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=[]
if ssbond!='':
#wrapper = textwrap.TextWrapper(width=70)
#word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
- if instance.unres_ff =='E0LL2Y':
+ 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 &
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')
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')
if instance.type == 'min':
os.chdir(instance.jobdirname)
- if instance.unres_ff =='E0LL2Y':
+ if instance.unres_ff =='FF2':
shutil.copy('../files/pbs.csh','.')
else:
shutil.copy('../files/pbs_new.csh','pbs.csh')
os.chdir('..')
elif instance.type == 'md':
os.chdir(instance.jobdirname)
- if instance.unres_ff =='E0LL2Y':
+ if instance.unres_ff =='FF2':
f1 = open('../files/pbs_md.csh', 'r')
else:
f1 = open('../files/pbs_md_new.csh', 'r')
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)
tmp_ss=' '.join(map(str,l))
os.chdir(instance.jobdirname)
- if instance.unres_ff =='E0LL2Y':
+ if instance.unres_ff =='FF2':
f1 = open('../files/pbs8.csh', 'r')
else:
f1 = open('../files/pbs8_new.csh', 'r')
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
if instance.md_pdbref:
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)+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)+
+ 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))
+ 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')
- fsaxs.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('{:79}'.format('nres='+str(len(seq))
+' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
+' 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:
projects / django_unres.git / blobdiff