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1 '''
2 Whole-cell data model
3
4 Author: Jonathan Karr, jkarr@stanford.edu
5 Affiliation: Covert Lab, Department of Bioengineering, Stanford University
6 Last updated: 2012-07-17
7 '''
8
9 from __future__ import unicode_literals
10 from Bio.Seq import Seq
11 from Bio.Alphabet import IUPAC
12 from django.contrib.auth.models import User
13 from django.core import validators
14 from django.core.exceptions import ValidationError, ObjectDoesNotExist
15 from django.core.urlresolvers import reverse
16 from django.db import models
17 from django.db.models import Model, OneToOneField, CharField, IntegerField, URLField, PositiveIntegerField, FloatField, ForeignKey, BooleanField, SlugField, ManyToManyField, TextField, DateTimeField, options, permalink, SET_NULL, Min, Max
18 from django.db.models.query import EmptyQuerySet
19 from django.utils.http import urlencode
20 from itertools import chain
21 from public.templatetags.templatetags import set_time_zone
22 import math
23 import re
24 import settings
25 import subprocess
26
27 ''' BEGIN: choices '''
28
29 CHOICES_DIRECTION = (
30 ('f', 'Forward'),
31 ('r', 'Reverse'),
32 )
33
34 CHOICES_REFERENCE_TYPE = (
35 ('article', 'Article'),
36 ('book', 'Book'),
37 ('thesis', 'Thesis'),
38 ('misc', 'Miscellaneous'),
39 )
40
41 CHOICES_STRANDEDNESS = (
42 ('dsDNA', 'dsDNA'),
43 ('ssDNA', 'ssDNA'),
44 ('xsDNA', 'xsDNA'),
45 )
46
47 CHOICES_VMAX_UNITS = (
48 ('1/min', '1/min'),
49 ('U/mg', 'U/mg'),
50 )
51
52 CHOICES_HOMOLOG_SPECIES = (
53 ('B. subtilis', 'B. subtilis'),
54 ('E. coli', 'E. coli'),
55 ('M. hyopneumoniae', 'M. hyopneumoniae'),
56 ('M. mobile', 'M. mobile'),
57 ('M. pneumoniae', 'M. pneumoniae'),
58 ('S. coelicolor', 'S. coelicolor'),
59 ('S. oneidensis', 'S. oneidensis'),
60 )
61
62 HOMOLOG_SPECIES_URLS = {
63 "B. subtilis": "http://www.genome.jp/dbget-bin/www_bget?bsu:%s",
64 "E. coli": "http://www.genome.jp/dbget-bin/www_bget?eco:%s",
65 "M. hyopneumoniae": "http://www.genome.jp/dbget-bin/www_bget?mhj:%s",
66 "M. mobile": "http://www.genome.jp/dbget-bin/www_bget?mmo:%s",
67 "M. pneumoniae": "http://www.genome.jp/dbget-bin/www_bget?mpn:%s",
68 "S. coelicolor": "http://www.genome.jp/dbget-bin/www_bget?sco:%s",
69 "S. oneidensis": "http://www.genome.jp/dbget-bin/www_bget?son:%s",
70 }
71
72 CHOICES_CROSS_REFERENCE_SOURCES = (
73 ('ATCC', 'ATCC'),
74 ('BiGG', 'BiGG'),
75 ('BioCyc', 'BioCyc'),
76 ('BioProject', 'BioProject'), #http://www.ncbi.nlm.nih.gov/bioproject/%s
77 ('CAS', 'CAS'),
78 ('ChEBI', 'ChEBI'),
79 ('CMR', 'CMR'),
80 ('EC', 'EC'),
81 ('GenBank', 'GenBank'),
82 ('ISBN', 'ISBN'),
83 ('KEGG', 'KEGG'),
84 ('KNApSAcK', 'KNApSAcK'),
85 ('LipidBank', 'LipidBank'),
86 ('LIPIDMAPS', 'LIPIDMAPS'),
87 ('PDB', 'PDB'),
88 ('PDBCCD', 'PDBCCD'),
89 ('PubChem', 'PubChem'),
90 ('PubMed', 'PubMed'),
91 ('RefSeq', 'RefSeq'),
92 ('SABIO-RK', 'SABIO-RK'),
93 ('SwissProt', 'SwissProt'),
94 ('Taxonomy', 'Taxonomy'),
95 ('ThreeDMET', 'ThreeDMET'),
96 ('URL', 'URL'),
97 )
98
99 CROSS_REFERENCE_SOURCE_URLS = {
100 "ATCC": "http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?Template=bacteria&ATCCNum=%s",
101 "BiGG": "http://bigg.ucsd.edu/bigg/postMet.pl?organism=3307911&organism=1461534&organism=222668&organism=3277493&organism=2795088&organism=2423527&organism=1823466&compartment_list=any&pathway_list=any&name_text=%s",
102 "BioCyc": "http://biocyc.org/MGEN243273/NEW-IMAGE?type=GENE&object=%s",
103 "BioProject": "http://www.ncbi.nlm.nih.gov/bioproject/%s",
104 "CAS": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=%s",
105 "ChEBI": "http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:%s",
106 "CMR": "http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=%s",
107 "EC": "http://www.expasy.ch/enzyme/%s",
108 "GenBank": "http://www.ncbi.nlm.nih.gov/sites/gquery?term=%s",
109 "ISBN": "http://isbndb.com/search-all.html?kw=%s",
110 "KEGG": "http://www.genome.jp/dbget-bin/www_bget?cpd:%s",
111 "KNApSAcK": "http://kanaya.naist.jp/knapsack_jsp/information.jsp?word=%s",
112 "LipidBank": "http://lipidbank.jp/cgi-bin/detail.cgi?id=%s",
113 "LIPIDMAPS": "http://www.lipidmaps.org/data/get_lm_lipids_dbgif.php?LM_ID=%s",
