Open dprada opened 5 years ago
MolMolMT rise an error when importing in jupyter-lab.
I imported the library as follows:
import os
import mdtraj as md
from pdbfixer import PDBFixer
import pdbfixer as pdb
from simtk.openmm.app import PDBFile
import molmodmt as mt
Then I got:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/openmoltools/amber.py in find_gaff_dat()
272 try:
--> 273 AMBERHOME = os.path.split(full_path)[0]
274 AMBERHOME = os.path.join(AMBERHOME, "../")
~/miniconda3/envs/AnalysisMD/lib/python3.6/posixpath.py in split(p)
106 everything after the final slash. Either part may be empty."""
--> 107 p = os.fspath(p)
108 sep = _get_sep(p)
TypeError: expected str, bytes or os.PathLike object, not NoneType
During handling of the above exception, another exception occurred:
ValueError Traceback (most recent call last)
<ipython-input-4-db124cf99dc6> in <module>
4 import pdbfixer as pdb
5 from simtk.openmm.app import PDBFile
----> 6 import molmodmt as mt
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/molmodmt/__init__.py in <module>
----> 1 from .multitool import *
2 from . import utils
3 from . import moldyn as moldyn
4 from . import molsys as molsys
5
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/molmodmt/multitool.py in <module>
10
11 ## Classes
---> 12 from .formats.classes import dict_is_form as _dict_classes_is_form, \
13 list_forms as _list_classes_forms, \
14 dict_converter as _dict_classes_converter, \
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/molmodmt/formats/classes/__init__.py in <module>
----> 1 from .base import *
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/molmodmt/formats/classes/base.py in <module>
18
19 for api_form in list_api_forms:
---> 20 module_api_form=_import_module('.'+api_form,base_package)
21 form_name=module_api_form.form_name
22 list_forms.append(form_name)
~/miniconda3/envs/AnalysisMD/lib/python3.6/importlib/__init__.py in import_module(name, package)
124 break
125 level += 1
--> 126 return _bootstrap._gcd_import(name[level:], package, level)
127
128
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/molmodmt/formats/classes/api_yank_Topography.py in <module>
1 from os.path import basename as _basename
----> 2 from yank import Topography as _yank_Topography
3
4 form_name=_basename(__file__).split('.')[0].replace('api_','').replace('_','.')
5
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/yank/__init__.py in <module>
12 from . import utils
13 from . import multistate
---> 14 from . import restraints
15 from . import pipeline
16 from . import experiment
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/yank/restraints.py in <module>
35 from simtk import openmm, unit
36
---> 37 from . import pipeline
38 from .utils import methoddispatch, generate_development_feature
39
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/yank/pipeline.py in <module>
29 import numpy as np
30 import openmmtools as mmtools
---> 31 import openmoltools as moltools
32 from pdbfixer import PDBFixer
33 from simtk import openmm, unit
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/openmoltools/__init__.py in <module>
24 """
25
---> 26 from openmoltools import amber_parser, system_checker, utils, packmol, openeye, amber, cirpy, gromacs, schrodinger
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/openmoltools/openeye.py in <module>
3 import mdtraj as md
4 from openmoltools.utils import import_, enter_temp_directory, create_ffxml_file
----> 5 from openmoltools.amber import run_antechamber
6 import logging
7
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/openmoltools/amber.py in <module>
281 return os.path.join(AMBERHOME, 'dat', 'leap', 'parm', 'gaff.dat')
282
--> 283 GAFF_DAT_FILENAME = find_gaff_dat()
284
285
~/miniconda3/envs/AnalysisMD/lib/python3.6/site-packages/openmoltools/amber.py in find_gaff_dat()
274 AMBERHOME = os.path.join(AMBERHOME, "../")
275 except:
--> 276 raise(ValueError("Cannot find AMBER GAFF"))
277
278 if AMBERHOME is None:
ValueError: Cannot find AMBER GAFF
It looks like I have to set the AMBER HOME path. Should I install Amber tools? I am managing the installation via Conda.
Can MolModMT include a method to predict the propensity of a given sequence segment to form secondary structures? Something similar to what APSSP server does, or any other similar tool.