text: # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  #
  #       http://www.apache.org/licenses/LICENSE-2.0
  #
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  
  from vaxrank.manufacturability import ManufacturabilityScores
  
  
  def test_c_terminal_proline():
      scores = ManufacturabilityScores.from_amino_acids("A" * 6 + "P")
      assert scores.c_terminal_proline
  
      scores = ManufacturabilityScores.from_amino_acids("A" * 7)
      assert not scores.c_terminal_proline
  
  
  def test_n_terminal_cysteine():
      scores = ManufacturabilityScores.from_amino_acids("C" + 6 * "A")
      assert scores.difficult_n_terminal_residue
  
      scores = ManufacturabilityScores.from_amino_acids(7 * "A")
      assert not scores.difficult_n_terminal_residue
  
  
  def test_n_terminal_glutamic_acid():
      scores = ManufacturabilityScores.from_amino_acids("E" + 6 * "A")
      assert scores.difficult_n_terminal_residue
  
      scores = ManufacturabilityScores.from_amino_acids(7 * "A")
      assert not scores.difficult_n_terminal_residue
  
  
  def test_n_terminal_glutamine():
      scores = ManufacturabilityScores.from_amino_acids("Q" + 6 * "A")
      assert scores.difficult_n_terminal_residue
  
      scores = ManufacturabilityScores.from_amino_acids(7 * "A")
      assert not scores.difficult_n_terminal_residue
  
  
  def test_asp_pro_bond_count():
      scores = ManufacturabilityScores.from_amino_acids("A" * 7)
      assert scores.asparagine_proline_bond_count == 0
  
      scores = ManufacturabilityScores.from_amino_acids("NP" + "A" * 7 + "NP")
      assert scores.asparagine_proline_bond_count == 2
  
  
  def test_cysteine_count():
      scores = ManufacturabilityScores.from_amino_acids("C" * 7)
      assert scores.cysteine_count == 7
  
  
  def cterm_7mer_gravy_score():
      scores = ManufacturabilityScores.from_amino_acids("QLFY" + "A" * 7)
      # hydropathy of alanine is 1.8 from Kyte & Doolittle 1982
      assert scores.cterm_7mer_gravy_score == 1.8
  
  
  def max_7mer_gravy_score():
      scores = ManufacturabilityScores.from_amino_acids("H" * 3 + "A" * 7)
      # hydropathy of alanine is 1.8, histidine is -3.2
      # from Kyte & Doolittle 1982
      assert scores.max_7mer_gravy_score == 1.8
  