Adds new features, based on amino acid swaps

deeprank/domain/amino_acid.py

@@ -1,48 +1,332 @@
 from deeprank.models.amino_acid import AminoAcid
+from deeprank.models.polarity import Polarity
 
 
-alanine = AminoAcid("Alanine", "ALA", "A")
-arginine = AminoAcid("Arginine", "ARG", "R")
-asparagine = AminoAcid("Asparagine", "ASN", "N")
-aspartate = AminoAcid("Aspartate", "ASP", "D")
-protonated_aspartate = AminoAcid("Protonated Aspartate", "ASH", "D")
-cysteine = AminoAcid("Cysteine", "CYS", "C")
-cysteine_metal = AminoAcid("Cysteine Metal Ligand", "CYM", "C")
-cysteine_iron = AminoAcid("Cysteine Iron Ligand", "CFE", "C")
-cysteine_zinc = AminoAcid("Cysteine Zinc Ligand", "CYF", "C")
-cysteine_phosphate = AminoAcid("Cysteine Phosphate", "CSP", "C")
-glutamate = AminoAcid("Glutamate", "GLU", "E")
-protonated_glutamate = AminoAcid("Protonated Glutamate", "GLH", "E")
-glutamine = AminoAcid("Glutamine", "GLN", "Q")
-glycine = AminoAcid("Glycine", "GLY", "G")
-histidine = AminoAcid("Histidine", "HIS", "H")
-histidine_phophate = AminoAcid("Histidine Phosphate", "NEP", "H")
-isoleucine = AminoAcid("Isoleucine", "ILE", "I")
-leucine = AminoAcid("Leucine", "LEU", "L")
-lysine = AminoAcid("Lysine", "LYS", "K")
-methionine = AminoAcid("Methionine", "MET", "M")
-phenylalanine = AminoAcid("Phenylalanine", "PHE", "F")
-proline = AminoAcid("Proline", "PRO", "P")
-serine = AminoAcid("Serine", "SER", "S")
-threonine = AminoAcid("Threonine", "THR", "T")
-tryptophan = AminoAcid("Tryptophan", "TRP", "W")
-tyrosine = AminoAcid("Tyrosine", "TYR", "Y")
-valine = AminoAcid("Valine", "VAL", "V")
-selenocysteine = AminoAcid("Selenocysteine", "SEC", "U")
-pyrrolysine = AminoAcid("Pyrrolysine", "PYL", "O")
-alysine = AminoAcid("Alysine", "ALY", "K")
-methyllysine = AminoAcid("Methyllysine", "MLZ", "K")
-dimethyllysine = AminoAcid("Dimethyllysine", "MLY", "K")
-trimethyllysine = AminoAcid("Trimethyllysine", "3ML", "K")
-epsilon_mthionine = AminoAcid("Epsilon Methionine", "MSE", "M")
-hydroxy_proline = AminoAcid("Hydroxy Proline", "HYP", "P")
-serine_phosphate = AminoAcid("Serine Phosphate", "SEP", "S")
-threonine_phosphate = AminoAcid("Threonine Phosphate", "TOP", "T")
-tyrosine_phosphate = AminoAcid("Tyrosine Phosphate", "TYP", "Y")
-tyrosine_sulphate = AminoAcid("Tyrosine Sulphate", "TYS", "Y")
-tyrosine_phosphate = AminoAcid("Tyrosine Phosphate", "PTR", "Y")
-cyclohexane_alanine = AminoAcid("Cyclohexane Alanine", "CHX", "?")
-unknown_amino_acid = AminoAcid("Unknown", "XXX", "X")
+alanine = AminoAcid("Alanine", "ALA", "A",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=1,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+arginine = AminoAcid("Arginine", "ARG", "R",
+    charge=-1.65,
+    polarity=Polarity.POSITIVE_CHARGE,
+    size=7,
+    count_hydrogen_bond_donors=5,
+    count_hydrogen_bond_acceptors=0
+)
+
+asparagine = AminoAcid("Asparagine", "ASN", "N",
+    charge=-1.22,
+    polarity=Polarity.POLAR,
+    size=4,
+    count_hydrogen_bond_donors=2,
+    count_hydrogen_bond_acceptors=2
+)
+
+aspartate = AminoAcid("Aspartate", "ASP", "D",
+    charge=-1.37,
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+protonated_aspartate = AminoAcid("Protonated Aspartate", "ASH", "D",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=4,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=3
+)
+
+cysteine = AminoAcid("Cysteine", "CYS", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+cysteine_metal = AminoAcid("Cysteine Metal Ligand", "CYM", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+cysteine_iron = AminoAcid("Cysteine Iron Ligand", "CFE", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+cysteine_zinc = AminoAcid("Cysteine Zinc Ligand", "CYF", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+cysteine_phosphate = AminoAcid("Cysteine Phosphate", "CSP", "C",
+    charge=-0.64,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+glutamate = AminoAcid("Glutamate", "GLU", "E",
+    charge=-1.37,
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=5,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4,
+)
+protonated_glutamate = AminoAcid("Protonated Glutamate", "GLH", "E",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=4,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=3
+)
+
+glutamine = AminoAcid("Glutamine", "GLN", "Q",
+    charge=-1.22,
+    polarity=Polarity.POLAR,
+    size=5,
+    count_hydrogen_bond_donors=2,
+    count_hydrogen_bond_acceptors=2,
+)
+
+glycine = AminoAcid("Glycine", "GLY", "G",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=0,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+histidine = AminoAcid("Histidine", "HIS", "H",
