Autopep8: E1 Indentions

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

Author: jlec

Diff for: aaindex.py

@@ -9,12 +9,12 @@
     aaindex2b
     pmf
 '''
- 
+
 import sys, os
- 
+
 _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
@@ -29,15 +29,15 @@ def search(pattern, searchtitle=True, casesensitive=False):
         if pattern in whatcase(record.desc) or searchtitle and pattern in whatcase(record.title):
             matches.append(record)
     return matches
- 
+
 def grep(pattern):
     '''
     Search for pattern in title and description of all records (case
     insensitive) and print results on standard output.
     '''
     for record in search(pattern):
         print record
- 
+
 class Record:
     '''
     Amino acid index (AAindex) Record
@@ -72,7 +72,7 @@ def median(self):
     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
@@ -107,20 +107,20 @@ def median(self):
         if len(x) % 2 == 1:
             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
     '''
     if len(_aaindex) == 0:
         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
@@ -141,10 +141,10 @@ def init(path=None, index='13'):
     if '3' in index:
         _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
@@ -157,15 +157,15 @@ def _parse(filename, rec, quiet=True):
         filename = urllib.urlretrieve(url, filename)[0]
         print 'Saved to "%s"' % (filename)
     f = open(filename)
- 
+
     current = rec()
     lastkey = None
- 
+
     for line in f:
         key = line[0:2]
         if key[0] == ' ':
             key = lastkey
- 
+
         if key == '//':
             _aaindex[current.key] = current
             current = rec()
@@ -217,63 +217,63 @@ def _parse(filename, rec, quiet=True):
                 current.extend(map(_float_or_None, a))
         elif not quiet:
             print 'Warning: line starts with "%s"' % (key)
- 
+
         lastkey = key
- 
+
 ########## PYMOL ###########
- 
+
 # from Bio.SCOP.Raf import to_one_letter_code
 # See also http://www.pymolwiki.org/index.php/Aa_codes
 to_one_letter_code = {'PAQ': 'Y', 'AGM': 'R', 'ILE': 'I', 'PR3': 'C',
-      'GLN': 'Q', 'DVA': 'V', 'CCS': 'C', 'ACL': 'R', 'GLX': 'Z', 'GLY': 'G',
-      'GLZ': 'G', 'DTH': 'T', 'OAS': 'S', 'C6C': 'C', 'NEM': 'H', 'DLY': 'K',
-      'MIS': 'S', 'SMC': 'C', 'GLU': 'E', 'NEP': 'H', 'BCS': 'C', 'ASQ': 'D',
-      'ASP': 'D', 'SCY': 'C', 'SER': 'S', 'LYS': 'K', 'SAC': 'S', 'PRO': 'P',
-      'ASX': 'B', 'DGN': 'Q', 'DGL': 'E', 'MHS': 'H', 'ASB': 'D', 'ASA': 'D',
-      'NLE': 'L', 'DCY': 'C', 'ASK': 'D', 'GGL': 'E', 'STY': 'Y', 'SEL': 'S',
-      'CGU': 'E', 'ASN': 'N', 'ASL': 'D', 'LTR': 'W', 'DAR': 'R', 'VAL': 'V',
-      'CHG': 'A', 'TPO': 'T', 'CLE': 'L', 'GMA': 'E', 'HAC': 'A', 'AYA': 'A',
-      'THR': 'T', 'TIH': 'A', 'SVA': 'S', 'MVA': 'V', 'SAR': 'G', 'LYZ': 'K',
-      'BNN': 'A', '5HP': 'E', 'IIL': 'I', 'SHR': 'K', 'HAR': 'R', 'FME': 'M',
-      'PYX': 'C', 'ALO': 'T', 'PHI': 'F', 'ALM': 'A', 'PHL': 'F', 'MEN': 'N',
-      'TPQ': 'A', 'GSC': 'G', 'PHE': 'F', 'ALA': 'A', 'MAA': 'A', 'MET': 'M',
-      'UNK': 'X', 'LEU': 'L', 'ALY': 'K', 'SET': 'S', 'GL3': 'G', 'TRG': 'K',
-      'CXM': 'M', 'TYR': 'Y', 'SCS': 'C', 'DIL': 'I', 'TYQ': 'Y', '3AH': 'H',
-      'DPR': 'P', 'PRR': 'A', 'CME': 'C', 'IYR': 'Y', 'CY1': 'C', 'TYY': 'Y',
-      'HYP': 'P', 'DTY': 'Y', '2AS': 'D', 'DTR': 'W', 'FLA': 'A', 'DPN': 'F',
-      'DIV': 'V', 'PCA': 'E', 'MSE': 'M', 'MSA': 'G', 'AIB': 'A', 'CYS': 'C',
-      'NLP': 'L', 'CYQ': 'C', 'HIS': 'H', 'DLE': 'L', 'CEA': 'C', 'DAL': 'A',
-      'LLP': 'K', 'DAH': 'F', 'HMR': 'R', 'TRO': 'W', 'HIC': 'H', 'CYG': 'C',
-      'BMT': 'T', 'DAS': 'D', 'TYB': 'Y', 'BUC': 'C', 'PEC': 'C', 'BUG': 'L',
-      'CYM': 'C', 'NLN': 'L', 'CY3': 'C', 'HIP': 'H', 'CSO': 'C', 'TPL': 'W',
-      'LYM': 'K', 'DHI': 'H', 'MLE': 'L', 'CSD': 'A', 'HPQ': 'F', 'MPQ': 'G',
-      'LLY': 'K', 'DHA': 'A', 'DSN': 'S', 'SOC': 'C', 'CSX': 'C', 'OMT': 'M',
-      'DSP': 'D', 'PTR': 'Y', 'TRP': 'W', 'CSW': 'C', 'EFC': 'C', 'CSP': 'C',
-      'CSS': 'C', 'SCH': 'C', 'OCS': 'C', 'NMC': 'G', 'SEP': 'S', 'BHD': 'D',
-      'KCX': 'K', 'SHC': 'C', 'C5C': 'C', 'HTR': 'W', 'ARG': 'R', 'TYS': 'Y',
-      'ARM': 'R', 'DNP': 'A'}
- 
+                      'GLN': 'Q', 'DVA': 'V', 'CCS': 'C', 'ACL': 'R', 'GLX': 'Z', 'GLY': 'G',
+                      'GLZ': 'G', 'DTH': 'T', 'OAS': 'S', 'C6C': 'C', 'NEM': 'H', 'DLY': 'K',
+                      'MIS': 'S', 'SMC': 'C', 'GLU': 'E', 'NEP': 'H', 'BCS': 'C', 'ASQ': 'D',
+                      'ASP': 'D', 'SCY': 'C', 'SER': 'S', 'LYS': 'K', 'SAC': 'S', 'PRO': 'P',
+                      'ASX': 'B', 'DGN': 'Q', 'DGL': 'E', 'MHS': 'H', 'ASB': 'D', 'ASA': 'D',
+                      'NLE': 'L', 'DCY': 'C', 'ASK': 'D', 'GGL': 'E', 'STY': 'Y', 'SEL': 'S',
+                      'CGU': 'E', 'ASN': 'N', 'ASL': 'D', 'LTR': 'W', 'DAR': 'R', 'VAL': 'V',
+                      'CHG': 'A', 'TPO': 'T', 'CLE': 'L', 'GMA': 'E', 'HAC': 'A', 'AYA': 'A',
+                      'THR': 'T', 'TIH': 'A', 'SVA': 'S', 'MVA': 'V', 'SAR': 'G', 'LYZ': 'K',
+                      'BNN': 'A', '5HP': 'E', 'IIL': 'I', 'SHR': 'K', 'HAR': 'R', 'FME': 'M',
+                      'PYX': 'C', 'ALO': 'T', 'PHI': 'F', 'ALM': 'A', 'PHL': 'F', 'MEN': 'N',
+                      'TPQ': 'A', 'GSC': 'G', 'PHE': 'F', 'ALA': 'A', 'MAA': 'A', 'MET': 'M',
+                      'UNK': 'X', 'LEU': 'L', 'ALY': 'K', 'SET': 'S', 'GL3': 'G', 'TRG': 'K',
+                      'CXM': 'M', 'TYR': 'Y', 'SCS': 'C', 'DIL': 'I', 'TYQ': 'Y', '3AH': 'H',
+                      'DPR': 'P', 'PRR': 'A', 'CME': 'C', 'IYR': 'Y', 'CY1': 'C', 'TYY': 'Y',
+                      'HYP': 'P', 'DTY': 'Y', '2AS': 'D', 'DTR': 'W', 'FLA': 'A', 'DPN': 'F',
+                      'DIV': 'V', 'PCA': 'E', 'MSE': 'M', 'MSA': 'G', 'AIB': 'A', 'CYS': 'C',
+                      'NLP': 'L', 'CYQ': 'C', 'HIS': 'H', 'DLE': 'L', 'CEA': 'C', 'DAL': 'A',
+                      'LLP': 'K', 'DAH': 'F', 'HMR': 'R', 'TRO': 'W', 'HIC': 'H', 'CYG': 'C',
+                      'BMT': 'T', 'DAS': 'D', 'TYB': 'Y', 'BUC': 'C', 'PEC': 'C', 'BUG': 'L',
+                      'CYM': 'C', 'NLN': 'L', 'CY3': 'C', 'HIP': 'H', 'CSO': 'C', 'TPL': 'W',
+                      'LYM': 'K', 'DHI': 'H', 'MLE': 'L', 'CSD': 'A', 'HPQ': 'F', 'MPQ': 'G',
+                      'LLY': 'K', 'DHA': 'A', 'DSN': 'S', 'SOC': 'C', 'CSX': 'C', 'OMT': 'M',
+                      'DSP': 'D', 'PTR': 'Y', 'TRP': 'W', 'CSW': 'C', 'EFC': 'C', 'CSP': 'C',
+                      'CSS': 'C', 'SCH': 'C', 'OCS': 'C', 'NMC': 'G', 'SEP': 'S', 'BHD': 'D',
+                      '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
- 
+
     "aaindex" looks up the Amino Acid Index from
       http://www.genome.jp/aaindex/
     for the given key and assignes b-factors to the given selection. Unknown
     residues get the average index value assigned.
