In [1]:

    

%matplotlib inline
import pymc
import seaborn
import numpy
import glob
import matplotlib as mpl
import matplotlib.pyplot as plt
from chemistry.charmm import CharmmParameterSet
import TorsionFitModel
import TorsionScanSet


    

In [2]:

    

param = CharmmParameterSet('../../charmm_ff/top_all36_cgenff.rtf', '../../charmm_ff/par_all36_cgenff.prm')
stream = '../../structures/Pyrrol/pyrrol.str'
structure = '../../structures/Pyrrol/pyrrol.psf'
scan = glob.glob('../../structures/Pyrrol/torsion-scan/*.log')
pyrrol = TorsionScanSet.read_scan_logfile(scan, structure)
pyrrol_opt = pyrrol.extract_geom_opt()


#create pymc model
model = TorsionFitModel.TorsionFitModel(param, stream, pyrrol_opt)
mcmc = pymc.MCMC(model.pymc_parameters)


    

    




loading ../../structures/Pyrrol/torsion-scan/PRL.scan2.neg.log
loading ../../structures/Pyrrol/torsion-scan/PRL.scan2.pos.log
loading ../../structures/Pyrrol/torsion-scan/PRL.scan3.neg.log
loading ../../structures/Pyrrol/torsion-scan/PRL.scan3.pos.log
loading ../../structures/Pyrrol/torsion-scan/PRL.scan4.neg.log
loading ../../structures/Pyrrol/torsion-scan/PRL.scan4.pos.log
loading ../../structures/Pyrrol/torsion-scan/PRL.scan5.neg.log
loading ../../structures/Pyrrol/torsion-scan/PRL.scan5.pos.log

In [5]:

    

# import database
db = pymc.database.sqlite.load('pyrrol.database')


    

In [14]:

    

plt.plot(pyrrol_opt.qm_energy), plt.plot(pyrrol_opt.mm_energy)


    

    
Out[14]:





([<matplotlib.lines.Line2D at 0x149fca090>],
 [<matplotlib.lines.Line2D at 0x149fca390>])






    

In [59]:

    

seaborn.tsplot(db.trace('mm_energy')[:], err_style='unit_traces'), plt.plot(pyrrol_opt.qm_energy, color='r')


    

    
Out[59]:





(<matplotlib.axes._subplots.AxesSubplot at 0x218b68f50>,
 [<matplotlib.lines.Line2D at 0x218d29350>])






    

In [64]:

    

plt.hist(db.trace('PRL1_offset')[:]) 
#seaborn.rugplot(db.trace('PRL1_offset')[:])


    

    
Out[64]:





(array([  873.,   931.,   970.,  1083.,  1084.,  1110.,  1064.,   966.,
          986.,   933.]),
 array([ -9.99011600e+00,  -7.99213170e+00,  -5.99414740e+00,
         -3.99616310e+00,  -1.99817880e+00,  -1.94500000e-04,
          1.99778980e+00,   3.99577410e+00,   5.99375840e+00,
          7.99174270e+00,   9.98972700e+00]),
 <a list of 10 Patch objects>)






    

In [18]:

    

plt.plot(db.trace('log_sigma')[:])


    

    
Out[18]:





[<matplotlib.lines.Line2D at 0x16d2430d0>]






    

In [19]:

    

plt.hist(db.trace('sigma')[:])


    

    
Out[19]:





(array([    7.,     0.,     0.,     0.,    74.,  1420.,  2312.,  1573.,
         1682.,  2932.]),
 array([ 0.01     ,  0.1089944,  0.2079888,  0.3069832,  0.4059776,
         0.504972 ,  0.6039664,  0.7029608,  0.8019552,  0.9009496,
         0.999944 ]),
 <a list of 10 Patch objects>)






    

In [39]:

    

plt.plot(db.trace('CG251O_NG3C51_CG321_HGA2_multiplicity_bitstring')[:])


    

    
Out[39]:





[<matplotlib.lines.Line2D at 0x198f27290>]






    

In [53]:

    

plt.hist(db.trace('CG251O_NG3C51_CG2R51_CG2R51_multiplicity_bitstring')[:], bins=15)


    

    
Out[53]:





(array([ 2810.,  2534.,  1462.,   698.,   803.,   254.,   221.,    43.,
          569.,   103.,   283.,    42.,   135.,    21.,    22.]),
 array([  0.        ,   0.93333333,   1.86666667,   2.8       ,
          3.73333333,   4.66666667,   5.6       ,   6.53333333,
          7.46666667,   8.4       ,   9.33333333,  10.26666667,
         11.2       ,  12.13333333,  13.06666667,  14.        ]),
 <a list of 15 Patch objects>)






    

In [57]:

    

plt.hist(db.CG251O_NG3C51_CG2R51_HGR52_multiplicity_bitstring[:], alpha=.3, bins=23)
seaborn.rugplot(db.trace('CG251O_NG3C51_CG2R51_HGR52_multiplicity_bitstring')[:])


    

    
Out[57]:





<matplotlib.axes._subplots.AxesSubplot at 0x1e8f2ef50>






    

In [23]:

    

plt.hist(db.CG251O_NG3C51_CG321_CG321_multiplicity_bitstring[:], alpha=.3)
seaborn.rugplot(db.trace('CG251O_NG3C51_CG321_CG321_multiplicity_bitstring')[:])


    

    
Out[23]:





<matplotlib.axes._subplots.AxesSubplot at 0x16be35790>






    

In [ ]: