from .models import MD_LANG
from .models import FF_CHOICE
import json
+import urllib
+
+def code_2d(line):
+ msg=''
+ set ='HEC-'
+ line2 = ''.join([c for c in line if c in set])
+ if line2 != line:
+ msg='use only H,E,C or - letters'
+ return(msg)
+
+def pdb_missing_res(file):
+ msg=''
+ newchain = True
+ ires=[]
+ for line in file:
+ if line[0:6] == 'ATOM ' and line[13:15] == 'CA':
+ i = int(line[22:26])
+ if ires and i==ires[-1]:
+ continue
+ if newchain or i==ires[-1]+1:
+ ires.append(i)
+ newchain = False
+ else:
+ msg = 'chain breaks between residues '+\
+ str(ires[-1])+' and '+str(i)+\
+ ', server cannot add missing residues to PDB file - please repair the structure using e.g. Modeller'
+ break
+ if line[0:3] == 'TER':
+ newchain = True
+ if line[0:3] == 'END':
+ break
+
+ return(msg)
class MultiWidgetBasic(forms.MultiWidget):
def __init__(self, count, attrs=None):
class TaskForm_min(forms.Form):
name = forms.CharField(max_length=20)
- file1 = forms.FileField(label='Upload a PDB file',
- help_text='continuous (without breaks) protein chains,use TER to divide chains')
-
+ file1 = forms.FileField(label='Upload a PDB file',required=False,
+ help_text='continuous (without breaks) protein chains,use TER to divide chains')
+ pdbid = forms.CharField(min_length=4,max_length=4,required=False,
+ widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
+ label='or PDB code')
+
+ def clean(self):
+ cleaned_data = super(TaskForm_min, self).clean()
+
+ pdbid = cleaned_data.get("pdbid")
+ file1 = cleaned_data.get("file1")
+
+ if not pdbid and not file1:
+ msg = 'provide pdb file or pdb code'
+ self.add_error('file1', msg)
+
+ if pdbid:
+ test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
+ if test.code != 200:
+ msg = 'wrong pdb code'
+ self.add_error('pdbid', msg)
+ else:
+ msg=pdb_missing_res(test)
+ if msg != '':
+ self.add_error('pdbid',msg)
+ test.close()
+
+ if file1:
+ msg=pdb_missing_res(file1)
+ if msg != '':
+ self.add_error('file1',msg)
+
class TaskForm_min_a(forms.Form):
name = forms.CharField(max_length=20)
help_text='maximum number of iterations')
min_maxfun = forms.IntegerField(label='MAXFUN',initial=15000,
help_text='maximum number of function evaluations')
- file1 = forms.FileField(label='Upload a PDB file',
+ file1 = forms.FileField(label='Upload a PDB file',required=False,
help_text='continuous (without breaks) protein chains,use TER to divide chains')
+ pdbid = forms.CharField(min_length=4,max_length=4,required=False,
+ widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
+ label='or PDB code')
min_unres_pdb = forms.BooleanField(required=False,label='uploaded input unres PDB',
help_text='(CA and CB atoms only, CB represents SC in UNRES)')
min_pdbout = forms.BooleanField(required=False,label='output PDB',initial='true')
+ boxx = forms.FloatField(label='Box X',initial=1000.0,
+ help_text='box x dimension')
+ boxy = forms.FloatField(label='Box Y',initial=1000.0,
+ help_text='box y dimension')
+ boxz = forms.FloatField(label='Box Z',initial=1000.0,
+ help_text='box z dimension')
+
+ def clean(self):
+ cleaned_data = super(TaskForm_min_a, self).clean()
+
+ pdbid = cleaned_data.get("pdbid")
+ file1 = cleaned_data.get("file1")
+
+ if not pdbid and not file1:
+ msg = 'provide pdb file or pdb code'
+ self.add_error('file1', msg)
+
+ if pdbid:
+ test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
+ if test.code != 200:
+ msg = 'wrong pdb code'
+ self.add_error('pdbid', msg)
+ else:
+ msg=pdb_missing_res(test)
+ if msg != '':
+ self.add_error('pdbid',msg)
+ test.close()
+
+ if file1:
+ msg=pdb_missing_res(file1)
+ if msg != '':
+ self.add_error('file1',msg)
class TaskForm_md(forms.Form):
widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
file1 = forms.FileField(label='Upload a PDB file',required=False,
help_text='starting structure for pdbstart/reference structure')
+ pdbid = forms.CharField(min_length=4,max_length=4,required=False,
+ widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
+ label='or PDB code')
md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
md_temp = forms.FloatField(label='temperature',initial=300,
help_text='bath temperature')
md_start = cleaned_data.get("md_start")
file1 = cleaned_data.get("file1")
+ pdbid = cleaned_data.get("pdbid")
md_seq = cleaned_data.get("md_seq")
md_pdbref = cleaned_data.get("md_pdbref")
- if md_start == 'pdbstart' and not file1:
- msg = 'pdbstart with no PDB file'
+ if md_start == 'pdbstart' and not (file1 or pdbid):
+ msg = 'pdbstart with no PDB file or code'
self.add_error('file1', msg)
- if md_pdbref and not file1:
- msg = 'pdbref with no PDB file'
+ if md_pdbref and not (file1 or pdbid):
+ msg = 'pdbref with no PDB file or code'
self.add_error('file1', msg)
msg = 'extended/random chain with no sequence'
self.add_error('md_seq', msg)
+ if pdbid:
+ test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
+ if test.code != 200:
+ msg = 'wrong pdb code'
+ self.add_error('pdbid', msg)
+ else:
+ msg=pdb_missing_res(test)
+ if msg != '':
+ self.add_error('pdbid',msg)
+ test.close()
+
+ if file1:
+ msg=pdb_missing_res(file1)
+ if msg != '':
+ self.add_error('file1',msg)
+
class TaskForm_md_a(forms.Form):
name = forms.CharField(max_length=20)
'field is ignored when uploading starting/reference PDB file',
required=False,
widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
+ md_2d = forms.CharField(label='Secondary structure restraints',
+ help_text='single letter code: H - helix, E - extended/beta, C or - no restraints',
+ required=False,
+ widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
+
file1 = forms.FileField(label='Upload a PDB file',required=False,
help_text='starting structure for pdbstart/reference structure')
+ pdbid = forms.CharField(min_length=4,max_length=4,required=False,
+ widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
+ label='or PDB code')
md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
md_temp = forms.FloatField(label='temperature',initial=300,
help_text='bath temperature')
help_text='coupling to the thermal bath (Berendsen)')
md_scal_fric = forms.FloatField(label='scal_froc',initial=0.02,
help_text='scaling of the friction coefficients (Langevin)')
+ md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
md_mdpdb = forms.BooleanField(required=False,label='trajectory as PDB')
+ boxx = forms.FloatField(label='Box X',initial=1000.0,
+ help_text='box x dimension')
+ boxy = forms.FloatField(label='Box Y',initial=1000.0,
+ help_text='box y dimension')
+ boxz = forms.FloatField(label='Box Z',initial=1000.0,
+ help_text='box z dimension')
+
def clean(self):
cleaned_data = super(TaskForm_md_a, self).clean()
md_start = cleaned_data.get("md_start")
file1 = cleaned_data.get("file1")
+ pdbid = cleaned_data.get("pdbid")
md_seq = cleaned_data.get("md_seq")
md_pdbref = cleaned_data.get("md_pdbref")
+ md_2d = cleaned_data.get("md_2d")
- if md_start == 'pdbstart' and not file1:
- msg = 'pdbstart with no PDB file'
+ if md_start == 'pdbstart' and not (file1 or pdbid):
+ msg = 'pdbstart with no PDB file or code'
self.add_error('file1', msg)
- if md_pdbref and not file1:
- msg = 'pdbref with no PDB file'
+ if md_pdbref and not (file1 or pdbid):
+ msg = 'pdbref with no PDB file or code'
self.add_error('file1', msg)
msg = 'extended/random chain with no sequence'
self.add_error('md_seq', msg)
+ if pdbid:
+ test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
+ if test.code != 200:
+ msg = 'wrong pdb code'
+ self.add_error('pdbid', msg)
+ else:
+ msg=pdb_missing_res(test)
+ if msg != '':
+ self.add_error('pdbid',msg)
+ test.close()
+
+ if file1:
+ msg=pdb_missing_res(file1)
+ if msg != '':
+ self.add_error('file1',msg)
+
+ if md_2d:
+ msg=code_2d(md_2d)
+ if msg != '':
+ self.add_error('md_2d',msg)
class TaskForm_remd(forms.Form):
name = forms.CharField(max_length=20)
widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
file1 = forms.FileField(label='Upload a PDB file',required=False,
help_text='starting structure for pdbstart/reference structure')
+ pdbid = forms.CharField(min_length=4,max_length=4,required=False,
+ widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
+ label='or PDB code')
md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
help_text='total number of steps')
md_start = cleaned_data.get("md_start")
file1 = cleaned_data.get("file1")
+ pdbid = cleaned_data.get("pdbid")
md_seq = cleaned_data.get("md_seq")
md_pdbref = cleaned_data.get("md_pdbref")
- if md_start == 'pdbstart' and not file1:
- msg = 'pdbstart with no PDB file'
+ if md_start == 'pdbstart' and not (file1 or pdbid):
+ msg = 'pdbstart with no PDB file or code'
self.add_error('file1', msg)
- if md_pdbref and not file1:
- msg = 'pdbref with no PDB file'
+ if md_pdbref and not (file1 or pdbid):
+ msg = 'pdbref with no PDB file or code'
self.add_error('file1', msg)
if md_start != 'pdbstart' and not md_pdbref and not md_seq:
msg = 'extended/random chain with no sequence'
self.add_error('md_seq', msg)
+ if pdbid:
+ test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
+ if test.code != 200:
+ msg = 'wrong pdb code'
+ self.add_error('pdbid', msg)
+ else:
+ msg=pdb_missing_res(test)
+ if msg != '':
+ self.add_error('pdbid',msg)
+ test.close()
+
+ if file1:
+ msg=pdb_missing_res(file1)
+ if msg != '':
+ self.add_error('file1',msg)
+
class TaskForm_remd_a(forms.Form):
name = forms.CharField(max_length=20)
'field is ignored when uploading starting/reference PDB file',
required=False,
widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
+ md_2d = forms.CharField(label='Secondary structure restraints',
+ help_text='single letter code: H - helix, E - extended/beta, C or - no restraints',
+ required=False,
+ widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
file1 = forms.FileField(label='Upload a PDB file',required=False,
help_text='starting structure for pdbstart/reference structure')
+ pdbid = forms.CharField(min_length=4,max_length=4,required=False,
+ widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
+ label='or PDB code')
md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
help_text='total number of steps')
help_text='number of replicas')
remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
help_text='exchange and write trajectory every nstex steps')
+ md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
+ help_text='write trajectory every ntwx steps')
remd_cluter_temp = forms.FloatField(label='TEMPER',
help_text='temperature for cluster analysis',initial=280)
# remd_traj1file = forms.BooleanField(required=False,label='single trajectory file',initial='true')
# remd_rest1file = forms.BooleanField(required=False,label='single restart file',initial='true')
+ md_respa = forms.BooleanField(required=False,initial=True,label='RESPA')
+
+ boxx = forms.FloatField(label='Box X',initial=1000.0,
+ help_text='box x dimension')
+ boxy = forms.FloatField(label='Box Y',initial=1000.0,
+ help_text='box y dimension')
+ boxz = forms.FloatField(label='Box Z',initial=1000.0,
+ help_text='box z dimension')
+
+
+ wsaxs = forms.FloatField(label='SAXS weight',initial=100.0,
+ help_text='weight for SAXS restraint term')
+ scal_rad = forms.FloatField(label='Scal_rad (SAXS)',initial=1.0,
+ help_text='downscaling factor of residue radii used in SAXS restraints')
+ saxs_data = forms.CharField(label='P(r) SAXS data',
+ help_text='distance distribution from SAXS, two columns: r and P(r)',
+ required=False,
+ widget=forms.Textarea(attrs={'cols': 25, 'rows': 20}))
+
+
def clean(self):
cleaned_data = super(TaskForm_remd_a, self).clean()
md_start = cleaned_data.get("md_start")
file1 = cleaned_data.get("file1")
+ pdbid = cleaned_data.get("pdbid")
md_seq = cleaned_data.get("md_seq")
md_pdbref = cleaned_data.get("md_pdbref")
+ md_2d = cleaned_data.get("md_2d")
- if md_start == 'pdbstart' and not file1:
- msg = 'pdbstart with no PDB file'
+ if md_start == 'pdbstart' and not (file1 or pdbid):
+ msg = 'pdbstart with no PDB file or code'
self.add_error('file1', msg)
- if md_pdbref and not file1:
- msg = 'pdbref with no PDB file'
+ if md_pdbref and not (file1 or pdbid):
+ msg = 'pdbref with no PDB file or code'
self.add_error('file1', msg)
msg = 'extended/random chain with no sequence'
self.add_error('md_seq', msg)
+ if pdbid:
+ test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
+ if test.code != 200:
+ msg = 'wrong pdb code'
+ self.add_error('pdbid', msg)
+ else:
+ msg=pdb_missing_res(test)
+ if msg != '':
+ self.add_error('pdbid',msg)
+ test.close()
+
+ if file1:
+ msg=pdb_missing_res(file1)
+ if msg != '':
+ self.add_error('file1',msg)
+
+ if md_2d:
+ msg=code_2d(md_2d)
+ if msg != '':
+ self.add_error('md_2d',msg)
+
+
class TaskForm_list(forms.Form):
name = forms.CharField(max_length=20,disabled=True,required=False)
projects / django_unres.git / blobdiff