From a2c993a7a81332719ecb024a7727f9de1dd04d8b Mon Sep 17 00:00:00 2001 From: Cezary Czaplewski Date: Mon, 9 Oct 2017 09:38:36 +0200 Subject: [PATCH] wham and cluster BOXX=1000. --- TODO | 2 ++ django_simple/todo/jobfiles.py | 15 +++++++++------ 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/TODO b/TODO index 0740ce8..109cf34 100644 --- a/TODO +++ b/TODO @@ -1,6 +1,7 @@ clean code and combine piasek and etoh versions make easy install on any system with pbs add javascript instead of separate forms +automatic download file from PDB using id check input pdb for: unknown residues, max length (1000), @@ -9,6 +10,7 @@ check input pdb for: and display error check input for other errors (sequence ?) add web viewer NGL WebGL +add BOXX BOXY BOXZ in advanced md and mremd dynamic dissulfides input - all and selected cys homology restraints input other restrains input diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py index af0b2c4..400a2f7 100644 --- a/django_simple/todo/jobfiles.py +++ b/django_simple/todo/jobfiles.py @@ -295,11 +295,13 @@ CUTOFF=7.00000 WCORR4=0.00000 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') + f.write('BOXX=1000. BOXY=1000. BOXZ=1000. \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') + f.write('BOXX=1000. BOXY=1000. BOXZ=1000. \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') @@ -325,9 +327,10 @@ CUTOFF=7.00000 WCORR4=0.00000 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') + +' temper='+str(instance.remd_cluter_temp))+'&\n') + f.write('BOXX=1000. BOXY=1000. BOXZ=1000. \n') f.write(w) for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') -- 1.7.9.5