PEP8 makeover.

biopython · Dec 6, 2012 · 514eb8f · 514eb8f
1 parent fd82a0a
commit 514eb8f
Showing 1 changed file with 63 additions and 64 deletions.
diff --git a/Scripts/Structure/hsexpo b/Scripts/Structure/hsexpo
@@ -10,7 +10,7 @@ from optparse import OptionParser
 from Bio.PDB import *
 import sys
 
-__doc__="""
+__doc__ = """
 This program calculates solvent exposure for all amino
 acids in a PDB file using 5 different methods:
 
@@ -24,116 +24,115 @@ A PDB file can be written out with the exposure in the B factor field.
 See --help for all options.
 """
 
-if len(sys.argv)==1:
+if len(sys.argv) == 1:
     print __doc__
     sys.exit()
 
 # Get the user's options
-parser=OptionParser(usage="usage: %prog [options] <PDB file>")
+parser = OptionParser(usage="usage: %prog [options] <PDB file>")
 
-parser.add_option("-t", "--type", dest="exp", 
+parser.add_option("-t", "--type", dest="exp",
-                  help="exposure type (HSEAU, HSEAD, HSEBU, HSEBD, CN, DSSPr, DSSPa, RD, RDa)",
+                  help="exposure type (HSEAU, HSEAD, HSEBU, HSEBD,\
-                  default="HSEb")
+                  CN, DSSPr, DSSPa, RD, RDa)", default="HSEb")
 
-parser.add_option("-o", "--out", dest="outfile", 
+parser.add_option("-o", "--out", dest="outfile",
                   help="output to PDB file (B factor=exposure)")
 
-parser.add_option("-r", "--radius", dest="radius", type="float", 
+parser.add_option("-r", "--radius", dest="radius", type="float",
-                  help="sphere radius (default 13.0 A)", 
+                  help="sphere radius (default 13.0 A)",
                   default=13.0)
 
-parser.add_option("-m", "--model", dest="model", type="int", 
+parser.add_option("-m", "--model", dest="model", type="int",
-                  help="model number (default 0)", 
+                  help="model number (default 0)",
                   default=0)
 
-(options, args)=parser.parse_args()
+(options, args) = parser.parse_args()
 
-pdbfile=args[0]
+pdbfile = args[0]
 
 # Get the structure
-p=PDBParser()
+p = PDBParser()
-s=p.get_structure('X', pdbfile)
+s = p.get_structure('X', pdbfile)
 
 # First model by default
-m=s[options.model]
+m = s[options.model]
 
-RADIUS=options.radius
+RADIUS = options.radius
 
 # d=dictionary of exposures
 # k=position in ntuple containing the desired exposure
 
-format="%4i"
+format = "%4i"
 
-options.exp=options.exp.upper()
+options.exp = options.exp.upper()
 
-if options.exp[0]=="H" and options.exp[3]=="A":
+if options.exp[0] == "H" and options.exp[3] == "A":
-    hse=HSExposureCA(m, RADIUS)
+    hse = HSExposureCA(m, RADIUS)
-    if options.exp[-1]=="D":
+    if options.exp[-1] == "D":
-        k='EXP_HSE_A_D'
+        k = 'EXP_HSE_A_D'
     else:
-        k='EXP_HSE_A_U'
+        k = 'EXP_HSE_A_U'
-elif options.exp[0]=="H" and options.exp[3]=="B":
+elif options.exp[0] == "H" and options.exp[3] == "B":
-    hse=HSExposureCB(m, RADIUS)
+    hse = HSExposureCB(m, RADIUS)
     #hse.write_pymol_script()
-    if options.exp[-1]=="D":
+    if options.exp[-1] == "D":
-        k='EXP_HSE_B_U'
+        k = 'EXP_HSE_B_U'
     else:
-        k='EXP_HSE_B_D'
+        k = 'EXP_HSE_B_D'
-elif options.exp=="CN":
+elif options.exp == "CN":
-    hse=ExposureCN(m, RADIUS)
+    hse = ExposureCN(m, RADIUS)
-    k='EXP_CN'
+    k = 'EXP_CN'
-elif options.exp=="ANGLE":
+elif options.exp == "ANGLE":
-    hse=HSExposureCA(m, RADIUS)
+    hse = HSExposureCA(m, RADIUS)
-    k='EXP_CB_PCB_ANGLE'
+    k = 'EXP_CB_PCB_ANGLE'
-    format="%4.1f"
+    format = "%4.1f"
-elif options.exp=="DSSPR":
+elif options.exp == "DSSPR":
-    d=DSSP(m, pdbfile)
+    d = DSSP(m, pdbfile)
-    k='EXP_DSSP_RASA'
+    k = 'EXP_DSSP_RASA'
-    format="%.4f"
+    format = "%.4f"
-elif options.exp=="DSSPA":
+elif options.exp == "DSSPA":
-    d=DSSP(m, pdbfile)
+    d = DSSP(m, pdbfile)
-    k='EXP_DSSP_ASA'
+    k = 'EXP_DSSP_ASA'
-elif options.exp=="RD":
+elif options.exp == "RD":
-    d=ResidueDepth(m, pdbfile)
+    d = ResidueDepth(m, pdbfile)
-    k='EXP_RD'
+    k = 'EXP_RD'
-    format="%4.1f"
+    format = "%4.1f"
-elif options.exp=="RDA":
+elif options.exp == "RDA":
-    d=ResidueDepth(m, pdbfile)
+    d = ResidueDepth(m, pdbfile)
-    k='EXP_RD_CA'
+    k = 'EXP_RD_CA'
-    format="%4.1f"
+    format = "%4.1f"
 else:
     print "ERROR: Unknown option."
     sys.exit()
 
-residue_list=Selection.unfold_entities(m, 'R')
+residue_list = Selection.unfold_entities(m, 'R')
 
 for r in residue_list:
 
-    if r.xtra.has_key(k):
+    if k in r.xtra:
 
-        exposure=r.xtra[k]
+        exposure = r.xtra[k]
 
-        if options.exp=="DSSPR":
+        if options.exp == "DSSPR":
             # to 0=exposed, 1=buried
-            exposure=1-exposure
+            exposure = 1 - exposure
 
         # Print info
-        hetflag, resseq, icode=r.get_id()
+        hetflag, resseq, icode = r.get_id()
 
-        if icode==' ':
+        if icode == ' ':
-            icode='_'
+            icode = '_'
 
-        resname=r.get_resname()
+        resname = r.get_resname()
 
-        print (("%s %4i %c\t"+format) % (resname, resseq, icode, exposure)) 
+        print (("%s %4i %c\t" + format) % (resname, resseq, icode, exposure))
     else:
-        exposure=0.0
+        exposure = 0.0
 
     for atom in r.get_iterator():
         atom.set_bfactor(exposure)
 
 if options.outfile:
-    io=PDBIO()
+    io = PDBIO()
     io.set_structure(s)
     io.save(options.outfile)
-