Merge branch 'interactions' into prody-cavifinder

.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", "3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2

MANIFEST.in

@@ -21,3 +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/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:

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/dynamics/rtbtools.c

@@ -419,7 +419,7 @@ void cross(double x[], double y[], double z[])
 int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB, 
 			int nres, int nblx, int bmx)
 {
-  double **X, **I, **IC, *CM, *W, **A, **ISQT;
+  double **X, **Ii, **IC, *CM, *W, **A, **ISQT;
   double x, tr, dd, df;
   int *IDX, nbp, b, i, j, k, ii, jj, aa, bb, elm;
 
@@ -429,7 +429,7 @@ int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB,
   X = dmatrix(1, bmx, 1, 3);
   IDX = ivector(1, bmx);
   CM = dvector(1, 3);
-  I = dmatrix(1, 3, 1, 3);
+  Ii = dmatrix(1, 3, 1, 3);
   IC = dmatrix(1, 3, 1, 3);
   W = dvector(1, 3);
   A = dmatrix(1, 3, 1, 3);
@@ -442,7 +442,7 @@ int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB,
     for(j=1; j<=3; j++)
     {
       CM[j] = 0.0;
-      for(i=1; i<=3; i++) I[i][j] = 0.0;
+      for(i=1; i<=3; i++) Ii[i][j] = 0.0;
       for(i=1; i<=bmx; i++) X[i][j] = 0.0;
     }
 
@@ -478,19 +478,19 @@ int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB,
       }
       for(i=1; i<=3; i++)
       {
-        I[i][i] += (dd - X[k][i] * X[k][i]);
+        Ii[i][i] += (dd - X[k][i] * X[k][i]);
         for(j=i+1; j<=3; j++)
         {
-          I[i][j] -= X[k][i]*X[k][j];
-          I[j][i] = I[i][j];
+          Ii[i][j] -= X[k][i]*X[k][j];
+          Ii[j][i] = Ii[i][j];
 	      }
       }
     }
 
     /* DIAGONALIZE INERTIA TENSOR */
     for (i=1; i<=3; i++)
       for (j=1; j<=3; j++)
-	      IC[i][j]=I[i][j];
+	      IC[i][j]=Ii[i][j];
     dsvdcmp(IC, 3, 3, W, A);
     deigsrt(W, A, 3);
     righthand2(W, A, 3);
@@ -545,7 +545,7 @@ int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB,
   free_dmatrix(X, 1, bmx, 1, 3);
   free_ivector(IDX, 1, bmx);
   free_dvector(CM, 1, 3);
-  free_dmatrix(I, 1, 3, 1, 3);
+  free_dmatrix(Ii, 1, 3, 1, 3);
   free_dmatrix(IC, 1, 3, 1, 3);
   free_dvector(W, 1, 3);
   free_dmatrix(A, 1, 3, 1, 3);

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: