From 18720bfd2db199afb2ebf034b3206fc07f16c1ad Mon Sep 17 00:00:00 2001 From: Cezary Czaplewski Date: Fri, 22 Dec 2017 01:21:02 +0100 Subject: [PATCH] saxs restraints --- django_simple/todo/forms.py | 10 +++++ django_simple/todo/jobfiles.py | 57 +++++++++++++++++++++------- django_simple/todo/models.py | 6 +++ django_simple/todo/templates/details.html | 25 +++++++++++- django_simple/todo/templates/details1.html | 26 ++++++++++++- django_simple/todo/templates/edit.html | 4 ++ django_simple/todo/views.py | 48 +++++++++++++++++++++++ files/pbs8.csh | 9 +++++ files/pbs8_new.csh | 10 +++++ files/plot_saxs.py | 30 +++++++++++++++ files/saxs_dist.awk | 33 ++++++++++++++++ 11 files changed, 242 insertions(+), 16 deletions(-) create mode 100755 files/plot_saxs.py create mode 100644 files/saxs_dist.awk diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py index 0a8f597..5eb67fb 100644 --- a/django_simple/todo/forms.py +++ b/django_simple/todo/forms.py @@ -411,6 +411,16 @@ 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() diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py index d09ab98..fd7fd7c 100644 --- a/django_simple/todo/jobfiles.py +++ b/django_simple/todo/jobfiles.py @@ -48,15 +48,13 @@ def write_on_task_save(sender, instance, **kwargs): WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 & WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 & WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25 & -CUTOFF=7.00000 WCORR4=0.00000 -""" +CUTOFF=7.00000 WCORR4=0.00000""" else: w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542 & WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000 & WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000 & WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000 & -CUTOFF=7.00000 WCORR4=0.00000 -""" +CUTOFF=7.00000 WCORR4=0.00000""" with open(instance.jobdirname+'/file.inp','w') as f: @@ -134,7 +132,16 @@ CUTOFF=7.00000 WCORR4=0.00000 if instance.md_pdbref: control_line = control_line+'pdbref ' - + + cntrl_saxs='' + if instance.saxs_data != '': + lines=instance.saxs_data.split('\n') + nsaxs=0 + for line in lines: + if len(line.split())==2: + nsaxs+=1 + cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad) + control_line += cntrl_saxs type_line = 'reset_vel='+ str(instance.remd_nstex)\ +' nstep='+str(instance.md_nstep)\ @@ -195,8 +202,10 @@ CUTOFF=7.00000 WCORR4=0.00000 for element in word_list[:-1]: f.write('{:79}'.format(element)+'&\n') f.write(word_list[-1]+'\n') - - f.write(w) + + if instance.saxs_data != '': + w+=' wsaxs='+str(instance.wsaxs) + f.write(w+'\n') if instance.type == 'min' or instance.md_start == 'pdbstart': @@ -223,7 +232,12 @@ CUTOFF=7.00000 WCORR4=0.00000 f.write(seq[i:i+80]+'\n') f.write('0\n0\n') - + if instance.saxs_data != '': + lines=instance.saxs_data.split('\n') + for line in lines: + tmp=line.split() + if len(tmp)==2: + f.write(tmp[0]+' '+tmp[1]+'\n') if instance.type == 'min': @@ -309,20 +323,29 @@ CUTOFF=7.00000 WCORR4=0.00000 f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+ ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n') f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+ - ' BOXZ='+str(instance.boxz) +'\n') + ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n') else: f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+ ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n') f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+ - ' BOXZ='+str(instance.boxz) +'\n') + ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n') f.write('nres='+str(len(seq))+' one_letter\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') f.write(write_ssbond(instance.ssbond)) - - f.write(w) + if instance.saxs_data != '': + fsaxs = open(instance.jobdirname+'/saxs.data', 'w') + lines=instance.saxs_data.split('\n') + for line in lines: + tmp=line.split() + if len(tmp)==2: + f.write(tmp[0]+' '+tmp[1]+'\n') + fsaxs.write(tmp[0]+' '+tmp[1]+'\n') + fsaxs.close() + + f.write(w+'\n') f.write('\n') f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n') tmp1=json.loads(instance.remd_multi_t) @@ -344,11 +367,17 @@ CUTOFF=7.00000 WCORR4=0.00000 +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1' +' temper='+str(instance.remd_cluter_temp))+'&\n') f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+ - ' BOXZ='+str(instance.boxz) +'\n') - f.write(w) + ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n') + f.write(w+'\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') f.write(write_ssbond(instance.ssbond)) + if instance.saxs_data != '': + lines=instance.saxs_data.split('\n') + for line in lines: + tmp=line.split() + if len(tmp)==2: + f.write(tmp[0]+' '+tmp[1]+'\n') os.chdir(instance.jobdirname) ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) diff --git a/django_simple/todo/models.py b/django_simple/todo/models.py index e74eca0..da15522 100644 --- a/django_simple/todo/models.py +++ b/django_simple/todo/models.py @@ -79,6 +79,12 @@ class Task(models.Model): remd_model3 = models.TextField(default='') remd_model4 = models.TextField(default='') remd_model5 = models.TextField(default='') + +#saxs + scal_rad = models.FloatField(default=1.0) + wsaxs = models.FloatField(default=100.0) + saxs_data = models.TextField(max_length=10000,default='') + # system ready = models.BooleanField(default=False) diff --git a/django_simple/todo/templates/details.html b/django_simple/todo/templates/details.html index 5c3e43c..c6ad8e9 100644 --- a/django_simple/todo/templates/details.html +++ b/django_simple/todo/templates/details.html @@ -280,7 +280,20 @@ Created {{ task.created_date }}
temperature for clustering
{{ task.remd_cluter_temp}}
- + {% if task.saxs_data != "" %} +
  • +
    wsaxs
    +
    {{ task.wsaxs }}
    +
    • +
  • +
    scal_rad (saxs)
    +
    {{ task.scal_rad }}
    +
    • +
  • +
    saxs distribution
    + 
     {{ task.saxs_data }}
    +
    • + {% endif %} {% endif %} @@ -479,6 +492,16 @@ Created {{ task.created_date }} width="500"> + {% if task.saxs_data != "" %} +
  • +
    P(r) of input SAXS data and + calculated for 5 models
    +
    +
    • + {% endif %} +
  • diff --git a/django_simple/todo/templates/details1.html b/django_simple/todo/templates/details1.html index 519ab0d..eaf6ff3 100644 --- a/django_simple/todo/templates/details1.html +++ b/django_simple/todo/templates/details1.html @@ -280,7 +280,21 @@ Created {{ task.created_date }}
    temperature for clustering
    {{ task.remd_cluter_temp}}
    • - + + {% if task.saxs_data != "" %} +
  • +
    wsaxs
    +
    {{ task.wsaxs }}
    +
    • +
  • +
    scal_rad (saxs)
    +
    {{ task.scal_rad }}
    +
    • +
  • +
    saxs distribution
    + 
     {{ task.saxs_data }}
    +
    • + {% endif %} {% endif %} @@ -478,6 +492,16 @@ Created {{ task.created_date }} src="/myfiles/download-file/{{task.jobdirname}}/remd_ex.png" width="500"> + {% if task.saxs_data != "" %} +
  • +
    P(r) of input SAXS data and + calculated for 5 models
    +
    +
    • + {% endif %} +
  • diff --git a/django_simple/todo/templates/edit.html b/django_simple/todo/templates/edit.html index 90cec38..940ab03 100644 --- a/django_simple/todo/templates/edit.html +++ b/django_simple/todo/templates/edit.html @@ -77,6 +77,10 @@ Calculation type {{ p_type }} + {% if p_type == "replica exchange molecular dynamics - advanced options" %} + + {% endif %} diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py index 61d5b61..c513fbf 100644 --- a/django_simple/todo/views.py +++ b/django_simple/todo/views.py @@ -413,6 +413,7 @@ def add_remd(request,task_id): @login_required def add_remd_a(request,task_id): + from django.core.files.uploadedfile import UploadedFile task = get_object_or_404(Task, id=task_id) if request.method == 'POST': if '_example' in request.POST: @@ -420,6 +421,49 @@ def add_remd_a(request,task_id): 'md_nstep':500000,'md_lang':'berendsen','unres_ff':'opt-wtfsa-2', 'remd_cluter_temp':280} form = TaskForm_remd_a(initial=data) + elif '_example_saxs' in request.POST: + data= {'name':task.name,'pdbid':'5UJQ','md_pdbref':True, + 'md_nstep':200000,'md_lang':'langevin','unres_ff':'E0LL2Y', + 'remd_cluter_temp':270, + 'scal_rad':4.0,'wsaxs':100.0,'saxs_data': +""" 0.5 1.33868e-02 + 1.5 1.95880e-02 + 2.5 2.68896e-02 + 3.5 3.43737e-02 + 4.5 4.07099e-02 + 5.5 4.47875e-02 + 6.5 4.63486e-02 + 7.5 4.60514e-02 + 8.5 4.49130e-02 + 9.5 4.36744e-02 +10.5 4.26085e-02 +11.5 4.17464e-02 +12.5 4.11217e-02 +13.5 4.07835e-02 +14.5 4.06776e-02 +15.5 4.06060e-02 +16.5 4.03241e-02 +17.5 3.96655e-02 +18.5 3.85756e-02 +19.5 3.70537e-02 +20.5 3.50982e-02 +21.5 3.27236e-02 +22.5 3.00046e-02 +23.5 2.70643e-02 +24.5 2.40044e-02 +25.5 2.08595e-02 +26.5 1.76342e-02 +27.5 1.43802e-02 +28.5 1.12281e-02 +29.5 8.34574e-03 +30.5 5.87354e-03 +31.5 3.88732e-03 +32.5 2.39755e-03 +33.5 1.36323e-03 +34.5 7.06686e-04 +35.5 3.30592e-04 +36.5 1.38359e-04"""} + form = TaskForm_remd_a(initial=data) else: form = TaskForm_remd_a(request.POST,request.FILES) if form.is_valid(): @@ -472,6 +516,10 @@ def add_remd_a(request,task_id): task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"] task.unres_ff=form.cleaned_data["unres_ff"] + task.scal_rad = form.cleaned_data["scal_rad"] + task.saxs_data = form.cleaned_data["saxs_data"] + task.wsaxs = form.cleaned_data["wsaxs"] + task.save() return redirect('addmlist',task_id=task.id) else: diff --git a/files/pbs8.csh b/files/pbs8.csh index 0e3867d..82e7143 100755 --- a/files/pbs8.csh +++ b/files/pbs8.csh @@ -89,5 +89,14 @@ rm tmp.pdb /users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out rm plik1.pdb +if (-e saxs.data) then +awk -f ../files/saxs_dist.awk MODEL1.pdb > MODEL1_saxs.data +awk -f ../files/saxs_dist.awk MODEL2.pdb > MODEL2_saxs.data +awk -f ../files/saxs_dist.awk MODEL3.pdb > MODEL3_saxs.data +awk -f ../files/saxs_dist.awk MODEL4.pdb > MODEL4_saxs.data +awk -f ../files/saxs_dist.awk MODEL5.pdb > MODEL5_saxs.data +../files/plot_saxs.py +endif + #END touch finished diff --git a/files/pbs8_new.csh b/files/pbs8_new.csh index ca528bb..67dcc8c 100755 --- a/files/pbs8_new.csh +++ b/files/pbs8_new.csh @@ -89,5 +89,15 @@ rm tmp.pdb /users2/local/bin/tmscore MODEL5.pdb plik1.pdb > tmscore5.out rm plik1.pdb +if (-e saxs.data) then +awk -f ../files/saxs_dist.awk MODEL1.pdb > MODEL1_saxs.data +awk -f ../files/saxs_dist.awk MODEL2.pdb > MODEL2_saxs.data +awk -f ../files/saxs_dist.awk MODEL3.pdb > MODEL3_saxs.data +awk -f ../files/saxs_dist.awk MODEL4.pdb > MODEL4_saxs.data +awk -f ../files/saxs_dist.awk MODEL5.pdb > MODEL5_saxs.data +../files/plot_saxs.py +endif + + #END touch finished diff --git a/files/plot_saxs.py b/files/plot_saxs.py new file mode 100755 index 0000000..292550b --- /dev/null +++ b/files/plot_saxs.py @@ -0,0 +1,30 @@ +#! /usr/bin/env python + +import matplotlib +#matplotlib.use('GTK') +matplotlib.use('Agg') +import matplotlib.pyplot as plt +import matplotlib.cm as cm +import numpy as np +import sys + +x,y= np.loadtxt('saxs.data',usecols=(0,1),unpack=True) +x1,y1= np.loadtxt('MODEL1_saxs.data',usecols=(0,2),unpack=True) +x2,y2= np.loadtxt('MODEL2_saxs.data',usecols=(0,2),unpack=True) +x3,y3= np.loadtxt('MODEL3_saxs.data',usecols=(0,2),unpack=True) +x4,y4= np.loadtxt('MODEL4_saxs.data',usecols=(0,2),unpack=True) +x5,y5= np.loadtxt('MODEL5_saxs.data',usecols=(0,2),unpack=True) + + +plt.clf() +plt.xlabel('r') +plt.ylabel('P(r)') +plt.xlim(x[0], x[-1]) +plt.plot(x,y,'-',color='black') +plt.plot(x1,y1,'-',color='red') +plt.plot(x2,y2,'-',color='lime') +plt.plot(x3,y3,'-',color='blue') +plt.plot(x4,y4,'-',color='magenta') +plt.plot(x5,y5,'-',color='cyan') +plt.legend(['reference','MODEL1','MODEL2','MODEL3','MODEL4','MODEL5']) +plt.savefig('saxs.png') diff --git a/files/saxs_dist.awk b/files/saxs_dist.awk new file mode 100644 index 0000000..347dfde --- /dev/null +++ b/files/saxs_dist.awk @@ -0,0 +1,33 @@ +{ + if ($1 == "ATOM" && $3 == "CA") { + nres = nres + 1 + x[nres] = substr($0,31,8) + y[nres] = substr($0,39,8) + z[nres] = substr($0,47,8) + +# print "nres",nres," x",x[nres],y[nres],z[nres] + } +}END{ +# print "nres",nres + sigma = 2.50 + for (i=1;i<=nres;i++) { + for (j=1;j