- 
+
 USAGE
- 
+
     aaindex2b [key [, selection]]
- 
+
 ARGUMENTS
- 
+
     key = string: Key of AAindex entry
- 
+
     selection = string: atoms to assign b-factors {default: (all)}
- 
+
 EXAMPLE
- 
+
     # Hydropathy index by Kyte-Doolittle
     aaindex2b KYTJ820101
     spectrumany b, white yellow forest
@@ -282,49 +282,49 @@ def aaindex2b(key='KYTJ820101', selection='(all)', quiet=0, var='b'):
     from pymol import cmd, stored
     entry = get(key)
     median = entry.median()
- 
+
     if int(quiet) != 0:
         print entry.desc.strip()
- 
+
     def lookup(resn):
         one_letter = to_one_letter_code.get(resn, 'X')
         value = entry.get(one_letter)
         if value is None:
             return median
         return value
     stored.aaindex = lookup
- 
+
     cmd.alter(selection, var + '=stored.aaindex(resn)')
- 
+
 def pmf(key, cutoff=7.0, selection1='(name CB)', selection2='', state=1, quiet=1):
     '''
 DESCRIPTION
- 
+
     Potential of Mean Force
- 
+
 ARGUMENTS
- 
+
     key = string: aaindex key
- 
+
     cutoff = float: distance cutoff {default: 7.0}
     cutoff = (float, float): distance shell
- 
+
     selection1 = string: atom selection {default: (name CB)}
- 
+
     selection2 = string: atom selection {default: selection1}
- 
+
 NOTES
- 
+
     Does also support a list of keys and a list of cutoffs to deal with
     multiple distance shells.
- 
+
 EXAMPLES
- 
+
     # distance dependent c-beta contact potentials
     pmf SIMK990101, 5,         /2x19//A//CB
     pmf SIMK990102, [5, 7.5],  /2x19//A//CB
     pmf [SIMK990101, SIMK990102, SIMK990103], [0, 5, 7.5, 10], /2x19//A//CB
- 
+
     # interface potential
     sidechaincenters 2x19_scc, 2x19
     pmf KESO980102, 7.0, /2x19_scc//A, /2x19_scc//B
@@ -354,21 +354,21 @@ def pmf(key, cutoff=7.0, selection1='(name CB)', selection2='', state=1, quiet=1
         print 'Distance shells:'
         for i in range(len(key)):
             print '%s %.1f-%.1f' % (key[i], cutoff[i], cutoff[i+1])
- 
+
     idmap = dict()
     cmd.iterate_state(state, '(%s) or (%s)' % (selection1, selection2),
-            'idmap[model,index] = [(resn,name),(x,y,z)]', space={'idmap': idmap})
+                      'idmap[model,index] = [(resn,name),(x,y,z)]', space={'idmap': idmap})
     twoN = cmd.count_atoms(selection1) + cmd.count_atoms(selection2)
     pairs = cmd.find_pairs(selection1, selection2, cutoff=max(cutoff),
-            state1=state, state2=state)
+                           state1=state, state2=state)
     if len(pairs) == 0:
         print 'Empty pair list'
         return 0.0
- 
+
     matrix = map(get, key)
     for i in matrix:
         assert isinstance(i, MatrixRecord)
- 
+
     i_list = range(len(key))
     u_sum = 0
     count = 0
@@ -385,12 +385,12 @@ def pmf(key, cutoff=7.0, selection1='(name CB)', selection2='', state=1, quiet=1
                     count += 1
                 except:
                     print 'Failed for', a1[0], a2[0]
- 
+
     value = float(u_sum) / twoN
     if not quiet:
         print 'PMF: %.4f (%d contacts, %d residues)' % (value, count, twoN)
     return value
- 
+
 try:
     from pymol import cmd
     cmd.extend('aaindex2b', aaindex2b)
@@ -413,5 +413,5 @@ def pymol_auto_arg_update():
     _pymol_auto_arg_update = pymol_auto_arg_update
 except:
     pass
- 
+
 # vi: ts=4:sw=4:smarttab:expandtab