X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fviews.py;h=4ffb0e73f59f2705f09fa5897ed693d1c6c91fd9;hb=00fcf7b84f8d27f314f1e5a6296e402ec6252bc1;hp=4f09e49f7a1f68eef57547c316611904b15946a3;hpb=a9bca6d4270387aa7e32b550da23cef62be47638;p=django_unres.git diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py index 4f09e49..4ffb0e7 100644 --- a/django_simple/todo/views.py +++ b/django_simple/todo/views.py @@ -6,6 +6,7 @@ from .models import Task import datetime import os import subprocess +import json res_codes = [ # 20 canonical amino acids @@ -34,18 +35,45 @@ def seq_add_x(sequence): def from_pdb(file): sequence = [] ssbond = [] + ssbond_ch = [] + ires = [] + chain_start = {} + chain_end = {} + unres_shift = {} + chain=[] + ichain=0 + newchain = True + for line in file: + if line[0:6] == 'COMPND' and line[11:17] == 'CHAIN:': + tmp=line[18:] + chain_=tmp.split(', ') + chain_[-1]=chain_[-1][0] + chain.extend(chain_) + if line[0:6] == 'ATOM ' and line[13:15] == 'CA': aa = three_to_one.get(line[17:20]) - sequence.append(aa) + i = int(line[22:26]) + if newchain or i!=ires[-1]: + sequence.append(aa) + ires.append(i) + if newchain: + chain_start[chain[ichain]]=i + newchain = False if line[0:3] == 'TER': sequence.append('XX') + chain_end[chain[ichain]]=i + ichain=ichain+1 + newchain = True if line[0:6] == 'SSBOND': b=[] b.append(int(line[17:21])) b.append(int(line[31:35])) ssbond.append(b) - + c = [] + c.append((line[15:16])) + c.append((line[29:30])) + ssbond_ch.append(c) if line[0:3] == 'END': break while sequence[-1] == 'XX': @@ -56,7 +84,15 @@ def from_pdb(file): if sequence[-1] != 'G': sequence.append('X') seq=''.join(sequence) - return seq,ssbond +# if ires[0] != 1: +# ssbond=[ [e[0]-ires[0]+1,e[1]-ires[0]+1] for e in ssbond] + i=0 + for c in chain: + unres_shift[c]=i+chain_start[c] + i=i-(chain_end[c]-chain_start[c])-3 + ssbond=[ [e[0]-unres_shift[c[0]]+1,e[1]-unres_shift[c[1]]+1] for e,c in zip(ssbond,ssbond_ch)] + + return seq,json.dumps(ssbond) @login_required @@ -125,6 +161,7 @@ def add_min_a(request,task_id): task.min_pdbout=form.cleaned_data["min_pdbout"] task.myfile1=form.cleaned_data["file1"] task.min_unres_pdb=form.cleaned_data["min_unres_pdb"] + task.unres_ff=form.cleaned_data["unres_ff"] seq,task.ssbond=from_pdb(task.myfile1) task.md_seq="" @@ -222,7 +259,7 @@ def add_md_a(request,task_id): task.md_tau=form.cleaned_data["md_tau"] task.md_scal_fric=form.cleaned_data["md_scal_fric"] task.md_mdpdb=form.cleaned_data["md_mdpdb"] - + task.unres_ff=form.cleaned_data["unres_ff"] task.ready=True basename = str(task.owner) @@ -249,6 +286,7 @@ def add_remd(request,task_id): task.md_start=form.cleaned_data["md_start"] task.myfile1=form.cleaned_data["file1"] task.md_pdbref=form.cleaned_data["md_pdbref"] + task.md_ntwx=task.remd_nstex task.md_seq="" if task.md_start == "pdbstart" or task.md_pdbref: @@ -312,10 +350,13 @@ def add_remd_a(request,task_id): task.md_scal_fric=form.cleaned_data["md_scal_fric"] task.remd_nrep=form.cleaned_data["remd_nrep"] task.remd_nstex=form.cleaned_data["remd_nstex"] + task.md_ntwx=form.cleaned_data["md_ntwx"] + task.md_ntwe=form.cleaned_data["md_ntwe"] # task.remd_traj1file=form.cleaned_data["remd_traj1file"] # task.remd_rest1file=form.cleaned_data["remd_rest1file"] task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"] + task.unres_ff=form.cleaned_data["unres_ff"] basename = str(task.owner) suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S") @@ -423,6 +464,30 @@ def refresh_done(request): elif i==5: task.remd_model5=' '.join(line.split()[-6:]) + for i in range(1,6): + with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f: + text='' + for line in f: + if 'RMSD of the common residues=' in line: + text=' RMSD='+line.split()[5] + if 'TM-score =' in line: + text=text+' TMscore='+line.split()[2] + if 'GDT-TS-score=' in line: + text=text+' GDT_TS='+line.split()[1] + + if i==1: + task.remd_model1=task.remd_model1+text + elif i==2: + task.remd_model2=task.remd_model2+text + elif i==3: + task.remd_model3=task.remd_model3+text + elif i==4: + task.remd_model4=task.remd_model4+text + elif i==5: + task.remd_model5=task.remd_model5+text + + + if task.type=='remd': with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f: @@ -434,15 +499,15 @@ def refresh_done(request): if i>6: break if i==1: - task.remd_model1=task.remd_model1+'Cluster1 probability= '+line1.split()[2] + task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[2] elif i==2: - task.remd_model2=task.remd_model2+'Cluster2 probability= '+line1.split()[2] + task.remd_model2=task.remd_model2+' Cluster2 probability= '+line1.split()[2] elif i==3: - task.remd_model3=task.remd_model3+'Cluster3 probability= '+line1.split()[2] + task.remd_model3=task.remd_model3+' Cluster3 probability= '+line1.split()[2] elif i==4: - task.remd_model4=task.remd_model4+'Cluster4 probability= '+line1.split()[2] + task.remd_model4=task.remd_model4+' Cluster4 probability= '+line1.split()[2] elif i==5: - task.remd_model5=task.remd_model5+'Cluster5 probability= '+line1.split()[2] + task.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[2]