Merge pull request #1940 from prod-feng/master

From Feng

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/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/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/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/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/waterbridges.py

@@ -15,7 +15,18 @@
 
 from itertools import combinations
 from collections import deque
-from enum import Enum, auto
+
+from prody import PY3K
+if PY3K:
+    from enum import Enum, auto
+else:
+    from enum import Enum
+    import enum
+    from itertools import count
+    def auto(it=count()):
+        return next(it)
+    enum.auto=auto
+
 from copy import copy
 
 from prody import LOGGER, SETTINGS
@@ -263,8 +274,10 @@ def getInfoOutput(waterBridgesAtomic):
         bridgeOutput = []
 
         for atom in bridge.proteins:
-            residueInfo = f"{atom.getResname()}{atom.getResnum()}"
-            atomInfo = f"{atom.getName()}_{atom.getIndex()}"
+            residueInfo = "{0}{1}".format(atom.getResname(), 
+                                          atom.getResnum())
+            atomInfo = "{0}_{1}".format(atom.getName(),
+                                        atom.getIndex())
             chainInfo = atom.getChid()
             bridgeOutput += [residueInfo, atomInfo, chainInfo]
 
@@ -273,7 +286,9 @@ def getInfoOutput(waterBridgesAtomic):
 
         bridgeOutput += [len(bridge.waters)]
         bridgeOutput += [
-            list(map(lambda w: f"{w.getChid()}_{w.getIndex()}", bridge.waters))]
+            list(map(lambda w: "{0}_{1}".format(w.getChid(),
+                                                w.getIndex()), 
+                     bridge.waters))]
 
         output.append(bridgeOutput)
 
@@ -314,7 +329,7 @@ def getAtomicOutput(waterBridges, relations):
 
 
 def getElementsRegex(elements):
-    return f'[{"|".join(elements)}].*'
+    return '[{0}].*'.format("|".join(elements))
 
 
 def calcWaterBridges(atoms, **kwargs):
@@ -417,7 +432,7 @@ def calcWaterBridges(atoms, **kwargs):
 
     relations = RelationList(len(atoms))
     tooFarAtoms = atoms.select(
-        f'water and not within {distWR} of protein')
+        'water and not within {0} of protein'.format(distWR))
     if tooFarAtoms is None:
         consideredAtoms = atoms
     else:
@@ -434,9 +449,10 @@ def calcWaterBridges(atoms, **kwargs):
         relations[oxygen].hydrogens.append(hydrogen)
 
     proteinHydrophilic = consideredAtoms.select(
-        f'protein and name "{getElementsRegex(set(donors+acceptors))}" and within {distWR} of water')
+        'protein and name "{0}" and within {1} of water'.format(
+            getElementsRegex(set(donors+acceptors)), distWR))
 
-    proteinHydrogens = consideredAtoms.select(f'protein and hydrogen') or []
+    proteinHydrogens = consideredAtoms.select('protein and hydrogen') or []
     proteinHydroPairs = findNeighbors(
         proteinHydrophilic, DIST_COVALENT_H, proteinHydrogens) if proteinHydrogens else []
     for hydrophilic in proteinHydrophilic:
@@ -474,7 +490,8 @@ def calcWaterBridges(atoms, **kwargs):
         waterBridgesWithIndices = getUniqueElements(
             waterBridgesWithIndices, getChainBridgeTuple)
 
-    log_string = f'{len(waterBridgesWithIndices)} water bridges detected using method {method}'
+    log_string = '{0} water bridges detected using method {1}'.format(
+        len(waterBridgesWithIndices), method)
     if prefix != '':
         log_string += ' for ' + prefix
     LOGGER.info(log_string)
@@ -715,7 +732,7 @@ def getResInfo(atoms):
     chids = atoms.select('protein').getChids()
 
     for i, num in enumerate(nums):
-        dict[num] = f"{names[i]}{num}{chids[i]}"
+        dict[num] = "{names[i]}{num}{chids[i]}"
 
     return dict
 
@@ -796,7 +813,8 @@ def calcWaterBridgesStatistics(frames, trajectory, **kwargs):
     interactionCount.removeDuplicateKeys(
         lambda keys, key: (key[1], key[0]) in keys)
 
