logging.basicConfig()
logger = logging.getLogger(__name__)
+def seq_2d_xx(line,seq):
+ line=line.replace(" ","")
+ lista=list(line)
+ for ii in range(0,len(line)):
+ if seq[ii]=='X':
+ if ii>0:
+ lista[ii-1]='-'
+ if ii+1<len(line):
+ lista[ii+1]='-'
+ return("".join(lista))
+
+def seq_2d_write(line):
+ line=line.replace(" ", "")
+ out='{:d}\n{:6.1f}\n'.format(len(line),50.0)
+ for i in range(1,4):
+ out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
+ for ii in range(1,len(line)-2):
+ i+=1
+ if line[ii:ii+2]=='HH':
+ out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
+ elif line[ii:ii+2]=='EE':
+ out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0)
+ else:
+ out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
+ return(out)
+
+def seq_2d_write_50(line):
+ line=line.replace(" ", "")
+ out='{:d}\n'.format(len(line))
+ for i in range(1,4):
+ out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
+ for ii in range(1,len(line)-2):
+ i+=1
+ if line[ii:ii+2]=='HH':
+ out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0,50.0)
+ elif line[ii:ii+2]=='EE':
+ out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0,50.0)
+ else:
+ out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
+ return(out)
+
def write_ssbond(ssbond):
- list=[]
+ list=[]
+ if ssbond!='':
+ ssbond=json.loads(ssbond)
for e in ssbond:
list.append(e[0])
list.append(e[1])
list_sorted=sorted(list)
- if len(list)>0:
+ if len(list)>0:
return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\
str(len(ssbond))+' '+' '.join(map(str,list))+'\n'
- else:
+ else:
return '0\n'
@receiver(post_save, sender=Task)
def write_on_task_save(sender, instance, **kwargs):
- if instance.ready and not instance.done and instance.running==0:
+ if instance.ready and not instance.done and instance.running==0 and instance.pbsjob=='':
if (not os.path.isdir(instance.jobdirname)):
os.mkdir(instance.jobdirname)
# os.chdir(instance.jobdirname)
#wrapper = textwrap.TextWrapper(width=70)
#word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
- w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
+ if instance.unres_ff =='FF2':
+ w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
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"""
+ elif instance.unres_ff =='NEWCT-9P':
+ w="""WSC=0.81230 WSCP=1.20420 WELEC=0.87690 WBOND=1.00000 WANG=1.97730 &
+WSCLOC=0.063657 WTOR=1.41540 WTORD=0.00000 WCORRH=0.00000 WCORR5=0.00000 &
+WCORR6=0.00000 WEL_LOC=0.036638 WTURN3=1.45110 WTURN4=0.00000 WTURN6=0.00000 &
+WSCCOR=0.00000 WVDWPP=0.33393 WHPB=1.00000 WSCP14=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"""
+
with open(instance.jobdirname+'/file.inp','w') as f:
f.write(instance.name + ' UNRES server job'+ '\n')
control_line = 'SEED='+str(instance.md_seed)+' ' \
+ instance.min_choice \
- + ' pdbstart pdbref BOXX=1000. BOXY=1000. BOXZ=1000. '
+ + ' pdbstart pdbref ' \
+ + ' BOXX='+str(instance.boxx) \
+ + ' BOXY='+str(instance.boxy) \
+ + ' BOXZ='+str(instance.boxz) +' '
if not instance.min_overlap:
control_line = control_line+'overlap '
if not instance.min_searchsc:
control_line = control_line+'pdbout '
if instance.min_unres_pdb:
control_line = control_line+'unres_pdb '
+ if instance.unres_ff =='NEWCT-9P':
+ control_line = control_line+'tormode=2 '
type_line = 'print_min_ini print_min_res print_min_stat'\
+' MAXMIN='+str(instance.min_maxmin)\
if seq[-1]=='X':
dimen3-=1
- nogly ='CDSQKIPTFNHLRWAVEYM'
+ nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym'
seq2 = ''.join([c for c in seq if c in nogly])
dimen3=(dimen3+len(seq2))*3
if instance.type == 'md' :
control_line = 'SEED='+str(instance.md_seed)+' '\
- +instance.md_start +' md one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
+ +instance.md_start +' md one_letter'\
