merge update

.github/workflows/main.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["2.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["2.7", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2

MANIFEST.in

@@ -9,6 +9,7 @@ include prody/*/*.cpp
 include prody/*/*/*.cpp
 include prody/*/*.h
 include prody/*/*/*.h
+include prody/*/*/*/*.so
 include prody/tests/*/*.py
 include prody/tests/datafiles/*.coo
 include prody/tests/datafiles/*.dcd
@@ -20,3 +21,4 @@ include prody/utilities/datafiles/*.dat
 include prody/utilities/datafiles/*.txt
 include scripts/prody*
 include scripts/evol*
+include prody/protein/tabulated_energies.txt

docs/about/people.rst

@@ -21,20 +21,22 @@ Development Team
 `James Krieger`_ was helping develop *ProDy* from 2017 and became the main 
 overseer and developer in mid 2020.
 
-`Hongchun Li`_ is currently maintaining and developing ANM and GNM servers, 
+`Hongchun Li`_ has helped maintain and develop ANM and GNM servers, 
 and made significant contributions to :mod:`.database` and :mod:`.dynamics` 
 including *SignDy* and Adaptive ANM.
 
+`JiYoung Lee`_ is the main developer of :mod:`.Pharmmaker`, for constructing pharmacophore models using the outputs from :mod:`.DruGUI`.
+
 `Yan Zhang`_ contributed significantly to the development of 
 the *cryo-EM* module, :mod:`.protein.emdmap`.
 
 `Burak Kaynak`_ contributed significantly to the development of 
 :mod:`.domain_decomposition`, :mod:`.dynamics.essa`, and
 :mod:`.dynamics.clustenm`. 
 
-`Karolina Mikulska-Ruminska`_ contributed significantly to the development of 
+`Karolina Mikulska-Ruminska`_ is one of the main developers since 2022, with the addition of the new modules 
 :mod:`.protein.interactions` (*InSty*), :mod:`.protein.waterbridges`
-(*WatFinder*), and :mod:`.dynamics.mechstiff` (*MechStiff*).
+(*WatFinder*), in addition to being the developer of :mod:`.dynamics.mechstiff` (*MechStiff*).
 
 `Anthony Bogetti`_ is overseeing the overall development of *ProDy* since 
 2024.
@@ -50,6 +52,12 @@ Blocks and Membrane ENM.
 `Lidio Meireles`_ provided insightful comments on the design of *ProDy*,
 and contributed to the development of :ref:`prody-apps`.
 
+`Mustafa Tekpinar`_ contributed to the development of MechStiff.
+
+`Luca Ponzoni`_ contributed to the development of SignDy.
+
+`David Koes`_ contributed to the development of drug discovery tools.
+
 Contributors
 ------------
 
@@ -67,17 +75,16 @@ contributions and feedback from the following individuals:
 insights.
 
 
-
 .. _Ahmet Bakan: https://scholar.google.com/citations?user=-QAYVgMAAAAJ&hl=en
 .. _Cihan Kaya: https://www.linkedin.com/in/cihan-kaya/
 .. _Bahar Lab: http://www.bahargroup.org/Faculty/bahar/
 .. _University of Pittsburgh: http://www.pitt.edu/
 .. _Anindita Dutta: http://www.linkedin.com/pub/anindita-dutta/5a/568/a90
 .. _Wenzhi Mao: http://www.linkedin.com/pub/wenzhi-mao/2a/29a/29
 .. _Lidio Meireles: http://www.linkedin.com/in/lidio
-.. _Ying Liu: http://www.linkedin.com/pub/ying-liu/15/48b/5a9
+.. _Ying Liu: https://www.linkedin.com/in/yingliu03/
 .. _Kian Ho: https://github.com/kianho
-.. _Gökçen Eraslan: http://blog.yeredusuncedernegi.com/
+.. _Gökçen Eraslan: https://github.com/gokceneraslan
 .. _Tim Lezon: https://scholar.google.pl/citations?user=1MwNI3EAAAAJ&hl=pl&oi=ao
 .. _Chakra Chennubhotla: http://www.csb.pitt.edu/Faculty/Chakra/
 .. _She (John) Zhang: https://www.linkedin.com/in/she-zhang-49164399/
@@ -87,4 +94,8 @@ insights.
 .. _Burak Kaynak: https://scholar.google.pl/citations?user=gP8RokwAAAAJ&hl=pl&oi=ao
 .. _Karolina Mikulska-Ruminska: https://scholar.google.pl/citations?user=IpyPHRwAAAAJ&hl=pl
 .. _Anthony Bogetti: https://scholar.google.pl/citations?hl=pl&user=9qQClIcAAAAJ
-.. _Frane Doljanin: https://github.com/fdoljanin
+.. _Frane Doljanin: https://github.com/fdoljanin
+.. _JiYoung Lee: https://scholar.google.com/citations?user=odKQmZcAAAAJ&hl=en
+.. _David Koes: https://bits.csb.pitt.edu/
+.. _Luca Ponzoni: https://scholar.google.it/citations?user=8vfPOYUAAAAJ&hl=en
+.. _Mustafa Tekpinar: https://scholar.google.com/citations?user=qeVv6o8AAAAJ&hl=en   

