Autopep8: E3 Blank lines

Signed-off-by: Justin Lecher <[email protected]>

Author: jlec

Diff for: aaindex.py

@@ -15,6 +15,7 @@
 _aaindex = dict()
 _pymol_auto_arg_update = lambda: None
 
+
 def search(pattern, searchtitle=True, casesensitive=False):
     '''
     Search for pattern in description and title (optional) of all records and
@@ -30,6 +31,7 @@ def search(pattern, searchtitle=True, casesensitive=False):
             matches.append(record)
     return matches
 
+
 def grep(pattern):
     '''
     Search for pattern in title and description of all records (case
@@ -38,11 +40,14 @@ def grep(pattern):
     for record in search(pattern):
         print record
 
+
 class Record:
+
     '''
     Amino acid index (AAindex) Record
     '''
     aakeys = 'ARNDCQEGHILKMFPSTWYV'
+
     def __init__(self):
         self.key = None
         self.desc = ''
@@ -53,41 +58,52 @@ def __init__(self):
         self.correlated = dict()
         self.index = dict()
         self.comment = ''
+
     def extend(self, row):
         i = len(self.index)
         for x in row:
             self.index[self.aakeys[i]] = x
             i += 1
+
     def get(self, aai, aaj=None, d=None):
         assert aaj is None
         return self.index.get(aai, d)
+
     def __getitem__(self, aai):
         return self.get(aai)
+
     def median(self):
         x = sorted(filter(None, self.index.values()))
         half = len(x)/2
         if len(x) % 2 == 1:
             return x[half]
         return (x[half-1] + x[half])/2.0
+
     def __str__(self):
         desc = self.desc.replace('\n', ' ').strip()
         return '%s(%s: %s)' % (self.__class__.__name__, self.key, desc)
 
+
 class MatrixRecord(Record):
+
     '''
     Matrix record for mutation matrices or pair-wise contact potentials
     '''
+
     def __init__(self):
         Record.__init__(self)
         self.index = []
         self.rows = dict()
         self.cols = dict()
+
     def extend(self, row):
         self.index.append(row)
+
     def _get(self, aai, aaj):
         i = self.rows[aai]
         j = self.cols[aaj]
         return self.index[i][j]
+
     def get(self, aai, aaj, d=None):
         try:
             return self._get(aai, aaj)
@@ -97,8 +113,10 @@ def get(self, aai, aaj, d=None):
             return self._get(aaj, aai)
         except:
             return d
+
     def __getitem__(self, aaij):
         return self.get(aaij[0], aaij[1])
+
     def median(self):
         x = []
         for y in self.index:
@@ -108,6 +126,7 @@ def median(self):
             return x[len(x)/2]
         return sum(x[len(x)/2-1:len(x)/2+1])/2.0
 
+
 def get(key):
     '''
     Get record for key
@@ -116,11 +135,13 @@ def get(key):
         init()
     return _aaindex[key]
 
+
 def _float_or_None(x):
     if x == 'NA' or x == '-':
         return None
     return float(x)
 
+
 def init(path=None, index='13'):
     '''
     Read in the aaindex files. You need to run this (once) before you can
@@ -142,9 +163,11 @@ def init(path=None, index='13'):
         _parse(path + '/aaindex3', MatrixRecord)
     _pymol_auto_arg_update()
 
+
 def init_from_file(filename, type=Record):
     _parse(filename, type)
 
+
 def _parse(filename, rec, quiet=True):
     '''
     Parse aaindex input file. `rec` must be `Record` for aaindex1 and
@@ -253,6 +276,7 @@ def _parse(filename, rec, quiet=True):
                       'KCX': 'K', 'SHC': 'C', 'C5C': 'C', 'HTR': 'W', 'ARG': 'R', 'TYS': 'Y',
                       'ARM': 'R', 'DNP': 'A'}
 
+
 def aaindex2b(key='KYTJ820101', selection='(all)', quiet=0, var='b'):
     '''
 DESCRIPTION
@@ -296,6 +320,7 @@ def lookup(resn):
 
     cmd.alter(selection, var + '=stored.aaindex(resn)')
 
+
 def pmf(key, cutoff=7.0, selection1='(name CB)', selection2='', state=1, quiet=1):
     '''
 DESCRIPTION
@@ -395,6 +420,7 @@ def pmf(key, cutoff=7.0, selection1='(name CB)', selection2='', state=1, quiet=1
     from pymol import cmd
     cmd.extend('aaindex2b', aaindex2b)
     cmd.extend('pmf', pmf)
+
     def pymol_auto_arg_update():
         aaindexkey_sc = cmd.Shortcut(_aaindex.keys())
         cmd.auto_arg[0].update({

Diff for: anglebetweenhelices.py

@@ -15,6 +15,7 @@ def get_unused_name(name):
     from pymol.cmd import get_unused_name
     STATE = -1
 
+
 def _vec_sum(vec_list):
     # this is the same as
     # return numpy.array(vec_list).sum(0).tolist()
@@ -23,6 +24,7 @@ def _vec_sum(vec_list):
         vec = cpv.add(vec, x)
     return vec
 
+
 def _mean_and_std(x):
     # this is the same as
     # return (numpy.mean(x), numpy.std(x, ddof=1))
@@ -33,6 +35,7 @@ def _mean_and_std(x):
     var = sum([(i - mu)**2 for i in x]) / float(N - 1)
     return (mu, var**0.5)
 
+
 def _common_orientation(selection, vec, visualize=1, quiet=0):
     '''
     Common part of different helix orientation functions. Does calculate
@@ -53,6 +56,7 @@ def _common_orientation(selection, vec, visualize=1, quiet=0):
         print 'Center: (%.2f, %.2f, %.2f) Direction: (%.2f, %.2f, %.2f)' % tuple(center + vec)
     return center, vec
 
+
 def visualize_orientation(direction, center=[0,0,0], scale=1.0, symmetric=False, color='green', color2='red'):
     '''
     Draw an arrow. Helper function for "helix_orientation" etc.
@@ -97,6 +101,7 @@ def visualize_orientation(direction, center=[0,0,0], scale=1.0, symmetric=False,
         ])
     cmd.load_cgo(obj, get_unused_name('oriVec'), zoom=0)
 
+
 def cafit_orientation(selection, visualize=1, quiet=0):
     '''
 DESCRIPTION
@@ -128,6 +133,7 @@ def cafit_orientation(selection, visualize=1, quiet=0):
         vec = cpv.negate(vec)
     return _common_orientation(selection, vec, visualize, quiet)
 
+
 def loop_orientation(selection, visualize=1, quiet=0):
     '''
 DESCRIPTION
@@ -160,6 +166,7 @@ def loop_orientation(selection, visualize=1, quiet=0):
     vec = cpv.normalize(vec)
     return _common_orientation(selection, vec, visualize, quiet)
 
+
 def helix_orientation(selection, visualize=1, sigma_cutoff=1.5, quiet=0):
     '''
 DESCRIPTION
@@ -210,6 +217,7 @@ def helix_orientation(selection, visualize=1, sigma_cutoff=1.5, quiet=0):
     vec = cpv.normalize(vec)
     return _common_orientation(selection, vec, visualize, quiet)
 
+
 def helix_orientation_hbond(selection, visualize=1, cutoff=3.5, quiet=0):
     '''
 DESCRIPTION
@@ -249,6 +257,7 @@ def helix_orientation_hbond(selection, visualize=1, cutoff=3.5, quiet=0):
     vec = cpv.normalize(vec)
     return _common_orientation(selection, vec, visualize, quiet)
 
+
 def angle_between_helices(selection1, selection2, method='helix_orientation', visualize=1, quiet=0):
     '''
 DESCRIPTION

Diff for: b2transparency.py

@@ -8,6 +8,7 @@
 
 from pymol import cmd, CmdException
 
+
 def b2transparency(selection='all', setting='transparency', minimum=None,
                    maximum=None, var='b', quiet=1):
     '''

Diff for: bbPlane.py

@@ -14,6 +14,7 @@
 
 from pymol import cmd
 
+
 def bbPlane(selection='(all)', color='gray', transp=0.3, state=-1, name=None, quiet=1):
     """
 DESCRIPTION

Diff for: ccp4_contact.py

@@ -26,6 +26,7 @@
 from pymol import cmd
 import re
 
+
 def parseCONTACTContacts( f ):
     # Lys    24A  ca  Asp   263D  CG   ...  4.94    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
     conParser = re.compile("(\S*)\s*(\d+)([A-Z])\s*(\w+)")
@@ -43,6 +44,7 @@ def parseCONTACTContacts( f ):
 
     return (s1, s2)
 
+
 def ccp4_contact( contactsfile, selName1 = "source", selName2 = "target" ):
     # read and parse contacts file into two lists of contact atoms and contact pair list
     s1, s2 = parseCONTACTContacts(open(contactsfile))

Diff for: ccp4_ncont.py

@@ -27,6 +27,7 @@
 from pymol import cmd
 import re
 
+
 def parseNCONTContacts( f ):
     # /1/B/ 282(PHE). / CE1[ C]:  /1/E/ 706(GLN). / O  [ O]:   3.32
     # * in the second group is needed when chain code is blank
@@ -54,6 +55,7 @@ def parseNCONTContacts( f ):
         else:
             print "Unknown mode", mode
 
+
 def ccp4_ncont( contactsfile, selName1 = "source", selName2 = "target" ):
     # read and parse contacts file into two lists of contact atoms and contact pair list
     s1, s2, pairs = parseNCONTContacts(open(contactsfile))

Diff for: ccp4_pisa.py

@@ -31,6 +31,7 @@
 from pymol import cmd
 from xml.etree import ElementTree
 
+
 def parseElement( element ):
     """ creates a dict for the sub elements of the element"""
     result = { }
@@ -39,10 +40,12 @@ def parseElement( element ):
             result[element[l].tag.strip()] = element[l].text.strip()
     return result;
 
+
 def parseBond( elementDir ):
     """ puts bond information into tuples"""
     return ((elementDir['chain-1'], elementDir['seqnum-1'], elementDir['atname-1']), (elementDir['chain-2'], elementDir['seqnum-2'], elementDir['atname-2']))
 
+
 def parseInterface( interface, bondname ):
     """ parses a single interface into the interface id, the two chain names connected 
         and two lists of atoms for each chain"""
@@ -62,11 +65,13 @@ def parseInterface( interface, bondname ):
         return id, (right_chain, left_chain), right, left
     return id, (left_chain, right_chain), left, right
 
+
 def createSelectionList( atomlist ):
     """creates a PYMOL selection string for a list of atoms"""
     atomnames = [chain+'/'+res+'/'+atom for chain, res, atom in atomlist]
     return " or ".join(atomnames)
 
+
 def createInterfaceSelection( interface, prefix ):
     """creates two selections for an interfaces"""
     id, e, l, r = interface
@@ -85,6 +90,7 @@ def createInterfaceSelection( interface, prefix ):
         print rightname, '\t', rightlist
     return leftname, rightname
 
+
 def ccp4_pisa( filename ):
     bond_types = [
         ('h-bonds', 'h-bonds/bond', 'hb'),

Diff for: center_of_mass.py

@@ -17,6 +17,7 @@
 
 from pymol import cmd
 
+
 def com(selection,state=None,mass=None,object=None, quiet=1, **kwargs):
     quiet = int(quiet)
     if (object == None):
@@ -43,6 +44,7 @@ def com(selection,state=None,mass=None,object=None, quiet=1, **kwargs):
 
 cmd.extend("com",com)
 
+
 def get_com(selection,state=1,mass=None, quiet=1):
     """
  DESCRIPTION

Diff for: cgo_arrow.py

@@ -8,6 +8,7 @@
 
 from pymol import cmd, cgo, CmdException
 
+
 def cgo_arrow(atom1='pk1', atom2='pk2', radius=0.5, gap=0.0, hlength=-1, hradius=-1,
               color='blue red', name=''):
     '''

Diff for: color_by_conservation.py

@@ -17,6 +17,8 @@
 '''
 
 from pymol import cmd
+
+
 def color_by_conservation(aln, names=(), color="rainbow", as_putty=0, _self=cmd):
     # PyMOL doesn't yet know about object:alignment
     # but we need to check that this exists or we might crash

Diff for: colorbydisplacement.py

@@ -43,9 +43,11 @@
 from pymol import cmd
 from pymol import stored
 
+
 def strTrue(p):
     return p[0].upper() == "T"
 
+
 def displacementUpdateBAll(objA, alnAri, objB, alnBri):
     print "This will take a while to go through the for loops. Give me around 3-5 minutes..."
     ### If residue is unassigned in one of the pdb files, we reset its value
@@ -67,6 +69,7 @@ def displacementUpdateBAll(objA, alnAri, objB, alnBri):
         cmd.delete(tempObject)
     cmd.sort(objA); cmd.sort(objB)
 
+
 def ColorByDisplacementAll(objSel1, objSel2, super1='all', super2='all', doColor="True", doAlign="True", AlignedWhite='yes'):
     ### First create backup copies; names starting with __ (underscores) are normally hidden by PyMOL
     tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln"

Diff for: colorbyrmsd.py

@@ -9,6 +9,7 @@
 
 from pymol import cmd, CmdException
 
+
 def colorbyrmsd(mobile, target, doAlign=1, doPretty=1, guide=1, method='super', quiet=1):
     '''
 DESCRIPTION

Diff for: com.py

@@ -41,6 +41,7 @@
 from pymol import stored
 from chempy import cpv
 
+
 def COM(selection='all', center=0, quiet=1):
 
     model = cmd.get_model(selection)