diff --git a/prody/proteins/interactions.py b/prody/proteins/interactions.py index c8d04acca..15c8d03f6 100644 --- a/prody/proteins/interactions.py +++ b/prody/proteins/interactions.py @@ -153,6 +153,28 @@ def filterInteractions(list_of_interactions, atoms, **kwargs): return final +def get_energy(pair, source): + """Return energies based on the pairs of interacting residues (without distance criteria) + Taking information from tabulated_energies.txt file""" + + import numpy as np + import importlib.resources as pkg_resources + + with pkg_resources.path('prody.proteins', 'tabulated_energies.txt') as file_path: + data = np.loadtxt(file_path, skiprows=1, dtype=str) + + sources = ["ivet_nosolv", "ivet_solv", "carlos"] + aa_pairs = [] + + for row in data: + aa_pairs.append(row[0]+row[1]) + + lookup = pair[0]+pair[1] + + return data[np.where(np.array(aa_pairs)==lookup)[0]][0][2:][np.where(np.array(sources)==source)][0] + + + def calcHydrophobicOverlapingAreas(atoms, **kwargs): """Provide information about hydrophobic contacts between pairs of residues based on the regsurf program. To use this function compiled hpb.so is needed. diff --git a/prody/proteins/tabulated_energies.txt b/prody/proteins/tabulated_energies.txt new file mode 100644 index 000000000..009c8c1b5 --- /dev/null +++ b/prody/proteins/tabulated_energies.txt @@ -0,0 +1,400 @@ +GLY GLY -0.27 -1.77 0.0 +GLY ALA 0.08 -2.24 0.0 +GLY VAL 0.17 -2.77 0.0 +GLY ILE 0.05 -3.5 0.0 +GLY LEU 0.33 -3.79 0.0 +GLY CYS -0.26 -3.43 0.0 +GLY MET 0.31 -3.02 0.0 +GLY PHE -0.15 -3.76 0.0 +GLY TYR -0.21 -3.34 0.0 +GLY TRP -0.31 -3.77 0.0 +GLY SER 0.08 -1.68 0.0 +GLY THR -0.11 -1.81 0.0 +GLY ASP 0.11 -1.84 0.0 +GLY ASN -0.09 -1.63 0.0 +GLY GLU 0.5 -1.58 0.0 +GLY GLN -0.11 -3.02 0.0 +GLY LYS -0.17 -1.32 0.0 +GLY ARG -0.1 -2.71 0.0 +GLY HIS 0.01 -2.47 0.0 +GLY PRO 0.13 -1.01 0.0 +ALA GLY 0.08 -2.24 0.0 +ALA ALA -0.38 -3.51 0.0 +ALA VAL -0.11 -3.86 0.0 +ALA ILE -0.08 -4.45 0.0 +ALA LEU -0.09 -5.02 0.0 +ALA CYS 0.0 -3.99 0.0 +ALA MET -0.27 -4.42 0.0 +ALA PHE 0.01 -4.43 0.0 +ALA TYR 0.0 -3.96 0.0 +ALA TRP -0.38 -4.66 0.0 +ALA SER 0.08 -2.49 0.0 +ALA THR 0.14 -2.38 0.0 +ALA ASP 0.02 -2.74 0.0 +ALA ASN 0.31 -2.06 0.0 +ALA GLU 0.2 -2.69 0.0 +ALA GLN 0.08 -3.65 0.0 +ALA LYS 0.06 -1.91 0.0 +ALA ARG 0.16 -3.26 0.0 +ALA HIS 0.01 -3.29 0.0 +ALA PRO 0.19 -1.78 0.0 +VAL GLY 0.17 -2.77 0.0 +VAL ALA -0.11 -3.86 0.0 +VAL VAL -0.49 -4.86 -1.0 +VAL ILE -0.33 -5.31 -1.2 +VAL LEU -0.48 -6.03 -1.0 +VAL CYS -0.22 -4.82 -0.4 +VAL MET -0.4 -5.16 -0.6 +VAL PHE -0.27 -5.33 -1.2 +VAL TYR 0.03 -4.54 -0.8 +VAL TRP 0.2 -4.7 -1.0 +VAL SER 0.25 -2.95 -1.0 +VAL THR 0.27 -2.87 -0.7 +VAL ASP 0.11 -3.28 0.0 +VAL ASN 0.22 -2.76 -0.5 +VAL GLU 0.3 -3.2 -0.2 +VAL GLN 0.05 -4.29 -1.1 +VAL LYS 0.4 -2.19 -1.1 +VAL ARG 0.35 -3.7 0.0 +VAL HIS -0.23 -4.14 -1.1 +VAL PRO 0.16 -2.43 0.0 +ILE GLY 0.05 -3.5 0.0 +ILE ALA -0.08 -4.45 0.0 +ILE VAL -0.33 -5.31 -1.2 +ILE ILE -0.37 -5.97 -0.6 +ILE LEU -0.5 -6.67 -1.1 +ILE CYS -0.3 -5.53 -0.4 +ILE MET 0.0 -5.37 -0.7 +ILE PHE -0.44 -6.11 -0.5 +ILE TYR -0.12 -5.39 -0.5 +ILE TRP -0.26 -5.79 -1.0 +ILE SER 0.33 -3.47 -0.9 +ILE THR 0.14 -3.61 -0.7 +ILE ASP 0.54 -3.46 -0.2 +ILE ASN 0.16 -3.42 -0.5 +ILE GLU 0.13 -3.99 -0.2 +ILE GLN 0.33 -4.65 -0.6 +ILE LYS 0.32 -2.88 -1.1 +ILE ARG 0.37 -4.29 0.0 +ILE HIS -0.02 -4.55 -1.1 +ILE PRO 0.11 -3.09 0.0 +LEU GLY 0.33 -3.79 0.0 +LEU ALA -0.09 -5.02 0.0 +LEU VAL -0.48 -6.03 -1.0 +LEU ILE -0.5 -6.67 -1.1 +LEU LEU -0.42 -7.16 -0.8 +LEU CYS -0.34 -6.13 -0.4 +LEU MET -0.3 -6.24 -0.6 +LEU PHE -0.4 -6.65 -1.2 +LEU TYR 0.08 -5.67 -1.3 +LEU TRP -0.31 -6.4 -1.0 +LEU SER 0.26 -4.12 -0.9 +LEU THR 0.04 -4.28 -0.7 +LEU ASP 0.41 -4.16 -0.2 +LEU ASN 0.23 -3.94 -0.5 +LEU GLU 0.34 -4.35 -0.2 +LEU GLN 0.17 -5.36 -1.1 +LEU LYS 0.52 -3.24 -1.1 +LEU ARG 0.21 -5.01 0.0 +LEU HIS 0.25 -4.85 -1.1 +LEU PRO 0.01 -3.75 0.0 +CYS GLY -0.26 -3.43 0.0 +CYS ALA 0.0 -3.99 0.0 +CYS VAL -0.22 -4.82 -0.4 +CYS ILE -0.3 -5.53 -0.4 +CYS LEU -0.34 -6.13 -0.4 +CYS CYS -2.38 -7.23 0.0 +CYS MET -0.08 -5.07 -0.4 +CYS PHE 0.49 -4.81 -1.3 +CYS TYR 0.1 -4.71 -1.3 +CYS TRP 0.44 4.7 -0.6 +CYS SER 0.02 -3.41 0.0 +CYS THR 0.46 -2.92 -0.8 +CYS ASP 0.06 -3.56 -0.2 +CYS ASN 1.46 -1.76 -0.9 +CYS GLU 0.72 -3.02 -0.2 +CYS GLN 0.21 -4.37 -0.9 +CYS LYS -0.5 -2.28 -0.2 +CYS ARG -0.12 -4.41 -0.2 +CYS HIS -0.64 -4.79 -0.8 +CYS PRO -0.15 -2.97 0.0 +MET GLY 0.31 -3.02 0.0 +MET ALA -0.27 -4.42 0.0 +MET VAL -0.4 -5.16 -0.6 +MET ILE 0.0 -5.37 -0.7 +MET LEU -0.3 -6.24 -0.6 +MET CYS -0.08 -5.07 -0.4 +MET MET -0.74 -5.89 -0.7 +MET PHE -0.14 -5.58 -0.8 +MET TYR -0.05 -5.01 -1.2 +MET TRP -0.2 -5.49 -1.0 +MET SER 0.25 -3.33 -0.6 +MET THR 0.19 -3.33 -1.0 +MET ASP 0.09 -3.69 0.0 +MET ASN 0.32 -3.05 -0.8 +MET GLU 0.13 -3.76 -0.2 +MET GLN 0.27 -4.46 -0.5 +MET LYS 0.61 -2.36 0.0 +MET ARG 0.3 -4.13 -0.8 +MET HIS -0.17 -4.47 -0.5 +MET PRO -0.14 -3.11 0.0 +PHE GLY -0.15 -3.76 0.0 +PHE ALA 0.01 -4.43 0.0 +PHE VAL -0.27 -5.33 -1.2 +PHE ILE -0.44 -6.11 -0.5 +PHE LEU -0.4 -6.65 -1.2 +PHE CYS 0.49 -4.81 -1.3 +PHE MET -0.14 -5.58 -0.8 +PHE PHE -0.71 -6.45 -1.2 +PHE TYR -0.07 -5.33 -1.2 +PHE TRP -0.13 -5.72 -1.2 +PHE SER -0.14 -4.01 -0.6 +PHE THR -0.02 -3.85 0.0 +PHE ASP 0.55 -3.52 0.0 +PHE ASN -0.22 -3.89 -0.2 +PHE GLU 0.09 -4.1 -0.4 +PHE GLN 0.14 -4.89 -1.7 +PHE LYS 0.57 -2.7 -0.9 +PHE ARG 0.22 -4.51 -1.1 +PHE HIS 0.79 -3.82 -0.6 +PHE PRO -0.19 -3.46 0.0 +TYR GLY -0.21 -3.34 0.0 +TYR ALA 0.0 -3.96 0.0 +TYR VAL 0.03 -4.54 -0.8 +TYR ILE -0.12 -5.39 -0.5 +TYR LEU 0.08 -5.67 -1.3 +TYR CYS 0.1 -4.71 -1.3 +TYR MET -0.05 -5.01 -1.2 +TYR PHE -0.07 -5.33 -1.2 +TYR TYR 0.2 -4.58 -1.5 +TYR TRP -0.02 -5.12 -1.2 +TYR SER -0.03 -3.43 -0.2 +TYR THR 0.0 -3.33 -0.6 +TYR ASP -0.04 -3.63 -0.6 +TYR ASN 0.04 -3.14 0.0 +TYR GLU 0.08 -3.62 -0.6 +TYR GLN -0.21 -4.75 -0.7 +TYR LYS 0.14 -2.64 -0.1 +TYR ARG -0.07 -4.32 -2.1 +TYR HIS 0.34 -3.78 -1.1 +TYR PRO -0.13 -2.92 0.0 +TRP GLY -0.31 -3.77 0.0 +TRP ALA -0.38 -4.66 0.0 +TRP VAL 0.2 -4.7 -1.0 +TRP ILE -0.26 -5.79 -1.0 +TRP LEU -0.31 -6.4 -1.0 +TRP CYS 0.44 4.7 -0.6 +TRP MET -0.2 -5.49 -1.0 +TRP PHE -0.13 -5.72 -1.2 +TRP TYR -0.02 -5.12 -1.2 +TRP TRP 0.27 -5.16 -1.2 +TRP SER 0.86 -2.86 -0.9 +TRP THR 0.18 -3.48 -0.9 +TRP ASP 0.11 -3.81 -0.5 +TRP ASN 0.2 -3.31 -1.3 +TRP GLU 0.2 -3.84 -0.5 +TRP GLN 0.01 -4.87 -1.3 +TRP LYS 1.0 -3.12 -1.2 +TRP ARG 0.04 -4.54 -1.8 +TRP HIS -0.05 -4.5 -1.7 +TRP PRO -0.85 -3.96 0.0 +SER GLY 0.08 -1.68 0.0 +SER ALA 0.08 -2.49 0.0 +SER VAL 0.25 -2.95 -1.0 +SER ILE 0.33 -3.47 -0.9 +SER LEU 0.26 -4.12 -0.9 +SER CYS 0.02 -3.41 0.0 +SER MET 0.25 -3.33 -0.6 +SER PHE -0.14 -4.01 -0.6 +SER TYR -0.03 -3.43 -0.2 +SER TRP 0.86 -2.86 -0.9 +SER SER -0.14 -2.14 -0.4 +SER THR -0.27 -2.22 -0.9 +SER ASP -0.13 -2.34 -0.2 +SER ASN -0.32 -2.13 0.2 +SER GLU -0.25 -2.57 -0.2 +SER GLN 0.1 -3.06 0.2 +SER LYS -0.5 -1.91 -1.2 +SER ARG 0.08 -2.78 -0.1 +SER HIS -0.38 -3.12 -0.5 +SER PRO -0.15 -1.56 0.0 +THR GLY -0.11 -1.81 0.0 +THR ALA 0.14 -2.38 0.0 +THR VAL 0.27 -2.87 -0.7 +THR ILE 0.14 -3.61 -0.7 +THR LEU 0.04 -4.28 -0.7 +THR CYS 0.46 -2.92 -0.8 +THR MET 0.19 -3.33 -1.0 +THR PHE -0.02 -3.85 0.0 +THR TYR 0.0 -3.33 -0.6 +THR TRP 0.18 -3.48 -0.9 +THR SER -0.27 -2.22 -0.9 +THR THR -0.22 -2.12 -0.9 +THR ASP -0.26 -2.41 -0.2 +THR ASN -0.3 -2.05 0.2 +THR GLU -0.07 -2.34 -0.5 +THR GLN -0.32 -3.44 0.2 +THR LYS -0.29 -1.64 -1.2 +THR ARG 0.38 -2.43 0.4 +THR HIS -0.05 -2.73 -0.5 +THR PRO 0.11 -1.24 0.0 +ASP GLY 0.11 -1.84 0.0 +ASP ALA 0.02 -2.74 0.0 +ASP VAL 0.11 -3.28 0.0 +ASP ILE 0.54 -3.46 -0.2 +ASP LEU 0.41 -4.16 -0.2 +ASP CYS 0.06 -3.56 -0.2 +ASP MET 0.09 -3.69 0.0 +ASP PHE 0.55 -3.52 0.0 +ASP TYR -0.04 -3.63 -0.6 +ASP TRP 0.11 -3.81 -0.5 +ASP SER -0.13 -2.34 -0.2 +ASP THR -0.26 -2.41 -0.2 +ASP ASP -0.07 -2.47 0.3 +ASP ASN -0.51 -2.5 -0.2 +ASP GLU 0.17 -2.35 0.3 +ASP GLN 0.21 -3.15 -0.2 +ASP LYS -0.87 -2.47 -1.4 +ASP ARG -0.87 -3.92 -1.4 +ASP HIS 0.0 -2.93 -0.4 +ASP PRO 0.36 -1.24 0.0 +ASN GLY -0.09 -1.63 0.0 +ASN ALA 0.31 -2.06 0.0 +ASN VAL 0.22 -2.76 -0.5 +ASN ILE 0.16 -3.42 -0.5 +ASN LEU 0.23 -3.94 -0.5 +ASN CYS 1.46 -1.76 -0.9 +ASN MET 0.32 -3.05 -0.8 +ASN PHE -0.22 -3.89 -0.2 +ASN TYR 0.04 -3.14 0.0 +ASN TRP 0.2 -3.31 -1.3 +ASN SER -0.32 -2.13 0.2 +ASN THR -0.3 -2.05 0.2 +ASN ASP -0.51 -2.5 -0.2 +ASN ASN -0.4 -1.99 -0.1 +ASN GLU -0.3 -2.43 0.1 +ASN GLN -0.05 -3.0 -0.1 +ASN LYS -0.44 -1.63 0.1 +ASN ARG -0.02 -2.67 0.2 +ASN HIS -0.52 -3.05 -1.2 +ASN PRO 0.19 -1.01 0.0 +GLU GLY 0.5 -1.58 0.0 +GLU ALA 0.2 -2.69 0.0 +GLU VAL 0.3 -3.2 -0.2 +GLU ILE 0.13 -3.99 -0.2 +GLU LEU 0.34 -4.35 -0.2 +GLU CYS 0.72 -3.02 -0.2 +GLU MET 0.13 -3.76 -0.2 +GLU PHE 0.09 -4.1 -0.4 +GLU TYR 0.08 -3.62 -0.6 +GLU TRP 0.2 -3.84 -0.5 +GLU SER -0.25 -2.57 -0.2 +GLU THR -0.07 -2.34 -0.5 +GLU ASP 0.17 -2.35 0.3 +GLU ASN -0.3 -2.43 0.1 +GLU GLU -0.2 -2.85 0.3 +GLU GLN 0.03 -3.45 0.1 +GLU LYS -1.11 -2.83 -1.0 +GLU ARG -0.87 -4.05 -1.6 +GLU HIS -0.1 -3.15 -0.4 +GLU PRO 0.01 -1.7 0.0 +GLN GLY -0.11 -3.02 0.0 +GLN ALA 0.08 -3.65 0.0 +GLN VAL 0.05 -4.29 -1.1 +GLN ILE 0.33 -4.65 -0.6 +GLN LEU 0.17 -5.36 -1.1 +GLN CYS 0.21 -4.37 -0.9 +GLN MET 0.27 -4.46 -0.5 +GLN PHE 0.14 -4.89 -1.7 +GLN TYR -0.21 -4.75 -0.7 +GLN TRP 0.01 -4.87 -1.3 +GLN SER 0.1 -3.06 0.2 +GLN THR -0.32 -3.44 0.2 +GLN ASP 0.21 -3.15 -0.2 +GLN ASN -0.05 -3.0 -0.1 +GLN GLU 0.03 -3.45 0.1 +GLN GLN -0.38 -4.71 -0.1 +GLN LYS 0.0 -2.56 0.1 +GLN ARG -0.11 -4.13 0.2 +GLN HIS -0.31 -4.2 -1.2 +GLN PRO -0.11 -2.67 0.0 +LYS GLY -0.17 -1.32 0.0 +LYS ALA 0.06 -1.91 0.0 +LYS VAL 0.4 -2.19 -1.1 +LYS ILE 0.32 -2.88 -1.1 +LYS LEU 0.52 -3.24 -1.1 +LYS CYS -0.5 -2.28 -0.2 +LYS MET 0.61 -2.36 0.0 +LYS PHE 0.57 -2.7 -0.9 +LYS TYR 0.14 -2.64 -0.1 +LYS TRP 1.0 -3.12 -1.2 +LYS SER -0.5 -1.91 -1.2 +LYS THR -0.29 -1.64 -1.2 +LYS ASP -0.87 -2.47 -1.4 +LYS ASN -0.44 -1.63 0.1 +LYS GLU -1.11 -2.83 -1.0 +LYS GLN 0.0 -2.56 0.1 +LYS LYS -0.22 -1.02 0.2 +LYS ARG 0.15 -2.11 0.0 +LYS HIS -0.01 -2.14 0.0 +LYS PRO 0.3 -0.5 0.0 +ARG GLY -0.1 -2.71 0.0 +ARG ALA 0.16 -3.26 0.0 +ARG VAL 0.35 -3.7 0.0 +ARG ILE 0.37 -4.29 0.0 +ARG LEU 0.21 -5.01 0.0 +ARG CYS -0.12 -4.41 -0.2 +ARG MET 0.3 -4.13 -0.8 +ARG PHE 0.22 -4.51 -1.1 +ARG TYR -0.07 -4.32 -2.1 +ARG TRP 0.04 -4.54 -1.8 +ARG SER 0.08 -2.78 -0.1 +ARG THR 0.38 -2.43 0.4 +ARG ASP -0.87 -3.92 -1.4 +ARG ASN -0.02 -2.67 0.2 +ARG GLU -0.87 -4.05 -1.6 +ARG GLN -0.11 -4.13 0.2 +ARG LYS 0.15 -2.11 0.0 +ARG ARG -0.26 -3.98 -0.6 +ARG HIS 0.35 -3.24 -0.4 +ARG PRO -0.17 -2.43 0.0 +HIS GLY 0.01 -2.47 0.0 +HIS ALA 0.01 -3.29 0.0 +HIS VAL -0.23 -4.14 -1.1 +HIS ILE -0.02 -4.55 -1.1 +HIS LEU 0.25 -4.85 -1.1 +HIS CYS -0.64 -4.79 -0.8 +HIS MET -0.17 -4.47 -0.5 +HIS PHE 0.79 -3.82 -0.6 +HIS TYR 0.34 -3.78 -1.1 +HIS TRP -0.05 -4.5 -1.7 +HIS SER -0.38 -3.12 -0.5 +HIS THR -0.05 -2.73 -0.5 +HIS ASP 0.0 -2.93 -0.4 +HIS ASN -0.52 -3.05 -1.2 +HIS GLU -0.1 -3.15 -0.4 +HIS GLN -0.31 -4.2 -1.2 +HIS LYS -0.01 -2.14 0.0 +HIS ARG 0.35 -3.24 -0.4 +HIS HIS 0.38 -3.08 -0.5 +HIS PRO 0.33 -1.8 0.0 +PRO GLY 0.13 -1.01 0.0 +PRO ALA 0.19 -1.78 0.0 +PRO VAL 0.16 -2.43 0.0 +PRO ILE 0.11 -3.09 0.0 +PRO LEU 0.01 -3.75 0.0 +PRO CYS -0.15 -2.97 0.0 +PRO MET -0.14 -3.11 0.0 +PRO PHE -0.19 -3.46 0.0 +PRO TYR -0.13 -2.92 0.0 +PRO TRP -0.85 -3.96 0.0 +PRO SER -0.15 -1.56 0.0 +PRO THR 0.11 -1.24 0.0 +PRO ASP 0.36 -1.24 0.0 +PRO ASN 0.19 -1.01 0.0 +PRO GLU 0.01 -1.7 0.0 +PRO GLN -0.11 -2.67 0.0 +PRO LYS 0.3 -0.5 0.0 +PRO ARG -0.17 -2.43 0.0 +PRO HIS 0.33 -1.8 0.0 +PRO PRO -0.03 -0.83 0.0