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AttributeError: 'DataFrame' object has no attribute 'components_ #7

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sbhakat opened this issue Jun 10, 2019 · 0 comments
Open

AttributeError: 'DataFrame' object has no attribute 'components_ #7

sbhakat opened this issue Jun 10, 2019 · 0 comments

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@sbhakat
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sbhakat commented Jun 10, 2019

I was trying to run the following script for tica rendering

#!/usr/bin/env python
import pandas as pd 
import mdtraj as md 
from msmbuilder.dataset import dataset
from msmbuilder.utils import load
from msmbuilder.featurizer import ContactFeaturizer
from msmbuilder.featurizer import RawPositionsFeaturizer
from tica_metadynamics.plumed_writer import render_tic

#python imports
import os,glob
import numpy as np
import pickle


ds = dataset("ca.xtc",  #38943.xtc",
              topology='ca.pdb')


#define our featurizer
feat = RawPositionsFeaturizer(atom_indices=np.array([7,   8,   9,  10,  11,  12,  13,  14,  15,  16,  17,  18,  19,
        20,  21,  22,  23,  24,  25,  26,  27,  28,  29,  30,  31,  32,
        33,  34,  35,  36,  37,  38,  39,  40,  41,  42,  43,  44,  45,
        46,  47,  48,  49,  50,  51,  52,  53,  54,  55,  56,  57,  58,
        59,  60,  61,  62,  63,  64,  65,  66,  67,  68,  69,  70,  71,
        72,  73,  74,  75,  76,  77,  78,  79,  80,  81,  82,  83,  84,
        85,  86,  87,  88,  89,  90,  91,  92,  93,  94,  95,  96,  97,
        98,  99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110,
       111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123,
       124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136,
       137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149,
       150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162,
       163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,
       176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188,
       189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201,
       202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214,
       215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227,
       228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240,
       241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253,
       254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266,
       267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279,
       280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292,
       293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305,
       306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318,
       319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331])-1)

top = md.load('ca.pdb')
# this basically maps every feature to atom indices. 
df = pd.DataFrame(feat.describe_features(ds[0]))

tica_mdl = load("tica_mdl_rawpos.pkl")

#Then to render tIC 0
print(render_tic(df,tica_mdl, 0))

But got an error like following:

Traceback (most recent call last):
  File "msm_ticawriter.py", line 54, in <module>
    print(render_tic(df,tica_mdl, 0))
  File "/lunarc/nobackup/users/sbhakat/tica_metadynamics-master/tica_metadynamics/pyplumed/render_tics.py", line 16, in render_tic
    inds = np.nonzero(tica_mdl.components_[tic_index,:])[0]
  File "/home/sbhakat/anaconda3/lib/python3.6/site-packages/pandas/core/generic.py", line 4372, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'components_'
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