Merge branch 'prody:main' into main

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-This is a first draft, which is based on the ProDy website page http://prody.csb.pitt.edu/manual/devel/develop.html. Please see that page for updates.
+This is a first draft, which is based on the ProDy website page http://www.bahargroup.org/prody/manual/devel/develop.html. Please see that page for updates.
 
 
 Install Git and a GUI

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

PKG-INFO

@@ -32,23 +32,23 @@ Description: .. image:: https://secure.travis-ci.org/prody/ProDy.png?branch=mast
         You can run ProDy on all major platforms.  For download and installation
         instructions see:
 
-        * http://prody.csb.pitt.edu/downloads
+        * http://www.bahargroup.org/prody/downloads
 
 
         DOCUMENTATION
         -------------
 
-        * Homepage: http://prody.csb.pitt.edu/
+        * Homepage: http://www.bahargroup.org/prody/
 
-        * Tutorials: http://prody.csb.pitt.edu/tutorials
+        * Tutorials: http://www.bahargroup.org/prody/tutorials
 
-        * Reference: http://prody.csb.pitt.edu/manual
+        * Reference: http://www.bahargroup.org/prody/manual
 
-        * Applications: http://prody.csb.pitt.edu/manual/apps
+        * Applications: http://www.bahargroup.org/prody/manual/apps
 
-        * NMWiz GUI: http://prody.csb.pitt.edu/nmwiz
+        * NMWiz GUI: http://www.bahargroup.org/prody/nmwiz
 
-        * Changes: http://prody.csb.pitt.edu/manual/release
+        * Changes: http://www.bahargroup.org/prody/manual/release
 
 
         SOURCE CODE

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/prody/index.rst

@@ -40,4 +40,4 @@ the output files are prefixed with :file:`p38_anm`::
 
 The output file :file:`p38_anm.nmd` can be visualized using `NMWiz`_.
 
-.. _NMWiz: http://prody.csb.pitt.edu/nmwiz/
+.. _NMWiz: http://www.bahargroup.org/prody/nmwiz/

docs/conf.py

@@ -158,13 +158,13 @@
     'numpy': ('http://docs.scipy.org/doc/numpy/', None),
     'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
     'matplotlib': ('http://matplotlib.sourceforge.net/', None),
-    'prodywebsite': ('http://prody.csb.pitt.edu/', None),
+    'prodywebsite': ('http://www.bahargroup.org/prody/', None),
 }
 
 rst_epilog = u"""
 
-.. _ProDy: http://prody.csb.pitt.edu
-.. _Tutorials: http://prody.csb.pitt.edu/tutorials
+.. _ProDy: http://www.bahargroup.org/prody
+.. _Tutorials: http://www.bahargroup.org/prody/tutorials
 .. _NMWiz: http://csb.pitt.edu/NMWiz
 .. _VMD: http://www.ks.uiuc.edu/Research/vmd
 .. _PDB: http://www.pdb.org

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/index.rst

@@ -11,7 +11,7 @@ ProDy Manual
 .. only:: rtd and html
 
     This is a partial copy of ProDy documentation.  Please visit
-    `ProDy Homepage <http://prody.csb.pitt.edu>`_ for complete
+    `ProDy Homepage <http://www.bahargroup.org/prody>`_ for complete
     documentation with tutorials.
 
 

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/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/compounds/pdbligands.py

@@ -8,6 +8,7 @@
 from prody import LOGGER, SETTINGS, getPackagePath, PY3K
 from prody.atomic import AtomGroup, ATOMIC_FIELDS
 from prody.utilities import openFile, makePath, openURL
+from .ccd import parseCCD
 
 __all__ = ['PDBLigandRecord', 'fetchPDBLigand', 'parsePDBLigand']
 
@@ -18,13 +19,20 @@ def __init__(self, data):
         self._rawdata = data
 
     def getCanonicalSMILES(self):
-        return self._rawdata['CACTVS_SMILES_CANONICAL']
+        canonical = None
+        for row in self._rawdata[2].data:
+            if row['_pdbx_chem_comp_descriptor.type'] == 'SMILES_CANONICAL':
+                canonical = row['_pdbx_chem_comp_descriptor.descriptor']
+        return canonical
 
 
 def fetchPDBLigand(cci, filename=None):
-    """Fetch PDB ligand data from PDB_ for chemical component *cci*.
+    """Handle PDB ligand data from PDB_ for chemical component *cci*.
     *cci* may be 3-letter chemical component identifier or a valid XML
-    filename.  If *filename* is given, XML file will be saved with that name.
+    filename. If *filename* is given, XML file will be saved with that name.
+
+    This function may not work as _PDB is not hosting ligand XML files anymore.
+    It is kept for use with existing ligand XML files.
 