+ + ' BOXX='+str(instance.boxx) \
+ + ' BOXY='+str(instance.boxy) \
+ + ' BOXZ='+str(instance.boxz) +' '
+
if instance.md_pdbref:
control_line = control_line+'pdbref '
+
+#---v
+ if instance.use_nmr:
+ control_line = control_line+' constr_dist=12 '
+#---^
+ if instance.unres_ff =='NEWCT-9P':
+ control_line = control_line+'tormode=2 cart'
- type_line = 'reset_vel=0'\
+ type_line = ' reset_vel=0'\
+' t_bath='+str(instance.md_temp)\
+' nstep='+str(instance.md_nstep)\
+' ntwe='+str(instance.md_ntwe)\
if instance.md_mdpdb:
type_line = type_line + ' mdpdb '
- if instance.type == 'remd' :
+ if instance.type == 'remd' or instance.type == 'dock':
control_line = 'SEED='+str(instance.md_seed)+' '\
- +instance.md_start +' re one_letter BOXX=1000. BOXY=1000. BOXZ=1000. '
+ +instance.md_start +' re one_letter'\
+ + ' BOXX='+str(instance.boxx) \
+ + ' BOXY='+str(instance.boxy) \
+ + ' BOXZ='+str(instance.boxz) +' '
+
+ if instance.type == 'dock':
+ control_line = control_line+'CONSTR_HOMOL=24 '
+
if instance.md_pdbref:
control_line = control_line+'pdbref '
-
+
+ if instance.unres_ff =='NEWCT-9P':
+ control_line = control_line+'tormode=2 cart'
+#---v
+ if instance.use_nmr:
+ control_line = control_line+' constr_dist=12 '
+#---^
+
+ 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)\
+ type_line = ' reset_vel='+ str(instance.remd_nstex)\
+' nstep='+str(instance.md_nstep)\
+' ntwe='+str(instance.md_ntwe)\
- +' ntwx='+str(instance.remd_nstex)\
+ +' ntwx='+str(instance.md_ntwx)\
+' dt='+str(instance.md_dt)
if instance.md_lang == 'langevin':
type_line = type_line + ' lang=1 '
type_line = type_line + 'tau_bath='+str(instance.md_tau)
if instance.md_respa:
type_line = type_line + ' respa '
- if instance.md_mdpdb:
- type_line = type_line + ' mdpdb '
+# if instance.md_mdpdb:
+# type_line = type_line + ' mdpdb '
type_line2 = 'nrep='+str(instance.remd_nrep) \
+' nstex='+str(instance.remd_nstex) \
+' tlist mlist sync nsyn='+str(instance.remd_nstex)\
- +' traj1file rest1file '
+ +' traj1file rest1file TRAJCACHE=200'
if instance.md_start == 'pdbstart':
type_line = type_line + ' preminim cart'
f.write('{:79}'.format(element)+'&\n')
f.write(word_list[-1]+'\n')
- if instance.md_start == 'pdbstart':
+ if instance.md_start == 'pdbstart' and instance.unres_ff !='NEWCT-9P':
+ if instance.type == 'remd' or instance.type == 'dock':
+ f.write('print_min_ini print_min_res print_min_stat maxfun='+
+ str(instance.min_maxfun)+'\n')
+ else:
f.write('print_min_ini print_min_res print_min_stat\n')
- if instance.type == 'remd' :
+ if instance.type == 'remd' or instance.type == 'dock':
word_list = wrapper.wrap(text=type_line2)
for element in word_list[:-1]:
f.write('{:79}'.format(element)+'&\n')
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':
- f.write('plik.pdb\n')
+ if instance.type == 'dock':
+ f.write('plik1ter.pdb\n')
+ else:
+ f.write('plik.pdb\n')
f.write(write_ssbond(instance.ssbond))
- f.write('0\n')
-
+ if instance.md_2d == '':
+ f.write('0\n')
+ else:
+ if instance.unres_ff =='NEWCT-9P':
+ f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+ else:
+ f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+
+ if instance.type == 'dock':
+ f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n')
+ f.write('READ2SIGMA START_FROM_MODELS\n')
+ for i in range(1,10):
+ f.write('model0'+str(i)+'.pdb\n')
+ for i in range(10,25):
+ f.write('model'+str(i)+'.pdb\n')
if instance.type == 'md' and instance.md_start != 'pdbstart':
f.write(str(len(seq))+'\n')
for i in range(0,len(seq),80):
f.write(seq[i:i+80]+'\n')
- f.write('0\n0\n')
+ f.write('0\n')
+ if instance.md_2d == '':
+ f.write('0\n')
+ else:
+ if instance.unres_ff =='NEWCT-9P':
+ f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+ else:
+ f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+#---v
+ if instance.use_nmr:
+ f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+ f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+ f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+ if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+ fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+ else:
+ fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+#---^
+
if instance.type == 'remd' and instance.md_start != 'pdbstart':
f.write(str(len(seq))+'\n')
for i in range(0,len(seq),80):
f.write(seq[i:i+80]+'\n')
- f.write('0\n0\n')
-
-
+ f.write('0\n')
+ if instance.md_2d == '':
+ f.write('0\n')
+ else:
+ if instance.unres_ff =='NEWCT-9P':
+ f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+ else:
+ f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+#---v
+ if instance.use_nmr:
+ f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+ f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+ f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+ if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+ fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+ else:
+ fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+#---^
+
+
+ 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':
os.chdir(instance.jobdirname)
- shutil.copy('../files/pbs.csh','.')
+ if instance.unres_ff =='FF2':
+ shutil.copy('../files/pbs.csh','.')
+ elif instance.unres_ff =='NEWCT-9P':
+ shutil.copy('../files/pbs_newct-9p.csh','pbs.csh')
+ else:
+ shutil.copy('../files/pbs_new.csh','pbs.csh')
ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
os.chdir('..')
elif instance.type == 'md':
os.chdir(instance.jobdirname)
- f1 = open('../files/pbs_md.csh', 'r')
+ if instance.unres_ff =='FF2':
+ f1 = open('../files/pbs_md.csh', 'r')
+ elif instance.unres_ff =='NEWCT-9P':
+ f1 = open('../files/pbs_md_newct-9p.csh', 'r')
+ else:
+ f1 = open('../files/pbs_md_new.csh', 'r')
f2 = open('pbs.csh', 'w')
for line in f1:
- f2.write(line.replace('$dimen3',str(dimen3) ))
+ f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
f1.close()
f2.close()
f1 = open('file.seq', 'w')
for i in range(0,len(seq),80):
f1.write(seq[i:i+80]+'\n')
+ f1.write('\n')
f1.close()
ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
os.chdir('..')
else:
+# instance.type == 'remd'
tmp1=json.loads(instance.remd_multi_m)
nreplicas=sum(map(int, tmp1))
-
# hardcoded for 4 core nodes with FGPROC=2
nodes=int(nreplicas*2/4)
reszta = nreplicas*2-nodes*4
pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
else:
pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
+
+ tmp_ss=''
+ if instance.ssbond!='':
+ ix=[]
+ ii=0
+ for i in range(0,len(seq)):
+ if seq[i]=='X':
+ ii=ii+1
+ ix.append(ii)
+ l=[]
+ ss=json.loads(instance.ssbond)
+ for e in ss:
+ l.append(e[0]-ix[e[0]])
+ l.append(e[1]-ix[e[1]])
+ tmp_ss=' '.join(map(str,l))
os.chdir(instance.jobdirname)
- f1 = open('../files/pbs8.csh', 'r')
+ if instance.unres_ff =='FF2':
+ f1 = open('../files/pbs8.csh', 'r')
+ elif instance.unres_ff =='NEWCT-9P':
+ f1 = open('../files/pbs8_newct-9p.csh', 'r')
+ else:
+ f1 = open('../files/pbs8_new.csh', 'r')
f2 = open('pbs8.csh', 'w')
for line in f1:
if '#PBS -l nodes=4:ppn=4' in line:
f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
+ elif '$ssbond' in line:
+ f2.write(line.replace('$ssbond',tmp_ss))
+ elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
+ f2.write(line)
+ if instance.md_seq2 !='':
+ f2.write("""setenv FGPROCS 2
+setenv POT GB
+setenv PREFIX file2
+setenv OUT1FILE YES
+/users2/local/mpich2-1.4.1p1_intel/bin/mpirun -machinefile $PBS_NODEFILE -np 2 $UNRES_BIN
+/users2/local/pulchra306/pulchra -q -g file2_MD000.pdb
+cat file2_MD000.rebuilt.pdb |grep -v TER |grep -v END > tmp_plik2.pdb
+/users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp_plik2.pdb > act.rebuilt.pdb
+/users2/local/scwrl4/Scwrl4 -h -i act.rebuilt.pdb -o plik2.pdb
+rm tmp_plik2.pdb act.rebuilt.pdb\n""")
+ if instance.dock_peptide:
+ f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n')
+ else:
+ f2.write('../files/generator_v13 plik.pdb plik2.pdb 0 \n')
+ f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n")
+ f2.write("echo TER >> plik1ter.pdb \n")
+ f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n")
else:
tmp1=json.loads(instance.remd_multi_t)
- f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'"'))
+ f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
f1.close()
f2.close()
+
+ f1 = open('file.seq', 'w')
+ for i in range(0,len(seq),80):
+ f1.write(seq[i:i+80]+'\n')
+ f1.write('\n')
+ f1.close()
+
os.chdir('..')
# write wham & cluster input
with open(instance.jobdirname+'/file_wham.inp','w') as f:
- if instance.md_nstep/instance.remd_nstex*nreplicas<=8000:
+ if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
isampl=1
else:
- isampl=int(instance.md_nstep/instance.remd_nstex*nreplicas/8000)
-
+ isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
+#---v
+ if instance.use_nmr:
+ f.write('{:79}'.format('with_dist_constr constr_dist=12')+'&\n')
+#---^
+ f.write('{:79}'.format(' isampl='+str(isampl))+'&\n')
if instance.md_pdbref:
- f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
- ' einicheck=1 rescale=2 delta=0.02 cxfile classify\n')
+ f.write('{:79}'.format('SEED='+str(instance.md_seed)+
+ ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
else:
- f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+
- ' einicheck=1 rescale=2 delta=0.02 cxfile\n')
+ f.write('{:79}'.format('SEED='+str(instance.md_seed)+
+ ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
+ if instance.md_2d != '':
+ f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
+ if instance.type == 'dock':
+ f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=24')+'&\n')
+ if instance.unres_ff =='NEWCT-9P':
+ f.write('{:79}'.format('tormode=2 ')+'&\n')
+ f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+ ' 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)
+#---v
+ if instance.use_nmr:
+ f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+ f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+ f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+ if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+ fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+ else:
+ fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+#---^
+
+ if instance.type == 'dock':
+ f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n')
+ f.write('READ2SIGMA \n')
+ for i in range(1,10):
+ f.write('model0'+str(i)+'.pdb\n')
+ for i in range(10,25):
+ f.write('model'+str(i)+'.pdb\n')
+
+ if instance.md_2d != '':
+ f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+
+ if instance.saxs_data != '':
+ saxs_r=[]
+ saxs_P=[]
+ saxs_norm=0
+ r_last=None
+ 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')
+ saxs_r.append(tmp[0])
+ saxs_P.append(float(tmp[1]))
+ if r_last==None:
+ r_last=float(tmp[0])
+ else:
+ saxs_norm += float(tmp[1])*(float(tmp[0])-r_last)
+ r_last=float(tmp[0])
+ for r,p in zip(saxs_r,saxs_P):
+ fsaxs.write('{} {}\n'.format(r,p/saxs_norm))
+ 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)
for element in tmp1:
f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
f.write('kh= 0.0 Q0=0.0\n')
- rec=instance.md_nstep/instance.remd_nstex
+ rec=instance.md_nstep/instance.md_ntwx
f.write('nfile_cx=1 rec_start='+str(rec/10)
+' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
f.write('file_MD000\n')
if instance.md_pdbref:
f.write('pdbref\n')
- f.write('plik.pdb\n')
+ if instance.type == 'dock':
+ f.write('plik1ter.pdb\n')
+ else:
+ f.write('plik.pdb\n')
with open(instance.jobdirname+'/file_cluster.inp','w') as f:
f.write(instance.name + ' UNRES server job'+ '\n')
- f.write('nres='+str(len(seq))
+ f.write('{:79}'.format('nres='+str(len(seq))
+' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
- +' temper='+str(instance.remd_cluter_temp)+'\n')
- f.write(w)
+ +' temper='+str(instance.remd_cluter_temp)
+ +' nclust='+str(instance.remd_cluster_n))+'&\n')
+ if instance.md_2d != '':
+ f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
+#---v
+ if instance.use_nmr:
+ f.write('{:79}'.format('constr_dist=12 ')+'&\n')
+#---^
+ if instance.type == 'dock':
+ f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n')
+ if instance.unres_ff =='NEWCT-9P':
+ f.write('{:79}'.format('tormode=2 ')+'&\n')
+ f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+ ' 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))
+
+#---v
+ if instance.use_nmr:
+ f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+ f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+ f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+ if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+ fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+ else:
+ fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+#---^
+
+ if instance.type == 'dock':
+ f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n')
+ f.write('READ2SIGMA \n')
+ for i in range(1,10):
+ f.write('model0'+str(i)+'.pdb\n')
+ for i in range(10,25):
+ f.write('model'+str(i)+'.pdb\n')
+ if instance.md_2d != '':
+ f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
+ 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 == 'dock' and instance.md_seq2 != '':
+ with open(instance.jobdirname+'/file2.inp','w') as f:
+ f.write(instance.name + ' chain2 random start'+ '\n')
+ control_line = 'SEED='+str(instance.md_seed)+' '\
+ +'rand_conf md one_letter'\
+ + ' BOXX=1000 BOXY=1000 BOXZ=1000 '
+
+ if instance.unres_ff =='NEWCT-9P':
+ control_line = control_line+'tormode=2 cart'
+
+ type_line = ' reset_vel=0'\
+ +' t_bath=300'\
+ +' nstep=100000'\
+ +' ntwe=10000'\
+ +' ntwx=100000'\
+ +' dt=0.2 lang=1 scal_fric=0.02 respa mdpdb '
+
+ wrapper = textwrap.TextWrapper(width=70)
+ word_list = wrapper.wrap(text=control_line)
+ for element in word_list[:-1]:
+ f.write('{:79}'.format(element)+'&\n')
+ f.write(word_list[-1]+'\n')
+
+ word_list = wrapper.wrap(text=type_line)
+ for element in word_list[:-1]:
+ f.write('{:79}'.format(element)+'&\n')
+ f.write(word_list[-1]+'\n')
+
+ f.write(w+'\n')
+
+ seq=instance.md_seq2.replace(" ","")
+ f.write(str(len(seq))+'\n')
+ for i in range(0,len(seq),80):
+ f.write(seq[i:i+80]+'\n')
+ f.write('0\n')
+ f.write('0\n')
+
os.chdir(instance.jobdirname)
ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
os.chdir('..')
+
+ output = str(ret_code.communicate()[0])
+ output=output.strip()
+ if output=='':
+ output='error'
+ logger.warning("PBS \"%s\" " % output)
+ instance.pbsjob = output
+ instance.save()
- print ret_code.stdout.readlines()
+# print ret_code.stdout.readlines()
logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
@receiver(post_delete, sender=Task)
def delete_on_task_del(sender, instance, **kwargs):
if instance.jobdirname:
if os.path.isdir(instance.jobdirname):
+ if not instance.done:
+ ret_code_qdel = subprocess.Popen(' /opt/torque/bin/qdel '+str(instance.pbsjob), shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+ output = str(ret_code_qdel.communicate()[0])
+ output=output.strip()
+ logger.warning("PBS qdel \"%s\" " % instance.pbsjob)
+ logger.warning("QDEL \"%s\" " % output)
shutil.rmtree(instance.jobdirname)
logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)
-
\ No newline at end of file
+
projects / django_unres.git / blobdiff