Révision 088cfdb3

b/dockOnSurf.sh
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only_ref=false
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coads_box=false
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removeHs=false
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rmsd_threshold=0.01
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for i in $@; do


  		





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  case $i in


  		





  ......




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      coads_box=true;;


  		





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    -H|--remove-Hs)


  		





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      removeHs=true;;


  		





  
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    -t=*|--rmsd-threshold=*)


  		





  
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      rmsd_threshold="${i#*=}";;


  		





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  esac


  		





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done


  		





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  ......




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  -b, --coadsorption-box \t When the surface file already contains an


  		





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\t \t \t \t adsorbed molecule, it creates a box around it to


  		





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\t \t \t \t prevent the second adsorbate to overlap the first.


  		





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  -H  --remove-Hs \t \t Remove hydrogens for the RMSD comparison."


  		





  
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  -H, --remove-Hs \t \t Remove hydrogens for the RMSD comparison.


  		





  
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  -t=NUM, --rmsd-threshold=NUM \t Sets the threshold for the RMSD check of 


  		





  
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\t \t \t \t different structures."


  		





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  exit


  		





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fi


  		





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  ......




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if [ "$only_ads" = false ] && [ "$only_ref" = false ] ; then


  		





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	### Generation des conformeres


  		





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  ${DockOnSurf_path}/modules/generation_conformeres.py $molecule 5000 $removeHs


  		





  
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  ${DockOnSurf_path}/modules/generation_conformeres.py $molecule 5000 $removeHs $rmsd_threshold


  		





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  echo ' -- CONFORMERS HAVE BEEN GENERATED --'


  		





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  ### Conversion des fichiers .mol en .xyz


  		





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  ${DockOnSurf_path}/modules/mol_to_xyz.sh $molecule


  		












  

    
      b/modules/generation_conformeres.py
    
  






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mol_input = sys.argv[1]  #nom du fichier d'entree


  		





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n = int(sys.argv[2])  #nombre de conformeres


  		





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remove_hydrogens = sys.argv[3].lower() in ("yes", "true", "t", "1") # converts the input argument to a boolean


  		





  
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rmsd_threshold = float(sys.argv[4])


  		





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m = Chem.MolFromMolFile('%s/%s.mol' % (Molecule_path, mol_input))  #lecture du fichier d'entree


  		





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  ......




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        else :


  		





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            if a != b :


  		





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                valeur = AllChem.GetBestRMS(m, m, prbId=b, refId=a) 


  		





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                if valeur < 0.01: #valeur de RMSD limite en dessous de laquelle les conformeres sont consideres comme identiques


  		





  
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                if valeur < rmsd_threshold: #valeur de RMSD limite en dessous de laquelle les conformeres sont consideres comme identiques


  		





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                    liste_suppr.append(a)


  		





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