Remove undesirable atoms

Dockerfile

@@ -1,7 +1,5 @@
 FROM centos:7
 
-MAINTAINER OSU OSL [email protected]
-
 EXPOSE 8000
 
 # Dockerfiles do not support "here documents"

pgd_constants.py

@@ -1,30 +1,8 @@
-# The possible values for the 'aa' field (in Protein and elsewhere)
-AA_CHOICES = (
-    ('a', 'Ala'),
-    ('r', 'Arg'),
-    ('n', 'Asn'),
-    ('d', 'Asp'),
-    ('c', 'Cys'),
-    ('q', 'Gln'),
-    ('e', 'Glu'),
-    ('g', 'Gly'),
-    ('h', 'His'),
-    ('i', 'Ile'),
-    ('l', 'Leu'),
-    ('k', 'Lys'),
-    ('m', 'Met'),
-    ('f', 'Phe'),
-    ('p', 'Pro'),
-    ('s', 'Ser'),
-    ('t', 'Thr'),
-    ('w', 'Trp'),
-    ('y', 'Tyr'),
-    ('v', 'Val'),
-)
+from Bio.Data.IUPACData import protein_letters_1to3
+import operator
 
-AA_CHOICES_DICT = {}
-for choice in AA_CHOICES:
-    AA_CHOICES_DICT[choice[0]] = choice[1]
+# The possible values for the 'aa' field (in Protein and elsewhere)
+AA_CHOICES = sorted(protein_letters_1to3.items(), key=operator.itemgetter(1))
 
 # The possible values for the 'ss' field (in Protein and elsewhere)
 '''SS_CHOICES = (

pgd_core/models.py

@@ -1,8 +1,9 @@
 import math
 
 from django.db import models
-from pgd_constants import AA_CHOICES, SS_CHOICES, AA_CHOICES_DICT
+from pgd_constants import AA_CHOICES, SS_CHOICES
 from django.contrib.auth.models import User
+from Bio.Data.IUPACData import protein_letters_1to3
 
 
 # Protein model
@@ -26,6 +27,9 @@ class Meta:
     def __unicode__(self):
         return self.code
 
+    def __str__(self):
+        return "<Protein %s>" % self.code
+
 # Chain model
 # Contains information about chains within a protein
 # 
@@ -43,6 +47,9 @@ class Chain (models.Model):
     class Meta:
         select_on_save = True
 
+    def __str__(self):
+        return "<Chain protein= code=%s>" % (self.protein.code, self.code)
+
 
 class Sidechain_ARG(models.Model):
     CB_CG = models.FloatField(null=True)
@@ -360,13 +367,13 @@ def __init__(self, *args, **kwargs):
 
     def __getattribute__(self,name):
         if name == 'aa_full':
-            return AA_CHOICES_DICT[self.aa]
+            return protein_letters_1to3[self.aa]
         # normal attribute
         else:
             return object.__getattribute__(self, name)
 
-
-
+    def __str__(self):
+        return "<Residue protein=%s chain=%s oldID=%s>" % (self.protein.code, self.chain.code, self.oldID)
 
 
 class Segmenter():

pgd_search/models.py

@@ -10,9 +10,10 @@
 from django.contrib.auth.models import User
 
 from pgd_core.models import Protein,Residue
-from pgd_constants import AA_CHOICES, AA_CHOICES_DICT, SS_CHOICES
+from pgd_constants import AA_CHOICES, SS_CHOICES
 from pgd_splicer.sidechain import bond_lengths_string_dict, bond_angles_string_dict
 from pgd_core.util import residue_indexes
+from Bio.Data.IUPACData import protein_letters_1to3
 
 
 range_re = re.compile("(?<=[^-<>=])-")
@@ -233,7 +234,7 @@ def compare(x,y):
             # ... handle sidechain query strings ...
             sidechain_fields = []
             if search_res.aa:
-                for aa_type in [AA_CHOICES_DICT[aa].upper() for aa in search_res.aa]:
+                for aa_type in [protein_letters_1to3[aa].upper() for aa in search_res.aa]:
                     if aa_type in bond_lengths_string_dict:
                         field_base = '%s__%%s' % aa_type
                         for field in bond_lengths_string_dict[aa_type]:

pgd_search/plot/views.py

@@ -132,7 +132,7 @@ def renderToPNG(request):
         height = 480
 
     writer = io.BytesIO()
-    response = HttpResponse(mimetype="image/png")
+    response = HttpResponse(content_type="image/png")
     response['Content-Disposition'] = 'attachment; filename="plot.png"'
     svg.render_png(writer, width, height+30)
     response.write(writer.getvalue())

pgd_search/statistics/views.py

@@ -7,12 +7,13 @@
 from django.http import HttpResponse
 from django.shortcuts import render_to_response
 from django.template import RequestContext
-from pgd_constants import AA_CHOICES, SS_CHOICES, AA_CHOICES_DICT
+from pgd_constants import AA_CHOICES, SS_CHOICES
 from pgd_search.statistics.aggregates import *
 from pgd_search.statistics.directional_stddev import *
 from pgd_search.statistics.form import StatsForm
 from pgd_search.views import settings_processor
 from pgd_splicer.sidechain import bond_angles_string_dict, bond_lengths_string_dict
+from Bio.Data.IUPACData import protein_letters_1to3
 
 stat_attributes = [('L1',u'C<sup>-1</sup>N'),
                         ('L2',u'NC<sup>&alpha;</sup>'),
@@ -54,7 +55,7 @@
 # rebuild bond angle list so they work with single letter codes
 BOND_ANGLES = {}
 BOND_LENGTHS = {}
-for k, v in AA_CHOICES_DICT.items():
+for k, v in protein_letters_1to3.items():
     v = v.upper()
     if v in bond_lengths_string_dict:
         BOND_LENGTHS[k] = [s.replace('-','_') for s in bond_lengths_string_dict[v]]
@@ -207,7 +208,7 @@ def calculate_aa_statistics(queryset, aa, iIndex=0):
     field_prefix = '%s%%s' % prefix  
 
     queryset = queryset.filter(**{'%saa'%prefix:aa})
-    full_aa = AA_CHOICES_DICT[aa].upper()
+    full_aa = protein_letters_1to3[aa].upper()
 
     angles = []
     if aa in BOND_LENGTHS:

pgd_search/templatetags/search_extras.py

@@ -3,8 +3,8 @@
 from django import template
 register = template.Library()
 
-from pgd_constants import AA_CHOICES_DICT
 from pgd_search.plot.PlotForm import PROPERTY_CHOICES_DICT
+from Bio.Data.IUPACData import protein_letters_1to3
 
 
 ROMAN_TO_GREEK = dict(
@@ -24,7 +24,7 @@ def full_aa(value):
     """
     Filter that returns the full AA code from the 1 letter AA code
     """
-    return AA_CHOICES_DICT[value]
+    return protein_letters_1to3[value]
 register.filter('full_aa',full_aa)
 
 

pgd_search/tests.py

@@ -362,7 +362,7 @@ def testSearchCode(self):
         )
 
     def testSearchAa(self):
-        aa_range = ('a', 'r', 'n', 'd', 'c')
+        aa_range = ('A', 'R', 'N', 'D', 'C')
         chainList = {}
         for t in zip(range(1,6), aa_range):
             i,aa_choice = t
@@ -400,7 +400,7 @@ def testSearchAa(self):
             )
 
         data['aa_i_0'] = 1
-        aa_choice = ('a', 'r', 'n')
+        aa_choice = ('A', 'R', 'N')
         data['aa_0'] = (aa_choice)
         search.data = data
         #data['aa_i'] = 0
@@ -412,7 +412,7 @@ def testSearchAa(self):
         )
 
         data['aa_i_0'] = 0
-        aa_choice = ('a', 'r', 'n')
+        aa_choice = ('A', 'R', 'N')
         data['aa_0'] = (aa_choice)
         search.data = data
         #data['aa_i'] = 0
@@ -776,14 +776,14 @@ def test_sidechain_statistics_present(self):
         # Each row has one element for each angle or length.
 
         ss_test_values = {
-            "aa_r": {
+            "aa_R": {
                 "CB_CG": {
-                    "avg": "1.521",
-                    "stddev": "0.014",
+                    "avg": "1.523",
+                    "stddev": "0.013",
                 },
                 "CA_CB_CG": {
-                    "avg": "112.6",
-                    "stddev": "2.8",
+                    "avg": "112.5",
+                    "stddev": "2.4",
                 },
             },
         }