham_iterative_10.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 0.1 13 | 14 | 15 | 16 | 17 | 18 | V 19 | 20 | iterativeHeatCapacityData/energy_135_time_10.data 21 | 22 | 23 | 24 | V 25 | 26 | iterativeHeatCapacityData/energy_136_time_10.data 27 | 28 | 29 | 30 | V 31 | 32 | iterativeHeatCapacityData/energy_137_time_10.data 33 | 34 | 35 | 36 | V 37 | 38 | iterativeHeatCapacityData/energy_138_time_10.data 39 | 40 | 41 | 42 | V 43 | 44 | iterativeHeatCapacityData/energy_139_time_10.data 45 | 46 | 47 | 48 | V 49 | 50 | iterativeHeatCapacityData/energy_140_time_10.data 51 | 52 | 53 | 54 | V 55 | 56 | iterativeHeatCapacityData/energy_141_time_10.data 57 | 58 | 59 | 60 | V 61 | 62 | iterativeHeatCapacityData/energy_142_time_10.data 63 | 64 | 65 | 66 | V 67 | 68 | iterativeHeatCapacityData/energy_143_time_10.data 69 | 70 | 71 | 72 | V 73 | 74 | iterativeHeatCapacityData/energy_144_time_10.data 75 | 76 | 77 | 78 | V 79 | 80 | iterativeHeatCapacityData/energy_145_time_10.data 81 | 82 | 83 | 84 | 85 | 86 | V 87 | 135,136,137,138,139,140,141,142,143,144,145 88 | 89 | 90 | 91 | -------------------------------------------------------------------------------- /tutorials/basic/04-FreeEnergySurface/inputs/1YPA_I_CA.contacts: -------------------------------------------------------------------------------- 1 | 1 1 1 63 2 | 1 1 1 24 3 | 1 1 1 44 4 | 1 1 1 42 5 | 1 2 1 23 6 | 1 2 1 24 7 | 1 2 1 63 8 | 1 2 1 6 9 | 1 2 1 7 10 | 1 2 1 19 11 | 1 3 1 63 12 | 1 3 1 61 13 | 1 3 1 62 14 | 1 3 1 42 15 | 1 4 1 61 16 | 1 4 1 62 17 | 1 4 1 60 18 | 1 5 1 60 19 | 1 5 1 61 20 | 1 5 1 9 21 | 1 5 1 19 22 | 1 5 1 20 23 | 1 5 1 23 24 | 1 5 1 24 25 | 1 5 1 47 26 | 1 5 1 62 27 | 1 5 1 63 28 | 1 6 1 60 29 | 1 7 1 11 30 | 1 7 1 19 31 | 1 7 1 23 32 | 1 8 1 61 33 | 1 8 1 16 34 | 1 8 1 57 35 | 1 8 1 59 36 | 1 8 1 19 37 | 1 8 1 15 38 | 1 8 1 20 39 | 1 9 1 61 40 | 1 9 1 57 41 | 1 9 1 59 42 | 1 9 1 58 43 | 1 9 1 60 44 | 1 10 1 57 45 | 1 10 1 56 46 | 1 11 1 57 47 | 1 11 1 16 48 | 1 11 1 51 49 | 1 11 1 55 50 | 1 11 1 56 51 | 1 11 1 15 52 | 1 12 1 56 53 | 1 12 1 55 54 | 1 12 1 16 55 | 1 12 1 57 56 | 1 13 1 55 57 | 1 13 1 49 58 | 1 13 1 57 59 | 1 13 1 17 60 | 1 13 1 31 61 | 1 13 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38 1 50 127 | 1 39 1 48 128 | 1 39 1 46 129 | 1 41 1 46 130 | 1 41 1 48 131 | 1 41 1 64 132 | 1 42 1 64 133 | 1 42 1 63 134 | 1 43 1 64 135 | 1 43 1 63 136 | 1 44 1 63 137 | 1 44 1 64 138 | 1 46 1 63 139 | 1 46 1 62 140 | 1 46 1 64 141 | 1 47 1 62 142 | 1 47 1 63 143 | 1 47 1 61 144 | 1 48 1 62 145 | 1 48 1 64 146 | 1 48 1 59 147 | 1 48 1 60 148 | 1 48 1 61 149 | 1 49 1 57 150 | 1 49 1 61 151 | 1 50 1 57 152 | 1 50 1 59 153 | 1 50 1 56 154 | 1 50 1 58 155 | 1 50 1 60 156 | 1 50 1 62 157 | 1 51 1 56 158 | 1 51 1 57 159 | 1 51 1 58 160 | 1 51 1 55 161 | 1 52 1 56 162 | 1 52 1 58 163 | 1 52 1 57 164 | 1 57 1 61 165 | -------------------------------------------------------------------------------- /tutorials/basic/04-FreeEnergySurface/inputs/pywham_Qf_RMSD_free_energy.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 0.05 17 | 18 | 19 | 0.45 20 | 21 | 22 | 0.1 23 | 24 | 25 | 26 | 27 | 28 | V 29 | 30 | simulationData/Qf_RMSD_00.data 31 | 32 | 33 | 34 | V 35 | 36 | simulationData/Qf_RMSD_01.data 37 | 38 | 39 | 40 | V 41 | 42 | simulationData/Qf_RMSD_02.data 43 | 44 | 45 | 46 | V 47 | 48 | simulationData/Qf_RMSD_03.data 49 | 50 | 51 | 52 | V 53 | 54 | simulationData/Qf_RMSD_04.data 55 | 56 | 57 | 58 | V 59 | 60 | simulationData/Qf_RMSD_05.data 61 | 62 | 63 | 64 | V 65 | 66 | simulationData/Qf_RMSD_06.data 67 | 68 | 69 | 70 | V 71 | 72 | simulationData/Qf_RMSD_07.data 73 | 74 | 75 | 76 | V 77 | 78 | simulationData/Qf_RMSD_08.data 79 | 80 | 81 | 82 | V 83 | 84 | simulationData/Qf_RMSD_09.data 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | V 95 | 136 96 | 97 | true 98 | 99 | 100 | 101 | 102 | -------------------------------------------------------------------------------- /tutorials/basic/04-FreeEnergySurface/inputs/pywham_Qf_free_energy.