Merge branch 'main' of github.com:prody/ProDy into scipion

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/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/fixer.py

@@ -28,7 +28,7 @@ def addMissingAtoms(infile, method='openbabel', pH=7.0, outfile=None, **kwargs):
     or PDBFixer with OpenMM. 
     
     There are also options whether to *model_residues* (default False), *remove_heterogens* 
-    (default False), *keep_waters* (default True), *overwrite* (default False).
+    (default False), *keep_waters* (default True), *overwrite* (default False), *keep_ids* (default True).
     
     :arg infile: PDB file name
     :type infile: str
@@ -41,9 +41,17 @@ def addMissingAtoms(infile, method='openbabel', pH=7.0, outfile=None, **kwargs):
             default is 'openbabel'
     :type method: str
     
-    :arg pH: pH value applyed only for PDBfixer.
+    :arg pH: pH value applied only for PDBfixer.
     :type pH: int, float
     
+    :arg model_residues: add all missing atoms from residues, applied only for PDBfixer.
+                    default is False
+    :type model_residues: bool
+    
+    :arg keep_ids: keep the original residue number, applied only for PDBfixer.
+                    default is True
+    :type keep_ids: bool
+
     Instalation of Openbabel:
     conda install -c conda-forge openbabel    
 
@@ -58,6 +66,7 @@ def addMissingAtoms(infile, method='openbabel', pH=7.0, outfile=None, **kwargs):
     remove_heterogens = kwargs.get("remove_heterogens", False)
     keep_water = kwargs.get("keep_water", True)
     overwrite = kwargs.get("overwrite", False)
+    keep_ids = kwargs.get("keep_ids", True)
 
     import os
 
@@ -70,6 +79,9 @@ def addMissingAtoms(infile, method='openbabel', pH=7.0, outfile=None, **kwargs):
     if not isinstance(keep_water, bool):
         raise TypeError('keep_water should be True or False')
 
+    if not isinstance(keep_ids, bool):
+        raise TypeError('keep_ids should be True or False')
+
     if not isinstance(overwrite, bool):
         raise TypeError('overwrite should be True or False')
 
@@ -136,7 +148,7 @@ def addMissingAtoms(infile, method='openbabel', pH=7.0, outfile=None, **kwargs):
             fixer.findMissingAtoms()
             fixer.addMissingAtoms()
             fixer.addMissingHydrogens(pH)
-            PDBFile.writeFile(fixer.topology, fixer.positions, open(outfile, 'w'))
+            PDBFile.writeFile(fixer.topology, fixer.positions, open(outfile, 'w'), keepIds=keep_ids)
             LOGGER.info("Hydrogens were added to the structure. New structure is saved as {0}.".format(outfile))
 
         except ImportError:
@@ -165,8 +177,16 @@ def fixStructuresMissingAtoms(infiles, method='openbabel', pH=7.0, outfiles=None
             'pdbfixer': PDBFixer and OpenMM
             default is 'openbabel'
     :type method: str
+
+    :arg model_residues: add all missing atoms from residues, applied only for PDBfixer.
+                    default is False
+    :type model_residues: bool
+    
+    :arg keep_ids: keep the original residue number, applied only for PDBfixer.
+                    default is True
+    :type keep_ids: bool
     
-    :arg pH: pH value applyed only for PDBfixer.
+    :arg pH: pH value applied only for PDBfixer.
     :type pH: int, float
     
     Instalation of Openbabel:

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()