from .models import MD_LANG
from .models import FF_CHOICE
from django.utils.safestring import mark_safe
+#---v
+from django.core.files import File
+#---^
import json
import urllib
msg='wrong chain id'
return(msg)
+#---v
+def nmr_bad_cols(file):
+ msg=''
+ for line in file:
+ line=line.rstrip()
+ if line:
+ data = line.split()
+ for x in (0, 1, 2):
+ lg = data[x].isdigit()
+ if not lg:
+ msg = 'NMR shifts data column '+repr(x+1)+' must be integer, not: '+data[x]
+ return(msg)
+ dlug = len(data)
+ if (dlug < 5):
+ msg = 'There have to be 5 or more columns in NMR shifts data file'
+ return(msg)
+ promien = data[3].replace('.', '')
+ lg2 = promien.isdigit()
+ if not lg2:
+ msg ='NMR shifts 4th data column must be decimal or integer radius, not: '+data[3]
+ return(msg)
+ lg3 = data[4].startswith('H') or data[4].startswith('Q')
+ if not lg3:
+ msg = 'NMR shifts 5th data column must be proton designation, not: '+data[4]
+ return(msg)
+ else:
+ msg = 'NMR shifts data contains blank lines. Remove them.'
+ return(msg)
+#---^
+
def code_2d(line):
msg=''
required=False,
widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
+#---v
+ use_nmr = forms.BooleanField(required=False,label='use NMR restraints',
+ help_text='this option requires the next four fields to be set.')
+ file3 = forms.FileField(label='Upload a NMR restraints file',required=False,
+ help_text='at least 5 columns required: 49 22 1 5.0 HD2 H; <i>Hint: if you are using <u>NMR example data</u> then the field will be filled out automatically</i>')
+ nmr_scal = forms.IntegerField(label='NMR option: scal_peak',initial=20)
+ nmr_fordepth = forms.FloatField(label='NMR option: FORDEPTH_PEAK',initial=0.5)
+ nmr_slope = forms.FloatField(label='NMR option: SLOPE_PEAK',initial=0.05)
file1 = forms.FileField(label='Upload a PDB file',required=False,
- help_text='starting structure for pdbstart/reference structure')
+ help_text='starting structure for pdbstart/reference structure; <i>Hint: if you are using <u>NMR example data</u> then the field will be filled out automatically</i>')
+#---^
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_md_a, self).clean()
+#---v
+ md_seq = cleaned_data.get("md_seq")
+ if (md_seq == 'TDELLERLRQLFEELHERGTEIVVEVHINGERDEIRVRNISKEELKKLLERIREKIEREGSSEVEVNVHSGGQTWTFNEK'):
+ reopn1 = open('files/6msp-from-THR.pdb', 'r')
+ file1 = File(reopn1)
+ else:
+#---^
+ file1 = cleaned_data.get("file1")
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")
+#---v
+ if (md_seq == 'TDELLERLRQLFEELHERGTEIVVEVHINGERDEIRVRNISKEELKKLLERIREKIEREGSSEVEVNVHSGGQTWTFNEK'):
+ reopn = open('files/N1008_AmbiR-trunc.txt', 'r')
+ file3 = File(reopn)
+ else:
+ file3 = cleaned_data.get("file3")
+ unres_ff = cleaned_data.get("unres_ff")
+ use_nmr = cleaned_data.get("use_nmr")
+ nmr_scal = cleaned_data.get("nmr_scal")
+ nmr_fordepth = cleaned_data.get("nmr_fordepth")
+ nmr_slope = cleaned_data.get("nmr_slope")
+ if (use_nmr and file3):
+ msg=nmr_bad_cols(file3)
+ if msg != '':
+ self.add_error('file3',msg)
+ else:
+ if (use_nmr and not file3):
+ self.add_error('file3','"Use NMR restarints" and "Upload a NMR restr. file" must be used together')
+
+ if (use_nmr and (unres_ff != 'NEWCT-9P')):
+ self.add_error('unres_ff','"Use NMR restarints" requires NEWCT-9P force field')
+
+#---^
if md_start == 'pdbstart' and not (file1 or pdbid):
msg = 'pdbstart with no PDB file or code'
self.add_error('file1', msg)
help_text='single letter code: H helix, E extended/beta, C or - no restraints',
required=False,
widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
+#---v
+ use_nmr = forms.BooleanField(required=False,label='use NMR restraints',
+ help_text='this option requires the next four fields to be set.')
+ file3 = forms.FileField(label='Upload a NMR restraints file',required=False,
+ help_text='at least 5 columns required: 49 22 1 5.0 HD2 H; <i>Hint: if you are using <u>NMR example data</u> then the field will be filled out automatically</i>')
+ nmr_scal = forms.IntegerField(label='NMR option: scal_peak',initial=20)
+ nmr_fordepth = forms.FloatField(label='NMR option: FORDEPTH_PEAK',initial=0.5)
+ nmr_slope = forms.FloatField(label='NMR option: SLOPE_PEAK',initial=0.05)
+#---^
file1 = forms.FileField(label='Upload a PDB file',required=False,
- help_text='starting structure for pdbstart/reference structure')
+ help_text='starting structure for pdbstart/reference structure; <i>Hint: if you are using <u>NMR example data</u> then the field will be filled out automatically</i>')
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)')
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")
+#---v
md_seq = cleaned_data.get("md_seq")
+ if (md_seq == 'TDELLERLRQLFEELHERGTEIVVEVHINGERDEIRVRNISKEELKKLLERIREKIEREGSSEVEVNVHSGGQTWTFNEK'):
+ reopn1 = open('files/6msp-from-THR.pdb', 'r')
+ file1 = File(reopn1)
+ else:
+ file1 = cleaned_data.get("file1")
+#---^
+ pdbid = cleaned_data.get("pdbid")
md_pdbref = cleaned_data.get("md_pdbref")
md_2d = cleaned_data.get("md_2d")
-
+#---v
+ if (md_seq == 'TDELLERLRQLFEELHERGTEIVVEVHINGERDEIRVRNISKEELKKLLERIREKIEREGSSEVEVNVHSGGQTWTFNEK'):
+ reopn = open('files/N1008_AmbiR-trunc.txt', 'r')
+ file3 = File(reopn)
+ else:
+ file3 = cleaned_data.get("file3")
+ unres_ff = cleaned_data.get("unres_ff")
+ use_nmr = cleaned_data.get("use_nmr")
+ nmr_scal = cleaned_data.get("nmr_scal")
+ nmr_fordepth = cleaned_data.get("nmr_fordepth")
+ nmr_slope = cleaned_data.get("nmr_slope")
+ if (use_nmr and file3):
+ msg=nmr_bad_cols(file3)
+ if msg != '':
+ self.add_error('file3',msg)
+ else:
+ if (use_nmr and not file3):
+ self.add_error('file3','"Use NMR restarints" and "Upload a NMR restr. file" must be used together')
+
+ if (use_nmr and (unres_ff != 'NEWCT-9P')):
+ self.add_error('unres_ff','"Use NMR restarints" requires NEWCT-9P force field')
+
+#---^
if md_start == 'pdbstart' and not (file1 or pdbid):
msg = 'pdbstart with no PDB file or code'
self.add_error('file1', msg)
self.fields['temperatures'] = MultiExampleField(self.count)
self.fields['multiplexing'] = MultiExampleField(self.count)
-
-
\ No newline at end of file
projects / django_unres.git / blobdiff