Moved createPDB function in gemmeAnal.py to sgemme.py.

gemmeAnal.py

@@ -54,24 +54,24 @@ import numpy as np
 # 	else:
 # 		return 0
 
-def createPDB(prot,seq):
-	"""
-		If there is not a real PDB file for a given sequence,
-		create a fake PDB containing only dummy CA atoms.  
-	"""
-	d = {'C': 'CYS', 'D': 'ASP', 'S': 'SER',  'Q': 'GLN', 'K': 'LYS',
-	'I': 'ILE', 'P': 'PRO', 'T': 'THR', 'F': 'PHE', 'N': 'ASN', 
-	'G': 'GLY',  'H': 'HIS', 'L': 'LEU', 'R': 'ARG', 'W': 'TRP', 
-	'A': 'ALA', 'V': 'VAL', 'E': 'GLU', 'Y': 'TYR', 'M': 'MET'}
+# def createPDB(prot,seq):
+# 	"""
+# 		If there is not a real PDB file for a given sequence,
+# 		create a fake PDB containing only dummy CA atoms.  
+# 	"""
+# 	d = {'C': 'CYS', 'D': 'ASP', 'S': 'SER',  'Q': 'GLN', 'K': 'LYS',
+# 	'I': 'ILE', 'P': 'PRO', 'T': 'THR', 'F': 'PHE', 'N': 'ASN', 
+# 	'G': 'GLY',  'H': 'HIS', 'L': 'LEU', 'R': 'ARG', 'W': 'TRP', 
+# 	'A': 'ALA', 'V': 'VAL', 'E': 'GLU', 'Y': 'TYR', 'M': 'MET'}
 
-	fOUT = open(prot+'.pdb','w')
-	i = 1
-	for let in seq:
-		if(let != '-'):
-			fOUT.write('ATOM%7d  CA  %s A%4d      43.524  70.381  46.465  1.00   0.0\n'%(i,d[let.upper()],i))
-			i += 1
+# 	fOUT = open(prot+'.pdb','w')
+# 	i = 1
+# 	for let in seq:
+# 		if(let != '-'):
+# 			fOUT.write('ATOM%7d  CA  %s A%4d      43.524  70.381  46.465  1.00   0.0\n'%(i,d[let.upper()],i))
+# 			i += 1
 		
-	fOUT.close()
+# 	fOUT.close()
 
 def editConfJET(N):
 	"""
@@ -121,7 +121,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 	n: int
 		Number of JET2 iterations.
 	N: int
-		Default 20000
+		Default 40000
 	nl: int
 		Number of lines after > character in the query sequences file.
 		It is obtained in extractQuerySeq() function.

sgemme.py

@@ -59,6 +59,26 @@ def getNbSeq(filename):
 		return int(proc.stdout.read())
 	else:
 		return 0
+        
+def createPDB(prot,seq):
+	"""
+		If there is not a real PDB file for a given sequence,
+		create a fake PDB containing only dummy CA atoms.  
+	"""
+	d = {'C': 'CYS', 'D': 'ASP', 'S': 'SER',  'Q': 'GLN', 'K': 'LYS',
+	'I': 'ILE', 'P': 'PRO', 'T': 'THR', 'F': 'PHE', 'N': 'ASN', 
+	'G': 'GLY',  'H': 'HIS', 'L': 'LEU', 'R': 'ARG', 'W': 'TRP', 
+	'A': 'ALA', 'V': 'VAL', 'E': 'GLU', 'Y': 'TYR', 'M': 'MET'}
+
+	fOUT = open(prot+'.pdb','w')
+	i = 1
+	for let in seq:
+		if(let != '-'):
+			fOUT.write('ATOM%7d  CA  %s A%4d      43.524  70.381  46.465  1.00   0.0\n'%(i,d[let.upper()],i))
+			i += 1
+		
+	fOUT.close()
+
 ###############################################################################
 def rankSortProteinData(dataArray, inverted=True):
     """