import json
import urllib
-def pdb_missing_res(file):
+aa_3letter = [
+ 'DPR','DLY','DAR','DHI','DAS','DGL','DSG','DGN','DSN','DTH',
+ 'DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY',
+ 'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
+ 'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO',
+ 'SME','AIB','ABU','DBZ']
+
+
+def pdb_code_chain(pdbid):
+
+ msg=''
+ chain=''
+ if len(pdbid)>4:
+ if pdbid[4]!=':':
+ return('use : between pdb code and chain id, like 5G3Q:B to select single chain')
+ chain=pdbid[5]
+ pdbid=pdbid[:4]
+
+ test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
+ if test.code != 200:
+ msg = 'wrong pdb code'
+ else:
+ msg=pdb_missing_res_chain(test,chain)
+ test.close()
+ return(msg)
+
+def pdb_missing_res_chain(file,chain):
msg=''
newchain = True
ires=[]
for line in file:
- if line[0:6] == 'ATOM ' and line[13:15] == 'CA':
+ if line[0:6] == 'ATOM ' and line[13:15] == 'CA' and (line[21] == chain or chain==''):
i = int(line[22:26])
+ ch = line[21]
+ if line[17:20] not in aa_3letter:
+ msg='residue '+line[17:20]+' '+str(i)+' not recognized'
+ return(msg)
if ires and i==ires[-1]:
continue
if newchain or i==ires[-1]+1:
newchain = False
else:
msg = 'chain breaks between residues '+\
- str(ires[-1])+' and '+str(i)+\
- ', server cannot add missing residues to PDB file'
+ str(ires[-1])+' and '+str(i)+' of chain '+ch+\
+ ', 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
+ if len(ires) == 0:
+ if chain == '':
+ msg='no CA atoms in this pdb'
+ else:
+ msg='wrong chain id'
return(msg)
+
+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)
+
+
class MultiWidgetBasic(forms.MultiWidget):
def __init__(self, count, attrs=None):
self.count=count
class TaskForm(forms.Form):
- name = forms.CharField(max_length=20)
+ name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
class TaskForm_min(forms.Form):
- name = forms.CharField(max_length=20)
+ name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
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')
+ pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+ widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+ label='or PDB code (:chain)')
def clean(self):
cleaned_data = super(TaskForm_min, self).clean()
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 != '':
+ msg=pdb_code_chain(pdbid)
+ if msg != '':
self.add_error('pdbid',msg)
- test.close()
if file1:
- msg=pdb_missing_res(file1)
+ msg=pdb_missing_res_chain(file1,'')
if msg != '':
self.add_error('file1',msg)
class TaskForm_min_a(forms.Form):
- name = forms.CharField(max_length=20)
+ name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
- label='Force Field',initial='E0LL2Y')
- min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
+ label='Force Field',initial='FF2')
+# min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
min_overlap = forms.BooleanField(required=False,label='remove overlap')
min_searchsc = forms.BooleanField(required=False,label='MC for sidechain overlap')
min_maxmin = forms.IntegerField(label='MAXMIN',initial=10000,
help_text='maximum number of function evaluations')
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')
+ pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+ widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+ label='or PDB code (:chain)')
min_unres_pdb = forms.BooleanField(required=False,label='uploaded input unres PDB',
help_text='(CA and CB atoms only, CB represents SC in UNRES)')
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)
+ msg=pdb_code_chain(pdbid)
if msg != '':
self.add_error('pdbid',msg)
- test.close()
if file1:
- msg=pdb_missing_res(file1)
+ msg=pdb_missing_res_chain(file1,'')
if msg != '':
self.add_error('file1',msg)
class TaskForm_md(forms.Form):
- name = forms.CharField(max_length=20)
+ name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
label='starting structure',initial='extconf')
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')
+ pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+ widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+ label='or PDB code (:chain)')
md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
md_temp = forms.FloatField(label='temperature',initial=300,
help_text='bath temperature')
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)
+ msg=pdb_code_chain(pdbid)
if msg != '':
self.add_error('pdbid',msg)
- test.close()
if file1:
- msg=pdb_missing_res(file1)
+ msg=pdb_missing_res_chain(file1,'')
if msg != '':
self.add_error('file1',msg)
class TaskForm_md_a(forms.Form):
- name = forms.CharField(max_length=20)
+ name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
- label='Force Field',initial='E0LL2Y')
+ label='Force Field',initial='FF2')
md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
label='starting structure',initial='extconf')
md_seq = forms.CharField(label='Sequence',
'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')
+ pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+ widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+ label='or PDB code (:chain)')
md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
md_temp = forms.FloatField(label='temperature',initial=300,
help_text='bath temperature')
md_ntwx = forms.IntegerField(label='NTWX',initial=1000,
help_text='write trajectory every ntwe steps')
md_dt = forms.FloatField(label='DT',initial=0.2,
- help_text='time step [mtu]')
+ help_text='time step [mtu=48.9 fs]')
md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
md_tau = forms.FloatField(label='tau_bath',initial=1.0,
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,
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 or pdbid):
msg = 'pdbstart with no PDB file or code'
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)
+ msg=pdb_code_chain(pdbid)
if msg != '':
self.add_error('pdbid',msg)
- test.close()
if file1:
- msg=pdb_missing_res(file1)
+ msg=pdb_missing_res_chain(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)
+ name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
label='starting structure',initial='extconf')
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')
+ pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+ widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+ label='or PDB code (:chain)')
md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
help_text='total number of steps')
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)
+ msg=pdb_code_chain(pdbid)
if msg != '':
self.add_error('pdbid',msg)
- test.close()
if file1:
- msg=pdb_missing_res(file1)
+ msg=pdb_missing_res_chain(file1,'')
if msg != '':
self.add_error('file1',msg)
class TaskForm_remd_a(forms.Form):
- name = forms.CharField(max_length=20)
+ name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40}))
unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
- label='Force Field',initial='E0LL2Y')
+ label='Force Field',initial='FF2')
md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
label='starting structure',initial='extconf')
md_seq = forms.CharField(label='Sequence',
'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')
+ pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+ widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+ label='or PDB code (:chain)')
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_ntwe = forms.IntegerField(label='NTWE',initial=1000,
help_text='write statfile every ntwe steps')
md_dt = forms.FloatField(label='DT',initial=0.2,
- help_text='time step [mtu]')
+ help_text='time step [mtu = 48.9 fs]')
md_lang = forms.ChoiceField(choices=MD_LANG,label='thermostat')
md_tau = forms.FloatField(label='tau_bath',initial=1.0,
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)')
+ min_maxfun = forms.IntegerField(label='MAXFUN',initial=5000,
+ help_text='preminim maximum number of function evaluations<br>'+
+ 'used for start from pdb or random start')
remd_nrep = forms.IntegerField(label='NREP',initial=8,
help_text='number of replicas')
remd_nstex = forms.IntegerField(label='NSTEX',initial=1000,
# 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 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()
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 or pdbid):
msg = 'pdbstart with no PDB file or code'
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)
+ msg=pdb_code_chain(pdbid)
if msg != '':
self.add_error('pdbid',msg)
- test.close()
if file1:
- msg=pdb_missing_res(file1)
+ msg=pdb_missing_res_chain(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)
+ name = forms.CharField(max_length=40,disabled=True,required=False)
nrep = forms.IntegerField(disabled=True,required=False,label='NREP')
def __init__(self, count, *args, **kwargs):
projects / django_unres.git / blobdiff