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# Values are taken from
# Rappe et al.
# "UFF, a Full Periodic Table Force Field
# for Molecular Mechanics and Molecular Dynamics Simulations"
# J Am Chem Soc, 114, 10024-10035 (1992)
# https://doi.org/10.1021/ja00051a040
#
#           valence               nonbond
#        ------------   --------------------------
# type   bond   angle   distance   energy    scale   charge

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#### General ####

extensions = ["sphinx.ext.autodoc",
              "sphinx.ext.autosummary",
              "sphinx.ext.doctest",
              "sphinx.ext.mathjax",
              "sphinx.ext.viewcode",
              "sphinxcontrib.bibtex"]

templates_path = ["templates"]

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import numpy as np
import biotite.structure as struc
import biotite.structure.io.pdbx as pdbx
import biotite.database.rcsb as rcsb

path = rcsb.fetch("1aki", "pdbx", ".")
pdbx_file = pdbx.PDBxFile.read(path)
atoms = pdbx.get_structure(pdbx_file, model=1)
sasa_per_atom = struc.sasa(atoms)
sasa_per_residue = struc.apply_residue_wise(atoms, sasa_per_atom, np.nansum)

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from os.path import join, isdir
from os import mkdir
import numpy as np
import biotite.structure as struc
import biotite.structure.io.pdb as pdb
import biotite.structure.io.pdbx as pdbx
import biotite.database.rcsb as rcsb


# The structural classifier

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# Code source: Patrick Kunzmann
# License: BSD 3 clause

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
import biotite
import biotite.sequence as seq
import biotite.sequence.graphics as graphics
import biotite.sequence.io.genbank as gb

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import numpy as np
import matplotlib.pyplot as plt
import biotite.sequence as seq
import biotite.sequence.align as align
import biotite.sequence.graphics as graphics

sequences = [
    seq.ProteinSequence(seq_str) for seq_str
    in ("BIQTITE", "TITANITE", "BISMITE", "IQLITE")
]

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import numpy as np
import biotite.structure as struc
import biotite.structure.io.mmtf as mmtf
import biotite.structure.info as info
import biotite.database.rcsb as rcsb


def remove_incomplete_residues(atoms):
    include_mask = np.zeros(atoms.array_length(), dtype=bool)
    residue_starts = struc.get_residue_starts(atoms, add_exclusive_stop=True)