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

jamesmkrieger · Aug 22, 2024 · 375179c · 375179c
2 parents f8cca17 + 9776bb5
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diff --git a/CONTRIBUTING.md b/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

diff --git a/PKG-INFO b/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

diff --git a/docs/apps/prody/index.rst b/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/
diff --git a/docs/conf.py b/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

diff --git a/docs/index.rst b/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.
 
 

diff --git a/prody/compounds/pdbligands.py b/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)
 
diff --git a/prody/ensemble/functions.py b/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):

diff --git a/prody/proteins/pdbfile.py b/prody/proteins/pdbfile.py
@@ -490,11 +490,10 @@ def _parsePDBLines(atomgroup, lines, split, model, chain, subset,
         elements = np.zeros(asize, dtype=ATOMIC_FIELDS['element'].dtype)
         bfactors = np.zeros(asize, dtype=ATOMIC_FIELDS['beta'].dtype)
         occupancies = np.zeros(asize, dtype=ATOMIC_FIELDS['occupancy'].dtype)
-        anisou = None
         siguij = None
     else:
         radii = np.zeros(asize, dtype=ATOMIC_FIELDS['radius'].dtype)
-
+    anisou = None
     asize = 2000 # increase array length by this much when needed
 
     start = split
@@ -537,19 +536,7 @@ def _parsePDBLines(atomgroup, lines, split, model, chain, subset,
     dec = True
     while i < stop:
         line = lines[i]
-        if not isPDB:
-            fields = line.split()
-            if len(fields) == 10:
-                fields.insert(4, '')
-            elif len(fields) != 11:
-                LOGGER.warn('wrong number of fields for PQR format at line %d'%i)
-                i += 1
-                continue
-
-        if isPDB:
-            startswith = line[0:6].strip()
-        else:
-            startswith = fields[0]
+        startswith = line[0:6].strip()
 
         if startswith == 'ATOM' or startswith == 'HETATM':
             if isPDB:
@@ -560,6 +547,17 @@ def _parsePDBLines(atomgroup, lines, split, model, chain, subset,
                 else:
                     resname = line[17:20].strip()
             else:
+                fields = line.split()
+                if fields[5].find('.') != -1:
+                    # coords too early as no chid
+                    fields.insert(4, '')
+                if len(fields) != 11:
+                    try:
+                        fields = fields[:6] + [line[30:38].strip(), line[38:46].strip(), line[46:54].strip()] + line[54:].split()
+                    except:
+                        LOGGER.warn('wrong number of fields for PQR format at line %d'%i)
+                        i += 1
+                        continue
                 atomname= fields[2]
                 resname = fields[3]
 
@@ -1689,7 +1687,10 @@ def writePQRStream(stream, atoms, **kwargs):
     write = stream.write
 
     calphas = atoms.ca
-    ssa = calphas.getSecstrs()
+    if calphas is not None:
+        ssa = calphas.getSecstrs()
+    else:
+        ssa = None
     helix = []
     sheet = []
     if ssa is not None:

diff --git a/prody/proteins/waterbridges.py b/prody/proteins/waterbridges.py
@@ -638,9 +638,9 @@ def analyseFrame(i, interactions_all):
 
             if max_proc == 1:
                 interactions_all = []
-                for j0, frame0 in enumerate(traj, start=start_frame):
+                for i in range(len(atoms.getCoordsets()[start_frame:stop_frame])):
                     interactions_all.append([])
-                    analyseFrame(j0, start_frame, frame0, interactions_all)
+                    analyseFrame(i, interactions_all)
             else:
                 with mp.Manager() as manager:
                     interactions_all = manager.list()

diff --git a/prody/tests/datafiles/__init__.py b/prody/tests/datafiles/__init__.py
@@ -381,6 +381,26 @@
         'file': 'pdb7pbl.pdb',
         'atoms': 31396,
         'nucleoside': 252
+    },
+    'pqrUnknown': {
+        'file': 'pqr_snippet1.pqr',
+        'atoms': 5,
+        'models': 1
+    },
+    'pqrTranscomp': {
+        'file': 'pqr_snippet2_transcomp.pqr',
+        'atoms': 5,
+        'models': 1
+    },
+    'pqrFpocket': {
+        'file': 'pqr_snippet3_fpocket.pqr',
+        'atoms': 5,
+        'models': 1
+    },
+    'pqrPymol': {
+        'file': 'pqr_snippet4_pymol.pqr',
+        'atoms': 5,
+        'models': 1
     }
 }
 

diff --git a/prody/tests/datafiles/pqr_snippet1.pqr b/prody/tests/datafiles/pqr_snippet1.pqr
@@ -0,0 +1,5 @@
+ATOM      1    C STP     1     -26.417  62.269-123.283    0.00     3.30
+ATOM      2    O STP     1     -30.495  65.669-122.669    0.00     3.08
+ATOM      3    O STP     1     -25.792  61.516-124.085    0.00     3.32
+ATOM      4    O STP     1     -25.262  61.506-124.230    0.00     3.05
+ATOM      5    O STP     1     -30.521  65.070-122.439    0.00     3.05
diff --git a/prody/tests/datafiles/pqr_snippet2_transcomp.pqr b/prody/tests/datafiles/pqr_snippet2_transcomp.pqr
@@ -0,0 +1,5 @@
+ATOM      1  N   VAL     1      16.783  48.812  26.447  0.0577   1.550
+ATOM      2  H1  VAL     1      15.848  48.422  26.463  0.2272   1.200
+ATOM      3  H2  VAL     1      16.734  49.803  26.251  0.2272   1.200
+ATOM      4  H3  VAL     1      17.195  48.663  27.359  0.2272   1.200
+ATOM      5  CA  VAL     1      17.591  48.101  25.416 -0.0054   1.700
diff --git a/prody/tests/datafiles/pqr_snippet3_fpocket.pqr b/prody/tests/datafiles/pqr_snippet3_fpocket.pqr
@@ -0,0 +1,5 @@
+ATOM      1    C STP     1     -26.417  62.269-123.283    0.00     3.30
+ATOM      2    O STP     1     -30.495  65.669-122.669    0.00     3.08
+ATOM      3    O STP     1     -25.792  61.516-124.085    0.00     3.32
+ATOM      4    O STP     1     -25.262  61.506-124.230    0.00     3.05
+ATOM      5    O STP     1     -30.521  65.070-122.439    0.00     3.05
diff --git a/prody/tests/datafiles/pqr_snippet4_pymol.pqr b/prody/tests/datafiles/pqr_snippet4_pymol.pqr
@@ -0,0 +1,5 @@
+ATOM     29  P     G    11     -17.189  -6.642 -23.827  0.00000000   0.000
+ATOM     30  C5'   G    11     -15.744  -5.986 -25.911  0.00000000   0.000
+ATOM     31  O5'   G    11     -16.783  -5.642 -25.005  0.00000000   0.000
+ATOM     32  C4'   G    11     -15.722  -5.012 -27.074  0.00000000   0.000
+ATOM     33  O4'   G    11     -16.947  -5.133 -27.838  0.00000000   0.000
diff --git a/prody/tests/proteins/test_pdbfile.py b/prody/tests/proteins/test_pdbfile.py
@@ -19,7 +19,7 @@
 class TestParsePDB(unittest.TestCase):
 
     def setUp(self):
-        """Set PDB file data and parse the PDB file."""
+        """Set PDB file data."""
 
         self.pdb = DATA_FILES['multi_model_truncated']
         self.one = DATA_FILES['oneatom']
@@ -108,14 +108,22 @@ def testSubsetArgument(self):
                         'failed to parse correct number of "bb" atoms')
 
     def testAgArgument(self):
-        """Test outcome of valid and invalid *ag* arguments."""
+        """Test outcome of 2 invalid and 2 valid *ag* arguments."""
 
         path = pathDatafile(self.pdb['file'])
         self.assertRaises(TypeError, parsePDB, path, ag='AtomGroup')
+
         ag = prody.AtomGroup('One atom')
         ag.setCoords(np.array([[0., 0., 0.]]))
         self.assertRaises(ValueError, parsePDB, path, ag=ag)
+
+        ag = prody.AtomGroup('Test')
+        self.assertEqual(parsePDB(path, ag=ag).numAtoms(),
+            self.pdb['atoms'],
+            'parsePDB failed to parse correct number of atoms')
+
         ag = prody.AtomGroup('Test')
+        ag.setCoords(np.array([[0., 0., 0.]]*self.pdb['atoms']))
         self.assertEqual(parsePDB(path, ag=ag).numAtoms(),
             self.pdb['atoms'],
             'parsePDB failed to parse correct number of atoms')