Unable to import pyemma after installation using jupyter notebook

[debanjansen48]

Thanks for submitting an issue!

Here's a quick checklist in what to include:

1. I created a conda env
2. activated conda env
3. using conda installed pyemma, mdshare, nglview, jupyter notebook.
4. inside the activated pyemma env I opend jupyter notebook 5.After issuing the command import pyemma it returns ModuleNotFoundError Traceback (most recent call last) /tmp/ipykernel_2239/684328617.py in ----> 1 import pyemma

ModuleNotFoundError: No module named 'pyemma'

6. after issuing the command !pip install 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

[clonker]

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]

[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)

— 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]

#after exploring the tutorial section I did the following things

1. conda activate pyemma to activate the env in side the working folder
2. conda activate pyemma jupyter nbextension enable toc2/main jupyter nbextension enable exercise2/main jupyter-notebook --browser=firefox 3.I am able to import pyemma successfully
3. but when i started the tutorial I am encountering the following issues. (installed conda install -c conda-forge pyemma mdshare nglview nbexamples jupyter_contrib_nbextensions)

**%matplotlib inline import matplotlib.pyplot as plt import numpy as np import mdshare

for visualization of molecular structures:

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..getinstance() 8 def getinstance(): 9 if cls not in instances: ---> 10 instances[cls] = cls() 11 return instances[cls]

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.ipython_display() 48 except NameError: 49 pass

File ~/anaconda3/envs/pyemma/lib/python3.9/site-packages/nglview/color.py:54, in _ColormakerRegistry.ipython_display(self, **kwargs) 52 if self._ready: 53 return ---> 54 super().ipython_display(**kwargs)

AttributeError: 'super' object has no attribute 'ipython_display'

#**In the tutorial i found 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]

i think issues are associated with nglview..

[clonker]

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]

#**In the tutorial i found 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]

You can use pyemma.coordinates.source for that. Please see to the relevant documentation.

[debanjansen48]

%matplotlib inline import matplotlib.pyplot as plt import numpy as np import mdshare import pyemma

for visualization of molecular structures:

import mdtraj from threading import Timer from pyemma import * pdb = pyemma.coordinates.source(md_100.pdb, features=feat) files = pyemma.coordinates.source(md_100-*.xtc, features=feat)

NameError Traceback (most recent call last) ~\AppData\Local\Temp/ipykernel_5568/2736778055.py in 1 from pyemma import * ----> 2 pdb = pyemma.coordinates.source(md_100.pdb, features=feat) 3 files = pyemma.coordinates.source(md_100.xtc, features=feat)

NameError: name 'md_100' is not defined

it returns above error.

[clonker]

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]

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 ----> 1 feat = pyemma.coordinates.featurizer(files) 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.feature_reader.FeatureReader'>, but only string or mdtraj.Topology allowed.

My trajectory is raw. contains water, ions and apo protein. It creating problem?i converted the md_100.gro to md_100.pdb utilizing pymol. As it says topol.top file not supported.

data = pyemma.coordinates.load(files, features=feat) print('type of data:', type(data)) print('lengths:', len(data)) print('shape of elements:', data[0].shape) print('n_atoms:', feat.topology.n_atoms)

NameError Traceback (most recent call last)~\AppData\Local\Temp/ipykernel_5568/2508888573.py in ----> 1 data = pyemma.coordinates.load(files, features=feat) 2 print('type of data:', type(data)) 3 print('lengths:', len(data)) 4 print('shape of elements:', data[0].shape) 5 print('n_atoms:', feat.topology.n_atoms) NameError: name 'feat' is not defined

Is there any straight forward protocol? I want to study the conformational changes of a apo protein and holoprotein. I am sorry, actually I am from Organic medicinal chemistry background and have limited idea about python coding.

On Mon, Sep 12, 2022 at 6:56 PM Moritz Hoffmann @.***> wrote:

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"].

— Reply to this email directly, view it on GitHub https://github.com/markovmodel/PyEMMA/issues/1575#issuecomment-1243742158, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4S6N65LVLOOJHPGJFDV54VSBANCNFSM6AAAAAAQJU5NXA . You are receiving this because you modified the open/close state.Message ID: @.***>

[hai-schrodinger]

AttributeError: 'super' object has no attribute 'ipython_display'

FYI: Downgrading to ipywidgets 7 would help.

[debanjansen48]

:( Downgrading to ipywidgets 7 would help.??

[hai-schrodinger]

:( 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]

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]

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]

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]

Not a problem, let us know how it goes!

[debanjansen48]

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 ----> 1 torsions_feat = pyemma.coordinates.featurizer(pdb) 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 'pyemma.coordinates.data.featurization.featurizer.MDFeaturizer'>, but only string or mdtraj.Topology allowed.

[clonker]

Hi, it should work if you use torsions_feat = pyemma.coordinates.featurizer("md_100.pdb") instead.

[debanjansen48]

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 1 torsions_feat = pyemma.coordinates.featurizer("md_100.pdb") 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 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]

i converted md_100.gro file to md_100.pdb using pymol. It contain TIP3P water ions

[clonker]

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]

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.

— 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]

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.

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[debanjansen48]

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: # save for later 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 13 fig, axes = plt.subplots(1, 3, figsize=(12, 3), sharey=True) 14 for ax, lag in zip(axes.flat, [5, 10, 20]): ---> 15 torsions_scores = score_cv(files, lag=lag, dim=dim) 16 scores = [torsions_scores.mean()] 17 errors = [torsions_scores.std()]

~\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.

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