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!='':
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:
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.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)\
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_seq_2d == '':
+ f.write('0\n')
+ else:
+ f.write(seq_2d_write(seq_2d_xx(instance.md_seq_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':
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) +'\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')
+ 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 != '':
+ 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)
+ 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)
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) +'\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.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)