X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;ds=inline;f=django_simple%2Ftodo%2Fforms.py;h=45e78bf31a54d9284dc97b576181155a1afe2795;hb=d82a989eec06a167258ff6d644dd77292310ddda;hp=e87cdcc2385241f6c43824a0708fec3e99de5b7b;hpb=787a0b201a638f0a7ac7cec85d172bf0619f2fc1;p=django_unres.git diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py index e87cdcc..45e78bf 100644 --- a/django_simple/todo/forms.py +++ b/django_simple/todo/forms.py @@ -7,21 +7,43 @@ 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): +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: @@ -29,7 +51,7 @@ def pdb_missing_res(file): newchain = False else: msg = 'chain breaks between residues '+\ - str(ires[-1])+' and '+str(i)+\ + 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': @@ -37,8 +59,23 @@ def pdb_missing_res(file): 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 @@ -71,16 +108,16 @@ class MultiExampleField(forms.fields.MultiValueField): 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() @@ -93,24 +130,18 @@ class TaskForm_min(forms.Form): 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='FF2') @@ -123,9 +154,9 @@ class TaskForm_min_a(forms.Form): 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)') @@ -148,24 +179,18 @@ class TaskForm_min_a(forms.Form): 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') @@ -176,9 +201,9 @@ 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') + 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') @@ -210,24 +235,18 @@ class TaskForm_md(forms.Form): 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='FF2') @@ -239,15 +258,15 @@ class TaskForm_md_a(forms.Form): 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', + 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') @@ -301,18 +320,12 @@ class TaskForm_md_a(forms.Form): 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) @@ -322,7 +335,7 @@ class TaskForm_md_a(forms.Form): 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') @@ -333,9 +346,9 @@ class TaskForm_remd(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') + 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') @@ -364,24 +377,18 @@ class TaskForm_remd(forms.Form): 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='FF2') @@ -393,14 +400,14 @@ class TaskForm_remd_a(forms.Form): 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', + 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') @@ -415,6 +422,9 @@ class TaskForm_remd_a(forms.Form): 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
'+ + '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, @@ -470,18 +480,12 @@ class TaskForm_remd_a(forms.Form): 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) @@ -491,9 +495,68 @@ class TaskForm_remd_a(forms.Form): self.add_error('md_2d',msg) +class TaskForm_dock(forms.Form): + name = forms.CharField(max_length=40,widget=forms.TextInput(attrs={'size':40, 'maxlength':40})) + + file1 = forms.FileField(label='Upload a PDB file1',required=False, + help_text='starting structure for chain1') + 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)') + + + file2 = forms.FileField(label='Upload a PDB file2',required=False, + help_text='starting structure for chain2') + pdbid2 = 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_nstep = forms.IntegerField(label='NSTEP',initial=200000, + help_text='total number of steps') + md_seed = forms.IntegerField(label='SEED',initial=-39912345, + help_text='seed for random number generator') + + def clean(self): + cleaned_data = super(TaskForm_dock, self).clean() + + file1 = cleaned_data.get("file1") + pdbid = cleaned_data.get("pdbid") + file2 = cleaned_data.get("file2") + pdbid2 = cleaned_data.get("pdbid2") + + + if not (file1 or pdbid): + msg = 'no PDB file or code for chain1' + self.add_error('file1', msg) + + if not (file2 or pdbid2): + msg = 'no PDB file or code for chain2' + self.add_error('file2', msg) + + if pdbid: + msg=pdb_code_chain(pdbid) + if msg != '': + self.add_error('pdbid',msg) + + if file1: + msg=pdb_missing_res_chain(file1,'') + if msg != '': + self.add_error('file1',msg) + + if pdbid2: + msg=pdb_code_chain(pdbid2) + if msg != '': + self.add_error('pdbid2',msg) + + if file2: + msg=pdb_missing_res_chain(file2,'') + if msg != '': + self.add_error('file2',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):