pKa/pKa_alascan.py
def local_defaults(pdbfile,target_residues,recalc_intpka):
    """
    # Set the parameters that are the same for all mutations
    """
    import pKa.Design_pKa as Design_pKa
    defaults=Design_pKa.get_defaults()
    # PDB file
    defaults['pdb'][0]=pdbfile
    #
    # pKa calculation parameters
    #
    defaults['pHstart'][0]=0.1
    defaults['pHstop'][0]=12.0
    defaults['pHstep'][0]=0.25
    defaults['pKMCsteps'][0]=200000
    #
    # Design settings
    #
    # Target
    #
    target_residues=target_residues.split(',')
    target_text=''
    for target in target_residues:
        target_text=target_text+target+'=0.0,' # Dummy pKa value
    defaults['pKas'][0]=target_text[:-1]
    #
    # Method
    #
    defaults['MC'][0]=1
    defaults['tabulated'][0]=1
    defaults['MCsteps'][0]=0
    #
    # Be not-so-noisy
    #
    defaults['verbose'][0]=3
    #
    # Minimum distance between target and mutation
    #
    #defaults['min_target_dist'][0]=min_dist
    #
    # Do not save the solutions
    #
    defaults['save_solutions'][0]=None
    #
    #
    defaults['recalc_intpka'][0]=recalc_intpka
    defaults['recalc_intpka_dist'][0]=10.0
    defaults['use_titration_curves'][0]=1
    defaults['calc_dpka'][0]=1
    defaults['generate_mutations'][0]=False
    defaults['ligands'][0]=[]
    defaults['allow_unknown_atoms'][0]=1
    defaults['unknown_rad'][0]=0.0
    return defaults

    # Set the parameters that are the same for all mutations
    
Set the parameters that are the same for all mutations
Set the parameters that are the same for all mutations
def local_defaults(pdbfile,target_residues,recalc_intpka):
    import pKa.Design_pKa as Design_pKa
    defaults=Design_pKa.get_defaults()
    defaults['pdb'][0]=pdbfile
     pKa calculation parameters
    defaults['pHstart'][0]=0.1
    defaults['pHstop'][0]=12.0
    defaults['pHstep'][0]=0.25
    defaults['pKMCsteps'][0]=200000
     Design settings
     Target
    target_residues=target_residues.split(',')
    target_text=''
    for target in target_residues:
        target_text=target_text+target+'=0.0,'  Dummy pKa value
    defaults['pKas'][0]=target_text[:-1]
     Method
    defaults['MC'][0]=1
    defaults['tabulated'][0]=1
    defaults['MCsteps'][0]=0
     Be not-so-noisy
    defaults['verbose'][0]=3
     Minimum distance between target and mutation
    defaults['min_target_dist'][0]=min_dist
     Do not save the solutions
    defaults['save_solutions'][0]=None
    defaults['recalc_intpka'][0]=recalc_intpka
    defaults['recalc_intpka_dist'][0]=10.0
    defaults['use_titration_curves'][0]=1
    defaults['calc_dpka'][0]=1
    defaults['generate_mutations'][0]=False
    defaults['ligands'][0]=[]
    defaults['allow_unknown_atoms'][0]=1
    defaults['unknown_rad'][0]=0.0
    return defaults
def local_defaults ( pdbfile , target_residues , recalc_intpka ) : import pKa . Design_pKa as Design_pKa defaults = Design_pKa . get_defaults ( ) defaults [ 'pdb' ] [ 0 ] = pdbfile defaults [ 'pHstart' ] [ 0 ] = 0.1 defaults [ 'pHstop' ] [ 0 ] = 12.0 defaults [ 'pHstep' ] [ 0 ] = 0.25 defaults [ 'pKMCsteps' ] [ 0 ] = 200000 target_residues = target_residues . split ( ',' ) target_text = '' for target in target_residues : target_text = target_text + target + '=0.0,' defaults [ 'pKas' ] [ 0 ] = target_text [ : - 1 ] defaults [ 'MC' ] [ 0 ] = 1 defaults [ 'tabulated' ] [ 0 ] = 1 defaults [ 'MCsteps' ] [ 0 ] = 0 defaults [ 'verbose' ] [ 0 ] = 3 defaults [ 'save_solutions' ] [ 0 ] = None defaults [ 'recalc_intpka' ] [ 0 ] = recalc_intpka defaults [ 'recalc_intpka_dist' ] [ 0 ] = 10.0 defaults [ 'use_titration_curves' ] [ 0 ] = 1 defaults [ 'calc_dpka' ] [ 0 ] = 1 defaults [ 'generate_mutations' ] [ 0 ] = False defaults [ 'ligands' ] [ 0 ] = [ ] defaults [ 'allow_unknown_atoms' ] [ 0 ] = 1 defaults [ 'unknown_rad' ] [ 0 ] = 0.0 return defaults
Set the parameters that are the same for all mutations
Set the parameters that are the same for all mutations
"""
    # Set the parameters that are the same for all mutations
    """ # PDB file # # pKa calculation parameters # # # Design settings # # Target # # Dummy pKa value # # Method # # # Be not-so-noisy # # # Minimum distance between target and mutation # #defaults['min_target_dist'][0]=min_dist # # Do not save the solutions # # #
pdbfile
target_residues
recalc_intpka