[med-svn] [Git][med-team/plip][upstream] New upstream version 2.1.7+dfsg

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / plip


Commits:
393877e4 by Nilesh Patra at 2020-12-19T02:53:32+05:30
New upstream version 2.1.7+dfsg
- - - - -


6 changed files:

- plip/basic/supplemental.py
- plip/plipcmd.py
- plip/structure/preparation.py
- plip/test/test_structure_processing.py
- + plip/test/test_visualization.py
- plip/visualization/visualize.py


Changes:

=====================================
plip/basic/supplemental.py
=====================================
@@ -1,7 +1,6 @@
 import gzip
 import itertools
 import os
-import platform
 import re
 import subprocess
 import sys
@@ -17,14 +16,6 @@ from plip.basic import config, logger
 
 logger = logger.get_logger()
 
-# Windows and MacOS
-if os.name != 'nt' and platform.system() != 'Darwin':  # Resource module not available for Windows
-    import resource
-
-# Settings
-np.seterr(all='ignore')  # No runtime warnings
-
-
 def tmpfile(prefix, direc):
     """Returns the path to a newly created temporary file."""
     return tempfile.mktemp(prefix=prefix, suffix='.pdb', dir=direc)
@@ -378,10 +369,6 @@ def int32_to_negative(int32):
 def read_pdb(pdbfname, as_string=False):
     """Reads a given PDB file and returns a Pybel Molecule."""
     pybel.ob.obErrorLog.StopLogging()  # Suppress all OpenBabel warnings
-    if os.name != 'nt':  # Resource module not available for Windows
-        maxsize = resource.getrlimit(resource.RLIMIT_STACK)[-1]
-        resource.setrlimit(resource.RLIMIT_STACK, (min(2 ** 28, maxsize), maxsize))
-    sys.setrecursionlimit(10 ** 5)  # increase Python recursion limit
     return readmol(pdbfname, as_string=as_string)
 
 


=====================================
plip/plipcmd.py
=====================================
@@ -225,9 +225,8 @@ def main():
     parser.add_argument("--nohydro", dest="nohydro", default=False,
                         help="Do not add polar hydrogens in case your structure already contains hydrogens.",
                         action="store_true")
-    parser.add_argument("--model", dest="model", default=1,
-                        help="Model number to be used for multi-model structures.",
-                        action="store_true")
+    parser.add_argument("--model", dest="model", default=1, type=int,
+                        help="Model number to be used for multi-model structures.")
     # Optional threshold arguments, not shown in help
     thr = namedtuple('threshold', 'name type')
     thresholds = [thr(name='aromatic_planarity', type='angle'),


=====================================
plip/structure/preparation.py
=====================================
@@ -63,6 +63,8 @@ class PDBParser:
                     corrected_line, newnum = self.fix_pdbline(line, lastnum)
                     if corrected_line is not None:
                         if corrected_line.startswith('MODEL'):
+                            # reset atom number when new model is encountered
+                            lastnum = 0
                             try:  # Get number of MODEL (1,2,3)
                                 model_num = int(corrected_line[10:14])
                                 # initialize storage for new model
@@ -72,7 +74,8 @@ class PDBParser:
                                     other_models = True
                             except ValueError:
                                 logger.debug(f'ignoring invalid MODEL entry: {corrected_line}')
-                        lastnum = newnum
+                        else:
+                            lastnum = newnum
                         model_dict[current_model].append(corrected_line)
                 # select model
                 try:


=====================================
plip/test/test_structure_processing.py
=====================================
@@ -22,10 +22,10 @@ class StructureProcessingTestCase(unittest.TestCase):
             all_hbonds = interactions.hbonds_ldon + interactions.hbonds_pdon
             all_hydrogen_bonds.add(len(all_hbonds))
         # models contain from 0-2 hydrogen bonds
-        self.assertEquals(all_hydrogen_bonds, {0, 1, 2})
+        self.assertEqual(all_hydrogen_bonds, {0, 1, 2})
 
     def test_nmr_invalid_model(self):
         config.MODEL = 11
         interactions = characterize_complex('./pdb/2ndo.pdb', 'SFQ:A:201')
         all_hbonds = interactions.hbonds_ldon + interactions.hbonds_pdon
-        self.assertEquals(len(all_hbonds), 1)
+        self.assertEqual(len(all_hbonds), 1)


=====================================
plip/test/test_visualization.py
=====================================
@@ -0,0 +1,31 @@
+import os
+import tempfile
+import unittest
+
+from plip.basic import config
+from plip.basic.remote import VisualizerData
+from plip.structure.preparation import PDBComplex
+from plip.visualization.visualize import visualize_in_pymol
+
+
+class VisualizationTest(unittest.TestCase):
+
+    def setUp(self) -> None:
+        self.tmp_dir = tempfile.mkdtemp()
+
+    def test_visualization(self) -> None:
+
+        pdb_file = './pdb/2ndo.pdb'
+        binding_site_id = 'SFQ:A:201'
+        config.PYMOL = True
+        config.MODEL = 2
+        config.OUTPATH = str(self.tmp_dir)
+        pdb_complex = PDBComplex()
+        pdb_complex.load_pdb(pdb_file)
+        for ligand in pdb_complex.ligands:
+            if ':'.join([ligand.hetid, ligand.chain, str(ligand.position)]) == binding_site_id:
+                pdb_complex.characterize_complex(ligand)
+        visualizer_complexes = [VisualizerData(pdb_complex, site) for site in sorted(pdb_complex.interaction_sets) if
+                                not len(pdb_complex.interaction_sets[site].interacting_res) == 0]
+        visualize_in_pymol(visualizer_complexes[0])
+        self.assertEqual(1, len(os.listdir(self.tmp_dir)))


=====================================
plip/visualization/visualize.py
=====================================
@@ -8,7 +8,7 @@ logger = logger.get_logger()
 
 
 def visualize_in_pymol(plcomplex):
-    """Visualizes the protein-ligand pliprofiler at one site in PyMOL."""
+    """Visualizes the given Protein-Ligand complex at one site in PyMOL."""
 
     vis = PyMOLVisualizer(plcomplex)
 
@@ -39,7 +39,8 @@ def visualize_in_pymol(plcomplex):
 
     cmd.load(plcomplex.sourcefile)
     current_name = cmd.get_object_list(selection='(all)')[0]
-    logger.debug(f'setting current_name to {current_name} and pdbid to {pdbid}')
+
+    logger.debug(f'setting current_name to {current_name} and PDB-ID to {pdbid}')
     cmd.set_name(current_name, pdbid)
     cmd.hide('everything', 'all')
     if config.PEPTIDES:



View it on GitLab: https://salsa.debian.org/med-team/plip/-/commit/393877e4a916749d393f71c0b38cd402d1990976

-- 
View it on GitLab: https://salsa.debian.org/med-team/plip/-/commit/393877e4a916749d393f71c0b38cd402d1990976
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