logging.basicConfig()
logger = logging.getLogger(__name__)
+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 e in line[:-3]:
+ i+=1
+ if e=='-':
+ out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
+ elif e=='H':
+ out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
+ elif e=='E':
+ out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0)
+ 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 e in line[:-3]:
+ i+=1
+ if e=='-':
+ out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
+ elif e=='H':
+ out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0,50.0)
+ elif e=='E':
+ out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0,50.0)
+ return(out)
+
def write_ssbond(ssbond):
list=[]
if ssbond!='':
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(instance.md_seq_2d))
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(instance.md_2d))
+
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(instance.md_2d))
+
if instance.saxs_data != '':
lines=instance.saxs_data.split('\n')
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(instance.md_2d))
+
if instance.saxs_data != '':
fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
lines=instance.saxs_data.split('\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(instance.md_2d))
if instance.saxs_data != '':
lines=instance.saxs_data.split('\n')
for line in lines: