Merge branch 'v0.3.0'

Author: blakeaw

README.md

@@ -1,11 +1,11 @@
 ![alt text](./_images/PyBILT_logo.png "PyBILT Logo")
 # *Py*thon based lipid *BIL*ayer molecular simulation analysis *T*oolkit
 ------
-![Python version badge](https://img.shields.io/badge/python-2.7%2C3.6%2C3.7-blue.svg)
+![Python version badge](https://img.shields.io/badge/python-3.7-blue.svg)
 [![license](https://img.shields.io/github/license/mashape/apistatus.svg)](LICENSE)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/2d6da71328a24ef6930ad8f554074292)](https://www.codacy.com/manual/blakeaw1102/PyBILT?utm_source=github.com&utm_medium=referral&utm_content=LoLab-VU/PyBILT&utm_campaign=Badge_Grade)
-![version](https://img.shields.io/badge/version-0.2.0-orange.svg)
-[![release](https://img.shields.io/github/release-pre/LoLab-VU/PyBILT.svg)](https://github.com/LoLab-VU/PyBILT/releases/tag/v0.2.0)
+![version](https://img.shields.io/badge/version-0.3.0-orange.svg)
+[![release](https://img.shields.io/github/release-pre/LoLab-VU/PyBILT.svg)](https://github.com/LoLab-VU/PyBILT/releases/tag/v0.3.0)
 [![Anaconda-Server Badge](https://anaconda.org/blakeaw/pybilt/badges/version.svg)](https://anaconda.org/blakeaw/pybilt)
 [![Documentation Status](https://readthedocs.org/projects/pybilt/badge/?version=latest)](http://pybilt.readthedocs.io/en/latest/?badge=latest)
 [![DOI](https://zenodo.org/badge/85123567.svg)](https://zenodo.org/badge/latestdoi/85123567)
@@ -33,7 +33,7 @@ The analyses include:
 
 ### Core dependencies
 **PyBILT** has the following core dependencies:
-   * [MDAnalysis](https://www.mdanalysis.org/)
+   * [MDAnalysis](https://www.mdanalysis.org/) > 1.0
    * [NumPy](http://www.numpy.org/)
    * [SciPy](https://www.scipy.org/)
    * [Matplotlib](https://matplotlib.org/)
@@ -42,16 +42,12 @@ The analyses include:
    * [future](http://python-future.org/)
 
 ### Python version support
-The `pybilt` package has been tested using [Anaconda Python](https://www.anaconda.com/) 2.7, 3.6, and 3.7.
-
-#### Sunsetting of Python 2
-Please be aware that Python 2 is scheduled to be sunset on January 1 2020. You can read about it here: [https://www.python.org/doc/sunset-python-2/](https://www.python.org/doc/sunset-python-2/)
-Parallel to the sunsetting of Python 2 many open source packages are also dropping support for Python 2 ([https://python3statement.org/](https://python3statement.org/)), including some of **PyBILT**'s core dependencies. As such, after January 1, 2020, **PyBILT** will also likely sunset its support for Python 2.7.  
+The `pybilt` package has been tested using [Anaconda Python](https://www.anaconda.com/) 3.7 and MDAnalysis=1.1.1.
 
 ### pip install
 You can install the latest version of the `pybilt` package using `pip` sourced from the GitHub repo:
 ```
-pip install -e git+https://github.com/LoLab-VU/PyBILT@v0.2.0#egg=pybilt
+pip install -e git+https://github.com/LoLab-VU/PyBILT@v0.3.0#egg=pybilt
 ```
 However, this will not automatically install the core dependencies. You will have to do that separately:
 ```

pybilt/bilayer_analyzer/analysis_protocols.py

@@ -3548,12 +3548,14 @@ def run_analysis(self, ba_settings, ba_reps, ba_mda_data):
         residues = self.selection.residues
         cos_run = RunningStats()
         for residue in residues:
-            atom_1 = eval("residue.{}".format(self.settings['ref_atom_1']))
-            atom_2 = eval("residue.{}".format(self.settings['ref_atom_2']))
+            #atom_1 = eval("residue.{}".format(self.settings['ref_atom_1']))
+            #atom_2 = eval("residue.{}".format(self.settings['ref_atom_2']))
+            atom_1 = residue.atoms.select_atoms('name {}'.format(self.settings['ref_atom_1']))
+            atom_2 = residue.atoms.select_atoms('name {}'.format(self.settings['ref_atom_2']))
             #atom_1 = ast.literal_eval("residue.{}".format(self.settings['ref_atom_1']))
             #atom_2 = ast.literal_eval("residue.{}".format(self.settings['ref_atom_2']))
-            atom_1_i = atom_1.index
-            atom_2_i = atom_2.index
+            atom_1_i = atom_1.indices[0]
+            atom_2_i = atom_2.indices[0]
             atom_1_coord = ba_reps['current_mda_frame'].positions[atom_1_i]
             atom_2_coord = ba_reps['current_mda_frame'].positions[atom_2_i]
             diff = atom_2_coord - atom_1_coord
@@ -3687,10 +3689,10 @@ def run_analysis(self, ba_settings, ba_reps, ba_mda_data):
         residues = self.selection.residues
         cos_run = RunningStats()
         for residue in residues:
-            atom_1 = eval("residue."+self.settings['ref_atom_1'])
-            atom_2 = eval("residue."+self.settings['ref_atom_2'])
-            atom_1_i = atom_1.index
-            atom_2_i = atom_2.index
+            atom_1 = residue.atoms.select_atoms('name {}'.format(self.settings['ref_atom_1']))
+            atom_2 = residue.atoms.select_atoms('name {}'.format(self.settings['ref_atom_2']))
+            atom_1_i = atom_1.indices[0]
+            atom_2_i = atom_2.indices[0]
             atom_1_coord = ba_reps['current_mda_frame'].positions[atom_1_i]
             atom_2_coord = ba_reps['current_mda_frame'].positions[atom_2_i]
             diff = atom_2_coord - atom_1_coord

pybilt/bilayer_analyzer/com_frame.py

@@ -66,12 +66,15 @@ def extract(self, mda_residue, unwrap=False, box=None, name_dict=None, make_whol
 
             self.atom_names = names
             n_names = len(names)
-            atom_group = mda.core.AtomGroup.AtomGroup([eval("mda_residue.atoms."+names[0])])
+            #print(mda_residue.atoms.select_atoms('name {}'.format(names[0])))
+            #atom_group = mda.core.groups.AtomGroup([eval("mda_residue.atoms."+names[0])])
+            atom_group = mda_residue.atoms.select_atoms('name {}'.format(names[0]))
             #if (not unwrap) and (n_names > 1):
             #    mda.lib.mdamath.make_whole(mda_residue.atoms, reference_atom=atom_group)
 
             for i in range(1, n_names):
-                atom_group+=eval("mda_residue.atoms."+names[i])
+                #atom_group+=eval("mda_residue.atoms."+names[i])
+                atom_group += mda_residue.atoms.select_atoms('name {}'.format(names[i]))
 
         #else:
         if (not unwrap) and make_whole:

setup.py

@@ -1,7 +1,7 @@
 from distutils.core import setup
 
 setup(name='pybilt',
-      version='0.2.0',
+      version='0.3.0',
       description='Lipid bilayer analysis toolkit.',
       author='Blake A. Wilson',
       author_email='[email protected]',
@@ -11,5 +11,5 @@
                 'pybilt.lipid_grid', 'pybilt.mda_tools',
                 'pybilt.plot_generation'],
       license='MIT',
-      keywords=['lipid bilayer', 'molecular dynamics', 'analysis']            
+      keywords=['lipid bilayer', 'molecular dynamics', 'analysis']
      )