-    tableHeader = f'{"RES1":<15}{"RES2":<15}{"PERC":<10}{"DIST_AVG":<10}{"DIST_STD":<10}'
+    tableHeader = '{0:<15}{1:<15}{2:<10}{3:<10}{4:<10}'.format(
+        "RES1", "RES2", "PERC", "DIST_AVG", "DIST_STD")
     LOGGER.info(tableHeader)
     info = {}
     file = open(filename, 'w') if filename else None
@@ -819,7 +837,8 @@ def calcWaterBridgesStatistics(frames, trajectory, **kwargs):
             key1, key2 = (x, y), (y, x)
             info[key1], info[key2] = pairInfo, pairInfo
 
-        tableRow = f'{resNames[x]:<15}{resNames[y]:<15}{percentage:<10.3f}{distAvg:<10.3f}{distStd:<10.3f}'
+        tableRow = '{0:<15}{1:<15}{2:<10.3f}{3:<10.3f}{4:<10.3f}'.format(
+            resNames[x], resNames[y], percentage, distAvg, distStd)
         LOGGER.info(tableRow)
         if file:
             file.write(tableRow + '\n')
@@ -885,7 +904,7 @@ def mofifyBeta(bridgeFrames, atoms):
     atoms.setBetas(0)
     for resnum, value in residueOccurances.items():
         residueAtoms = atoms.select(
-            f'resnum {resnum}')
+            'resnum {0}'.format(resnum))
         beta = value/len(bridgeFrames)
 
         residueAtoms.setBetas(beta)
@@ -1075,7 +1094,7 @@ def calcWaterBridgesDistribution(frames, res_a, res_b=None, **kwargs):
         plt.hist(result, rwidth=0.95, density=True)
         plt.xlabel('Value')
         plt.ylabel('Probability')
-        plt.title(f'Distribution: {metric}')
+        plt.title('Distribution: {0}'.format(metric))
         if SETTINGS['auto_show']:
             showFigure()
 
@@ -1108,7 +1127,8 @@ def savePDBWaterBridges(bridges, atoms, filename):
     waterOxygens = reduceTo1D(
         bridges, lambda w: w.getIndex(), lambda b: b.waters)
     waterAtoms = atoms.select(
-        f'same residue as water within 1.6 of index {" ".join(map(str, waterOxygens))}')
+        'same residue as water within 1.6 of index {0}'.format(
+            " ".join(map(str, waterOxygens))))
 
     atomsToSave = proteinAtoms.toAtomGroup() + waterAtoms.toAtomGroup()
     return writePDB(filename, atomsToSave)
@@ -1147,21 +1167,23 @@ def saveBridgesFrame(trajectory, atoms, frameIndex, frame):
 
         waterAtoms = reduceTo1D(frame, sublistSel=lambda b: b.waters)
         waterResidues = atoms.select(
-            f'same residue as water within 1.6 of index {" ".join(map(lambda a: str(a.getIndex()), waterAtoms))}')
+            'same residue as water within 1.6 of index {0}'.format(
+                " ".join(map(lambda a: str(a.getIndex()), waterAtoms))))
 
         bridgeProteinAtoms = reduceTo1D(
             frame, lambda p: p.getResnum(), lambda b: b.proteins)
         atoms.setOccupancies(0)
-        atoms.select(
-            f'resid {" ".join(map(str, bridgeProteinAtoms))}').setOccupancies(1)
+        atoms.select('resid {0}'.format(
+            " ".join(map(str, bridgeProteinAtoms)))).setOccupancies(1)
 
         atomsToSave = atoms.select(
             'protein').toAtomGroup() + waterResidues.toAtomGroup()
 
         if trajectory:
-            writePDB(f'{filename}_{frameIndex}.pdb', atomsToSave)
+            writePDB('{0}_{1}.pdb'.format(filename, frameIndex),
+                     atomsToSave)
         else:
-            writePDB(f'{filename}_{frameIndex}.pdb',
+            writePDB('{0}_{1}.pdb'.format(filename, frameIndex),
                      atomsToSave, csets=frameIndex)
 
     if max_proc == 1:
@@ -1210,7 +1232,7 @@ def saveWaterBridges(atomicBridges, filename):
     if isInfoOutput:
         info = getWaterBridgesInfoOutput(atomicBridges)
         for frameIndex, frame in enumerate(info):
-            file.write(f'FRAME {frameIndex}\n')
+            file.write('FRAME {0}\n'.format(frameIndex))
             for bridge in frame:
                 file.write(' '.join(map(str, bridge)) + '\n')