update code to Hex v. 8.0; still some issues (#26, #25)

graik · Aug 2, 2018 · d2d4965 · d2d4965
1 parent 8be2eac
commit d2d4965
Show file tree

Hide file tree

Showing 4 changed files with 9 additions and 8 deletions.
diff --git a/biskit/dock/docker.py b/biskit/dock/docker.py
@@ -566,7 +566,7 @@ def dry_or_wet_run( self, run=True ):
         # dock rec 1 vs. lig 2 on localhost
         fmac1, fout = self.d.createHexInp( 1, 1 )
         if run:
-            self.d.runHex( fmac1, log=1, ncpu=4, host='localhost' )
+            self.d.runHex( fmac1, log=1, ncpu=6, host='localhost' )
 
             self.d.waitForLastHex()
 

diff --git a/biskit/dock/hexparser.py b/biskit/dock/hexparser.py
@@ -60,7 +60,7 @@ def __init__(self, hexFile, rec_dic, lig_dic, forceModel=None):
         self.lig_models = lig_dic
         self.forceModel = forceModel
         ## pattern for analyzing single line of type "Value: -1.23":
-        self.ex_line = re.compile("^(\S+):\s*([-0-9\.\s]*)")
+        self.ex_line = re.compile("^(\S+):\s*(nan|[-0-9\.\s]*)")
         ## pattern to find one line of transformation matrix
         self.ex_matrix = re.compile("([-0-9]+\.[0-9]+e[-+0-9]+)")
 
@@ -127,6 +127,8 @@ def nextComplex(self):
                         i['hex_etotal'] = float(m[1])
                     elif m[0] == 'Eshape':
                         i['hex_eshape'] = float(m[1])
+                    elif m[0] == 'Eair':
+                        i['hex_eair'] = float(m[1])
                     elif m[0] == 'LigandMatrix':
                         ## get all numbers of matrix as list of strings
                         strings = self.ex_matrix.findall( l )
@@ -204,7 +206,7 @@ def test_hexParser(self):
         rec_dic = t.load( t.testRoot() + "/dock/rec/1A2P_model.dic" )
         lig_dic = t.load( t.testRoot() + "/dock/lig/1A19_model.dic" )
 
-        self.h = HexParser( t.testRoot() + "/dock/hex/1A2P-1A19_hex.out",
+        self.h = HexParser( t.testRoot() + "/dock/hex/1A2P-1A19_hex8.out",
                             rec_dic, lig_dic)
 
         c_lst = self.h.parseHex()
@@ -217,7 +219,8 @@ def test_hexParser(self):
 
         self.assertSetEqual( set(c_lst[1].info.keys()),
                              set(['soln', 'rms', 'hex_clst', 'hex_eshape',
-                                  'model2', 'model1', 'hex_etotal', 'date']) )
+                                  'model2', 'model1', 'hex_etotal', 'hex_eair',
+                                  'date']) )
 
 if __name__ == '__main__':
 

diff --git a/biskit/testdata/dock/generate_pickles.py b/biskit/testdata/dock/generate_pickles.py
@@ -2,7 +2,6 @@
 import biskit.tools as T
 import biskit.dock.hexparser as H
 
-## generate PDBModel and model dictionary pickles for receptor and ligand
 rec = B.XplorModel(source='rec/1A2P_clean.pdb', fPsf='1A2P.psf', pdbCode='1A2P')
 rec.saveAs('rec/1A2P.model')
 
@@ -17,7 +16,7 @@
 T.dump(lig_dic, 'lig/1A19_model.dic')
 
 ## generate complex list from Hex docking result for this rec and lig
-h = H.HexParser('hex/1A2P-1A19_hex.out', rec_dic, lig_dic)
+h = H.HexParser('hex/1A2P-1A19_hex5.out', rec_dic, lig_dic)
 c_lst = h.parseHex()
 
 T.dump(c_lst, 'hex/complexes.cl')
diff --git a/scripts2/Dock/hex2complex.py b/scripts2/Dock/hex2complex.py
@@ -71,7 +71,7 @@ def setOptions():
 
     o.setTest( lig= osp.join(f, 'dock/lig/1A19_model.dic'),
                rec= osp.join(f, 'dock/rec/1A2P_model.dic'),
-               hex= osp.join(f, 'dock/hex/1A2P-1A19_hex.out'),
+               hex= osp.join(f, 'dock/hex/1A2P-1A19_hex5.out'),
                o=   osp.join(ftemp, 'complexes.cl'),
                p= 0,
                fsuccess=testSuccess )
@@ -153,7 +153,6 @@ def plot( complex_lst ):
 def main( o ):
     """@param o: options dictionary"""
 
-    ## load pickeled model dictionaries with XplorModels indexed by hex model
     ## number
     rec_lst = load( o['rec'] )
     lig_lst = load( o['lig'] )