dynetan 2.2.0__tar.gz → 2.2.2__tar.gz

{dynetan-2.2.0 → dynetan-2.2.2}/PKG-INFO

@@ -1,9 +1,9 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: dynetan
-Version: 2.2.0
+Version: 2.2.2
 Summary: A Python implementation for Dynamical Network Analysis.
-Project-URL: Homepage, https://github.com/melomcr/dynetan
-Project-URL: Bug Tracker, https://github.com/melomcr/dynetan/issues
+Project-URL: Homepage, https://gitlab.com/comp-biochem-csu/dynetan
+Project-URL: Bug Tracker, https://gitlab.com/comp-biochem-csu/dynetan/-/issues
 Project-URL: Documentation, https://dynamical-network-analysis.readthedocs.io
 Author-email: "Marcelo C. R. Melo" <melomcr@gmail.com>
 License-File: LICENSE
@@ -26,12 +26,13 @@ Description-Content-Type: text/markdown
 Dynamical Network Analysis
 ===========================
 
-![GitHub release (latest by date)](https://img.shields.io/github/v/release/melomcr/dynetan)
+![last release](https://img.shields.io/gitlab/v/release/comp-biochem-csu/dynetan)
 [![PyPI](https://img.shields.io/pypi/v/dynetan)](https://pypi.org/project/dynetan/)
-[![Documentation Status](https://readthedocs.org/projects/dynamical-network-analysis/badge/?version=latest)](https://dynamical-network-analysis.readthedocs.io/en/latest/?badge=latest)
-[![GH CI Tests](https://github.com/melomcr/dynetan/actions/workflows/github-actions-ci.yml/badge.svg)](https://github.com/melomcr/dynetan/actions/workflows/github-actions-ci.yml)
-[![codecov](https://codecov.io/gh/melomcr/dynetan/branch/master/graph/badge.svg)](https://codecov.io/gh/melomcr/dynetan)
-![GitHub](https://img.shields.io/github/license/melomcr/dynetan)
+[![Read-The-Docs Status](https://readthedocs.org/projects/dynamical-network-analysis/badge/?version=latest)](https://dynamical-network-analysis.readthedocs.io/en/latest/?badge=latest)
+[![CI/CD Status](https://img.shields.io/gitlab/pipeline-status/comp-biochem-csu/dynetan)](https://gitlab.com/comp-biochem-csu/dynetan/-/pipelines)
+[![Codecov](https://codecov.io/gl/comp-biochem-csu/dynetan/branch/master/graph/badge.svg)](https://codecov.io/gl/comp-biochem-csu/dynetan)
+![License](https://img.shields.io/gitlab/license/comp-biochem-csu/dynetan)
+
 
 The Python implementation of Dynamical Network Analysis was built to provide all
 functionalities necessary to the analysis of Molecular Dynamics (MD) simulations
@@ -40,7 +41,7 @@ using the Dynamical Network Analysis method.
 Install
 -------
 
-Install the latest version of Dynamical Network Analysis::
+Install the latest version of Dynamical Network Analysis:
 
     $ pip install dynetan
 
@@ -49,18 +50,14 @@ For additional details, please see `INSTALL.md`.
 Tutorial
 --------
 
-For an introduction to this implementation, a jupyter notebook tutorial has been
-prepared and released along with its latest publication:
+Several jupyter notebook tutorials have been prepared as an introduction to this package and were released in an independent repository:
 
-* [Generalized correlation-based dynamical network analysis: a new high-performance
-approach for identifying allosteric communications in molecular dynamics
-trajectories. J. Chem. Phys. (2020).
-DOI: 10.1063/5.0018980](https://doi.org/10.1063/5.0018980)
+https://gitlab.com/comp-biochem-csu/dynetan_tutorial
 
 Documentation
 ------------------------
 
-A full documentation can be found at
+The full documentation can be found at
 https://dynamical-network-analysis.readthedocs.io/en/latest/index.html
 
 Resources and References

{dynetan-2.2.0 → dynetan-2.2.2}/README.md

@@ -1,12 +1,13 @@
 Dynamical Network Analysis
 ===========================
 
-![GitHub release (latest by date)](https://img.shields.io/github/v/release/melomcr/dynetan)
+![last release](https://img.shields.io/gitlab/v/release/comp-biochem-csu/dynetan)
 [![PyPI](https://img.shields.io/pypi/v/dynetan)](https://pypi.org/project/dynetan/)
-[![Documentation Status](https://readthedocs.org/projects/dynamical-network-analysis/badge/?version=latest)](https://dynamical-network-analysis.readthedocs.io/en/latest/?badge=latest)
-[![GH CI Tests](https://github.com/melomcr/dynetan/actions/workflows/github-actions-ci.yml/badge.svg)](https://github.com/melomcr/dynetan/actions/workflows/github-actions-ci.yml)
-[![codecov](https://codecov.io/gh/melomcr/dynetan/branch/master/graph/badge.svg)](https://codecov.io/gh/melomcr/dynetan)
-![GitHub](https://img.shields.io/github/license/melomcr/dynetan)
+[![Read-The-Docs Status](https://readthedocs.org/projects/dynamical-network-analysis/badge/?version=latest)](https://dynamical-network-analysis.readthedocs.io/en/latest/?badge=latest)
+[![CI/CD Status](https://img.shields.io/gitlab/pipeline-status/comp-biochem-csu/dynetan)](https://gitlab.com/comp-biochem-csu/dynetan/-/pipelines)
+[![Codecov](https://codecov.io/gl/comp-biochem-csu/dynetan/branch/master/graph/badge.svg)](https://codecov.io/gl/comp-biochem-csu/dynetan)
+![License](https://img.shields.io/gitlab/license/comp-biochem-csu/dynetan)
+
 
 The Python implementation of Dynamical Network Analysis was built to provide all
 functionalities necessary to the analysis of Molecular Dynamics (MD) simulations
@@ -15,7 +16,7 @@ using the Dynamical Network Analysis method.
 Install
 -------
 
-Install the latest version of Dynamical Network Analysis::
+Install the latest version of Dynamical Network Analysis:
 
     $ pip install dynetan
 
@@ -24,18 +25,14 @@ For additional details, please see `INSTALL.md`.
 Tutorial
 --------
 
-For an introduction to this implementation, a jupyter notebook tutorial has been
-prepared and released along with its latest publication:
+Several jupyter notebook tutorials have been prepared as an introduction to this package and were released in an independent repository:
 
-* [Generalized correlation-based dynamical network analysis: a new high-performance
-approach for identifying allosteric communications in molecular dynamics
-trajectories. J. Chem. Phys. (2020).
-DOI: 10.1063/5.0018980](https://doi.org/10.1063/5.0018980)
+https://gitlab.com/comp-biochem-csu/dynetan_tutorial
 
 Documentation
 ------------------------
 
-A full documentation can be found at
+The full documentation can be found at
 https://dynamical-network-analysis.readthedocs.io/en/latest/index.html
 
 Resources and References

{dynetan-2.2.0 → dynetan-2.2.2}/docs/source/Tutorial.rst

@@ -12,7 +12,7 @@ using Jupyter Notebooks, as well as command-line-interface (CLI) scripts that ca
 deployed for execution in remote computer clusters.
 
 For the latest version of the tutorial, download the
-`tutorial files here <https://github.com/melomcr/dynetan_tutorial>`_
+`tutorial files here <https://gitlab.com/comp-biochem-csu/dynetan_tutorial>`_
 along with accompanying
 `trajectory data here <https://compbiophysics.auburn.edu/DyNetAn_Tutorial/data/DynamicNetworkAnalysis_MDdata.tar.gz>`_
 (trajectory files are approximately 500MB in size).

{dynetan-2.2.0 → dynetan-2.2.2}/docs/source/conf.py

@@ -94,6 +94,8 @@ if not on_rtd:  # only import and set the theme if we're building docs locally
     import sphinx_rtd_theme
     html_theme = "sphinx_rtd_theme"
     html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+else:
+    html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

{dynetan-2.2.0 → dynetan-2.2.2}/docs/source/index.rst

@@ -6,21 +6,24 @@ Dynamical Network Analysis
 
 This package was built to provide an updated and enhanced Python implementation
 of the Dynamical Network Analysis method, for the analysis of Molecular Dynamics
-simulations. The package was optimized for interactive use through Jupyter
-Notebooks (see :ref:`Tutorial <Tutorial>`), and allows for extensive
-customization of analysis to suit research-specific needs.
+simulations. The package was optimized for interactive data analysis and
+visualization through Jupyter Notebooks (see :ref:`Tutorial <Tutorial>`),
+and provides an interface for rendering publication-quality figures using
+`VMD <https://www.ks.uiuc.edu/Research/vmd/>`_.
+It allows for extensive customization of analysis workflows to suit
+research-specific needs.
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
-   
+
    Introduction
    Installation
    Tutorial
    Usage
    Citing
    Reference
-   
+
 
 Indices and tables
 ==================

{dynetan-2.2.0 → dynetan-2.2.2}/pyproject.toml

@@ -34,8 +34,8 @@ classifiers = [
 ]
 
 [project.urls]
-"Homepage" = "https://github.com/melomcr/dynetan"
-"Bug Tracker" = "https://github.com/melomcr/dynetan/issues"
+"Homepage" = "https://gitlab.com/comp-biochem-csu/dynetan"
+"Bug Tracker" = "https://gitlab.com/comp-biochem-csu/dynetan/-/issues"
 "Documentation" = "https://dynamical-network-analysis.readthedocs.io"
 
 [tool.hatch.version]
@@ -66,10 +66,11 @@ filterwarnings = [
     "error",  #converts all warnings to errors
     "ignore:.*numpy.ndarray size changed.*:RuntimeWarning",
 #    "ignore::UserWarning",
-    # note the use of single quote below to denote "raw" strings in TOML
+    # note the use of the single quotes below to denote "raw" strings in TOML
     'ignore:.*np.MachAr.* is deprecated:DeprecationWarning',
     'ignore::DeprecationWarning:jupyter*',
-    'ignore:.*DCDReader.*independent timesteps.*:DeprecationWarning:MDAnalysis'
+    'ignore:.*DCDReader.*independent timesteps.*:DeprecationWarning:MDAnalysis',
+    "ignore::UserWarning:nglview.*"
 ]
 
 [tool.mypy]

{dynetan-2.2.0 → dynetan-2.2.2}/src/dynetan/proctraj.py

@@ -19,7 +19,7 @@ import networkx as nx
 
 import community
 
-from networkx import eigenvector_centrality_numpy as nxeigencentrality
+from networkx import eigenvector_centrality as nxeigencentrality
 from networkx import edge_betweenness_centrality as nxbetweenness
 from networkx.algorithms.shortest_paths.dense import \
     floyd_warshall_predecessor_and_distance as nxFWPD
@@ -509,6 +509,48 @@ class DNAproc:
         self.notSelResNamesSet = notSelResNamesSet
         self.notSelSegidSet = notSelSegidSet
 
+    def _get_sel_check_set(self, with_solvent: bool) -> Union[mda.AtomGroup, None]:
+        """
+        Returns an atom selection object or None for selection of structural
+        solvent, ions, and other molecules.
+
+        Args:
+            with_solvent (bool): Whether solvent molecules should be automatically
+                selected for analysis.
+
+        Returns:
+            mda.AtomGroup
+        """
+        if with_solvent:
+            # For automatic solvent detection, we use the segIDs that were
+            # not selected by the user as targets for network analysis.
+            if self.notSelSegidSet:
+                selStr = "(not (name H* or name [123]H*)) "
+                selStr += "and segid " + " ".join(self.notSelSegidSet)
+                checkSet = self.workU.select_atoms(selStr)
+            else:
+                print("WARNING: All segments have been selected for Network "
+                      "Analysis, none are left for automatic identification "
+                      "of structural solvent molecules or lipids.")
+                checkSet = None
+        else:
+            # Without solvent detection, the new selection removes all solvent
+            # molecules from the selection but keeps selected segments.
+            # Those may have ions or ligands that may be structural and
+            # necessary for the analysis.
+            if self.notSelSegidSet:
+                selStr = "segid " + " ".join(self.notSelSegidSet)
+                selStr += " and not resname " + " ".join(self.solventNames)
+                selStr += " and not (name H* or name [123]H*)"
+                checkSet = self.workU.select_atoms(selStr)
+            else:
+                print("WARNING: All segments have been selected for Network "
+                      "Analysis, none are left for automatic identification "
+                      "of transient contacts.")
+                checkSet = None
+
+        return checkSet
+
     def selectSystem(self,
                      withSolvent: bool = False,
                      inputSelStr: str = "",
@@ -563,41 +605,38 @@ class DNAproc:
             initialSel = self.workU.select_atoms(inputSelStr)
 
         else:
-            if withSolvent:
-                # For automatic solvent detection, we use the segIDs that were
-                # not selected by the user as targets for network analysis.
-                if self.notSelSegidSet:
-                    selStr = "(not (name H* or name [123]H*)) "
-                    selStr += "and segid " + " ".join(self.notSelSegidSet)
-                    checkSet = self.workU.select_atoms(selStr)
-                else:
-                    print("WARNING: All segments have been selected for Network "
-                          "Analysis, none are left for automatic identification "
-                          "of structural solvent molecules or lipids.")
-                    checkSet = None
-            else:
-                # Without solvent detection, the new selection removes all solvent
-                # molecules from the selection but keeps other segments that may
-                # ions or ligands that may be structural and necessary for the
-                # analysis.
-                if self.notSelSegidSet:
-                    selStr = "segid " + " ".join(self.notSelSegidSet)
-                    selStr += " and not resname " + " ".join(self.solventNames)
-                    selStr += " and not (name H* or name [123]H*)"
-                    checkSet = self.workU.select_atoms(selStr)
-                else:
-                    print("WARNING: All segments have been selected for Network "
-                          "Analysis, none are left for automatic identification "
-                          "of transient contacts.")
-                    checkSet = None
+
+            checkSet = self._get_sel_check_set(withSolvent)
 
             if checkSet:
                 numAutoFrames: int = self.numSampledFrames * self.numWinds
 
                 stride = int(np.floor(len(self.workU.trajectory) / numAutoFrames))
 
-                print("Checking {0} frames (striding {1})...".format(
-                    numAutoFrames, stride))
+                if stride > 0:
+                    print("Checking {0} frames (striding {1})...".format(
+                        numAutoFrames, stride))
+                if stride <= 0:  # Sanity check
+
+                    n_frames = int(len(self.workU.trajectory))
+                    n_frames_w = len(self.workU.trajectory)/self.numWinds
+                    errorStr = f"The trajectory has {n_frames} frames, " \
+                               f"or {n_frames_w} frames per window, which is " \
+                               f"less than the number of sampled " \
+                               f"frames: {self.numSampledFrames}. We need at " \
+                               f"least one sampled frame per window!"
+                    print(errorStr)
+
+                    errorStr = f"Check the number of sampled " \
+                               f"frames ({self.numSampledFrames}) and the number " \
+                               f"of windows ({self.numWinds}) chosen for this analysis."
+                    print(errorStr)
+
+                    errorStr = (Fore.RED + "ERROR!" + Fore.RESET +
+                                f" Stride was set to {stride}!")
+                    print(errorStr)
+
+                    raise Exception(errorStr)
 
                 selRes = self.workU.select_atoms("segid " + " ".join(self.segIDs))
                 searchSelRes = selRes.select_atoms("not (name H* or name [123]H*)")
@@ -2121,7 +2160,7 @@ class DNAproc:
         """
         for win in range(self.numWinds):
             # Calc all node centrality values in the system.
-            cent = nxeigencentrality(self.nxGraphs[win], weight='weight')
+            cent = nxeigencentrality(self.nxGraphs[win], weight='weight', max_iter=5000)
             nx.set_node_attributes(self.nxGraphs[win], cent, 'eigenvector')
 
     def calcCommunities(self) -> None:

dynetan-2.2.2/src/dynetan/version.py

@@ -0,0 +1 @@
+__version__ = "2.2.2"

{dynetan-2.2.0 → dynetan-2.2.2}/tests/test_proctraj_checksys_selectsys.py

@@ -102,6 +102,33 @@ class TestPackageSysVerificationSelection:
         dnap_fail.checkSystem()
         dnap_fail.selectSystem(withSolvent=False, inputSelStr="")
 
+    @pytest.mark.xfail(strict=True)
+    def test_select_system_stride(self, test_data_dir):
+        psfFile = os.path.join(test_data_dir, psf_fn_omp)
+        dcdFiles = [os.path.join(test_data_dir, dcd_fn_omp)]
+
+        dnap_fail = dna.proctraj.DNAproc(notebookMode=False)
+
+        # Test the default wrapper for loading a list of paths to DCDs
+        dnap_fail.loadSystem(psfFile, dcdFiles)
+
+        node_grps = {"OMP": {}}
+        node_grps["OMP"]["N1"] = set("N1 C2 O2 N3 C4 O4 C5 C6 C7 OA OB".split())
+        node_grps["OMP"]["P"] = set("P OP1 OP2 OP3 O5' C5' C4' O4' C1' C3' C2' "
+                                    "O2' O3'".split())
+
+        # TEST STRIDE LENGTH
+        dnap_fail.setNumWinds(1)
+        dnap_fail.setNumSampledFrames(200)  # INDUCE HUGE STRIDE
+        # STRIDE WILL BE TOO LARGE FOR WINDOW LENGTH
+
+        dnap_fail.setSolvNames(["TIP3"])
+        dnap_fail.setSegIDs(["OMP", "ENZY"])
+        dnap_fail.setNodeGroups(node_grps)
+
+        dnap_fail.checkSystem()
+        dnap_fail.selectSystem(withSolvent=True)
+
     @pytest.mark.parametrize(("solv", "sel", "verb", "n_atoms"), [
         (True, "protein", 0, 3291),
         (True, "protein and (not (name H* or name [123]H*))", 0, 1635),

{dynetan-2.2.0 → dynetan-2.2.2}/tests/test_proctraj_graph.py

@@ -270,15 +270,15 @@ class TestGraph:
 
         # Window, Node, Eigenvector Centrality
         ref_vals = [[0, 0,   0.2518],
-                    [0, 215, 0.10615],
-                    [0, 216, 0.04137],
-                    [1, 0,   0.00585],
-                    [1, 215, 0.00055],
-                    [1, 216, 0.00731]
+                    [0, 215, 0.1061],
+                    [0, 216, 0.0414],
+                    [1, 0,   0.0059],
+                    [1, 215, 0.0006],
+                    [1, 216, 0.0073]
                     ]
 
         for window, node, ref_val in ref_vals:
-            ev_val = round(dnap.nxGraphs[window].nodes[node]['eigenvector'], 5)
+            ev_val = round(dnap.nxGraphs[window].nodes[node]['eigenvector'], 4)
             assert ev_val == ref_val
 
     @pytest.mark.parametrize(

dynetan-2.2.0/src/dynetan/version.py

@@ -1 +0,0 @@
-__version__ = "2.2.0"