114 "PDB": "http://www.pdb.org/pdb/explore/explore.do?structureId=%s",
115 "PDBCCD": "http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/%s",
116 "PubChem": "http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?viewopt=PubChem&sid=%s",
117 "PubMed": "http://www.ncbi.nlm.nih.gov/pubmed/%s",
118 "RefSeq": "http://www.ncbi.nlm.nih.gov/nuccore/%s",
119 "SABIO-RK": "http://sabio.villa-bosch.de/kineticLawEntry.jsp?kinlawid=%s&viewData=true",
120 "SwissProt": "http://www.uniprot.org/uniprot/%s",
121 "Taxonomy": "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%s",
122 "ThreeDMET": "http://www.3dmet.dna.affrc.go.jp/bin2/show_data.e?acc=%s",
123 "URL": "%s",
124 }
125
126 CHOICES_GENETIC_CODE = (
127 ('1', 'Standard'),
128 ('2', 'Vertebrate'),
129 ('3', 'Yeast'),
130 ('4', 'Mold, protozoa, coelenterate mitochondria, mycoplasma, and spiroplasma'),
131 ('5', 'Invertebrate mitochondria'),
132 ('6', 'Ciliate, dasycladacean and hexamita'),
133 ('9', 'Echinoderm and flatworm mitochondria'),
134 ('10', 'Euplotid'),
135 ('11', 'Bacteria, archaea and plant plastids'),
136 ('12', 'Alternative yeast'),
137 ('13', 'Ascidian mitochondria'),
138 ('14', 'Alternative flatworm mitochondria'),
139 ('15', 'Blepharisma'),
140 ('16', 'Chlorophycean mitochondria'),
141 ('21', 'Trematode mitochondria'),
142 ('22', 'Scenedesmus obliquus mitochondria'),
143 ('23', 'Thraustochytrium mitochondria'),
144 ('24', 'Pterobranchia mitochondria'),
145 )
146
147 CHOICES_REACTION_DIRECTION = (
148 ('f', 'Forward'),
149 ('b', 'Backward'),
150 ('r', 'Reversible'),
151 )
152
153 CHOICES_SIGNAL_SEQUENCE_LOCATION = (
154 ('N', 'N-terminus'),
155 ('C', 'C-terminus'),
156 )
157
158 CHOICES_SIGNAL_SEQUENCE_TYPE = (
159 ('lipoprotein', 'Lipoprotein'),
160 ('secretory', 'Secretory'),
161 )
162
163 ''' END: CHOICES '''
164
165 # add model options
166 options.DEFAULT_NAMES = options.DEFAULT_NAMES + (
167 'concrete_entry_model',
168 'hide_public',
169 'fieldsets',
170 'field_list',
171 'facet_fields',
172 'clean',
173 'validate_unique',
174 )
175
176 ''' BEGIN: validators '''
178 validators.RegexValidator(regex=r'^[ACGT]+$', message='Enter a valid DNA sequence consisting of only the letters A, C, G, and T')(seq)
179
181 if direction == 'f':
182 prop_name = 'kinetics_forward'
183 else:
184 prop_name = 'kinetics_backward'
185 kinetics = reaction[prop_name]
186
187 wids = []
188 for s in reaction['stoichiometry']:
189 if (direction == 'f' and s['coefficient'] < 0) or (direction == 'r' and s['coefficient'] > 0):
190 wids.append(s['molecule'])
191
192 #rate law
193 usedKmMax = 0
194 usedVmax = 0
195 for match in re.finditer(r'([a-z][a-z0-9_]*)', kinetics['rate_law'], flags=re.I):
196 if match.group(1) == 'Vmax':
197 usedVmax = 1
198 elif match.group(1)[0:2] == 'Km':
199 if len(match.group(1)) == 2:
200 usedKmMax = max(usedKmMax, 1);
201 elif match.group(1)[2:].isnumeric():
202 usedKmMax = max(usedKmMax, int(float(match.group(1)[2:])))
203 else:
204 raise ValidationError({prop_name: 'Invalid rate law'})
205 elif match.group(1) not in wids:
206 raise ValidationError({prop_name: 'Invalid rate law, unknown molecule: "%s"' % (match.group(1), )})
207
208 #Vmax
209 if usedVmax and kinetics['vmax'] is None:
210 raise ValidationError({prop_name: 'Invalid rate law'})
211 if usedVmax and kinetics['vmax_unit'] not in ["1/min", "U/mg"]:
212 raise ValidationError({prop_name: 'Invalid rate law'})
213
214 #Km
215 if not ((kinetics['rate_law'] is None or kinetics['rate_law'] == '') or (kinetics['km'] == '' and usedKmMax == 0) or (kinetics['km'] != '' and usedKmMax == len(kinetics['km'].split(', ')))):
216 raise ValidationError({prop_name: 'Invalid rate law'})
217
218 '''
219 Test cases:
220 tests = [
221 "!(ATP)",
222 " ( ATP ) ",
223 "CTP ( ATP ) ",
224 "CTP | ( ATP ) ",
225 "CTP | ( ATP & !ATP & GTP ) ",
226 "CTP | ( ATP & !ATP & GTP)( ) ",
227 "CTP | ( ATP & !ATP & GTP ) | ()",
228 "CTP | ( ATP & !ATP & GTP ) | (H)",
229 "CTP | ( ATP & !ATP & GTP ) | (H) K",
230 "!!CTP",
231 "CTP | !!( ATP & !ATP & GTP ) | (H) & K",
232 "CTP | !( ATP & !ATP & GTP ) | (H) & K",
233 "CTP | !( ATP & (!ATP | UTP) & GTP ) | (H) & K",
234 ]
235 for test in tests:
236 try:
237 models.parse_regulatory_rule(test)
238 except:
239 print test
240 '''
242 from public.helpers import getModel, getEntry
243 import settings
244
245 pre = ''
246 blocks = []
247 posts = []
248 pattern = '%s'
249 begin = 0
250 end = 0
251 sense = 0
252
253 equation = equation or ''
254 equation = equation.replace(" ", "")
255
256 match = re.match(r'^([!\-]{0,1})\((.+)\)$', equation)
257 if match:
258 pattern = pattern.replace('%s', match.group(1) + '(%s)')
259 equation = match.group(2)
260
261 match = re.match(r'^([!\-]{0,1})(.+)$', equation)
262 if match:
263 pattern = pattern.replace('%s', match.group(1) + '%s')
264 equation = match.group(2)
265
266 if equation == '':
267 raise ValidationError({'regulatory_rule': 'Invalid regulatory rule'})
268
269 #split into blocks
270 for i in range(len(equation)):
271 if equation[i] == '(':
272 sense += 1
273 if equation[i] == ')':
274 sense -= 1
275 if sense < 0:
276 raise ValidationError({'regulatory_rule': 'Invalid regulatory rule'})
277
278 if sense == 0:
279 if len(blocks) == 0:
280 pre = equation[0:begin]
281 if equation[i] in ["|", "&", "-", "+"]:
282 blocks.append(equation[begin:i])
283 posts.append(equation[i])
284 begin = i + 1
285 elif equation[i:i+2] in [">=", "<=", "=="]:
286 blocks.append(equation[begin:i])
287 posts.append(equation[i:i+1])
288 begin = i + 2
289 elif equation[i] in [">", "<"]:
290 blocks.append(equation[begin:i])
291 posts.append(equation[i])
292 begin = i + 1
293 blocks.append(equation[begin:])
294 posts.append('')
295
296 #check parenthesis match
297 if sense != 0:
298 raise ValidationError({'regulatory_rule': 'Invalid regulatory rule'})
299
300 #if no further substructure
301 if len(blocks) == 1:
302 if '(' in blocks[0]:
303 raise ValidationError({'regulatory_rule': 'Invalid regulatory rule'})
304 elif '!' in blocks[0]:
305 raise ValidationError({'regulatory_rule': 'Invalid regulatory rule'})
306 elif blocks[0].isnumeric() or blocks[0] in ["true", "false"]:
307 return pattern % (pre + ' '.join([block + ' ' + post for block, post in zip(blocks, posts)]))
308
309 wid = blocks[0]
310 molecule = None
311 if all_obj_data is None:
312 molecule = getEntry(species_wid=species_wid, wid=wid)
313 elif all_obj_data.has_key(wid):
314 molecule = all_obj_data[wid]
315
316 if molecule is not None:
317 if isinstance(molecule, Entry):
318 molecule_model = molecule.__class__
319 else:
320 molecule_model = getModel(molecule['model_type'])
321 if issubclass(molecule_model, Molecule):
322 return pattern % (pre + ' '.join([block + ' ' + post for block, post in zip(blocks, posts)]))
323 else:
324 raise ValidationError({'regulatory_rule': 'Invalid regulatory rule, referenced invalid object %s' % wid})
325 try:
326 obj = Molecule.objects.get(species__wid=species_wid, wid=wid)
327 blocks[0] = '<a href="%s">%s</a>' % (obj.get_absolute_url(), wid, )
328 return pattern % (pre + ' '.join([block + ' ' + post for block, post in zip(blocks, posts)]))
329 except:
330 pass
331 raise ValidationError({'regulatory_rule': 'Invalid object "%s" in regulatory rule' % wid})
332
333 #recurse on blocks
334 for i in range(len(blocks)):
335 blocks[i] = parse_regulatory_rule(blocks[i], all_obj_data, species_wid)
336
337 return pattern % (pre + ' '.join([block + ' ' + post for block, post in zip(blocks, posts)]))
338
339 ''' END: validators '''
343 user = OneToOneField(User)
344 affiliation = CharField(max_length=255, blank=True, default='', verbose_name='Affiliation')
345 website = URLField(max_length=255, blank=True, default='', verbose_name='Website')
346 phone = CharField(max_length=255, blank=True, default='', verbose_name='Phone')
347 address = CharField(max_length=255, blank=True, default='', verbose_name='Address')
348 city = CharField(max_length=255, blank=True, default='', verbose_name='City')
349 state = CharField(max_length=255, blank=True, default='', verbose_name='State')
350 zip = CharField(max_length=255, blank=True, default='', verbose_name='Zip')
351 country = CharField(max_length=255, blank=True, default='', verbose_name='Country')
352
354 verbose_name='User profile'
355 verbose_name_plural = 'User profiles'
356 ordering = ['user__last_name', 'user__first_name']
357 get_latest_by = 'user__date_joined'
358
359 ''' BEGIN: helper models '''
361 value = TextField(blank=True, default='', verbose_name='Value')
362 units = CharField(max_length=255, blank=True, null=True, verbose_name='Units')
363 is_experimentally_constrained = BooleanField(verbose_name='Is experimentally <br/>constrained')
364 species = CharField(max_length=255, blank=True, null=True, verbose_name='Species')
365 media = CharField(max_length=255, blank=True, null=True, verbose_name='Media')
366 pH = FloatField(blank=True, null=True, verbose_name='pH')
367 temperature = FloatField(blank=True, null=True, verbose_name='Temperature (C)')
368 comments = TextField(blank=True, default='', verbose_name='Comments')
369 references = ManyToManyField('Reference', blank=True, null=True, related_name='evidence', verbose_name='References')
370
371 species_component = ForeignKey('SpeciesComponent', verbose_name='Species omponent', related_name='+')
372
374 arr = []
375 for field in self.__class__._meta.fields:
376 if not field.auto_created and getattr(self, field.name) is not None and not (isinstance(getattr(self, field.name), (str, unicode, )) and getattr(self, field.name) == ''):
377 arr.append('%s: %s' % (field.name, unicode(getattr(self, field.name))))
378 for field in self.__class__._meta.many_to_many:
379 arr.append('%s: %s' % (field.name, unicode(getattr(self, field.name).all())))
380 return ', '.join(arr)
381
383 ordering = ['value', 'units']
384 verbose_name = 'Evidence'
385 verbose_name_plural = 'Evidence'
386
388
390 arr = []
391 txt = unicode('')
392 nFields = 0
393 for field in self.__class__._meta.fields:
394 if not field.auto_created:
395 nFields += 1
396 try:
397 txt = unicode(getattr(self, field.name))
398 arr.append('%s: %s' % (field.name, txt))
399 except ObjectDoesNotExist:
400 pass
401 for field in self.__class__._meta.many_to_many:
402 nFields += 1
403 txt = unicode(getattr(self, field.name).all())
404 arr.append('%s: %s' % (field.name, txt))
405
406 if nFields == 1:
407 return txt
408 else:
409 return ', '.join(arr)
410
412 abstract = True
413
415 evidence = ManyToManyField(Evidence, blank=True, null=True, verbose_name='Evidence')
416
418 abstract = True
419
422 value = BooleanField(verbose_name='Value')
423
425 ordering = ['value']
426 verbose_name = 'Entry Boolean data'
427 verbose_name_plural = 'Entry Boolean data'
428
430 value = CharField(max_length = 255, blank=True, default='', verbose_name='Value')
431 units = CharField(max_length = 255, blank=True, default='', verbose_name='Units')
432
434 ordering = ['value', 'units']
435 verbose_name = 'Entry char data'
436 verbose_name_plural = 'Entry char data'
437
439 value = FloatField(verbose_name='Value')
440 units = CharField(max_length = 255, blank=True, default='', verbose_name='Units')
441
443 ordering = ['value', 'units']
444 verbose_name = 'Entry float data'
445 verbose_name_plural = 'Entry float data'
446
448 value = FloatField(verbose_name='Value', validators=[validators.MinValueValidator(0)])
449 units = CharField(max_length = 255, blank=True, default='', verbose_name='Units')
450
452 ordering = ['value', 'units']
453 verbose_name = 'Entry positive float data'
454 verbose_name_plural = 'Entry positive float data'
455
457 value = TextField(blank=True, default='', verbose_name='Value')
458 units = CharField(max_length = 255, blank=True, default='', verbose_name='Units')
459
461 ordering = ['value', 'units']
462 verbose_name = 'Entry text data'
463 verbose_name_plural = 'Entry text data'
464
467 coordinate = PositiveIntegerField(verbose_name='Coordinate (nt)')
468 length = PositiveIntegerField(verbose_name='Length (nt)')
469 direction = CharField(max_length=10, choices=CHOICES_DIRECTION, verbose_name='Direction')
470
471 #getter
474
476 ordering = ['coordinate', 'length']
477 verbose_name = 'Binding site'
478 verbose_name_plural = 'Binding sites'
479
481 concentration = FloatField(verbose_name='Concentration (mmol gDCW<sup>-1</sup>)', validators=[validators.MinValueValidator(0)])
482 compartment = ForeignKey('Compartment', related_name='biomass_compositions', verbose_name='Compartment')
483
485 ordering = ['-concentration']
486 verbose_name = 'Biomass composition'
487 verbose_name_plural = 'Biomass composition'
488
490 sequence = CharField(max_length=3, verbose_name='Sequence', validators=[
491 validate_dna_sequence,
492 validators.MinLengthValidator(3),
493 ])
494
499
501 metabolite = ForeignKey('Metabolite', related_name='coenzyme_participants', verbose_name='Metabolite')
502 compartment = ForeignKey('Compartment', related_name='+', verbose_name='Compartment')
503 coefficient = FloatField(blank=True, null=True, verbose_name='Coefficient', validators=[validators.MinValueValidator(0)])
504
506 ordering = []
507 verbose_name='Coenzyme participant'
508 verbose_name_plural = 'Coenzyme participants'
509
511 xid = CharField(max_length=255, verbose_name='External ID')
512 source = CharField(max_length=20, choices=CHOICES_CROSS_REFERENCE_SOURCES, verbose_name='Source')
513
515 ordering = ['xid']
516 verbose_name='Cross reference'
517 verbose_name_plural = 'Cross references'
518
520 protein_monomer = ForeignKey('ProteinMonomer', related_name = 'disulfide_bonds', verbose_name='Protein monomer')
521 residue_1 = PositiveIntegerField(verbose_name='Residue-1')
522 residue_2 = PositiveIntegerField(verbose_name='Residue-2')
523
528
530 length = PositiveIntegerField(null=True, blank=True, verbose_name='Length (nt)')
531 binding = CharField(max_length=10, blank=True, default='', verbose_name='Binding', choices=CHOICES_STRANDEDNESS)
532 region = CharField(max_length=10, blank=True, default='', verbose_name='Region', choices=CHOICES_STRANDEDNESS)
533
538
540 protein = ForeignKey('Protein', related_name='enzyme_participants', verbose_name='Protein')
541 compartment = ForeignKey('Compartment', related_name='+', verbose_name='Compartment')
542
544 ordering = []
545 verbose_name='Enzyme participant'
546 verbose_name_plural = 'Enzyme participants'
547
549 xid = CharField(max_length=255, verbose_name='External ID')
550 species = CharField(max_length=20, choices=CHOICES_HOMOLOG_SPECIES, verbose_name='Species')
551
556
558 rate_law = CharField(blank=True, default='', max_length=255, verbose_name='Rate law')
559 km = CharField(max_length=255, blank=True, verbose_name='K<sub>m</sub> (μM)', validators=[validators.RegexValidator(r'^([0-9\.]+)(, [0-9\.]+)*$')])
560 vmax = FloatField(blank=True, null=True, verbose_name='V<sub>max</sub>', validators=[validators.MinValueValidator(0)])
561 vmax_unit = CharField(blank=True, max_length=255, choices=CHOICES_VMAX_UNITS, verbose_name='V<sub>max</sub> Unit')
562
564 from public.helpers import getModel
565
566 if vmax_unit.name == 'U/mg':
567 enz = self.reactions.all()[0].enzyme
568 enz = getModel(enz.model_type).objects.get(id=enz.id)
569 return self.vmax * enz.get_molecular_weight() * 1e-3
570 else:
571 return self.vmax
572
577
579 concentration = FloatField(verbose_name='Concentration (mM)', validators=[validators.MinValueValidator(0)])
580 is_diffused = BooleanField(verbose_name='Is diffused')
581
583 ordering = ['-concentration']
584 verbose_name='Media composition'
585 verbose_name_plural = 'Media composition'
586
588 compartment = ForeignKey('Compartment', related_name='+', verbose_name='Compartment')
589 x = FloatField(verbose_name='X')
590 y = FloatField(verbose_name='Y')
591
593 ordering = ['x', 'y', 'compartment']
594 verbose_name='Metabolite map coordinate'
595 verbose_name_plural = 'Metabolite map coordinates'
596
598 molecule = ForeignKey('Molecule', related_name='modification_reactions', verbose_name='Molecule')
599 compartment = ForeignKey('Compartment', related_name='+', verbose_name='Compartment')
600 position = PositiveIntegerField(blank=True, null=True, verbose_name='Position')
601
606
608 metabolite = ForeignKey('Metabolite', related_name='prosthetic_group_participants', verbose_name='Metabolite')
609 compartment = ForeignKey('Compartment', related_name='+', verbose_name='Compartment')
610 coefficient = PositiveIntegerField(blank=True, null=True, verbose_name='Coefficient')
611
613 ordering = []
614 verbose_name='Prosthetic group participant'
615 verbose_name_plural = 'Prosthetic group participants'
616
618 molecule = ForeignKey('Molecule', related_name='protein_complex_biosythesis_participants', verbose_name='Molecule')
619 residue = PositiveIntegerField(blank=True, null=True, verbose_name='Residue')
620 coefficient = FloatField(verbose_name='Coefficient')
621 compartment = ForeignKey('Compartment', related_name='+', verbose_name='Compartment')
622
624 ordering = []
625 verbose_name='Protein complex biosythesis participant'
626 verbose_name_plural = 'Protein complex biosythesis participants'
627
629 path = TextField(verbose_name='Path')
630 value_x = FloatField(verbose_name='Label-X')
631 value_y = FloatField(verbose_name='Label-Y')
632 label_x = FloatField(verbose_name='Value-X')
633 label_y = FloatField(verbose_name='Value-Y')
634
636 ordering = ['value_x', 'value_y', 'label_x', 'label_y']
637 verbose_name='Reaction map coordinate'
638 verbose_name_plural = 'Reaction map coordinates'
639
641 molecule = ForeignKey('Molecule', related_name='reaction_stoichiometry_participants', verbose_name='Molecule')
642 coefficient = FloatField(verbose_name='Coefficient')
643 compartment = ForeignKey('Compartment', related_name='+', verbose_name='Compartment')
644
646 ordering = []
647 verbose_name='Molecule coefficient compartment'
648 verbose_name_plural = 'Molecule coefficient compartments'
649
651 type = CharField(max_length=20, choices=CHOICES_SIGNAL_SEQUENCE_TYPE, verbose_name='Type')
652 location = CharField(max_length=1, choices=CHOICES_SIGNAL_SEQUENCE_LOCATION, verbose_name='Location')
653 length = PositiveIntegerField(verbose_name='Length (nt)')
654
656 ordering = ['type', 'location', 'length']
657 verbose_name = 'Signal sequence'
658 verbose_name_plural = 'Signal sequences'
659
661 class_name = TextField(verbose_name = 'Class', db_index=True)
662 property_name = CharField(max_length = 255, verbose_name = 'Property', db_index=True)
663
666
668 ordering = ['class_name', 'property_name']
669 verbose_name = 'Simulation property'
670 verbose_name_plural = 'Simulation properties'
671
679
680 ''' END: helper models '''
681
682
683 ''' BEGIN: Base classes for all knowledge base objects '''
685 model_type = CharField(max_length=255, editable=False, verbose_name='Model')
686 wid = SlugField(max_length=150, verbose_name='WID', validators=[validators.validate_slug])
687 name = CharField(max_length=255, blank=True, default='', verbose_name='Name')
688 synonyms = ManyToManyField(Synonym, blank=True, null=True, related_name='entry', verbose_name='Synonyms')
689 cross_references = ManyToManyField(CrossReference, blank=True, null=True, related_name='cross_referenced_entries', verbose_name='Cross references')
690 comments = TextField(blank=True, default='', verbose_name='Comments')
691
692 created_user = ForeignKey(User, related_name='+', editable=False, verbose_name='Created user')
693 created_date = DateTimeField(auto_now=False, auto_now_add=True, verbose_name='Created date')
694
695 last_updated_user = ForeignKey(User, related_name='+', editable=False, verbose_name='Last updated user')
696 last_updated_date = DateTimeField(auto_now=True, auto_now_add=True, verbose_name='Last updated date')
697
699 return self.wid
700
702 return self.wid
703
705 setattr(self, 'model_type', self.__class__.__name__)
706 super(Entry, self).save(*args, **kwargs)
707
708 #html formatting
711
713 results = []
714 for cr in self.cross_references.all():
715 results.append('%s: <a href="%s">%s</a>' % (cr.source, CROSS_REFERENCE_SOURCE_URLS[cr.source] % cr.xid, cr.xid))
716 return format_list_html(results, separator=', ')
717
719 if is_user_anonymous:
720 return '%s' % (self.created_date.strftime("%Y-%m-%d %H:%M:%S"))
721 else:
722 return '<a href="%s">%s %s</a> on %s' % (self.created_user.get_absolute_url(), self.created_user.first_name, self.created_user.last_name, self.created_date.strftime("%Y-%m-%d %H:%M:%S"))
723
725 if is_user_anonymous:
726 return '%s' % (self.last_updated_date.strftime("%Y-%m-%d %H:%M:%S"))
727 else:
728 return '<a href="%s">%s %s</a> on %s' % (self.last_updated_user.get_absolute_url(), self.last_updated_user.first_name, self.last_updated_user.last_name, self.last_updated_date.strftime("%Y-%m-%d %H:%M:%S"))
729
730 #meta information
732 concrete_entry_model = False
733 fieldsets = [
734 ('Type', {'fields': ['model_type']}),
735 ('Name', {'fields': ['wid', 'name', 'synonyms', 'cross_references']}),
736 ('Comments', {'fields': ['comments']}),
737 ('Metadata', {'fields': [{'verbose_name': 'Created', 'name': 'created_user'}, {'verbose_name': 'Last updated', 'name': 'last_updated_user'}]}),
738 ]
739 field_list = [
740 'id', 'wid', 'name', 'synonyms', 'cross_references', 'comments', 'created_user', 'created_date', 'last_updated_user', 'last_updated_date',
741 ]
742 facet_fields = []
743 ordering = ['wid']
744 get_latest_by = 'createdDate'
745 verbose_name = 'Entry'
746 verbose_name_plural = 'Entries'
747
749 #parent pointer
750 parent_ptr_entry = OneToOneField(Entry, related_name='child_ptr_species_component', parent_link=True, verbose_name='Entry')
751
752 #additional fields
753 species = ForeignKey('Species', related_name='components', verbose_name='Species')
754 type = ManyToManyField('Type', blank=True, null=True, related_name='members', verbose_name='Type')
755 references = ManyToManyField('Reference', blank=True, null=True, related_name='referenced_entries', verbose_name='References')
756
757 #getters
758 @permalink
761
763 return self.references.all() | Reference.objects.filter(evidence__species_component__id = self.id)
764
765 #html formatting
767 results = []
768 for p in self.parameters.all():
769 results.append('<a href="%s">%s</a>: <i>%s</i> = %s %s' % (p.get_absolute_url(), p.wid, p.name, p.value.value, p.value.units))
770 return format_list_html(results)
771
773 txt = self.comments
774
775 #provide links to references
776 return re.sub(r'\[(PUB_\d{4,4})(, PUB_\d{4,4})*\]',
777 lambda match: '[' + ', '.join(['<a href="%s">%s</a>' % (reverse('public.views.detail', kwargs={'species_wid':self.species.wid, 'wid': x}), x, ) for x in match.group(0)[1:-1].split(', ')]) + ']',
778 txt)
779
781 results = {}
782 for r in self.get_all_references():
783 key = r.authors + ' ' + r.editors
784 results[key] = r.get_citation(True)
785
786 keys = results.keys()
787 keys.sort()
788 ordered_results = []
789 for key in keys:
790 ordered_results.append(results[key])
791 return format_list_html(ordered_results, numbered=True, force_list=True)
792
793 #meta information
795 concrete_entry_model = False
796 fieldsets = [
797 ('Type', {'fields': ['model_type']}),
798 ('Name', {'fields': ['wid', 'name', 'synonyms', 'cross_references']}),
799 ('Classification', {'fields': ['type']}),
800 ('Comments', {'fields': ['comments', 'references']}),
801 ('Metadata', {'fields': [{'verbose_name': 'Created', 'name': 'created_user'}, {'verbose_name': 'Last updated', 'name': 'last_updated_user'}]}),
802 ]
803 field_list = [
804 'id', 'wid', 'name', 'synonyms', 'cross_references', 'type', 'comments', 'references', 'created_user', 'created_date', 'last_updated_user', 'last_updated_date',
805 ]
806 facet_fields = ['type']
807 verbose_name = 'Species component'
808 verbose_name_plural = 'Species components'
809
811 #parent pointer
812 parent_ptr_species_component = OneToOneField(SpeciesComponent, related_name='child_ptr_molecule', parent_link=True, verbose_name='Species component')
813
814 #additional fields
815
816 #getters
820
823
825 return sum(self.get_empirical_formula().values())
826
828 return 1 / self.get_extinction_coefficient()
829
830 #html formatting
833
835 return self.get_molecular_weight()
836
838 return self.get_extinction_coefficient()
839
841 return self.get_absorbance_factor()
842
848
850 results = []
851 for obj in self.modification_reactions.all():
852 if len(obj.reactions.all()) == 0:
853 continue
854 rxn = obj.reactions.all()[0]
855 results.append('<a href="%s">%s</a><br/>%s' % (rxn.get_absolute_url(), rxn.name, rxn.get_as_html_stoichiometry(is_user_anonymous)))
856 return format_list_html(results, vertical_spacing=True)
857
859 results = []
860 for obj in self.reaction_stoichiometry_participants.all():
861 if len(obj.reactions.all()) == 0:
862 continue
863 rxn = obj.reactions.all()[0]
864 results.append('<a href="%s">%s</a><br/>%s' % (rxn.get_absolute_url(), rxn.name, rxn.get_as_html_stoichiometry(is_user_anonymous)))
865 return format_list_html(list(set(results)), vertical_spacing=True)
866
868 results = []
869 for obj in self.protein_complex_biosythesis_participants.all():
870 if len(obj.protein_complexes.all()) == 0:
871 continue
872 pc = obj.protein_complexes.all()[0]
873 results.append('<a href="%s">%s</a><br/>%s' % (pc.get_absolute_url(), pc.name, pc.get_as_html_biosynthesis(is_user_anonymous)))
874 return format_list_html(results)
875
876 #meta information
878 concrete_entry_model = False
879 fieldsets = [
880 ('Type', {'fields': ['model_type']}),
881 ('Name', {'fields': ['wid', 'name', 'synonyms', 'cross_references']}),
882 ('Classification', {'fields': ['type']}),
883 ('Function', {'fields': [
884 {'verbose_name': 'Reaction participant', 'name':'reaction_stoichiometry_participants'},
885 {'verbose_name': 'Complex subunit', 'name':'protein_complex_biosythesis_participants'},
886 ]}),
887 ('Parameters', {'fields': ['parameters']}),
888 ('Comments', {'fields': ['comments', 'references']}),
889 ('Metadata', {'fields': [{'verbose_name': 'Created', 'name': 'created_user'}, {'verbose_name': 'Last updated', 'name': 'last_updated_user'}]}),
890 ]
891 field_list = [
892 'id', 'wid', 'name', 'synonyms', 'cross_references', 'type', 'comments', 'references', 'created_user', 'created_date', 'last_updated_user', 'last_updated_date',
893 ]
894 facet_fields = ['type']
895 verbose_name = 'Molecule'
896 verbose_name_plural = 'Molecules'
897
899 #parent pointer
900 parent_ptr_molecule = OneToOneField(Molecule, related_name='child_ptr_protein', parent_link=True, verbose_name='Molecule')
901
902 #additional fields
903 prosthetic_groups = ManyToManyField(ProstheticGroupParticipant, blank=True, null=True, related_name='proteins', verbose_name='Prosthetic groups')
904 chaperones = ManyToManyField('self', symmetrical=False, blank=True, null=True, related_name='chaperone_substrates', verbose_name='Chaperones')
905 dna_footprint = ForeignKey(DNAFootprint, null=True, blank=True, related_name='proteins', verbose_name='DNA footprint')
906 regulatory_rule = ForeignKey(EntryCharData, null=True, blank=True, on_delete=SET_NULL, verbose_name='Regulatory rule', related_name='+')
907
908 #html formatting
910 results = []
911 for p in self.prosthetic_groups.all():
912 results.append(format_with_evidence(list_item = True, obj = p, txt = '(%s) <a href="%s">%s</a> [<a href="%s">%s</a>]' % (p.coefficient, p.metabolite.get_absolute_url(), p.metabolite.wid, p.compartment.get_absolute_url(), p.compartment.wid)))
913 return format_list_html(results, force_list=True)
914
916 results = [];
917 for c in self.chaperones.all():
918 results.append('<a href="%s">%s</a>' % (c.get_absolute_url(), c.wid))
919 return format_list_html(results, comma_separated=True)
920
922 results = [];
923 for p in self.chaperone_substrates.all():
924 results.append('<a href="%s">%s</a>' % (p.get_absolute_url(), p.wid))
925 return format_list_html(results, comma_separated=True)
926
928 if self.dna_footprint is None:
929 return None
930 return format_with_evidence(obj = self.dna_footprint, txt = 'Length: %s (nt), Binding: %s, Region: %s' % (self.dna_footprint.length, self.dna_footprint.binding, self.dna_footprint.region))
931
933 if self.regulatory_rule is not None and self.regulatory_rule.value is not None and self.regulatory_rule.value != '':
934 return parse_regulatory_rule(self.regulatory_rule.value, {}, self.species.wid)
935 return ''
936
938 results = [];
939 for r in self.transcriptional_regulations.all():
940 results.append('<a href="%s">%s</a>: <a href="%s">%s</a>' % (r.get_absolute_url(), r.wid, r.transcription_unit.get_absolute_url(), r.transcription_unit.wid))
941 return format_list_html(results)
942
944 results = [];
945 for obj in self.enzyme_participants.all():
946 if len(obj.reactions.all()) == 0:
947 continue
948 rxn = obj.reactions.all()[0]
949 results.append('<a href="%s">%s</a><br/>%s' % (rxn.get_absolute_url(), rxn.name, rxn.get_as_html_stoichiometry(is_user_anonymous)))
950 return format_list_html(results, vertical_spacing=True)
951
953 return self.get_half_life()
954
955 #meta information
957 concrete_entry_model = False
958 fieldsets = [
959 ('Type', {'fields': ['model_type']}),
960 ('Name', {'fields': ['wid', 'name', 'synonyms', 'cross_references']}),
961 ('Classification', {'fields': ['type']}),
962 ('Structure', {'fields': ['prosthetic_groups', 'chaperones', 'dna_footprint']}),
963 ('Regulation', {'fields': ['regulatory_rule']}),
964