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 0.05 15 | 16 | 17 | 0.1 18 | 19 | 20 | 21 | 22 | 23 | V 24 | 25 | simulationData/Qf_00.data 26 | 27 | 28 | 29 | V 30 | 31 | simulationData/Qf_01.data 32 | 33 | 34 | 35 | V 36 | 37 | simulationData/Qf_02.data 38 | 39 | 40 | 41 | V 42 | 43 | simulationData/Qf_03.data 44 | 45 | 46 | 47 | V 48 | 49 | simulationData/Qf_04.data 50 | 51 | 52 | 53 | V 54 | 55 | simulationData/Qf_05.data 56 | 57 | 58 | 59 | V 60 | 61 | simulationData/Qf_06.data 62 | 63 | 64 | 65 | V 66 | 67 | simulationData/Qf_07.data 68 | 69 | 70 | 71 | V 72 | 73 | simulationData/Qf_08.data 74 | 75 | 76 | 77 | V 78 | 79 | simulationData/Qf_09.data 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | V 89 | 136 90 | 91 | true 92 | 93 | 94 | 95 | 96 | -------------------------------------------------------------------------------- /tutorials/basic/04-FreeEnergySurface/inputs/pywham_RMSD_free_energy.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 0.45 15 | 16 | 17 | 0.1 18 | 19 | 20 | 21 | 22 | 23 | V 24 | 25 | simulationData/RMSD_00.data 26 | 27 | 28 | 29 | V 30 | 31 | simulationData/RMSD_01.data 32 | 33 | 34 | 35 | V 36 | 37 | simulationData/RMSD_02.data 38 | 39 | 40 | 41 | V 42 | 43 | simulationData/RMSD_03.data 44 | 45 | 46 | 47 | V 48 | 49 | simulationData/RMSD_04.data 50 | 51 | 52 | 53 | V 54 | 55 | simulationData/RMSD_05.data 56 | 57 | 58 | 59 | V 60 | 61 | simulationData/RMSD_06.data 62 | 63 | 64 | 65 | V 66 | 67 | simulationData/RMSD_07.data 68 | 69 | 70 | 71 | V 72 | 73 | simulationData/RMSD_08.data 74 | 75 | 76 | 77 | V 78 | 79 | simulationData/RMSD_09.data 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | V 89 | 136 90 | 91 | true 92 | 93 | 94 | 95 | 96 | -------------------------------------------------------------------------------- /tutorials/basic/05-MultiBasin/input/AK_close_CA.contacts: -------------------------------------------------------------------------------- 1 | 1 1 1 26 2 | 1 1 1 79 3 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1 202 1 206 588 | 1 203 1 207 589 | 1 204 1 208 590 | 1 204 1 211 591 | 1 205 1 209 592 | 1 206 1 210 593 | 1 207 1 211 594 | 1 208 1 212 595 | 1 209 1 213 596 | 1 209 1 214 597 | 1 210 1 214 598 | -------------------------------------------------------------------------------- /tutorials/basic/05-MultiBasin/input/fe_wham.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 2 17 | 18 | 19 | 0.05 20 | 21 | 22 | 0.05 23 | 24 | 25 | 26 | 27 | 28 | V 29 | 30 | simulationData/Qf_01.data 31 | 32 | 33 | 34 | V 35 | 36 | simulationData/Qf_02.data 37 | 38 | 39 | 40 | V 41 | 42 | simulationData/Qf_03.data 43 | 44 | 45 | 46 | V 47 | 48 | simulationData/Qf_04.data 49 | 50 | 51 | 52 | V 53 | 54 | simulationData/Qf_05.data 55 | 56 | 57 | 58 | V 59 | 60 | simulationData/Qf_06.data 61 | 62 | 63 | 64 | V 65 | 66 | simulationData/Qf_07.data 67 | 68 | 69 | 70 | V 71 | 72 | simulationData/Qf_08.data 73 | 74 | 75 | 76 | V 77 | 78 | simulationData/Qf_09.data 79 | 80 | 81 | 82 | V 83 | 84 | simulationData/Qf_10.data 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | V 95 | 123.75 96 | 97 | true 98 | 99 | 100 | 101 | 102 | -------------------------------------------------------------------------------- /tutorials/folding/01-FoxP1_equilibrium_folding/other_notebooks/getTStrajectory.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 1, 6 | "metadata": {}, 7 | "outputs": [], 8 | "source": [ 9 | "import numpy as np\n", 10 | "import mdtraj as md\n", 11 | "import os\n", 12 | "import gc" 13 | ] 14 | }, 15 | { 16 | "cell_type": "code", 17 | "execution_count": 2, 18 | "metadata": {}, 19 | "outputs": [], 20 | "source": [ 21 | "# Store aligned trajectory files\n", 22 | "folder = '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/'\n", 23 | "trajectory_files = {}\n", 24 | "for d in sorted(os.listdir(folder)):\n", 25 | " if os.path.isdir(folder+d):\n", 26 | " for f in sorted(os.listdir(folder+d)):\n", 27 | " if f.endswith('.dcd'):\n", 28 | " index = f.split('_')[0]\n", 29 | " trajectory_files[index] = folder+d+'/'+f" 30 | ] 31 | }, 32 | { 33 | "cell_type": "code", 34 | "execution_count": 3, 35 | "metadata": {}, 36 | "outputs": [], 37 | "source": [ 38 | "# Define an SBMOpenMM All-Atom SBM from the forcefield parameters file\n", 39 | "topology = '../input/FoxP_monomer.pdb'" 40 | ] 41 | }, 42 | { 43 | "cell_type": "code", 44 | "execution_count": 4, 45 | "metadata": {}, 46 | "outputs": [], 47 | "source": [ 48 | "# Load TS frames' indexes\n", 49 | "folder = '../output'\n", 50 | "ts_frames = {}\n", 51 | "for f in sorted(os.listdir(folder)):\n", 52 | " if f.endswith('.npy') and f.startswith('ts_frames'):\n", 53 | " index = f.split('.')[0].replace('ts_frames','')\n", 54 | " ts_frames[index] = np.loadtxt(folder+'/'+f).astype(int)" 55 | ] 56 | }, 57 | { 58 | "cell_type": "code", 59 | "execution_count": 5, 60 | "metadata": {}, 61 | "outputs": [ 62 | { 63 | "name": "stdout", 64 | "output_type": "stream", 65 | "text": [ 66 | "\n" 67 | ] 68 | } 69 | ], 70 | "source": [ 71 | "# Merge all TS frames into one trajectory\n", 72 | "trajectory = None\n", 73 | "for i in trajectory_files:\n", 74 | " traj = md.load(trajectory_files[i], top=topology)\n", 75 | " # slice trajectory by the TS frames\n", 76 | " traj = traj[ts_frames[i]]\n", 77 | " if isinstance(topology, str):\n", 78 | " topology = traj.topology\n", 79 | " if isinstance(trajectory, type(None)):\n", 80 | " trajectory = traj\n", 81 | " else:\n", 82 | " if trajectory.xyz.shape[1:] != traj.xyz.shape[1:]:\n", 83 | " print('Trajectory file: '+trajectory_files[i]+' has different number of atoms \\\n", 84 | " than the reference topology! Discarding it')\n", 85 | " continue \n", 86 | " traj = md.Trajectory(traj.xyz, topology)\n", 87 | " trajectory = md.join((trajectory, traj))\n", 88 | " gc.collect() # Free memory before moving to the next trajectory file\n", 89 | "\n", 90 | "print(trajectory)" 91 | ] 92 | }, 93 | { 94 | "cell_type": "code", 95 | "execution_count": 6, 96 | "metadata": {}, 97 | "outputs": [], 98 | "source": [ 99 | "# Save trajectory\n", 100 | "trajectory.save('../output/ts_trajectory.dcd')" 101 | ] 102 | }, 103 | { 104 | "cell_type": "code", 105 | "execution_count": null, 106 | "metadata": {}, 107 | "outputs": [], 108 | "source": [] 109 | } 110 | ], 111 | "metadata": { 112 | "kernelspec": { 113 | "display_name": "Python 3", 114 | "language": "python", 115 | "name": "python3" 116 | }, 117 | "language_info": { 118 | "codemirror_mode": { 119 | "name": "ipython", 120 | "version": 3 121 | }, 122 | "file_extension": ".py", 123 | "mimetype": "text/x-python", 124 | "name": "python", 125 | "nbconvert_exporter": "python", 126 | "pygments_lexer": "ipython3", 127 | "version": "3.7.8" 128 | } 129 | }, 130 | "nbformat": 4, 131 | "nbformat_minor": 4 132 | } 133 | -------------------------------------------------------------------------------- /tutorials/folding/01-FoxP1_equilibrium_folding/other_notebooks/radiusOfGyration.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 1, 6 | "metadata": {}, 7 | "outputs": [], 8 | "source": [ 9 | "import os\n", 10 | "import numpy as np\n", 11 | "import mdtraj as md\n", 12 | "import gc" 13 | ] 14 | }, 15 | { 16 | "cell_type": "code", 17 | "execution_count": 3, 18 | "metadata": {}, 19 | "outputs": [ 20 | { 21 | "name": "stdout", 22 | "output_type": "stream", 23 | "text": [ 24 | "['/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/01/01_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/02/02_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/03/03_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/04/04_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/05/05_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/06/06_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/07/07_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/08/08_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/09/09_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/10/10_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/11/11_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/12/12_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/13/13_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/14/14_trajectory.dcd', '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/15/15_trajectory.dcd']\n" 25 | ] 26 | } 27 | ], 28 | "source": [ 29 | "# Store aligned trajectory files\n", 30 | "folder = '/home/martin/Projects/FoxP/AA/FoldingSimulation_Tf/kx/'\n", 31 | "trajectory_files = []\n", 32 | "for d in sorted(os.listdir(folder)):\n", 33 | " if os.path.isdir(folder+d):\n", 34 | " for f in sorted(os.listdir(folder+d)):\n", 35 | " if f.endswith('.dcd'):\n", 36 | " trajectory_files.append(folder+d+'/'+f)\n", 37 | "print(trajectory_files)" 38 | ] 39 | }, 40 | { 41 | "cell_type": "code", 42 | "execution_count": 4, 43 | "metadata": {}, 44 | "outputs": [], 45 | "source": [ 46 | "# Define an SBMOpenMM All-Atom SBM from the forcefield parameters file\n", 47 | "topology = '../input/FoxP_monomer.pdb'" 48 | ] 49 | }, 50 | { 51 | "cell_type": "code", 52 | "execution_count": 6, 53 | "metadata": {}, 54 | "outputs": [], 55 | "source": [ 56 | "# Compute radius of gyration\n", 57 | "rg = []\n", 58 | "for t in trajectory_files:\n", 59 | " traj = md.load(t, top=topology)\n", 60 | " rg.append(md.compute_rg(traj))\n", 61 | " traj = None\n", 62 | " gc.collect() # Free memory before moving to the next estimation\n", 63 | "rg_concatenated = np.concatenate(rg)" 64 | ] 65 | }, 66 | { 67 | "cell_type": "code", 68 | "execution_count": 7, 69 | "metadata": {}, 70 | "outputs": [], 71 | "source": [ 72 | "np.save('../output/radiusOfGyration', rg_concatenated)" 73 | ] 74 | } 75 | ], 76 | "metadata": { 77 | "kernelspec": { 78 | "display_name": "Python 3", 79 | "language": "python", 80 | "name": "python3" 81 | }, 82 | "language_info": { 83 | "codemirror_mode": { 84 | "name": "ipython", 85 | "version": 3 86 | }, 87 | "file_extension": ".py", 88 | "mimetype": "text/x-python", 89 | "name": "python", 90 | "nbconvert_exporter": "python", 91 | "pygments_lexer": "ipython3", 92 | "version": "3.7.8" 93 | } 94 | }, 95 | "nbformat": 4, 96 | "nbformat_minor": 4 97 | } 98 | -------------------------------------------------------------------------------- /tutorials/folding/01-FoxP1_equilibrium_folding/output/radiusOfGyration.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/tutorials/folding/01-FoxP1_equilibrium_folding/output/radiusOfGyration.npy -------------------------------------------------------------------------------- /tutorials/folding/01-FoxP1_equilibrium_folding/output/ts_trajectory.dcd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CompBiochBiophLab/sbm-openmm/113b04eb2c78664a48600a05ff6778898fbb2fd9/tutorials/folding/01-FoxP1_equilibrium_folding/output/ts_trajectory.dcd --------------------------------------------------------------------------------