update pdb2sql related code

.gitignore

@@ -32,3 +32,4 @@ example/training_set/kernel/*
 example/training_set/test/kernel/*
 example/training_set/test/graph/*
 _training_set_/*
+.vscode/*

iScore/energetic/internal_energy.py

@@ -1,6 +1,6 @@
 import os
 import numpy as np
-from pdb2sql.pdb2sqlcore import pdb2sql
+from pdb2sql import pdb2sql
 
 class InternalEnergy(object):
 

iScore/graphrank/graph.py

@@ -3,8 +3,8 @@
 import scipy.io as spio
 import pickle
 import h5py
-from pdb2sql.pdb2sqlcore import pdb2sql
-from pdb2sql.interface import interface
+from pdb2sql import pdb2sql
+from pdb2sql import interface
 from Bio import pairwise2
 import warnings
 
@@ -301,7 +301,7 @@ def __init__(self,pdbfile,pssmfile, aligned=True, export=True,
 
         # pdb file
         self.pdbfile = pdbfile
-        self.pdb = pdb2sql(self.pdbfile,no_extra=True)
+        self.pdb = pdb2sql(self.pdbfile)
 
         # residue name translation dict
         self.resmap = {
@@ -556,7 +556,7 @@ def get_graph(self,name=None):
 
         if name is None:
             name = os.path.splitext(self.pdbfile)[0]
-            
+
         return Graph(name = name,
                       nodes_pssm = nodes_pssm,
                       nodes_info = nodes_info,

iScore/h5x/baseimport.py

@@ -3,7 +3,7 @@
 import os
 import subprocess as sp
 
-from pdb2sql.pdb2sqlcore import pdb2sql
+from pdb2sql import pdb2sql
 
 
 def launchPyMol(grp):
@@ -34,8 +34,8 @@ def launchPyMol(grp):
 
     for n in grp['nodes']:
         db.exportpdb(tmp_file,append=True,
-                             chainID=n[0].decode('utf-8'), 
-                             resSeq= n[1].decode('utf-8'), 
+                             chainID=n[0].decode('utf-8'),
+                             resSeq= n[1].decode('utf-8'),
                              resName=n[2].decode('utf-8'))
 
     f.write("# load the contact\n")
@@ -46,8 +46,8 @@ def launchPyMol(grp):
     nodes  = []
     f.write('graph = [\n')
     for n in grp['nodes']:
-        xyz = db.get('x,y,z',chainID=n[0].decode('utf-8'), 
-                             resSeq= n[1].decode('utf-8'), 
+        xyz = db.get('x,y,z',chainID=n[0].decode('utf-8'),
+                             resSeq= n[1].decode('utf-8'),
                              resName=n[2].decode('utf-8'))
         xyz = np.mean(xyz,0)
         nodes.append(xyz)

iScore/pssm/pssm.py

@@ -1,6 +1,6 @@
 import os, glob, shutil
 from Bio.Blast.Applications import NcbipsiblastCommandline
-from pdb2sql.pdb2sqlcore import pdb2sql
+from pdb2sql import pdb2sql
 
 from iScore.pssm.map_pssm2pdb import write_mapped_pssm_pdb
 
@@ -236,4 +236,3 @@ def map_pssm(self,pssm_dir='pssm_raw',outdir='pssm',chain=['A','B']):
             for c in chain:
                 pssm = os.path.join(pssm_dir,pssm_files[c])
                 write_mapped_pssm_pdb(pssm, pdb, c, outdir)
-

test/test_graph.py

@@ -41,7 +41,3 @@ def setUp(self):
 
 if __name__ == '__main__':
     unittest.main()
-
-
-
-