Changeset 1655 in rotdif


Ignore:
Timestamp:
Feb 18, 2019, 10:44:23 PM (17 months ago)
Author:
yuexi
Message:

rotdif subfolder

Files:
3 edited

Legend:

Unmodified
Added
Removed
  • bin/main_rotdif.py

    r1647 r1655  
    11#!/usr/bin/python
     2from os.path import join
    23import os
    34import glob
     
    4142from indicator_chain import dock
    4243from StringIO import StringIO
     44import shutil
    4345
    4446if __name__ == "__main__":
     
    5052    json_variables = json.load(argv_io_string)
    5153    relax_location = json_variables['relax_location']
    52     relax_loc = relax_location[0]
    53     to_dock = dock(relax_loc)
    54     output_res, base_dir, dyna_flag, elm_flag, elmdock_flag = rotdif(to_dock)
    55     exp_graph,exp_keys,exp_resi,dyna_resi = exp_plot(color_list, dyna_flag, elm_flag, elmdock_flag,relax_loc)
     54    old_relax = os.path.basename(relax_location[0])
     55    to_dock = dock(old_relax)
     56    pdb_location = json_variables['pdb_location']
     57    old_pdb = os.path.basename(pdb_location[0])
     58
     59    run_name = json_variables['run_name']
     60    sub_dir = "ROTDIF_" + run_name
     61    if os.path.isdir(sub_dir):
     62        pass
     63    else:
     64        os.mkdir(sub_dir)
     65
     66    new_relax = join(sub_dir,old_relax)
     67    new_pdb = join(sub_dir,old_pdb)
     68    shutil.move(old_relax,new_relax)
     69    shutil.move(old_pdb, new_pdb)
     70    os.chdir(sub_dir)
     71    output_res, base_dir, dyna_flag, elm_flag, elmdock_flag = rotdif(to_dock,old_pdb,old_relax,sub_dir)
     72    exp_graph,exp_keys,exp_resi,dyna_resi = exp_plot(color_list, dyna_flag, elm_flag, elmdock_flag,old_relax)
    5673    outputmd_arr_files = []
    57     log_out = [str(base_dir) + "/" + 'rotdif_log.out']
    58     ani_out = [str(base_dir) + "/"+ 'out_ani.py']
    59     axi_out = [str(base_dir) + "/" + 'out_axial.py']
     74    log_out = [join(str(base_dir),join(sub_dir,'rotdif_log.out'))]
     75    ani_out = [join(str(base_dir),join(sub_dir, 'out_ani.py'))]
     76    axi_out = [join(str(base_dir),join(sub_dir, 'out_axial.py'))]
    6077
    6178    if dyna_flag == True:
     
    6683    if elm_flag == True:
    6784        save_elm(dyna_flag, elm_flag, elmdock_flag)
    68         elm_out = [str(base_dir) + "/" + 'ELM_prediction']
     85        elm_out = [join(str(base_dir),join(sub_dir,'ELM_prediction'))]
    6986        output_res[ 'elm_out' ] = elm_out   
    7087
    7188    if elmdock_flag == True:
    7289        save_dock(dyna_flag, elm_flag, elmdock_flag)
    73         dock_out = [str(base_dir) + "/" + 'ELMDOCK']     
     90        dock_out = [join(str(base_dir),join(sub_dir, 'ELMDOCK'))]     
    7491        output_res[ 'elmdock' ] = dock_out
    75         dock_pdb = [str(base_dir) + "/" + 'out_dock.pdb']
     92        dock_pdb = [join(str(base_dir),join(sub_dir, 'out_dock.pdb'))]
    7693        output_res[ 'pdb'] = dock_pdb
    7794        output_res['outputpdb'] = dock_pdb
  • bin/run_rotdif.py

    r1653 r1655  
    11#!/usr/bin/python
     2from os.path import join
    23import os
    34import glob
     
    4647    return
    4748
    48 def rotdif(in_dock,sub_dir):
     49def rotdif(in_dock,Pdbfilename,Relaxfilename,sub_dir):
    4950    output_res = {}
    5051    json_variables = " "
     
    5253    argv_io_string = StringIO(sys.argv[1])
    5354    json_variables = json.load(argv_io_string)
    54     relax_location = json_variables['relax_location']
    55     RelaxStr = relax_location[0]
    56     Relaxfilename = os.path.basename(RelaxStr)
    57     pdb_location   = json_variables['pdb_location']
    58     PdbStr = pdb_location[0]
    59     Pdbfilename = os.path.basename(PdbStr)
     55    #relax_location = json_variables['relax_location']
     56    #RelaxStr = relax_location[0]
     57    #Relaxfilename = os.path.basename(RelaxStr)
     58    #pdb_location   = json_variables['pdb_location']
     59    #PdbStr = pdb_location[0]
     60    #Pdbfilename = os.path.basename(PdbStr)
    6061## UDP messaging ##################################################
    6162    UDP_IP = json_variables['_udphost']
     
    116117    stdout_rotdif = os.fdopen(master_rotdif, 'r', 0)
    117118    rotdif_log = open('rotdif_log.out','w')
    118     path_to_live_log = str(base_dir) + "/" + 'rotdif_log.out'
     119    path_to_live_log = join(str(base_dir),join(sub_dir,'rotdif_log.out'))
    119120    error_string_md = ''
    120121    timeout = 4 # seconds
  • files/acknowledgements_my.html

    r1647 r1655  
    1717
    1818<div style= "font-size:16pt;font-family:'Avenir'">
    19   <p>GenApp framework development: Dr. Emre Brookes@UTHSC</p>
    20   <p>ROTDIF integration: Yuexi Chen@UMD, Dr. Alexey Savelyev@UTHSC</p>
    21   <p>Feedback and suggestions: Dr. David Fushman@UMD, Andrew Boughton@UMD</p>
     19  <p>GenApp framework development: Emre Brookes@UTHSC</p>
     20  <p>ROTDIF integration: Yuexi Chen@UMD, Alexey Savelyev@UTHSC</p>
     21  <p>Guidance and design: David Fushman@UMD</p>
     22  <p>Examples, feedback and suggestions: David Fushman@UMD, Andrew Boughton@UMD</p>
    2223</div>
    2324
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