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'
if instance.ready and not instance.done and instance.running==0:
if (not os.path.isdir(instance.jobdirname)):
os.mkdir(instance.jobdirname)
- os.chdir(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"""
+ 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('file.inp','w') as f:
+ with open(instance.jobdirname+'/file.inp','w') as f:
f.write(instance.name + ' UNRES server job'+ '\n')
if instance.type == 'min' :
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:
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 '
if instance.type == 'remd' :
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.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)\
+' 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_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(word_list[-1]+'\n')
if instance.md_start == 'pdbstart':
+ if instance.type == 'remd' :
+ 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')
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')
f.write(write_ssbond(instance.ssbond))
- f.write('0\n')
-
+ if instance.md_2d == '':
+ f.write('0\n')
+ else:
+ f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
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:
+ f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+
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:
+ f.write(seq_2d_write(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 == 'min':
- shutil.copy('../files/pbs.csh','.')
+ os.chdir(instance.jobdirname)
+ if instance.unres_ff =='FF2':
+ shutil.copy('../files/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':
- f1 = open('../files/pbs_md.csh', 'r')
+ os.chdir(instance.jobdirname)
+ if instance.unres_ff =='FF2':
+ f1 = open('../files/pbs_md.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)
-
- f1 = open('../files/pbs8.csh', 'r')
+
+ 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)
+ if instance.unres_ff =='FF2':
+ f1 = open('../files/pbs8.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))
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()
+ 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('file_wham.inp','w') as f:
- if instance.md_nstep/instance.remd_nstex*nreplicas<=8000:
+ with open(instance.jobdirname+'/file_wham.inp','w') as f:
+ 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)
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)+' isampl='+str(isampl)+
+ ' 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)+' isampl='+str(isampl)+
+ ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
+ if instance.md_2d != '':
+ f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\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)
+ 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')
f.write('plik.pdb\n')
- with open('file_cluster.inp','w') as f:
+ 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))+'&\n')
+ if instance.md_2d != '':
+ f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\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))
-
+ 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')
+
+ os.chdir(instance.jobdirname)
ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+ os.chdir('..')
print ret_code.stdout.readlines()
- os.chdir('..')
logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
@receiver(post_delete, sender=Task)
projects / django_unres.git / blobdiff