docs/apps/docapps.py

@@ -1,15 +1,18 @@
 #!/usr/bin/python
 
 import os
-import imp
+import sys
 import importlib
 from subprocess import Popen, PIPE
 
-path = [importlib.util.find_spec("prody").submodule_search_locations[0]]
-apps = imp.load_module('prody.apps',
-                           *imp.find_module('apps', path))
+from prody.utilities.misctools import impLoadModule
 
-for cmd, subcmds in [('prody', apps.PRODY_APPS), ('evol', apps.EVOL_APPS)]:
+path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+
+prody_apps = impLoadModule('prody.apps.prody_apps', path_apps + '/prody_apps/', '__init__')
+evol_apps = impLoadModule('prody.apps.evol_apps', path_apps + '/evol_apps/', '__init__')
+
+for cmd, subcmds in [('prody', prody_apps.PRODY_APPS), ('evol', evol_apps.EVOL_APPS)]:
 
     pipe = Popen([cmd, '-h'], stdout=PIPE, stderr=PIPE)
     with open(os.path.join(cmd, cmd + '.txt'), 'w') as rst:

docs/devel/website.rst

@@ -14,7 +14,7 @@ This is a short guide for building the ProDy website.
 Environment Setup
 --------------
 
-First log in to the ProDy webserver (prody.csb.pitt.edu) then run the following::
+First log in to your ProDy webserver and then run the following::
 
   $ conda deactivate
 
@@ -34,7 +34,7 @@ ProDy-website-workdir. You can then copy files back over afterwards.
 
 It's recommended to have the symbolic link called test_prody pointing to 
 your build directory instead and then you can monitor changes by going to 
-http://prody.csb.pitt.edu/test_prody/_build/html/ in your web browser.
+http://yourdomainname/test_prody/_build/html/ in your web browser.
 
 
 Updating from GitHub

docs/docs

@@ -1 +1 @@
-.
+ProDy/docs

docs/reference/proteins/waterbridges.rst

@@ -3,4 +3,4 @@ Water bridge finder (WatFinder)
 
 .. automodule:: prody.proteins.waterbridges
    :members:
-   :undoc-members:
+   :undoc-members:

docs/release/index.rst

@@ -9,7 +9,8 @@ Release Notes
 .. toctree::
    :maxdepth: 2
    :glob:
-
+
+   v2.5_series
    v2.4_series
    v2.3_series
    v2.2_series

prody/apps/evol_apps/__init__.py

@@ -1,6 +1,5 @@
 """This module defines some sequence evolution applications."""
 
-import imp
 import importlib
 import sys
 
@@ -9,14 +8,22 @@
 except ImportError:
     from .. import argparse
 
-from ..apptools import *
+from prody.apps.apptools import *
+from prody.utilities.misctools import impLoadModule
 
 if sys.version_info[0] == 2:
+    import imp
     path_prody = imp.find_module('prody')[1]
 else:
     path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
-path_apps = imp.find_module('apps', [path_prody])[1]
-path_apps = imp.find_module('evol_apps', [path_apps])[1]
+
+try:
+    import imp
+    path_apps = imp.find_module('apps', [path_prody])[1]
+    path_apps = imp.find_module('evol_apps', [path_apps])[1]
+except ModuleNotFoundError:
+    path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+    path_apps += '/evol_apps/'
 
 EVOL_APPS = ['search', 'fetch', 'filter', 'refine', 'merge', 'occupancy',
              'conserv', 'coevol', 'rankorder']
@@ -81,8 +88,7 @@
 
 for cmd in EVOL_APPS:
     cmd = 'evol_' + cmd
-    mod = imp.load_module('prody.apps.evol_apps.' + cmd,
-                          *imp.find_module(cmd, [path_apps]))
+    mod = impLoadModule('prody.apps.evol_apps.', cmd, path_apps)
     mod.APP.addApplication(evol_commands)
 
 

prody/apps/prody_apps/__init__.py

@@ -1,6 +1,5 @@
 """This module defines structure and dynamics analysis applications."""
 
-import imp
 import importlib
 import sys
 
@@ -9,14 +8,22 @@
 except ImportError:
     from .. import argparse
 
-from ..apptools import *
+from prody.apps.apptools import *
+from prody.utilities.misctools import impLoadModule
 
 if sys.version_info[0] == 2:
+    import imp
     path_prody = imp.find_module('prody')[1]
 else:
     path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
-path_apps = imp.find_module('apps', [path_prody])[1]
-path_apps = imp.find_module('prody_apps', [path_apps])[1]
+
+try:
+    import imp
+    path_apps = imp.find_module('apps', [path_prody])[1]
+    path_apps = imp.find_module('prody_apps', [path_apps])[1]
+except ModuleNotFoundError:
+    path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+    path_apps += '/prody_apps/'
 
 PRODY_APPS = ['anm', 'gnm', 'pca', 'eda', 'align', 'blast', 'biomol',
                   'catdcd', 'contacts', 'fetch', 'select', 'energy', 
@@ -44,11 +51,9 @@
 
 for cmd in PRODY_APPS:
     cmd = 'prody_' + cmd
-    mod = imp.load_module('prody.apps.prody_apps.' + cmd,
-                          *imp.find_module(cmd, [path_apps]))
+    mod = impLoadModule('prody.apps.prody_apps.', cmd, path_apps)
     mod.addCommand(prody_commands)
 
-
 def prody_main():
 
     if len(sys.argv) == 1:

prody/atomic/functions.py

@@ -346,7 +346,10 @@ def extendAtoms(nodes, atoms, is3d=False):
         if res is None:
             raise ValueError('atoms must contain a residue for all atoms')
         if isinstance(res, list):
-            raise ValueError('not enough data to get a single residue for all atoms')
+            if len(res) == 1:
+                res = res[0]
+            else:
+                raise ValueError('not enough data to get a single residue for all atoms')
 
         res_atom_indices = res._getIndices()
         if not fastin(res, residues):

prody/chromatin/functions.py

@@ -212,7 +212,7 @@ def showEmbedding(modes, labels=None, trace=True, headtail=True, cmap='prism'):
         X, Y, Z = V[:,:3].T
 
         f = figure()
-        ax = f.add_subplot(projection="3d")
+        ax = f.add_subplot(1,1,1,projection="3d")
         if trace:
             ax.plot(X, Y, Z, ':', color=[0.3, 0.3, 0.3])
         if labels is None:
@@ -240,4 +240,4 @@ def getDomainList(labels):
     ends = sites[1:]
     domains = np.array([starts, ends]).T
 
-    return domains
+    return domains

prody/dynamics/__init__.py

@@ -119,6 +119,14 @@
 
   * :class:`.AdaptiveANM` - generate transitions between two conformers using best overlapping modes 
 
+ENM-MD hybrid methods
+===================
+
+The following classes and functions can be used to generate conformers using ENM-MD hybrid methods:
+
+  * :class:`.ClustENM` - generate conformers by exploring combinations of modes and clustering, using minimisation and optionally MD
+  * :function:`.ANMD` - generate conformers by traversing a number of individual modes, applying minimisation to each conformer
+
 Essential Site Scanning Analysis (ESSA)
 ========================================
 
@@ -367,3 +375,7 @@
 from . import logistic
 from .logistic import *
 __all__.extend(logistic.__all__)
+
+from . import anmd
+from .anmd import *
+__all__.extend(anmd.__all__)