3.5.1.1.2.1. crysolの対話モードの自動応答での実行

できるだけわかりやすいように、無駄な部分は省いている。

出力の文字列が乱れているが、気になるのならprintがある文をコメントアウトすればよい。

def auto_crysol(pdb_base,dat_base):

    import pexpect


    p = pexpect.spawn("crysol")
    #2-1.  Enter your option ...................... <            0 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")
    #2-2.  Brookhaven file name ................... <         .pdb >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline(pdb_base)
    #2-3. Maximum order of  harmonics ........... <           15 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")
    #2-4. Order of Fibonacci grid ............... <           17 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")
    #2-5. Maximum s value ........................ <        .5000 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")
    #2-6.  Number of points ....................... <           51 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("201")
    #2-7.  Account for explicit hydrogens? [ Y / N ] <           No >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")

    #4-1.   Fit the experimental curve [ Y / N ] .. <          Yes >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")
    #4-2.  Enter data file ........................ <         .dat >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline(dat_base)
    #5-1. Subtract constant ...................... <           no >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("N")

    #5-2. 2 *  sin(theta)/lambda [1/nm]  (4) ..... <            1 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")

    #6. Electron density of the solvent, e/A**3  <        .3340 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")

    #7. Plot the fit [ Y / N ] ................. <          Yes >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("N")

    #8-1.  Another set of parameters [ Y / N ] .... <           No >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("Y")

    #8-2. Minimize again with new limits [ Y / N ] <           No >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("Y")


    p.expect(r"Minimum")
    ret=str(p.before)
    # print ('ret',ret)
    #Average atomic radius is ............................... :
    m=ret.split(':')
    # print('m',m[-1].split("\\")[0])
    Ra=float(m[-1].split("\\")[0])

    # 9-1. Minimum radius of atomic group ......... <        1.400 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline(str(Ra))

    # 9-2.  Maximum radius of atomic group ......... <        1.800 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline(str(Ra))

    # 9-3. Smax in the fitting range .............. <       0.4984 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")

    # 9-4.  Minimum contrast in the shell .......... <        0.000 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")

    # 9-5.  Maximum contrast in the shell .......... <  7.5000E-002 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")

    p.expect(r"Minimum")
    ret=str(p.before)
    # print ('ret',ret)
    #Van der Waals volume is ................................ :
    m=ret.split(':')
    # print('m',m[-1].split("\\")[0])
    ExVol=float(m[-1].split("\\")[0])

    # 9-6  Minimum excluded volume ................ <  1.6108E+004 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline(str(ExVol))

    # 9-7.  Maximum excluded volume ................ <  1.8720E+004 >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline(str(ExVol))

    # 9-7. Subtract constant ...................... <           no >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")

    # 10-1. Plot the fit [ Y / N ] ................. <          Yes >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("N")

    # 10-2. Another set of parameters [ Y / N ] .... <           No >:
    p.expect(r">:")
    print (p.before+p.after)
    p.sendline("")

    #p.terminate()
    p.expect(pexpect.EOF)

    return

• 6lyz.pdb : 結晶構造
• lyzexp.dat : 実験データ

を入力して上の関数auto_crysolを実行する。

auto_crysol('6lyz.pdb','lyzexp.dat')