Open debanjansen48 opened 1 year ago
clonker
commented
1 year ago Hi, have you activated the correct environment before starting the server? Also please make sure your jupyter kernel is pointing to the right path (see eg here https://ipython.readthedocs.io/en/stable/install/kernel_install.htm)
debanjansen48
commented
1 year ago [image: image.png] unable to open the given page.
On Sun, Sep 11, 2022 at 11:55 PM Moritz Hoffmann @.***> wrote:
Hi, have you activated the correct environment before starting the server? Also please make sure your jupyter kernel is pointing to the right path (see eg here https://ipython.readthedocs.io/en/stable/install/kernel_install.htm)
ā Reply to this email directly, view it on GitHub https://github.com/markovmodel/PyEMMA/issues/1575#issuecomment-1243017332, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4Q55UBAYS724M4RVMTV5YPZBANCNFSM6AAAAAAQJU5NXA . You are receiving this because you authored the thread.Message ID: @.***>
debanjansen48
commented
1 year ago **%matplotlib inline import matplotlib.pyplot as plt import numpy as np import mdshare
import nglview import mdtraj from threading import * from nglview.player import ** AttributeError Traceback (most recent call last) Cell In [8], line 6 4 import mdshare 5 # for visualization of molecular structures: ----> 6 import nglview 7 import mdtraj 8 from threading import
File ~/anaconda3/envs/pyemma/lib/python3.9/site-packages/nglview/init.py:4 1 import warnings 3 # for doc ----> 4 from . import adaptor, datafiles, show, widget 5 from ._version import get_versions 6 from .adaptor import *
File ~/anaconda3/envs/pyemma/lib/python3.9/site-packages/nglview/show.py:13 3 from . import datafiles 4 from .adaptor import (ASEStructure, ASETrajectory, BiopythonStructure, 5 FileStructure, HTMDTrajectory, IODataStructure, 6 IOTBXStructure, MDAnalysisTrajectory, MDTrajTrajectory, (...) 11 RdkitStructure, 12 TextStructure) ---> 13 from .widget import NGLWidget 15 all = [ 16 'demo', 17 'show_pdbid', (...) 40 'show_biopython', 41 ] 44 def show_pdbid(pdbid, **kwargs):
File ~/anaconda3/envs/pyemma/lib/python3.9/site-packages/nglview/widget.py:19 15 from traitlets import (Bool, CaselessStrEnum, Dict, Instance, Int, Integer, 16 List, Unicode, observe, validate) 17 import traitlets ---> 19 from . import color, interpolate 20 from .adaptor import Structure, Trajectory 21 from .component import ComponentViewer
File ~/anaconda3/envs/pyemma/lib/python3.9/site-packages/nglview/color.py:114 110 else: 111 raise ValueError(f"{obj} must be either list of list or string") --> 114 ColormakerRegistry = _ColormakerRegistry()
File ~/anaconda3/envs/pyemma/lib/python3.9/site-packages/nglview/base.py:10, in _singleton.
File ~/anaconda3/envs/pyemma/lib/python3.9/site-packages/nglview/color.py:47, in _ColormakerRegistry.init(self, *args, **kwargs) 45 try: 46 get_ipython() # only display in notebook ---> 47 self._ipythondisplay() 48 except NameError: 49 pass
File ~/anaconda3/envs/pyemma/lib/python3.9/site-packages/nglview/color.py:54, in _ColormakerRegistry._ipythondisplay(self, kwargs) 52 if self._ready: 53 return ---> 54 super()._ipythondisplay(kwargs)
AttributeError: 'super' object has no attribute '_ipythondisplay'
file = mdshare.fetch('hmm-doublewell-2d-100k.npz', working_directory='data') or pdb = mdshare.fetch('alanine-dipeptide-nowater.pdb', working_directory='data') files = mdshare.fetch('alanine-dipeptide-*-250ns-nowater.xtc', working_directory='data') print(pdb) print(files)
I have three 100ns gromacs MD trajectory entitled md_100ns-0.xtc,md_100ns-1.xtc,md_100ns-2.xtc and md_100ns.gro files. how to load them. each trajectory contains 10k snapshots. kindly help**
debanjansen48
commented
1 year ago i think issues are associated with nglview..
clonker
commented
1 year ago Hi, yes, the error message suggests that there is something wrong with your nglview / ipython setup. It is however not crucial to work with NGLView, you can also use, e.g., VMD. :slightly_smiling_face:
debanjansen48
commented
1 year ago file = mdshare.fetch('hmm-doublewell-2d-100k.npz', working_directory='data') or pdb = mdshare.fetch('alanine-dipeptide-nowater.pdb', working_directory='data') files = mdshare.fetch('alanine-dipeptide-*-250ns-nowater.xtc', working_directory='data') print(pdb) print(files)
I have three 100ns gromacs MD trajectory entitled md_100ns-0.xtc,md_100ns-1.xtc,md_100ns-2.xtc and md_100ns.gro files. how to load them. each trajectory contains 10k snapshots. kindly help**
clonker
commented
1 year ago You can use pyemma.coordinates.source for that. Please see to the [relevant documentation](http://www.emma-project.org/latest/tutorials/notebooks/01-data-io-and-featurization.html#load()-versus-source()).
debanjansen48
commented
1 year ago %matplotlib inline import matplotlib.pyplot as plt import numpy as np import mdshare import pyemma
NameError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_5568/2736778055.py in
NameError: name 'md_100' is not defined
it returns above error.
clonker
commented
1 year ago Hi, you can't use it like that :) PyEMMA does not support wildcards and strings should also be declared as such: use "md_100.pdb" over just md_100.pdb. For lists of files use a Python list of strings like ["a.xtc", "b.xtc"].
debanjansen48
commented
1 year ago files=pyemma.coordinates.source("md_100.xtc",top="md_100.pdb") print(files)
output:-<pyemma.coordinates.data.feature_reader.FeatureReader object at 0x000001D9CB806100>
feat = pyemma.coordinates.featurizer(files)
---------------------------------------------------------------------------ValueError Traceback (most recent call last)~\AppData\Local\Temp/ipykernel_5568/3492995895.py in
hai-schrodinger
commented
1 year ago AttributeError: 'super' object has no attribute 'ipython_display'
FYI: Downgrading to ipywidgets 7 would help.
debanjansen48
commented
1 year ago :( Downgrading to ipywidgets 7 would help.??
hai-schrodinger
commented
1 year ago :( Downgrading to ipywidgets 7 would help.??
Why do you need to use double ??
But yes, downgrading helps. v8 breaks a lot of things that requires time to migrate.
debanjansen48
commented
1 year ago Sir, actually I am unable to get your suggestions... I want to.build msm model...not.double... during execution as per protocol given in tutorial. I am getting those errors..I have limited idea about python
clonker
commented
1 year ago I would like to remind all of you that this is an open and collaborative platform, so please remain civil with each other and exercise yourselves in leniency.
Thanks @hai-schrodinger for the hint to downgrade ipywidgets.
@debanjansen48 assuming you use conda for dependency management, running conda remove jupyter and conda install jupyter "ipywidgets<8" should fix things. Be aware that it might take a while for the conda dependency solver to figure things out.
debanjansen48
commented
1 year ago Apologies If I say something wrong....as a non native English speaker...I may not used correct words. With limited python knowledge I did not understood ipywdget things.... However, I am installing things as per your guidance...thanks
clonker
commented
1 year ago Not a problem, let us know how it goes!
debanjansen48
commented
1 year ago it takes long....but able to install successfully. During my learning with my trajectory. "http://www.emma-project.org/latest/tutorials/notebooks/00-pentapeptide-showcase.html" getting following error.
%matplotlib inline import matplotlib.pyplot as plt import matplotlib as mpl import numpy as np import mdshare import mdtraj import pyemma from pyemma.util.contexts import settings
pdb =pyemma.coordinates.featurizer('md_100.pdb') pdb.add_backbone_torsions() files = pyemma.coordinates.source("md_100.xtc", features=pdb) traj = mdtraj.load('md_100.pdb')
print(pdb) print(files) MDFeaturizer with features: MDFeaturizer with features: ['PHI 0 TRP 2', 'PSI 0 MET 1', 'PHI 0 PRO 3', 'PSI 0 TRP 2', 'PHI 0 PHE 4', 'PSI 0 PRO 3', 'PHI 0 VAL 5', 'PSI 0 PHE 4', 'PHI 0 SER 6', 'PSI 0 VAL 5', ...] <pyemma.coordinates.data.feature_reader.FeatureReader object at 0x000001D709D1B7F0>
torsions_feat = pyemma.coordinates.featurizer(pdb) torsions_feat.add_backbone_torsions(cossin=True, periodic=False) torsions_data = pyemma.coordinates.load(files, features=torsions_feat) labels = ['backbone\ntorsions']
ValueError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_7948/2952867051.py in
C:\ProgramData\Miniconda3\envs\pyemma\lib\site-packages\pyemma\coordinates\api.py in featurizer(topfile) 142 """ 143 from pyemma.coordinates.data.featurization.featurizer import MDFeaturizer --> 144 return MDFeaturizer(topfile) 145 146
C:\ProgramData\Miniconda3\envs\pyemma\lib\site-packages\pyemma\coordinates\data\featurization\featurizer.py in init(self, topfile, **kwargs) 59 """ 60 self.topology = None ---> 61 self.topologyfile = topfile 62 self.active_features = [] 63
C:\ProgramData\Miniconda3\envs\pyemma\lib\site-packages\pyemma\coordinates\data\featurization\featurizer.py in topologyfile(self, topfile) 77 self.topology = topfile.topology 78 else: ---> 79 raise ValueError("no valid topfile arg: type was %s, " 80 "but only string or mdtraj.Topology allowed." % type(topfile)) 81
ValueError: no valid topfile arg: type was <class 'pyemma.coordinates.data.featurization.featurizer.MDFeaturizer'>, but only string or mdtraj.Topology allowed.
clonker
commented
1 year ago Hi, it should work if you use torsions_feat = pyemma.coordinates.featurizer("md_100.pdb") instead.
debanjansen48
commented
1 year ago Sir, again error torsions_feat = pyemma.coordinates.featurizer("md_100.pdb") torsions_feat.add_backbone_torsions(cossin=True, periodic=False) torsions_data = pyemma.coordinates.load(files, features=torsions_feat) labels = ['backbone\ntorsions']
ValueError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_7948/3503107185.py in
C:\ProgramData\Miniconda3\envs\pyemma\lib\site-packages\pyemma\coordinates\api.py in load(trajfiles, features, top, stride, chunksize, **kw) 250 return trajs 251 else: --> 252 raise ValueError('unsupported type (%s) of input' % type(trajfiles)) 253 254
ValueError: unsupported type (<class 'pyemma.coordinates.data.feature_reader.FeatureReader'>) of input
debanjansen48
commented
1 year ago i converted md_100.gro file to md_100.pdb using pymol. It contain TIP3P water ions
clonker
commented
1 year ago Hey sorry, the problem is that files in your case is the result of pyemma.coordinates.source, which is a feature reader, not a list of file names :-) If you provide a list of file names instead, the call to pyemma.coordinates.load should work as expected.
debanjansen48
commented
1 year ago Ok sir
On Tue, 13 Sept 2022, 5:44 pm Moritz Hoffmann, @.***> wrote:
Hey sorry, the problem is that files in your case is the result of pyemma.coordinates.source, which is a feature reader, not a list of file names :-) If you provide a list of file names instead, the call to pyemma.coordinates.load should work as expected.
ā Reply to this email directly, view it on GitHub https://github.com/markovmodel/PyEMMA/issues/1575#issuecomment-1245327313, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4X7P6RM2MV6PLSMAR3V6BV23ANCNFSM6AAAAAAQJU5NXA . You are receiving this because you were mentioned.Message ID: @.***>
debanjansen48
commented
1 year ago Same error pdb =pyemma.coordinates.featurizer('md_100.pdb') pdb.add_backbone_torsions() files = pyemma.coordinates.load("md_100.xtc", features=pdb) print(pdb) print(files)
MDFeaturizer with features: ['PHI 0 TRP 2', 'PSI 0 MET 1', 'PHI 0 PRO 3', 'PSI 0 TRP 2', 'PHI 0 PHE 4', 'PSI 0 PRO 3', 'PHI 0 VAL 5', 'PSI 0 PHE 4', 'PHI 0 SER 6', 'PSI 0 VAL 5', ...] [[-2.7803931 -0.55992097 0.8125005 ... -0.9663092 3.060793 -2.0096664 ] [-3.1387906 -0.52576107 0.9709076 ... -1.2261833 2.9609232 -2.078714 ] [-2.8843434 -0.5206821 1.4275188 ... -1.1710676 -3.0772657 -1.4840003 ] ... [ 2.7466419 -0.40174305 0.8194104 ... -1.8518398 3.0417266 -1.8356031 ] [ 2.8462875 -0.851876 1.1383928 ... -2.0212262 -3.139257 -1.0744576 ] [ 2.9985669 -0.5661735 0.97182405 ... -1.1841456 -2.9308317 -0.67333 ]]
torsions_feat = pyemma.coordinates.featurizer(pdb) torsions_feat.add_backbone_torsions(cossin=True, periodic=False) torsions_data = pyemma.coordinates.load(files, features=torsions_feat) labels = ['backbone\ntorsions']
---------------------------------------------------------------------------ValueError
Traceback (most recent call
last)~\AppData\Local\Temp/ipykernel_7160/857609899.py in
On Tue, Sep 13, 2022 at 6:26 PM Debanjan Sen @.***> wrote:
Ok sir
On Tue, 13 Sept 2022, 5:44 pm Moritz Hoffmann, @.***> wrote:
Hey sorry, the problem is that files in your case is the result of pyemma.coordinates.source, which is a feature reader, not a list of file names :-) If you provide a list of file names instead, the call to pyemma.coordinates.load should work as expected.
ā Reply to this email directly, view it on GitHub https://github.com/markovmodel/PyEMMA/issues/1575#issuecomment-1245327313, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4X7P6RM2MV6PLSMAR3V6BV23ANCNFSM6AAAAAAQJU5NXA . You are receiving this because you were mentioned.Message ID: @.***>
debanjansen48
commented
1 year ago Hi Sir, gradually I am getting success.. pdb =pyemma.coordinates.featurizer('md_100.pdb') files = pyemma.coordinates.source(["md_100.xtc","md_100-1.xtc","md_100-2.xtc"], features=pdb) torsions_feat = pyemma.coordinates.featurizer("md_100.pdb") torsions_feat.add_backbone_torsions(cossin=True, periodic=False) torsions_data = pyemma.coordinates.source(files, features=torsions_feat) labels = ['backbone\ntorsions'] positions_feat = pyemma.coordinates.featurizer("md_100.pdb") positions_feat.add_selection(positions_feat.select_Backbone()) positions_data = pyemma.coordinates.source(files, features=positions_feat) labels += ['backbone atom\npositions'] distances_feat = pyemma.coordinates.featurizer("md_100.pdb") distances_feat.add_distances( distances_feat.pairs(distances_feat.select_Backbone(), excluded_neighbors=2), periodic=False) distances_data = pyemma.coordinates.source(files, features=distances_feat) labels += ['backbone atom\ndistances']
upto above code it returns no error however def score_cv(data, dim, lag, number_of_splits=10, validation_fraction=0.5): with pyemma.util.contexts.settings(show_progress_bars=False): nval = int(len(data) * validation_fraction) scores = np.zeros(number_of_splits) for n in range(number_of_splits): ival = np.random.choice(len(data), size=nval, replace=False) vamp = pyemma.coordinates.vamp( [d for i, d in enumerate(data) if i not in ival], lag=lag, dim=dim) scores[n] = vamp.score([d for i, d in enumerate(data) if i in ival]) return scores dim = 15
fig, axes = plt.subplots(1, 3, figsize=(12, 3), sharey=True) for ax, lag in zip(axes.flat, [5, 10, 20]): torsions_scores = score_cv(files, lag=lag, dim=dim) scores = [torsions_scores.mean()] errors = [torsions_scores.std()] positions_scores = score_cv(positions_data, lag=lag, dim=dim) scores += [positions_scores.mean()] errors += [positions_scores.std()] distances_scores = score_cv(distances_data, lag=lag, dim=dim) scores += [distances_scores.mean()] errors += [distances_scores.std()] ax.bar(labels, scores, yerr=errors, color=['C0', 'C1', 'C2']) ax.set_title(r'lag time $\tau$={:.1f}ns'.format(lag * 0.1)) if lag == 5:
vamp_bars_plot = dict(
labels=labels, scores=scores, errors=errors, dim=dim, lag=lag)axes[0].set_ylabel('VAMP2 score') fig.tight_layout()
returns len error
TypeError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_4636/4284533947.py in
~\AppData\Local\Temp/ipykernel_4636/4284533947.py in score_cv(data, dim, lag, number_of_splits, validation_fraction) 1 def score_cv(data, dim, lag, number_of_splits=10, validation_fraction=0.5): 2 with pyemma.util.contexts.settings(show_progress_bars=False): ----> 3 nval = int(len(data) * validation_fraction) 4 scores = np.zeros(number_of_splits) 5 for n in range(number_of_splits):
TypeError: object of type 'FeatureReader' has no len()
shall i need to install some tools?
On Wed, Sep 14, 2022 at 12:53 AM Debanjan Sen @.***> wrote:
Same error pdb =pyemma.coordinates.featurizer('md_100.pdb') pdb.add_backbone_torsions() files = pyemma.coordinates.load("md_100.xtc", features=pdb) print(pdb) print(files)
MDFeaturizer with features: ['PHI 0 TRP 2', 'PSI 0 MET 1', 'PHI 0 PRO 3', 'PSI 0 TRP 2', 'PHI 0 PHE 4', 'PSI 0 PRO 3', 'PHI 0 VAL 5', 'PSI 0 PHE 4', 'PHI 0 SER 6', 'PSI 0 VAL 5', ...] [[-2.7803931 -0.55992097 0.8125005 ... -0.9663092 3.060793 -2.0096664 ] [-3.1387906 -0.52576107 0.9709076 ... -1.2261833 2.9609232 -2.078714 ] [-2.8843434 -0.5206821 1.4275188 ... -1.1710676 -3.0772657 -1.4840003 ] ... [ 2.7466419 -0.40174305 0.8194104 ... -1.8518398 3.0417266 -1.8356031 ] [ 2.8462875 -0.851876 1.1383928 ... -2.0212262 -3.139257 -1.0744576 ] [ 2.9985669 -0.5661735 0.97182405 ... -1.1841456 -2.9308317 -0.67333 ]]
torsions_feat = pyemma.coordinates.featurizer(pdb) torsions_feat.add_backbone_torsions(cossin=True, periodic=False) torsions_data = pyemma.coordinates.load(files, features=torsions_feat) labels = ['backbone\ntorsions']
---------------------------------------------------------------------------ValueError Traceback (most recent call last)~\AppData\Local\Temp/ipykernel_7160/857609899.py in
----> 1 torsions_feat = pyemma.coordinates.featurizer(files) 2 torsions_feat.add_backbone_torsions(cossin=True, periodic=False) 3 torsions_data = pyemma.coordinates.load(files, features=torsions_feat) 4 labels = ['backbone\ntorsions'] C:\ProgramData\Miniconda3\envs\pyemma\lib\site-packages\pyemma\coordinates\api.py in featurizer(topfile) 142 """ 143 from pyemma.coordinates.data.featurization.featurizer import MDFeaturizer--> 144 return MDFeaturizer(topfile) 145 146 C:\ProgramData\Miniconda3\envs\pyemma\lib\site-packages\pyemma\coordinates\data\featurization\featurizer.py in init(self, topfile, **kwargs) 59 """ 60 self.topology = None---> 61 self.topologyfile = topfile 62 self.active_features = [] 63 C:\ProgramData\Miniconda3\envs\pyemma\lib\site-packages\pyemma\coordinates\data\featurization\featurizer.py in topologyfile(self, topfile) 77 self.topology = topfile.topology 78 else:---> 79 raise ValueError("no valid topfile arg: type was %s, " 80 "but only string or mdtraj.Topology allowed." % type(topfile)) 81 ValueError: no valid topfile arg: type was <class 'numpy.ndarray'>, but only string or mdtraj.Topology allowed. On Tue, Sep 13, 2022 at 6:26 PM Debanjan Sen @.***> wrote:
Ok sir
On Tue, 13 Sept 2022, 5:44 pm Moritz Hoffmann, @.***> wrote:
Hey sorry, the problem is that files in your case is the result of pyemma.coordinates.source, which is a feature reader, not a list of file names :-) If you provide a list of file names instead, the call to pyemma.coordinates.load should work as expected.
ā Reply to this email directly, view it on GitHub https://github.com/markovmodel/PyEMMA/issues/1575#issuecomment-1245327313, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4X7P6RM2MV6PLSMAR3V6BV23ANCNFSM6AAAAAAQJU5NXA . You are receiving this because you were mentioned.Message ID: @.***>
stale[bot]
commented
1 year ago This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.
Thanks for submitting an issue!
Here's a quick checklist in what to include:
ModuleNotFoundError: No module named 'pyemma'
Requirement already satisfied: pyemma in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (2.5.11) Requirement already satisfied: tqdm>=4.23 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (4.64.1) Requirement already satisfied: h5py>=2.7.1 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (3.7.0) Requirement already satisfied: matplotlib in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (3.5.3) Requirement already satisfied: scipy>=0.11 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (1.9.1) Requirement already satisfied: numpy>=1.8.0 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (1.23.2) Requirement already satisfied: mdtraj>=1.9.2 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (1.9.7) Requirement already satisfied: pathos in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (0.2.9) Requirement already satisfied: psutil>=3.1.1 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (5.9.2) Requirement already satisfied: decorator>=4.0.0 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (5.1.1) Requirement already satisfied: msmtools>=1.2 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (1.2.6) Requirement already satisfied: pyyaml in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (6.0) Requirement already satisfied: deeptime in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (0.4.3) Requirement already satisfied: bhmm<0.7,>=0.6 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pyemma) (0.6.3) Requirement already satisfied: six in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from bhmm<0.7,>=0.6->pyemma) (1.16.0) Requirement already satisfied: pyparsing in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from mdtraj>=1.9.2->pyemma) (3.0.9) Requirement already satisfied: astunparse in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from mdtraj>=1.9.2->pyemma) (1.6.3) Requirement already satisfied: scikit-learn>=0.14.1 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from deeptime->pyemma) (1.1.2) Requirement already satisfied: threadpoolctl>=2.0.0 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from deeptime->pyemma) (3.1.0) Requirement already satisfied: python-dateutil>=2.7 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from matplotlib->pyemma) (2.8.2) Requirement already satisfied: fonttools>=4.22.0 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from matplotlib->pyemma) (4.37.1) Requirement already satisfied: kiwisolver>=1.0.1 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from matplotlib->pyemma) (1.4.4) Requirement already satisfied: pillow>=6.2.0 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from matplotlib->pyemma) (9.2.0) Requirement already satisfied: cycler>=0.10 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from matplotlib->pyemma) (0.11.0) Requirement already satisfied: packaging>=20.0 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from matplotlib->pyemma) (21.3) Requirement already satisfied: ppft>=1.7.6.5 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pathos->pyemma) (1.7.6.5) Requirement already satisfied: multiprocess>=0.70.13 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pathos->pyemma) (0.70.13) Requirement already satisfied: pox>=0.3.1 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pathos->pyemma) (0.3.1) Requirement already satisfied: dill>=0.3.5.1 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from pathos->pyemma) (0.3.5.1) Requirement already satisfied: joblib>=1.0.0 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from scikit-learn>=0.14.1->deeptime->pyemma) (1.1.0) Requirement already satisfied: wheel<1.0,>=0.23.0 in /home/debanjan/anaconda3/envs/pyemma/lib/python3.9/site-packages (from astunparse->mdtraj>=1.9.2->pyemma) (0.37.1)
Unable to figure out.. kindly help me out thanks