dynetan 2.2.2__tar.gz → 2.3.0__tar.gz

{dynetan-2.2.2 → dynetan-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dynetan
-Version: 2.2.2
+Version: 2.3.0
 Summary: A Python implementation for Dynamical Network Analysis.
 Project-URL: Homepage, https://gitlab.com/comp-biochem-csu/dynetan
 Project-URL: Bug Tracker, https://gitlab.com/comp-biochem-csu/dynetan/-/issues
@@ -29,7 +29,7 @@ Dynamical Network Analysis
 ![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/)
 [![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)
+[![CI/CD Status](https://gitlab.com/comp-biochem-csu/dynetan/badges/master/pipeline.svg)](https://gitlab.com/comp-biochem-csu/dynetan/-/commits/master)
 [![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)
 

{dynetan-2.2.2 → dynetan-2.3.0}/README.md

@@ -4,7 +4,7 @@ Dynamical Network Analysis
 ![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/)
 [![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)
+[![CI/CD Status](https://gitlab.com/comp-biochem-csu/dynetan/badges/master/pipeline.svg)](https://gitlab.com/comp-biochem-csu/dynetan/-/commits/master)
 [![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)
 

{dynetan-2.2.2 → dynetan-2.3.0}/docs/source/Tutorial.rst

@@ -14,5 +14,5 @@ deployed for execution in remote computer clusters.
 For the latest version of the tutorial, download the
 `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 data here <https://compbiochem.colostate.edu/public_data/dynetan_tutorial_data/decarboxylase.1.dcd>`_
 (trajectory files are approximately 500MB in size).

{dynetan-2.2.2 → dynetan-2.3.0}/src/dynetan/gencor.py

@@ -56,6 +56,7 @@ def stand_vars_c(traj: npt.NDArray[np.float64],
 
 
 def prep_mi_c(universe: MDAnalysis.Universe,
+              nodesAtmSel,
               traj: npt.NDArray[np.float64],
               beg: int,
               end: int,
@@ -92,9 +93,13 @@ def prep_mi_c(universe: MDAnalysis.Universe,
     # Copy trajectory
     for frame_index, ts in enumerate(universe.trajectory[beg:end]):
 
-        for atm_index in range(num_nodes):
+        for node_index in range(num_nodes):
+
+            # Convert atom index in MDanalysis universe to node index in Dynetan
+            atm_index = int(nodesAtmSel[node_index].index)
+
             for dim in range(num_dims):
-                traj[atm_index, dim, frame_index] = ts.positions[atm_index, dim]
+                traj[node_index, dim, frame_index] = ts.positions[atm_index, dim]
 
     stand_vars_c(traj, num_nodes, num_dims)
 

{dynetan-2.2.2 → dynetan-2.3.0}/src/dynetan/proctraj.py

@@ -1679,7 +1679,7 @@ class DNAproc:
             traj.fill(0)
 
             # Prepares data for fast calculation of the current window.
-            gc.prep_mi_c(self.workU, traj, beg, end, self.numNodes, num_dims)
+            gc.prep_mi_c(self.workU, self.nodesAtmSel, traj, beg, end, self.numNodes, num_dims)
 
             if ncores == 1:
 
@@ -1687,13 +1687,13 @@ class DNAproc:
                     print("- > Using single-core implementation.")
 
                 # Iterates over all pairs of nodes that are in contact.
-                for atmList in self.progBar(pair_array,
+                for node_list in self.progBar(pair_array,
                                             desc="Contact Pair",
                                             leave=False,
                                             ascii=self.asciiMode):
 
                     # Calls the Numba-compiled function.
-                    mir = gc.calc_mir_numba_2var(traj[atmList, :, :],
+                    mir = gc.calc_mir_numba_2var(traj[node_list, :, :],
                                                  win_len,
                                                  num_dims,
                                                  self.kNeighb,
@@ -1702,8 +1702,8 @@ class DNAproc:
 
                     corr = gc.mir_to_corr(mir)
 
-                    self.corrMatAll[winIndx, atmList[0], atmList[1]] = corr
-                    self.corrMatAll[winIndx, atmList[1], atmList[0]] = corr
+                    self.corrMatAll[winIndx, node_list[0], node_list[1]] = corr
+                    self.corrMatAll[winIndx, node_list[1], node_list[0]] = corr
 
             else:
 
@@ -1715,8 +1715,8 @@ class DNAproc:
                 results_queue: queue.Queue = mp.Queue()
 
                 # Loads the node pairs in the input queue
-                for atmList in pair_array:
-                    data_queue.put(atmList)
+                for node_list in pair_array:
+                    data_queue.put(node_list)
 
                 # Creates processes.
                 procs = []

dynetan-2.3.0/src/dynetan/version.py

@@ -0,0 +1 @@
+__version__ = "2.3.0"

dynetan-2.2.2/src/dynetan/version.py

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