+    charge=-0.29,
+    polarity=Polarity.POLAR,
+    size=6,
+    count_hydrogen_bond_donors=2,
+    count_hydrogen_bond_acceptors=2
+)
+
+histidine_phosphate = AminoAcid("Histidine Phosphate", "NEP", "H",
+    charge=-0.29,
+    polarity=Polarity.POLAR,
+    size=6,
+    count_hydrogen_bond_donors=2,
+    count_hydrogen_bond_acceptors=2
+)
+
+isoleucine = AminoAcid("Isoleucine", "ILE", "I",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0,
+)
+
+leucine = AminoAcid("Leucine", "LEU", "L",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+lysine = AminoAcid("Lysine", "LYS", "K",
+    charge=-0.36,
+    polarity=Polarity.POSITIVE_CHARGE,
+    size=5,
+    count_hydrogen_bond_donors=3,
+    count_hydrogen_bond_acceptors=0
+)
+
+methionine = AminoAcid("Methionine", "MET", "M",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+phenylalanine = AminoAcid("Phenylalanine", "PHE", "F",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=7,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+proline = AminoAcid("Proline", "PRO", "P",
+    charge=0.0,
+    polarity=Polarity.APOLAR,
+    size=3,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+serine = AminoAcid("Serine", "SER", "S",
+    charge=-0.80,
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=2
+)
+
+threonine = AminoAcid("Threonine", "THR", "T",
+    charge=-0.80,
+    polarity=Polarity.POLAR,
+    size=3,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=2
+)
+
+tryptophan = AminoAcid("Tryptophan", "TRP", "W",
+    charge=-0.79,
+    polarity=Polarity.POLAR,
+    size=10,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=0
+)
+
+tyrosine = AminoAcid("Tyrosine", "TYR", "Y",
+    charge=-0.80,
+    polarity=Polarity.POLAR,
+    size=8,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=1
+)
+
+valine = AminoAcid("Valine", "VAL", "V",
+    charge=-0.37,
+    polarity=Polarity.APOLAR,
+    size=3,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+selenocysteine = AminoAcid("Selenocysteine", "SEC", "U",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=2,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=2,
+)
+
+pyrrolysine = AminoAcid("Pyrrolysine", "PYL", "O",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=13,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+alysine = AminoAcid("Alysine", "ALY", "K",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=13,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+methyllysine = AminoAcid("Methyllysine", "MLZ", "K",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=14,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+dimethyllysine = AminoAcid("Dimethyllysine", "MLY", "K",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=15,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+trimethyllysine = AminoAcid("Trimethyllysine", "3ML", "K",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=16,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=4
+)
+
+epsilon_methionine = AminoAcid("Epsilon Methionine", "MSE", "M",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.APOLAR,
+    size=4,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+hydroxy_proline = AminoAcid("Hydroxy Proline", "HYP", "P",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.POLAR,
+    size=4,
+    count_hydrogen_bond_donors=1,
+    count_hydrogen_bond_acceptors=2
+)
+
+serine_phosphate = AminoAcid("Serine Phosphate", "SEP", "S",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=7,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+threonine_phosphate = AminoAcid("Threonine Phosphate", "TOP", "T",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=8,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+tyrosine_phosphate = AminoAcid("Tyrosine Phosphate", "TYP", "Y",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=13,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+tyrosine_sulphate = AminoAcid("Tyrosine Sulphate", "TYS", "Y",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.NEGATIVE_CHARGE,
+    size=13,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=4
+)
+
+cyclohexane_alanine = AminoAcid("Cyclohexane Alanine", "CHX", "?",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.APOLAR,
+    size=7,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
+
+unknown_amino_acid = AminoAcid("Unknown", "XXX", "X",
+    charge=0.0,  # unknown, but needs a numerical value
+    polarity=Polarity.APOLAR,
+    size=0,
+    count_hydrogen_bond_donors=0,
+    count_hydrogen_bond_acceptors=0
+)
 
 
 amino_acids = [alanine, arginine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine,