X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;ds=sidebyside;f=django_simple%2Ftodo%2Fforms.py;h=38fe634365c75955d151c8149fd47d74346d3714;hb=87aa2f76c91baef63391400d7df4a7ca72cd3fb4;hp=bfbd0945fbde8d785b4f4abc321d6d8f27d4b0a5;hpb=0e76b9e206d73ead2b1dfe7b894e580225f210b3;p=django_unres.git diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py index bfbd094..38fe634 100644 --- a/django_simple/todo/forms.py +++ b/django_simple/todo/forms.py @@ -7,6 +7,74 @@ from .models import FF_CHOICE import json import urllib +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' 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: + ires.append(i) + newchain = False + else: + msg = 'chain breaks between residues '+\ + 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): @@ -47,9 +115,9 @@ class TaskForm_min(forms.Form): name = forms.CharField(max_length=20) 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() @@ -62,18 +130,22 @@ 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) - test.close() + 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) + class TaskForm_min_a(forms.Form): name = forms.CharField(max_length=20) 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, @@ -82,9 +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)') @@ -107,11 +179,14 @@ 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) - test.close() + 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) class TaskForm_md(forms.Form): @@ -126,9 +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') @@ -160,18 +235,21 @@ 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) - test.close() + 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) class TaskForm_md_a(forms.Form): name = forms.CharField(max_length=20) 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', @@ -179,11 +257,16 @@ class TaskForm_md_a(forms.Form): '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') @@ -197,12 +280,13 @@ class TaskForm_md_a(forms.Form): 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, @@ -220,6 +304,7 @@ class TaskForm_md_a(forms.Form): 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' @@ -235,12 +320,19 @@ 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) - test.close() - + 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 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) @@ -254,9 +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') @@ -285,18 +377,21 @@ 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) - test.close() + 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) class TaskForm_remd_a(forms.Form): name = forms.CharField(max_length=20) 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', @@ -304,11 +399,15 @@ class TaskForm_remd_a(forms.Form): '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') @@ -317,12 +416,15 @@ class TaskForm_remd_a(forms.Form): 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
'+ + '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, @@ -334,6 +436,8 @@ class TaskForm_remd_a(forms.Form): # 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, @@ -342,6 +446,16 @@ class TaskForm_remd_a(forms.Form): 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() @@ -350,6 +464,7 @@ class TaskForm_remd_a(forms.Form): 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' @@ -365,11 +480,19 @@ 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) - test.close() + 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 md_2d: + msg=code_2d(md_2d) + if msg != '': + self.add_error('md_2d',msg)