MIN_CHOICE = (('minimize cart','minimize'),('minimize regular','regularize'),('minimize softreg','soft regularize'),('minimize','minimize internal coordinates'))
MD_START= (('extconf','extended chain'),('pdbstart','start from pdb'),('rand_conf','random chain'))
MD_LANG = (('langevin','Langevin'),('berendsen','Berendsen'))
-FF_CHOICE = (('E0LL2Y','JCC 30 2127 (2009) + JCTC 11 817831 (2015)'),('opt-wtfsa-2','JCIM 10.1021/acs.jcim.7b00254 (2017)'))
+FF_CHOICE = (('FF2','FF2 = JCC 30 2127 (2009) + JCTC 11 817-831 (2015)'),('opt-wtfsa-2','OPT-WTFSA-2 = JCIM 57 2364-2377 (2017)'),('NEWCT-9P','NEWCT-9P = JCP 150 155104 (2019)'))
logger = logging.getLogger(__name__)
# file will be uploaded to MEDIA_ROOT/<jobdirname>/plik.pdb
return '{0}/{1}'.format(instance.jobdirname, 'plik.pdb')
+def user_directory_path2(instance, filename):
+ # file will be uploaded to MEDIA_ROOT/<jobdirname>/plik2.pdb
+ return '{0}/{1}'.format(instance.jobdirname, 'plik2.pdb')
+
# Create your models here.
class Task(models.Model):
# def getssbond(self):
# return json.loads(self.ssbond)
- unres_ff = models.CharField(max_length=20,choices=FF_CHOICE,default='E0LL2Y')
+ unres_ff = models.CharField(max_length=20,choices=FF_CHOICE,default='FF2')
+ pdbcode = models.CharField(max_length=6,default='')
# minimization
min_choice = models.CharField(max_length=20,choices=MIN_CHOICE,default='minimize cart')
min_overlap = models.BooleanField(default=False)
min_pdbout = models.BooleanField(default=True)
myfile1 = models.FileField(default='',upload_to=user_directory_path)
min_unres_pdb = models.BooleanField(default=False)
+ boxx = models.FloatField(default=1000.0)
+ boxy = models.FloatField(default=1000.0)
+ boxz = models.FloatField(default=1000.0)
# minimization output
etot = models.FloatField(default=0)
md_temp = models.FloatField(default=300.0)
md_nstep = models.IntegerField(default=200000)
md_ntwe = models.IntegerField(default=100)
- md_ntwx = models.IntegerField(default=100)
+ md_ntwx = models.IntegerField(default=1000)
md_dt = models.FloatField(default=0.20)
md_lang = models.CharField(max_length=10,choices=MD_LANG,default='langevin')
md_tau = models.FloatField(default=1.0)
md_scal_fric = models.FloatField(default=0.02)
- md_mdpdb = models.BooleanField(default=False)
+ md_mdpdb = models.BooleanField(default=True)
md_seq = models.TextField(max_length=2000,default='')
+ md_2d = models.TextField(max_length=2000,default='')
+ md_total_steps = models.IntegerField(default=200000)
#remd
remd_nrep = models.IntegerField(default=8)
remd_model3 = models.TextField(default='')
remd_model4 = models.TextField(default='')
remd_model5 = models.TextField(default='')
+
+#saxs
+ scal_rad = models.FloatField(default=1.0)
+ wsaxs = models.FloatField(default=1000.0)
+ saxs_data = models.TextField(max_length=10000,default='')
+
+#dock
+ myfile2 = models.FileField(default='',upload_to=user_directory_path2)
+ pdbcode2 = models.CharField(max_length=6,default='')
# system
ready = models.BooleanField(default=False)
owner = models.ForeignKey(User,default=1)
created_date = models.DateTimeField(default=timezone.now)
jobdirname = models.CharField(max_length=100,default='')
+ example = models.CharField(max_length=10,default='')
+ damino = models.BooleanField(default=False)
def __str__(self):
if self.done: