Secondary structure prediction for sequence segments

[dprada]

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.

[AngelRuizMoreno]

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.