     If you query ligand data frequently, you may configure ProDy to save XML
     files in your computer.  Set ``ligand_xml_save`` option **True**, i.e.
@@ -50,6 +58,7 @@ def fetchPDBLigand(cci, filename=None):
     ideal (energy minimized) coordinate sets:
 
     .. ipython:: python
+       :okexcept:
 
        from prody import *
        ligand_data = fetchPDBLigand('STI')
@@ -233,8 +242,8 @@ def fetchPDBLigand(cci, filename=None):
     return dict_
 
 
-def parsePDBLigand(cci, filename=None):
+def parsePDBLigand(cci):
     """See :func:`.fetchPDBLigand`"""
-    lig_dict = fetchPDBLigand(cci, filename)
+    lig_dict = parseCCD(cci)
     return PDBLigandRecord(lig_dict)
 

prody/dynamics/plotting.py

@@ -110,7 +110,7 @@ def showEllipsoid(modes, onto=None, n_std=2, scale=1., *args, **kwargs):
             show = child
             break
     if show is None:
-        show = cf.add_subplot(projection="3d")
+        show = cf.add_subplot(111,projection="3d")
     show.plot_wireframe(x, y, z, rstride=6, cstride=6, *args, **kwargs)
     if onto is not None:
         onto = list(onto)
@@ -421,7 +421,7 @@ def showProjection(ensemble=None, modes=None, projection=None, *args, **kwargs):
                 show = child
                 break
         if show is None:
-            show = cf.add_subplot(projection="3d")
+            show = cf.add_subplot(111,projection="3d")
         plot = show.plot
         text = show.text
 

prody/dynamics/sampling.py

@@ -51,9 +51,10 @@ def sampleModes(modes, atoms=None, n_confs=1000, rmsd=1.0):
 
     RMSD of the new conformation from :math:`R_0` can be calculated as
 
+
     .. math::
 
-      RMSD^k = \\sqrt{ {\\left( s \\sum_{i=1}^{m} r_i^k \\lambda^{-0.5}_i u_i  \\right)}^{2} / N } = \\frac{s}{ \\sqrt{N}} \\sqrt{ \\sum_{i=1}^{m} (r_i^k)^2 \\lambda^{-1}_i  }
+      RMSD^k = \\sqrt{  \\left[ s \\sum_{i=1}^{m} r_i^k \\lambda^{-0.5}_i u_i \\right] ^{2} / N } = \\frac{s}{ \\sqrt{N}} \\sqrt{ \\sum_{i=1}^{m} (r_i^k)^2 \\lambda^{-1}_i  }
 
 
     Average :math:`RMSD` of the generated conformations from the initial conformation is:

prody/ensemble/functions.py

@@ -411,7 +411,7 @@ def buildPDBEnsemble(atomics, ref=None, title='Unknown', labels=None, atommaps=N
 
     if 'mapping_func' in kwargs:
         raise DeprecationWarning('mapping_func is deprecated. Please see release notes for '
-                                 'more details: http://prody.csb.pitt.edu/manual/release/v1.11_series.html')
+                                 'more details: http://www.bahargroup.org/prody/manual/release/v1.11_series.html')
     start = time.time()
 
     if not isListLike(atomics):

prody/proteins/functions.py

@@ -266,7 +266,7 @@ def showProtein(*atoms, **kwargs):
                 show = child
                 break
         if show is None:
-            show = cf.add_subplot(projection="3d")
+            show = cf.add_subplot(1,1,1,projection="3d")
         from matplotlib import colors
         cnames = dict(colors.cnames)
         wcolor = kwargs.get('water', 'red').lower()

prody/proteins/interactions.py

@@ -163,7 +163,7 @@ def calcHydrophobicOverlapingAreas(atoms, **kwargs):
     :arg selection: selection string of hydrophobic residues
     :type selection: str
     
-    :arg hpb_cutoff: cutoff for hydrophobic overlaping area values
+    :arg hpb_cutoff: cutoff for hydrophobic overlapping area values
         default is 0.0
     :type hpb_cutoff: float, int
     
@@ -200,7 +200,7 @@ def calcHydrophobicOverlapingAreas(atoms, **kwargs):
         lA = [ [x[i] + str(y[i]), z[i] +'_'+ str(w[i]), ch[i]] for i in range(len(x))]
 
         output = hpb.hpb((lB,lA))
-        LOGGER.info("Hydrophobic Overlaping Areas are computed.")
+        LOGGER.info("Hydrophobic Overlapping Areas are computed.")
         output_final = [i for i in output if i[-1] >= hpb_cutoff]
 
         if cumulative_values == None:            
@@ -1000,11 +1000,11 @@ def calcHydrophobic(atoms, **kwargs):
                         non_standard works too
     :type non_standard_Hph: dict
 
-    :arg zerosHPh: zero values of hydrophobic overlaping areas included
+    :arg zerosHPh: zero values of hydrophobic overlapping areas included
         default is False
     :type zerosHPh: bool
 
-    Last value in the output corresponds to the total hydrophobic overlaping area for two residues
+    Last value in the output corresponds to the total hydrophobic overlapping area for two residues
     not only for the atoms that are included in the list. Atoms that which are listed are the closest
     between two residues and they will be inluded to draw the line in VMD_.
     
@@ -1065,7 +1065,7 @@ def calcHydrophobic(atoms, **kwargs):
     aromatic_nr = list(set(zip(atoms.aromatic.getResnums(),atoms.aromatic.getChids())))   
     aromatic = list(set(atoms.aromatic.getResnames()))
 
-    # Computing hydrophobic overlaping areas for pairs of residues:
+    # Computing hydrophobic overlapping areas for pairs of residues:
     try:
         hpb_overlaping_results = calcHydrophobicOverlapingAreas(atoms_hydrophobic, cumulative_values='pairs')
     except: