propy.QuasiSequenceOrder

Compute the quasi sequence order descriptors based on the given protein sequence. We can obtain two types of descriptors: Sequence-order-coupling number and quasi-sequence-order descriptors. Two distance matrixes between 20 amino acids are employed.

References

[1](1, 2) Kuo-Chen Chou. Prediction of Protein Subcellar Locations by Incorporating Quasi-Sequence-Order Effect. Biochemical and Biophysical Research Communications 2000, 278, 477-483.
[2]Kuo-Chen Chou and Yu-Dong Cai. Prediction of Protein sucellular locations by GO-FunD-PseAA predictor, Biochemical and Biophysical Research Communications, 2004, 320, 1236-1239.
[3]Gisbert Schneider and Paul wrede. The Rational Design of Amino Acid Sequences by Artifical Neural Networks and Simulated Molecular Evolution: Do Novo Design of an Idealized Leader Cleavge Site. Biophys Journal, 1994, 66, 335-344.

Authors: Dongsheng Cao and Yizeng Liang. Date: 2012.09.03 Email: oriental-cds@163.com

propy.QuasiSequenceOrder.GetAAComposition(ProteinSequence: str) → Dict[str, float][source]

Calculate the composition of Amino acids for a given protein sequence.

Parameters:ProteinSequence (str) – a pure protein sequence
Returns:result – contains the composition of 20 amino acids.
Return type:Dict[str, float]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> from propy.AAComposition import CalculateAAComposition
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = CalculateAAComposition(protein)
propy.QuasiSequenceOrder.GetQuasiSequenceOrder(ProteinSequence: str, maxlag: int = 30, weight: float = 0.1) → Dict[Any, Any][source]

Compute quasi-sequence-order descriptors for a given protein.

See [1] for details.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger than maxlag
  • weight (float, optional (default: 0.1)) – a weight factor. Please see reference 1 for its choice.
Returns:

result – contains all quasi-sequence-order descriptors

Return type:

Dict

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetQuasiSequenceOrder(protein)
propy.QuasiSequenceOrder.GetQuasiSequenceOrder1(ProteinSequence: str, maxlag: int = 30, weight: float = 0.1, distancematrix=None)[source]

Compute the first 20 quasi-sequence-order descriptors for a given protein sequence.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetQuasiSequenceOrder1(protein)

see GetQuasiSequenceOrder() for the choice of parameters.

propy.QuasiSequenceOrder.GetQuasiSequenceOrder1Grant(ProteinSequence: str, maxlag: int = 30, weight: float = 0.1, distancematrix={'AA': 0.0, 'AC': 0.112, 'AD': 0.819, 'AE': 0.827, 'AF': 0.54, 'AG': 0.208, 'AH': 0.696, 'AI': 0.407, 'AK': 0.891, 'AL': 0.406, 'AM': 0.379, 'AN': 0.318, 'AP': 0.191, 'AQ': 0.372, 'AR': 1.0, 'AS': 0.094, 'AT': 0.22, 'AV': 0.273, 'AW': 0.739, 'AY': 0.552, 'CA': 0.114, 'CC': 0.0, 'CD': 0.847, 'CE': 0.838, 'CF': 0.437, 'CG': 0.32, 'CH': 0.66, 'CI': 0.304, 'CK': 0.887, 'CL': 0.301, 'CM': 0.277, 'CN': 0.324, 'CP': 0.157, 'CQ': 0.341, 'CR': 1.0, 'CS': 0.176, 'CT': 0.233, 'CV': 0.167, 'CW': 0.639, 'CY': 0.457, 'DA': 0.729, 'DC': 0.742, 'DD': 0.0, 'DE': 0.124, 'DF': 0.924, 'DG': 0.697, 'DH': 0.435, 'DI': 0.847, 'DK': 0.249, 'DL': 0.841, 'DM': 0.819, 'DN': 0.56, 'DP': 0.657, 'DQ': 0.584, 'DR': 0.295, 'DS': 0.667, 'DT': 0.649, 'DV': 0.797, 'DW': 1.0, 'DY': 0.836, 'EA': 0.79, 'EC': 0.788, 'ED': 0.133, 'EE': 0.0, 'EF': 0.932, 'EG': 0.779, 'EH': 0.406, 'EI': 0.86, 'EK': 0.143, 'EL': 0.854, 'EM': 0.83, 'EN': 0.599, 'EP': 0.688, 'EQ': 0.598, 'ER': 0.234, 'ES': 0.726, 'ET': 0.682, 'EV': 0.824, 'EW': 1.0, 'EY': 0.837, 'FA': 0.508, 'FC': 0.405, 'FD': 0.977, 'FE': 0.918, 'FF': 0.0, 'FG': 0.69, 'FH': 0.663, 'FI': 0.128, 'FK': 0.903, 'FL': 0.131, 'FM': 0.169, 'FN': 0.541, 'FP': 0.42, 'FQ': 0.459, 'FR': 1.0, 'FS': 0.548, 'FT': 0.499, 'FV': 0.252, 'FW': 0.207, 'FY': 0.179, 'GA': 0.206, 'GC': 0.312, 'GD': 0.776, 'GE': 0.807, 'GF': 0.727, 'GG': 0.0, 'GH': 0.769, 'GI': 0.592, 'GK': 0.894, 'GL': 0.591, 'GM': 0.557, 'GN': 0.381, 'GP': 0.323, 'GQ': 0.467, 'GR': 1.0, 'GS': 0.158, 'GT': 0.272, 'GV': 0.464, 'GW': 0.923, 'GY': 0.728, 'HA': 0.896, 'HC': 0.836, 'HD': 0.629, 'HE': 0.547, 'HF': 0.907, 'HG': 1.0, 'HH': 0.0, 'HI': 0.848, 'HK': 0.566, 'HL': 0.842, 'HM': 0.825, 'HN': 0.754, 'HP': 0.777, 'HQ': 0.716, 'HR': 0.697, 'HS': 0.865, 'HT': 0.834, 'HV': 0.831, 'HW': 0.981, 'HY': 0.821, 'IA': 0.403, 'IC': 0.296, 'ID': 0.942, 'IE': 0.891, 'IF': 0.134, 'IG': 0.592, 'IH': 0.652, 'II': 0.0, 'IK': 0.892, 'IL': 0.013, 'IM': 0.057, 'IN': 0.457, 'IP': 0.311, 'IQ': 0.383, 'IR': 1.0, 'IS': 0.443, 'IT': 0.396, 'IV': 0.133, 'IW': 0.339, 'IY': 0.213, 'KA': 0.889, 'KC': 0.871, 'KD': 0.279, 'KE': 0.149, 'KF': 0.957, 'KG': 0.9, 'KH': 0.438, 'KI': 0.899, 'KK': 0.0, 'KL': 0.892, 'KM': 0.871, 'KN': 0.667, 'KP': 0.757, 'KQ': 0.639, 'KR': 0.154, 'KS': 0.825, 'KT': 0.759, 'KV': 0.882, 'KW': 1.0, 'KY': 0.848, 'LA': 0.405, 'LC': 0.296, 'LD': 0.944, 'LE': 0.892, 'LF': 0.139, 'LG': 0.596, 'LH': 0.653, 'LI': 0.013, 'LK': 0.893, 'LL': 0.0, 'LM': 0.062, 'LN': 0.452, 'LP': 0.309, 'LQ': 0.376, 'LR': 1.0, 'LS': 0.443, 'LT': 0.397, 'LV': 0.133, 'LW': 0.341, 'LY': 0.205, 'MA': 0.383, 'MC': 0.276, 'MD': 0.932, 'ME': 0.879, 'MF': 0.182, 'MG': 0.569, 'MH': 0.648, 'MI': 0.058, 'MK': 0.884, 'ML': 0.062, 'MM': 0.0, 'MN': 0.447, 'MP': 0.285, 'MQ': 0.372, 'MR': 1.0, 'MS': 0.417, 'MT': 0.358, 'MV': 0.12, 'MW': 0.391, 'MY': 0.255, 'NA': 0.424, 'NC': 0.425, 'ND': 0.838, 'NE': 0.835, 'NF': 0.766, 'NG': 0.512, 'NH': 0.78, 'NI': 0.615, 'NK': 0.891, 'NL': 0.603, 'NM': 0.588, 'NN': 0.0, 'NP': 0.266, 'NQ': 0.175, 'NR': 1.0, 'NS': 0.361, 'NT': 0.368, 'NV': 0.503, 'NW': 0.945, 'NY': 0.641, 'PA': 0.22, 'PC': 0.179, 'PD': 0.852, 'PE': 0.831, 'PF': 0.515, 'PG': 0.376, 'PH': 0.696, 'PI': 0.363, 'PK': 0.875, 'PL': 0.357, 'PM': 0.326, 'PN': 0.231, 'PP': 0.0, 'PQ': 0.228, 'PR': 1.0, 'PS': 0.196, 'PT': 0.161, 'PV': 0.244, 'PW': 0.72, 'PY': 0.481, 'QA': 0.512, 'QC': 0.462, 'QD': 0.903, 'QE': 0.861, 'QF': 0.671, 'QG': 0.648, 'QH': 0.765, 'QI': 0.532, 'QK': 0.881, 'QL': 0.518, 'QM': 0.505, 'QN': 0.181, 'QP': 0.272, 'QQ': 0.0, 'QR': 1.0, 'QS': 0.461, 'QT': 0.389, 'QV': 0.464, 'QW': 0.831, 'QY': 0.522, 'RA': 0.919, 'RC': 0.905, 'RD': 0.305, 'RE': 0.225, 'RF': 0.977, 'RG': 0.928, 'RH': 0.498, 'RI': 0.929, 'RK': 0.141, 'RL': 0.92, 'RM': 0.908, 'RN': 0.69, 'RP': 0.796, 'RQ': 0.668, 'RR': 0.0, 'RS': 0.86, 'RT': 0.808, 'RV': 0.914, 'RW': 1.0, 'RY': 0.859, 'SA': 0.1, 'SC': 0.185, 'SD': 0.801, 'SE': 0.812, 'SF': 0.622, 'SG': 0.17, 'SH': 0.718, 'SI': 0.478, 'SK': 0.883, 'SL': 0.474, 'SM': 0.44, 'SN': 0.289, 'SP': 0.181, 'SQ': 0.358, 'SR': 1.0, 'SS': 0.0, 'ST': 0.174, 'SV': 0.342, 'SW': 0.827, 'SY': 0.615, 'TA': 0.251, 'TC': 0.261, 'TD': 0.83, 'TE': 0.812, 'TF': 0.604, 'TG': 0.312, 'TH': 0.737, 'TI': 0.455, 'TK': 0.866, 'TL': 0.453, 'TM': 0.403, 'TN': 0.315, 'TP': 0.159, 'TQ': 0.322, 'TR': 1.0, 'TS': 0.185, 'TT': 0.0, 'TV': 0.345, 'TW': 0.816, 'TY': 0.596, 'VA': 0.275, 'VC': 0.165, 'VD': 0.9, 'VE': 0.867, 'VF': 0.269, 'VG': 0.471, 'VH': 0.649, 'VI': 0.135, 'VK': 0.889, 'VL': 0.134, 'VM': 0.12, 'VN': 0.38, 'VP': 0.212, 'VQ': 0.339, 'VR': 1.0, 'VS': 0.322, 'VT': 0.305, 'VV': 0.0, 'VW': 0.472, 'VY': 0.31, 'WA': 0.658, 'WC': 0.56, 'WD': 1.0, 'WE': 0.931, 'WF': 0.196, 'WG': 0.829, 'WH': 0.678, 'WI': 0.305, 'WK': 0.892, 'WL': 0.304, 'WM': 0.344, 'WN': 0.631, 'WP': 0.555, 'WQ': 0.538, 'WR': 0.968, 'WS': 0.689, 'WT': 0.638, 'WV': 0.418, 'WW': 0.0, 'WY': 0.204, 'YA': 0.587, 'YC': 0.478, 'YD': 1.0, 'YE': 0.932, 'YF': 0.202, 'YG': 0.782, 'YH': 0.678, 'YI': 0.23, 'YK': 0.904, 'YL': 0.219, 'YM': 0.268, 'YN': 0.512, 'YP': 0.444, 'YQ': 0.404, 'YR': 0.995, 'YS': 0.612, 'YT': 0.557, 'YV': 0.328, 'YW': 0.244, 'YY': 0.0})[source]

Compute the first 20 quasi-sequence-order descriptors for a given protein sequence.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetQuasiSequenceOrder1Grant(protein)

see GetQuasiSequenceOrder() for the choice of parameters.

propy.QuasiSequenceOrder.GetQuasiSequenceOrder1SW(ProteinSequence: str, maxlag=30, weight=0.1, distancematrix={'AA': 0.0, 'AC': 0.112, 'AD': 0.819, 'AE': 0.827, 'AF': 0.54, 'AG': 0.208, 'AH': 0.696, 'AI': 0.407, 'AK': 0.891, 'AL': 0.406, 'AM': 0.379, 'AN': 0.318, 'AP': 0.191, 'AQ': 0.372, 'AR': 1.0, 'AS': 0.094, 'AT': 0.22, 'AV': 0.273, 'AW': 0.739, 'AY': 0.552, 'CA': 0.114, 'CC': 0.0, 'CD': 0.847, 'CE': 0.838, 'CF': 0.437, 'CG': 0.32, 'CH': 0.66, 'CI': 0.304, 'CK': 0.887, 'CL': 0.301, 'CM': 0.277, 'CN': 0.324, 'CP': 0.157, 'CQ': 0.341, 'CR': 1.0, 'CS': 0.176, 'CT': 0.233, 'CV': 0.167, 'CW': 0.639, 'CY': 0.457, 'DA': 0.729, 'DC': 0.742, 'DD': 0.0, 'DE': 0.124, 'DF': 0.924, 'DG': 0.697, 'DH': 0.435, 'DI': 0.847, 'DK': 0.249, 'DL': 0.841, 'DM': 0.819, 'DN': 0.56, 'DP': 0.657, 'DQ': 0.584, 'DR': 0.295, 'DS': 0.667, 'DT': 0.649, 'DV': 0.797, 'DW': 1.0, 'DY': 0.836, 'EA': 0.79, 'EC': 0.788, 'ED': 0.133, 'EE': 0.0, 'EF': 0.932, 'EG': 0.779, 'EH': 0.406, 'EI': 0.86, 'EK': 0.143, 'EL': 0.854, 'EM': 0.83, 'EN': 0.599, 'EP': 0.688, 'EQ': 0.598, 'ER': 0.234, 'ES': 0.726, 'ET': 0.682, 'EV': 0.824, 'EW': 1.0, 'EY': 0.837, 'FA': 0.508, 'FC': 0.405, 'FD': 0.977, 'FE': 0.918, 'FF': 0.0, 'FG': 0.69, 'FH': 0.663, 'FI': 0.128, 'FK': 0.903, 'FL': 0.131, 'FM': 0.169, 'FN': 0.541, 'FP': 0.42, 'FQ': 0.459, 'FR': 1.0, 'FS': 0.548, 'FT': 0.499, 'FV': 0.252, 'FW': 0.207, 'FY': 0.179, 'GA': 0.206, 'GC': 0.312, 'GD': 0.776, 'GE': 0.807, 'GF': 0.727, 'GG': 0.0, 'GH': 0.769, 'GI': 0.592, 'GK': 0.894, 'GL': 0.591, 'GM': 0.557, 'GN': 0.381, 'GP': 0.323, 'GQ': 0.467, 'GR': 1.0, 'GS': 0.158, 'GT': 0.272, 'GV': 0.464, 'GW': 0.923, 'GY': 0.728, 'HA': 0.896, 'HC': 0.836, 'HD': 0.629, 'HE': 0.547, 'HF': 0.907, 'HG': 1.0, 'HH': 0.0, 'HI': 0.848, 'HK': 0.566, 'HL': 0.842, 'HM': 0.825, 'HN': 0.754, 'HP': 0.777, 'HQ': 0.716, 'HR': 0.697, 'HS': 0.865, 'HT': 0.834, 'HV': 0.831, 'HW': 0.981, 'HY': 0.821, 'IA': 0.403, 'IC': 0.296, 'ID': 0.942, 'IE': 0.891, 'IF': 0.134, 'IG': 0.592, 'IH': 0.652, 'II': 0.0, 'IK': 0.892, 'IL': 0.013, 'IM': 0.057, 'IN': 0.457, 'IP': 0.311, 'IQ': 0.383, 'IR': 1.0, 'IS': 0.443, 'IT': 0.396, 'IV': 0.133, 'IW': 0.339, 'IY': 0.213, 'KA': 0.889, 'KC': 0.871, 'KD': 0.279, 'KE': 0.149, 'KF': 0.957, 'KG': 0.9, 'KH': 0.438, 'KI': 0.899, 'KK': 0.0, 'KL': 0.892, 'KM': 0.871, 'KN': 0.667, 'KP': 0.757, 'KQ': 0.639, 'KR': 0.154, 'KS': 0.825, 'KT': 0.759, 'KV': 0.882, 'KW': 1.0, 'KY': 0.848, 'LA': 0.405, 'LC': 0.296, 'LD': 0.944, 'LE': 0.892, 'LF': 0.139, 'LG': 0.596, 'LH': 0.653, 'LI': 0.013, 'LK': 0.893, 'LL': 0.0, 'LM': 0.062, 'LN': 0.452, 'LP': 0.309, 'LQ': 0.376, 'LR': 1.0, 'LS': 0.443, 'LT': 0.397, 'LV': 0.133, 'LW': 0.341, 'LY': 0.205, 'MA': 0.383, 'MC': 0.276, 'MD': 0.932, 'ME': 0.879, 'MF': 0.182, 'MG': 0.569, 'MH': 0.648, 'MI': 0.058, 'MK': 0.884, 'ML': 0.062, 'MM': 0.0, 'MN': 0.447, 'MP': 0.285, 'MQ': 0.372, 'MR': 1.0, 'MS': 0.417, 'MT': 0.358, 'MV': 0.12, 'MW': 0.391, 'MY': 0.255, 'NA': 0.424, 'NC': 0.425, 'ND': 0.838, 'NE': 0.835, 'NF': 0.766, 'NG': 0.512, 'NH': 0.78, 'NI': 0.615, 'NK': 0.891, 'NL': 0.603, 'NM': 0.588, 'NN': 0.0, 'NP': 0.266, 'NQ': 0.175, 'NR': 1.0, 'NS': 0.361, 'NT': 0.368, 'NV': 0.503, 'NW': 0.945, 'NY': 0.641, 'PA': 0.22, 'PC': 0.179, 'PD': 0.852, 'PE': 0.831, 'PF': 0.515, 'PG': 0.376, 'PH': 0.696, 'PI': 0.363, 'PK': 0.875, 'PL': 0.357, 'PM': 0.326, 'PN': 0.231, 'PP': 0.0, 'PQ': 0.228, 'PR': 1.0, 'PS': 0.196, 'PT': 0.161, 'PV': 0.244, 'PW': 0.72, 'PY': 0.481, 'QA': 0.512, 'QC': 0.462, 'QD': 0.903, 'QE': 0.861, 'QF': 0.671, 'QG': 0.648, 'QH': 0.765, 'QI': 0.532, 'QK': 0.881, 'QL': 0.518, 'QM': 0.505, 'QN': 0.181, 'QP': 0.272, 'QQ': 0.0, 'QR': 1.0, 'QS': 0.461, 'QT': 0.389, 'QV': 0.464, 'QW': 0.831, 'QY': 0.522, 'RA': 0.919, 'RC': 0.905, 'RD': 0.305, 'RE': 0.225, 'RF': 0.977, 'RG': 0.928, 'RH': 0.498, 'RI': 0.929, 'RK': 0.141, 'RL': 0.92, 'RM': 0.908, 'RN': 0.69, 'RP': 0.796, 'RQ': 0.668, 'RR': 0.0, 'RS': 0.86, 'RT': 0.808, 'RV': 0.914, 'RW': 1.0, 'RY': 0.859, 'SA': 0.1, 'SC': 0.185, 'SD': 0.801, 'SE': 0.812, 'SF': 0.622, 'SG': 0.17, 'SH': 0.718, 'SI': 0.478, 'SK': 0.883, 'SL': 0.474, 'SM': 0.44, 'SN': 0.289, 'SP': 0.181, 'SQ': 0.358, 'SR': 1.0, 'SS': 0.0, 'ST': 0.174, 'SV': 0.342, 'SW': 0.827, 'SY': 0.615, 'TA': 0.251, 'TC': 0.261, 'TD': 0.83, 'TE': 0.812, 'TF': 0.604, 'TG': 0.312, 'TH': 0.737, 'TI': 0.455, 'TK': 0.866, 'TL': 0.453, 'TM': 0.403, 'TN': 0.315, 'TP': 0.159, 'TQ': 0.322, 'TR': 1.0, 'TS': 0.185, 'TT': 0.0, 'TV': 0.345, 'TW': 0.816, 'TY': 0.596, 'VA': 0.275, 'VC': 0.165, 'VD': 0.9, 'VE': 0.867, 'VF': 0.269, 'VG': 0.471, 'VH': 0.649, 'VI': 0.135, 'VK': 0.889, 'VL': 0.134, 'VM': 0.12, 'VN': 0.38, 'VP': 0.212, 'VQ': 0.339, 'VR': 1.0, 'VS': 0.322, 'VT': 0.305, 'VV': 0.0, 'VW': 0.472, 'VY': 0.31, 'WA': 0.658, 'WC': 0.56, 'WD': 1.0, 'WE': 0.931, 'WF': 0.196, 'WG': 0.829, 'WH': 0.678, 'WI': 0.305, 'WK': 0.892, 'WL': 0.304, 'WM': 0.344, 'WN': 0.631, 'WP': 0.555, 'WQ': 0.538, 'WR': 0.968, 'WS': 0.689, 'WT': 0.638, 'WV': 0.418, 'WW': 0.0, 'WY': 0.204, 'YA': 0.587, 'YC': 0.478, 'YD': 1.0, 'YE': 0.932, 'YF': 0.202, 'YG': 0.782, 'YH': 0.678, 'YI': 0.23, 'YK': 0.904, 'YL': 0.219, 'YM': 0.268, 'YN': 0.512, 'YP': 0.444, 'YQ': 0.404, 'YR': 0.995, 'YS': 0.612, 'YT': 0.557, 'YV': 0.328, 'YW': 0.244, 'YY': 0.0})[source]

Compute the first 20 quasi-sequence-order descriptors for a given protein sequence.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetQuasiSequenceOrder1SW(protein)

see GetQuasiSequenceOrder() for the choice of parameters.

propy.QuasiSequenceOrder.GetQuasiSequenceOrder2(ProteinSequence: str, maxlag=30, weight=0.1, distancematrix=None)[source]

Compute the last maxlag quasi-sequence-order descriptors for a given protein sequence.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetQuasiSequenceOrder2(protein)

see GetQuasiSequenceOrder() for the choice of parameters.

propy.QuasiSequenceOrder.GetQuasiSequenceOrder2Grant(ProteinSequence: str, maxlag: int = 30, weight: float = 0.1, distancematrix={'AA': 0.0, 'AC': 0.112, 'AD': 0.819, 'AE': 0.827, 'AF': 0.54, 'AG': 0.208, 'AH': 0.696, 'AI': 0.407, 'AK': 0.891, 'AL': 0.406, 'AM': 0.379, 'AN': 0.318, 'AP': 0.191, 'AQ': 0.372, 'AR': 1.0, 'AS': 0.094, 'AT': 0.22, 'AV': 0.273, 'AW': 0.739, 'AY': 0.552, 'CA': 0.114, 'CC': 0.0, 'CD': 0.847, 'CE': 0.838, 'CF': 0.437, 'CG': 0.32, 'CH': 0.66, 'CI': 0.304, 'CK': 0.887, 'CL': 0.301, 'CM': 0.277, 'CN': 0.324, 'CP': 0.157, 'CQ': 0.341, 'CR': 1.0, 'CS': 0.176, 'CT': 0.233, 'CV': 0.167, 'CW': 0.639, 'CY': 0.457, 'DA': 0.729, 'DC': 0.742, 'DD': 0.0, 'DE': 0.124, 'DF': 0.924, 'DG': 0.697, 'DH': 0.435, 'DI': 0.847, 'DK': 0.249, 'DL': 0.841, 'DM': 0.819, 'DN': 0.56, 'DP': 0.657, 'DQ': 0.584, 'DR': 0.295, 'DS': 0.667, 'DT': 0.649, 'DV': 0.797, 'DW': 1.0, 'DY': 0.836, 'EA': 0.79, 'EC': 0.788, 'ED': 0.133, 'EE': 0.0, 'EF': 0.932, 'EG': 0.779, 'EH': 0.406, 'EI': 0.86, 'EK': 0.143, 'EL': 0.854, 'EM': 0.83, 'EN': 0.599, 'EP': 0.688, 'EQ': 0.598, 'ER': 0.234, 'ES': 0.726, 'ET': 0.682, 'EV': 0.824, 'EW': 1.0, 'EY': 0.837, 'FA': 0.508, 'FC': 0.405, 'FD': 0.977, 'FE': 0.918, 'FF': 0.0, 'FG': 0.69, 'FH': 0.663, 'FI': 0.128, 'FK': 0.903, 'FL': 0.131, 'FM': 0.169, 'FN': 0.541, 'FP': 0.42, 'FQ': 0.459, 'FR': 1.0, 'FS': 0.548, 'FT': 0.499, 'FV': 0.252, 'FW': 0.207, 'FY': 0.179, 'GA': 0.206, 'GC': 0.312, 'GD': 0.776, 'GE': 0.807, 'GF': 0.727, 'GG': 0.0, 'GH': 0.769, 'GI': 0.592, 'GK': 0.894, 'GL': 0.591, 'GM': 0.557, 'GN': 0.381, 'GP': 0.323, 'GQ': 0.467, 'GR': 1.0, 'GS': 0.158, 'GT': 0.272, 'GV': 0.464, 'GW': 0.923, 'GY': 0.728, 'HA': 0.896, 'HC': 0.836, 'HD': 0.629, 'HE': 0.547, 'HF': 0.907, 'HG': 1.0, 'HH': 0.0, 'HI': 0.848, 'HK': 0.566, 'HL': 0.842, 'HM': 0.825, 'HN': 0.754, 'HP': 0.777, 'HQ': 0.716, 'HR': 0.697, 'HS': 0.865, 'HT': 0.834, 'HV': 0.831, 'HW': 0.981, 'HY': 0.821, 'IA': 0.403, 'IC': 0.296, 'ID': 0.942, 'IE': 0.891, 'IF': 0.134, 'IG': 0.592, 'IH': 0.652, 'II': 0.0, 'IK': 0.892, 'IL': 0.013, 'IM': 0.057, 'IN': 0.457, 'IP': 0.311, 'IQ': 0.383, 'IR': 1.0, 'IS': 0.443, 'IT': 0.396, 'IV': 0.133, 'IW': 0.339, 'IY': 0.213, 'KA': 0.889, 'KC': 0.871, 'KD': 0.279, 'KE': 0.149, 'KF': 0.957, 'KG': 0.9, 'KH': 0.438, 'KI': 0.899, 'KK': 0.0, 'KL': 0.892, 'KM': 0.871, 'KN': 0.667, 'KP': 0.757, 'KQ': 0.639, 'KR': 0.154, 'KS': 0.825, 'KT': 0.759, 'KV': 0.882, 'KW': 1.0, 'KY': 0.848, 'LA': 0.405, 'LC': 0.296, 'LD': 0.944, 'LE': 0.892, 'LF': 0.139, 'LG': 0.596, 'LH': 0.653, 'LI': 0.013, 'LK': 0.893, 'LL': 0.0, 'LM': 0.062, 'LN': 0.452, 'LP': 0.309, 'LQ': 0.376, 'LR': 1.0, 'LS': 0.443, 'LT': 0.397, 'LV': 0.133, 'LW': 0.341, 'LY': 0.205, 'MA': 0.383, 'MC': 0.276, 'MD': 0.932, 'ME': 0.879, 'MF': 0.182, 'MG': 0.569, 'MH': 0.648, 'MI': 0.058, 'MK': 0.884, 'ML': 0.062, 'MM': 0.0, 'MN': 0.447, 'MP': 0.285, 'MQ': 0.372, 'MR': 1.0, 'MS': 0.417, 'MT': 0.358, 'MV': 0.12, 'MW': 0.391, 'MY': 0.255, 'NA': 0.424, 'NC': 0.425, 'ND': 0.838, 'NE': 0.835, 'NF': 0.766, 'NG': 0.512, 'NH': 0.78, 'NI': 0.615, 'NK': 0.891, 'NL': 0.603, 'NM': 0.588, 'NN': 0.0, 'NP': 0.266, 'NQ': 0.175, 'NR': 1.0, 'NS': 0.361, 'NT': 0.368, 'NV': 0.503, 'NW': 0.945, 'NY': 0.641, 'PA': 0.22, 'PC': 0.179, 'PD': 0.852, 'PE': 0.831, 'PF': 0.515, 'PG': 0.376, 'PH': 0.696, 'PI': 0.363, 'PK': 0.875, 'PL': 0.357, 'PM': 0.326, 'PN': 0.231, 'PP': 0.0, 'PQ': 0.228, 'PR': 1.0, 'PS': 0.196, 'PT': 0.161, 'PV': 0.244, 'PW': 0.72, 'PY': 0.481, 'QA': 0.512, 'QC': 0.462, 'QD': 0.903, 'QE': 0.861, 'QF': 0.671, 'QG': 0.648, 'QH': 0.765, 'QI': 0.532, 'QK': 0.881, 'QL': 0.518, 'QM': 0.505, 'QN': 0.181, 'QP': 0.272, 'QQ': 0.0, 'QR': 1.0, 'QS': 0.461, 'QT': 0.389, 'QV': 0.464, 'QW': 0.831, 'QY': 0.522, 'RA': 0.919, 'RC': 0.905, 'RD': 0.305, 'RE': 0.225, 'RF': 0.977, 'RG': 0.928, 'RH': 0.498, 'RI': 0.929, 'RK': 0.141, 'RL': 0.92, 'RM': 0.908, 'RN': 0.69, 'RP': 0.796, 'RQ': 0.668, 'RR': 0.0, 'RS': 0.86, 'RT': 0.808, 'RV': 0.914, 'RW': 1.0, 'RY': 0.859, 'SA': 0.1, 'SC': 0.185, 'SD': 0.801, 'SE': 0.812, 'SF': 0.622, 'SG': 0.17, 'SH': 0.718, 'SI': 0.478, 'SK': 0.883, 'SL': 0.474, 'SM': 0.44, 'SN': 0.289, 'SP': 0.181, 'SQ': 0.358, 'SR': 1.0, 'SS': 0.0, 'ST': 0.174, 'SV': 0.342, 'SW': 0.827, 'SY': 0.615, 'TA': 0.251, 'TC': 0.261, 'TD': 0.83, 'TE': 0.812, 'TF': 0.604, 'TG': 0.312, 'TH': 0.737, 'TI': 0.455, 'TK': 0.866, 'TL': 0.453, 'TM': 0.403, 'TN': 0.315, 'TP': 0.159, 'TQ': 0.322, 'TR': 1.0, 'TS': 0.185, 'TT': 0.0, 'TV': 0.345, 'TW': 0.816, 'TY': 0.596, 'VA': 0.275, 'VC': 0.165, 'VD': 0.9, 'VE': 0.867, 'VF': 0.269, 'VG': 0.471, 'VH': 0.649, 'VI': 0.135, 'VK': 0.889, 'VL': 0.134, 'VM': 0.12, 'VN': 0.38, 'VP': 0.212, 'VQ': 0.339, 'VR': 1.0, 'VS': 0.322, 'VT': 0.305, 'VV': 0.0, 'VW': 0.472, 'VY': 0.31, 'WA': 0.658, 'WC': 0.56, 'WD': 1.0, 'WE': 0.931, 'WF': 0.196, 'WG': 0.829, 'WH': 0.678, 'WI': 0.305, 'WK': 0.892, 'WL': 0.304, 'WM': 0.344, 'WN': 0.631, 'WP': 0.555, 'WQ': 0.538, 'WR': 0.968, 'WS': 0.689, 'WT': 0.638, 'WV': 0.418, 'WW': 0.0, 'WY': 0.204, 'YA': 0.587, 'YC': 0.478, 'YD': 1.0, 'YE': 0.932, 'YF': 0.202, 'YG': 0.782, 'YH': 0.678, 'YI': 0.23, 'YK': 0.904, 'YL': 0.219, 'YM': 0.268, 'YN': 0.512, 'YP': 0.444, 'YQ': 0.404, 'YR': 0.995, 'YS': 0.612, 'YT': 0.557, 'YV': 0.328, 'YW': 0.244, 'YY': 0.0})[source]

Compute the last maxlag quasi-sequence-order descriptors for a given protein sequence.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetQuasiSequenceOrder2Grant(protein)

see GetQuasiSequenceOrder() for the choice of parameters.

propy.QuasiSequenceOrder.GetQuasiSequenceOrder2SW(ProteinSequence: str, maxlag=30, weight=0.1, distancematrix={'AA': 0.0, 'AC': 0.112, 'AD': 0.819, 'AE': 0.827, 'AF': 0.54, 'AG': 0.208, 'AH': 0.696, 'AI': 0.407, 'AK': 0.891, 'AL': 0.406, 'AM': 0.379, 'AN': 0.318, 'AP': 0.191, 'AQ': 0.372, 'AR': 1.0, 'AS': 0.094, 'AT': 0.22, 'AV': 0.273, 'AW': 0.739, 'AY': 0.552, 'CA': 0.114, 'CC': 0.0, 'CD': 0.847, 'CE': 0.838, 'CF': 0.437, 'CG': 0.32, 'CH': 0.66, 'CI': 0.304, 'CK': 0.887, 'CL': 0.301, 'CM': 0.277, 'CN': 0.324, 'CP': 0.157, 'CQ': 0.341, 'CR': 1.0, 'CS': 0.176, 'CT': 0.233, 'CV': 0.167, 'CW': 0.639, 'CY': 0.457, 'DA': 0.729, 'DC': 0.742, 'DD': 0.0, 'DE': 0.124, 'DF': 0.924, 'DG': 0.697, 'DH': 0.435, 'DI': 0.847, 'DK': 0.249, 'DL': 0.841, 'DM': 0.819, 'DN': 0.56, 'DP': 0.657, 'DQ': 0.584, 'DR': 0.295, 'DS': 0.667, 'DT': 0.649, 'DV': 0.797, 'DW': 1.0, 'DY': 0.836, 'EA': 0.79, 'EC': 0.788, 'ED': 0.133, 'EE': 0.0, 'EF': 0.932, 'EG': 0.779, 'EH': 0.406, 'EI': 0.86, 'EK': 0.143, 'EL': 0.854, 'EM': 0.83, 'EN': 0.599, 'EP': 0.688, 'EQ': 0.598, 'ER': 0.234, 'ES': 0.726, 'ET': 0.682, 'EV': 0.824, 'EW': 1.0, 'EY': 0.837, 'FA': 0.508, 'FC': 0.405, 'FD': 0.977, 'FE': 0.918, 'FF': 0.0, 'FG': 0.69, 'FH': 0.663, 'FI': 0.128, 'FK': 0.903, 'FL': 0.131, 'FM': 0.169, 'FN': 0.541, 'FP': 0.42, 'FQ': 0.459, 'FR': 1.0, 'FS': 0.548, 'FT': 0.499, 'FV': 0.252, 'FW': 0.207, 'FY': 0.179, 'GA': 0.206, 'GC': 0.312, 'GD': 0.776, 'GE': 0.807, 'GF': 0.727, 'GG': 0.0, 'GH': 0.769, 'GI': 0.592, 'GK': 0.894, 'GL': 0.591, 'GM': 0.557, 'GN': 0.381, 'GP': 0.323, 'GQ': 0.467, 'GR': 1.0, 'GS': 0.158, 'GT': 0.272, 'GV': 0.464, 'GW': 0.923, 'GY': 0.728, 'HA': 0.896, 'HC': 0.836, 'HD': 0.629, 'HE': 0.547, 'HF': 0.907, 'HG': 1.0, 'HH': 0.0, 'HI': 0.848, 'HK': 0.566, 'HL': 0.842, 'HM': 0.825, 'HN': 0.754, 'HP': 0.777, 'HQ': 0.716, 'HR': 0.697, 'HS': 0.865, 'HT': 0.834, 'HV': 0.831, 'HW': 0.981, 'HY': 0.821, 'IA': 0.403, 'IC': 0.296, 'ID': 0.942, 'IE': 0.891, 'IF': 0.134, 'IG': 0.592, 'IH': 0.652, 'II': 0.0, 'IK': 0.892, 'IL': 0.013, 'IM': 0.057, 'IN': 0.457, 'IP': 0.311, 'IQ': 0.383, 'IR': 1.0, 'IS': 0.443, 'IT': 0.396, 'IV': 0.133, 'IW': 0.339, 'IY': 0.213, 'KA': 0.889, 'KC': 0.871, 'KD': 0.279, 'KE': 0.149, 'KF': 0.957, 'KG': 0.9, 'KH': 0.438, 'KI': 0.899, 'KK': 0.0, 'KL': 0.892, 'KM': 0.871, 'KN': 0.667, 'KP': 0.757, 'KQ': 0.639, 'KR': 0.154, 'KS': 0.825, 'KT': 0.759, 'KV': 0.882, 'KW': 1.0, 'KY': 0.848, 'LA': 0.405, 'LC': 0.296, 'LD': 0.944, 'LE': 0.892, 'LF': 0.139, 'LG': 0.596, 'LH': 0.653, 'LI': 0.013, 'LK': 0.893, 'LL': 0.0, 'LM': 0.062, 'LN': 0.452, 'LP': 0.309, 'LQ': 0.376, 'LR': 1.0, 'LS': 0.443, 'LT': 0.397, 'LV': 0.133, 'LW': 0.341, 'LY': 0.205, 'MA': 0.383, 'MC': 0.276, 'MD': 0.932, 'ME': 0.879, 'MF': 0.182, 'MG': 0.569, 'MH': 0.648, 'MI': 0.058, 'MK': 0.884, 'ML': 0.062, 'MM': 0.0, 'MN': 0.447, 'MP': 0.285, 'MQ': 0.372, 'MR': 1.0, 'MS': 0.417, 'MT': 0.358, 'MV': 0.12, 'MW': 0.391, 'MY': 0.255, 'NA': 0.424, 'NC': 0.425, 'ND': 0.838, 'NE': 0.835, 'NF': 0.766, 'NG': 0.512, 'NH': 0.78, 'NI': 0.615, 'NK': 0.891, 'NL': 0.603, 'NM': 0.588, 'NN': 0.0, 'NP': 0.266, 'NQ': 0.175, 'NR': 1.0, 'NS': 0.361, 'NT': 0.368, 'NV': 0.503, 'NW': 0.945, 'NY': 0.641, 'PA': 0.22, 'PC': 0.179, 'PD': 0.852, 'PE': 0.831, 'PF': 0.515, 'PG': 0.376, 'PH': 0.696, 'PI': 0.363, 'PK': 0.875, 'PL': 0.357, 'PM': 0.326, 'PN': 0.231, 'PP': 0.0, 'PQ': 0.228, 'PR': 1.0, 'PS': 0.196, 'PT': 0.161, 'PV': 0.244, 'PW': 0.72, 'PY': 0.481, 'QA': 0.512, 'QC': 0.462, 'QD': 0.903, 'QE': 0.861, 'QF': 0.671, 'QG': 0.648, 'QH': 0.765, 'QI': 0.532, 'QK': 0.881, 'QL': 0.518, 'QM': 0.505, 'QN': 0.181, 'QP': 0.272, 'QQ': 0.0, 'QR': 1.0, 'QS': 0.461, 'QT': 0.389, 'QV': 0.464, 'QW': 0.831, 'QY': 0.522, 'RA': 0.919, 'RC': 0.905, 'RD': 0.305, 'RE': 0.225, 'RF': 0.977, 'RG': 0.928, 'RH': 0.498, 'RI': 0.929, 'RK': 0.141, 'RL': 0.92, 'RM': 0.908, 'RN': 0.69, 'RP': 0.796, 'RQ': 0.668, 'RR': 0.0, 'RS': 0.86, 'RT': 0.808, 'RV': 0.914, 'RW': 1.0, 'RY': 0.859, 'SA': 0.1, 'SC': 0.185, 'SD': 0.801, 'SE': 0.812, 'SF': 0.622, 'SG': 0.17, 'SH': 0.718, 'SI': 0.478, 'SK': 0.883, 'SL': 0.474, 'SM': 0.44, 'SN': 0.289, 'SP': 0.181, 'SQ': 0.358, 'SR': 1.0, 'SS': 0.0, 'ST': 0.174, 'SV': 0.342, 'SW': 0.827, 'SY': 0.615, 'TA': 0.251, 'TC': 0.261, 'TD': 0.83, 'TE': 0.812, 'TF': 0.604, 'TG': 0.312, 'TH': 0.737, 'TI': 0.455, 'TK': 0.866, 'TL': 0.453, 'TM': 0.403, 'TN': 0.315, 'TP': 0.159, 'TQ': 0.322, 'TR': 1.0, 'TS': 0.185, 'TT': 0.0, 'TV': 0.345, 'TW': 0.816, 'TY': 0.596, 'VA': 0.275, 'VC': 0.165, 'VD': 0.9, 'VE': 0.867, 'VF': 0.269, 'VG': 0.471, 'VH': 0.649, 'VI': 0.135, 'VK': 0.889, 'VL': 0.134, 'VM': 0.12, 'VN': 0.38, 'VP': 0.212, 'VQ': 0.339, 'VR': 1.0, 'VS': 0.322, 'VT': 0.305, 'VV': 0.0, 'VW': 0.472, 'VY': 0.31, 'WA': 0.658, 'WC': 0.56, 'WD': 1.0, 'WE': 0.931, 'WF': 0.196, 'WG': 0.829, 'WH': 0.678, 'WI': 0.305, 'WK': 0.892, 'WL': 0.304, 'WM': 0.344, 'WN': 0.631, 'WP': 0.555, 'WQ': 0.538, 'WR': 0.968, 'WS': 0.689, 'WT': 0.638, 'WV': 0.418, 'WW': 0.0, 'WY': 0.204, 'YA': 0.587, 'YC': 0.478, 'YD': 1.0, 'YE': 0.932, 'YF': 0.202, 'YG': 0.782, 'YH': 0.678, 'YI': 0.23, 'YK': 0.904, 'YL': 0.219, 'YM': 0.268, 'YN': 0.512, 'YP': 0.444, 'YQ': 0.404, 'YR': 0.995, 'YS': 0.612, 'YT': 0.557, 'YV': 0.328, 'YW': 0.244, 'YY': 0.0})[source]

Compute the last maxlag quasi-sequence-order descriptors for a given protein sequence.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetQuasiSequenceOrder2SW(protein)

see GetQuasiSequenceOrder() for the choice of parameters.

propy.QuasiSequenceOrder.GetQuasiSequenceOrderp(ProteinSequence: str, maxlag: int = 30, weight: float = 0.1, distancematrix: Dict[Any, Any] = None) → Dict[Any, Any][source]

Compute quasi-sequence-order descriptors for a given protein.

See [1] for details.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger than maxlag
  • weight (float, optional (default: 0.1)) – a weight factor. Please see reference 1 for its choice.
  • distancematrix (Dict[Any, Any]) – contains 400 distance values
Returns:

result – contains all quasi-sequence-order descriptors

Return type:

Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetQuasiSequenceOrderp(protein)
propy.QuasiSequenceOrder.GetSequenceOrderCouplingNumber(ProteinSequence: str, d: int = 1, distancematrix: Dict[str, float] = {'AA': 0.0, 'AC': 0.112, 'AD': 0.819, 'AE': 0.827, 'AF': 0.54, 'AG': 0.208, 'AH': 0.696, 'AI': 0.407, 'AK': 0.891, 'AL': 0.406, 'AM': 0.379, 'AN': 0.318, 'AP': 0.191, 'AQ': 0.372, 'AR': 1.0, 'AS': 0.094, 'AT': 0.22, 'AV': 0.273, 'AW': 0.739, 'AY': 0.552, 'CA': 0.114, 'CC': 0.0, 'CD': 0.847, 'CE': 0.838, 'CF': 0.437, 'CG': 0.32, 'CH': 0.66, 'CI': 0.304, 'CK': 0.887, 'CL': 0.301, 'CM': 0.277, 'CN': 0.324, 'CP': 0.157, 'CQ': 0.341, 'CR': 1.0, 'CS': 0.176, 'CT': 0.233, 'CV': 0.167, 'CW': 0.639, 'CY': 0.457, 'DA': 0.729, 'DC': 0.742, 'DD': 0.0, 'DE': 0.124, 'DF': 0.924, 'DG': 0.697, 'DH': 0.435, 'DI': 0.847, 'DK': 0.249, 'DL': 0.841, 'DM': 0.819, 'DN': 0.56, 'DP': 0.657, 'DQ': 0.584, 'DR': 0.295, 'DS': 0.667, 'DT': 0.649, 'DV': 0.797, 'DW': 1.0, 'DY': 0.836, 'EA': 0.79, 'EC': 0.788, 'ED': 0.133, 'EE': 0.0, 'EF': 0.932, 'EG': 0.779, 'EH': 0.406, 'EI': 0.86, 'EK': 0.143, 'EL': 0.854, 'EM': 0.83, 'EN': 0.599, 'EP': 0.688, 'EQ': 0.598, 'ER': 0.234, 'ES': 0.726, 'ET': 0.682, 'EV': 0.824, 'EW': 1.0, 'EY': 0.837, 'FA': 0.508, 'FC': 0.405, 'FD': 0.977, 'FE': 0.918, 'FF': 0.0, 'FG': 0.69, 'FH': 0.663, 'FI': 0.128, 'FK': 0.903, 'FL': 0.131, 'FM': 0.169, 'FN': 0.541, 'FP': 0.42, 'FQ': 0.459, 'FR': 1.0, 'FS': 0.548, 'FT': 0.499, 'FV': 0.252, 'FW': 0.207, 'FY': 0.179, 'GA': 0.206, 'GC': 0.312, 'GD': 0.776, 'GE': 0.807, 'GF': 0.727, 'GG': 0.0, 'GH': 0.769, 'GI': 0.592, 'GK': 0.894, 'GL': 0.591, 'GM': 0.557, 'GN': 0.381, 'GP': 0.323, 'GQ': 0.467, 'GR': 1.0, 'GS': 0.158, 'GT': 0.272, 'GV': 0.464, 'GW': 0.923, 'GY': 0.728, 'HA': 0.896, 'HC': 0.836, 'HD': 0.629, 'HE': 0.547, 'HF': 0.907, 'HG': 1.0, 'HH': 0.0, 'HI': 0.848, 'HK': 0.566, 'HL': 0.842, 'HM': 0.825, 'HN': 0.754, 'HP': 0.777, 'HQ': 0.716, 'HR': 0.697, 'HS': 0.865, 'HT': 0.834, 'HV': 0.831, 'HW': 0.981, 'HY': 0.821, 'IA': 0.403, 'IC': 0.296, 'ID': 0.942, 'IE': 0.891, 'IF': 0.134, 'IG': 0.592, 'IH': 0.652, 'II': 0.0, 'IK': 0.892, 'IL': 0.013, 'IM': 0.057, 'IN': 0.457, 'IP': 0.311, 'IQ': 0.383, 'IR': 1.0, 'IS': 0.443, 'IT': 0.396, 'IV': 0.133, 'IW': 0.339, 'IY': 0.213, 'KA': 0.889, 'KC': 0.871, 'KD': 0.279, 'KE': 0.149, 'KF': 0.957, 'KG': 0.9, 'KH': 0.438, 'KI': 0.899, 'KK': 0.0, 'KL': 0.892, 'KM': 0.871, 'KN': 0.667, 'KP': 0.757, 'KQ': 0.639, 'KR': 0.154, 'KS': 0.825, 'KT': 0.759, 'KV': 0.882, 'KW': 1.0, 'KY': 0.848, 'LA': 0.405, 'LC': 0.296, 'LD': 0.944, 'LE': 0.892, 'LF': 0.139, 'LG': 0.596, 'LH': 0.653, 'LI': 0.013, 'LK': 0.893, 'LL': 0.0, 'LM': 0.062, 'LN': 0.452, 'LP': 0.309, 'LQ': 0.376, 'LR': 1.0, 'LS': 0.443, 'LT': 0.397, 'LV': 0.133, 'LW': 0.341, 'LY': 0.205, 'MA': 0.383, 'MC': 0.276, 'MD': 0.932, 'ME': 0.879, 'MF': 0.182, 'MG': 0.569, 'MH': 0.648, 'MI': 0.058, 'MK': 0.884, 'ML': 0.062, 'MM': 0.0, 'MN': 0.447, 'MP': 0.285, 'MQ': 0.372, 'MR': 1.0, 'MS': 0.417, 'MT': 0.358, 'MV': 0.12, 'MW': 0.391, 'MY': 0.255, 'NA': 0.424, 'NC': 0.425, 'ND': 0.838, 'NE': 0.835, 'NF': 0.766, 'NG': 0.512, 'NH': 0.78, 'NI': 0.615, 'NK': 0.891, 'NL': 0.603, 'NM': 0.588, 'NN': 0.0, 'NP': 0.266, 'NQ': 0.175, 'NR': 1.0, 'NS': 0.361, 'NT': 0.368, 'NV': 0.503, 'NW': 0.945, 'NY': 0.641, 'PA': 0.22, 'PC': 0.179, 'PD': 0.852, 'PE': 0.831, 'PF': 0.515, 'PG': 0.376, 'PH': 0.696, 'PI': 0.363, 'PK': 0.875, 'PL': 0.357, 'PM': 0.326, 'PN': 0.231, 'PP': 0.0, 'PQ': 0.228, 'PR': 1.0, 'PS': 0.196, 'PT': 0.161, 'PV': 0.244, 'PW': 0.72, 'PY': 0.481, 'QA': 0.512, 'QC': 0.462, 'QD': 0.903, 'QE': 0.861, 'QF': 0.671, 'QG': 0.648, 'QH': 0.765, 'QI': 0.532, 'QK': 0.881, 'QL': 0.518, 'QM': 0.505, 'QN': 0.181, 'QP': 0.272, 'QQ': 0.0, 'QR': 1.0, 'QS': 0.461, 'QT': 0.389, 'QV': 0.464, 'QW': 0.831, 'QY': 0.522, 'RA': 0.919, 'RC': 0.905, 'RD': 0.305, 'RE': 0.225, 'RF': 0.977, 'RG': 0.928, 'RH': 0.498, 'RI': 0.929, 'RK': 0.141, 'RL': 0.92, 'RM': 0.908, 'RN': 0.69, 'RP': 0.796, 'RQ': 0.668, 'RR': 0.0, 'RS': 0.86, 'RT': 0.808, 'RV': 0.914, 'RW': 1.0, 'RY': 0.859, 'SA': 0.1, 'SC': 0.185, 'SD': 0.801, 'SE': 0.812, 'SF': 0.622, 'SG': 0.17, 'SH': 0.718, 'SI': 0.478, 'SK': 0.883, 'SL': 0.474, 'SM': 0.44, 'SN': 0.289, 'SP': 0.181, 'SQ': 0.358, 'SR': 1.0, 'SS': 0.0, 'ST': 0.174, 'SV': 0.342, 'SW': 0.827, 'SY': 0.615, 'TA': 0.251, 'TC': 0.261, 'TD': 0.83, 'TE': 0.812, 'TF': 0.604, 'TG': 0.312, 'TH': 0.737, 'TI': 0.455, 'TK': 0.866, 'TL': 0.453, 'TM': 0.403, 'TN': 0.315, 'TP': 0.159, 'TQ': 0.322, 'TR': 1.0, 'TS': 0.185, 'TT': 0.0, 'TV': 0.345, 'TW': 0.816, 'TY': 0.596, 'VA': 0.275, 'VC': 0.165, 'VD': 0.9, 'VE': 0.867, 'VF': 0.269, 'VG': 0.471, 'VH': 0.649, 'VI': 0.135, 'VK': 0.889, 'VL': 0.134, 'VM': 0.12, 'VN': 0.38, 'VP': 0.212, 'VQ': 0.339, 'VR': 1.0, 'VS': 0.322, 'VT': 0.305, 'VV': 0.0, 'VW': 0.472, 'VY': 0.31, 'WA': 0.658, 'WC': 0.56, 'WD': 1.0, 'WE': 0.931, 'WF': 0.196, 'WG': 0.829, 'WH': 0.678, 'WI': 0.305, 'WK': 0.892, 'WL': 0.304, 'WM': 0.344, 'WN': 0.631, 'WP': 0.555, 'WQ': 0.538, 'WR': 0.968, 'WS': 0.689, 'WT': 0.638, 'WV': 0.418, 'WW': 0.0, 'WY': 0.204, 'YA': 0.587, 'YC': 0.478, 'YD': 1.0, 'YE': 0.932, 'YF': 0.202, 'YG': 0.782, 'YH': 0.678, 'YI': 0.23, 'YK': 0.904, 'YL': 0.219, 'YM': 0.268, 'YN': 0.512, 'YP': 0.444, 'YQ': 0.404, 'YR': 0.995, 'YS': 0.612, 'YT': 0.557, 'YV': 0.328, 'YW': 0.244, 'YY': 0.0})[source]

Compute the dth-rank sequence order coupling number for a protein.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • d (int) – the gap between two amino acids.
  • distancematrix (Dict[str, float]) –
Returns:

tau

Return type:

float

Example

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetSequenceOrderCouplingNumber(protein)
propy.QuasiSequenceOrder.GetSequenceOrderCouplingNumberGrant(ProteinSequence: str, maxlag: int = 30, distancematrix={'AA': 0.0, 'AC': 0.112, 'AD': 0.819, 'AE': 0.827, 'AF': 0.54, 'AG': 0.208, 'AH': 0.696, 'AI': 0.407, 'AK': 0.891, 'AL': 0.406, 'AM': 0.379, 'AN': 0.318, 'AP': 0.191, 'AQ': 0.372, 'AR': 1.0, 'AS': 0.094, 'AT': 0.22, 'AV': 0.273, 'AW': 0.739, 'AY': 0.552, 'CA': 0.114, 'CC': 0.0, 'CD': 0.847, 'CE': 0.838, 'CF': 0.437, 'CG': 0.32, 'CH': 0.66, 'CI': 0.304, 'CK': 0.887, 'CL': 0.301, 'CM': 0.277, 'CN': 0.324, 'CP': 0.157, 'CQ': 0.341, 'CR': 1.0, 'CS': 0.176, 'CT': 0.233, 'CV': 0.167, 'CW': 0.639, 'CY': 0.457, 'DA': 0.729, 'DC': 0.742, 'DD': 0.0, 'DE': 0.124, 'DF': 0.924, 'DG': 0.697, 'DH': 0.435, 'DI': 0.847, 'DK': 0.249, 'DL': 0.841, 'DM': 0.819, 'DN': 0.56, 'DP': 0.657, 'DQ': 0.584, 'DR': 0.295, 'DS': 0.667, 'DT': 0.649, 'DV': 0.797, 'DW': 1.0, 'DY': 0.836, 'EA': 0.79, 'EC': 0.788, 'ED': 0.133, 'EE': 0.0, 'EF': 0.932, 'EG': 0.779, 'EH': 0.406, 'EI': 0.86, 'EK': 0.143, 'EL': 0.854, 'EM': 0.83, 'EN': 0.599, 'EP': 0.688, 'EQ': 0.598, 'ER': 0.234, 'ES': 0.726, 'ET': 0.682, 'EV': 0.824, 'EW': 1.0, 'EY': 0.837, 'FA': 0.508, 'FC': 0.405, 'FD': 0.977, 'FE': 0.918, 'FF': 0.0, 'FG': 0.69, 'FH': 0.663, 'FI': 0.128, 'FK': 0.903, 'FL': 0.131, 'FM': 0.169, 'FN': 0.541, 'FP': 0.42, 'FQ': 0.459, 'FR': 1.0, 'FS': 0.548, 'FT': 0.499, 'FV': 0.252, 'FW': 0.207, 'FY': 0.179, 'GA': 0.206, 'GC': 0.312, 'GD': 0.776, 'GE': 0.807, 'GF': 0.727, 'GG': 0.0, 'GH': 0.769, 'GI': 0.592, 'GK': 0.894, 'GL': 0.591, 'GM': 0.557, 'GN': 0.381, 'GP': 0.323, 'GQ': 0.467, 'GR': 1.0, 'GS': 0.158, 'GT': 0.272, 'GV': 0.464, 'GW': 0.923, 'GY': 0.728, 'HA': 0.896, 'HC': 0.836, 'HD': 0.629, 'HE': 0.547, 'HF': 0.907, 'HG': 1.0, 'HH': 0.0, 'HI': 0.848, 'HK': 0.566, 'HL': 0.842, 'HM': 0.825, 'HN': 0.754, 'HP': 0.777, 'HQ': 0.716, 'HR': 0.697, 'HS': 0.865, 'HT': 0.834, 'HV': 0.831, 'HW': 0.981, 'HY': 0.821, 'IA': 0.403, 'IC': 0.296, 'ID': 0.942, 'IE': 0.891, 'IF': 0.134, 'IG': 0.592, 'IH': 0.652, 'II': 0.0, 'IK': 0.892, 'IL': 0.013, 'IM': 0.057, 'IN': 0.457, 'IP': 0.311, 'IQ': 0.383, 'IR': 1.0, 'IS': 0.443, 'IT': 0.396, 'IV': 0.133, 'IW': 0.339, 'IY': 0.213, 'KA': 0.889, 'KC': 0.871, 'KD': 0.279, 'KE': 0.149, 'KF': 0.957, 'KG': 0.9, 'KH': 0.438, 'KI': 0.899, 'KK': 0.0, 'KL': 0.892, 'KM': 0.871, 'KN': 0.667, 'KP': 0.757, 'KQ': 0.639, 'KR': 0.154, 'KS': 0.825, 'KT': 0.759, 'KV': 0.882, 'KW': 1.0, 'KY': 0.848, 'LA': 0.405, 'LC': 0.296, 'LD': 0.944, 'LE': 0.892, 'LF': 0.139, 'LG': 0.596, 'LH': 0.653, 'LI': 0.013, 'LK': 0.893, 'LL': 0.0, 'LM': 0.062, 'LN': 0.452, 'LP': 0.309, 'LQ': 0.376, 'LR': 1.0, 'LS': 0.443, 'LT': 0.397, 'LV': 0.133, 'LW': 0.341, 'LY': 0.205, 'MA': 0.383, 'MC': 0.276, 'MD': 0.932, 'ME': 0.879, 'MF': 0.182, 'MG': 0.569, 'MH': 0.648, 'MI': 0.058, 'MK': 0.884, 'ML': 0.062, 'MM': 0.0, 'MN': 0.447, 'MP': 0.285, 'MQ': 0.372, 'MR': 1.0, 'MS': 0.417, 'MT': 0.358, 'MV': 0.12, 'MW': 0.391, 'MY': 0.255, 'NA': 0.424, 'NC': 0.425, 'ND': 0.838, 'NE': 0.835, 'NF': 0.766, 'NG': 0.512, 'NH': 0.78, 'NI': 0.615, 'NK': 0.891, 'NL': 0.603, 'NM': 0.588, 'NN': 0.0, 'NP': 0.266, 'NQ': 0.175, 'NR': 1.0, 'NS': 0.361, 'NT': 0.368, 'NV': 0.503, 'NW': 0.945, 'NY': 0.641, 'PA': 0.22, 'PC': 0.179, 'PD': 0.852, 'PE': 0.831, 'PF': 0.515, 'PG': 0.376, 'PH': 0.696, 'PI': 0.363, 'PK': 0.875, 'PL': 0.357, 'PM': 0.326, 'PN': 0.231, 'PP': 0.0, 'PQ': 0.228, 'PR': 1.0, 'PS': 0.196, 'PT': 0.161, 'PV': 0.244, 'PW': 0.72, 'PY': 0.481, 'QA': 0.512, 'QC': 0.462, 'QD': 0.903, 'QE': 0.861, 'QF': 0.671, 'QG': 0.648, 'QH': 0.765, 'QI': 0.532, 'QK': 0.881, 'QL': 0.518, 'QM': 0.505, 'QN': 0.181, 'QP': 0.272, 'QQ': 0.0, 'QR': 1.0, 'QS': 0.461, 'QT': 0.389, 'QV': 0.464, 'QW': 0.831, 'QY': 0.522, 'RA': 0.919, 'RC': 0.905, 'RD': 0.305, 'RE': 0.225, 'RF': 0.977, 'RG': 0.928, 'RH': 0.498, 'RI': 0.929, 'RK': 0.141, 'RL': 0.92, 'RM': 0.908, 'RN': 0.69, 'RP': 0.796, 'RQ': 0.668, 'RR': 0.0, 'RS': 0.86, 'RT': 0.808, 'RV': 0.914, 'RW': 1.0, 'RY': 0.859, 'SA': 0.1, 'SC': 0.185, 'SD': 0.801, 'SE': 0.812, 'SF': 0.622, 'SG': 0.17, 'SH': 0.718, 'SI': 0.478, 'SK': 0.883, 'SL': 0.474, 'SM': 0.44, 'SN': 0.289, 'SP': 0.181, 'SQ': 0.358, 'SR': 1.0, 'SS': 0.0, 'ST': 0.174, 'SV': 0.342, 'SW': 0.827, 'SY': 0.615, 'TA': 0.251, 'TC': 0.261, 'TD': 0.83, 'TE': 0.812, 'TF': 0.604, 'TG': 0.312, 'TH': 0.737, 'TI': 0.455, 'TK': 0.866, 'TL': 0.453, 'TM': 0.403, 'TN': 0.315, 'TP': 0.159, 'TQ': 0.322, 'TR': 1.0, 'TS': 0.185, 'TT': 0.0, 'TV': 0.345, 'TW': 0.816, 'TY': 0.596, 'VA': 0.275, 'VC': 0.165, 'VD': 0.9, 'VE': 0.867, 'VF': 0.269, 'VG': 0.471, 'VH': 0.649, 'VI': 0.135, 'VK': 0.889, 'VL': 0.134, 'VM': 0.12, 'VN': 0.38, 'VP': 0.212, 'VQ': 0.339, 'VR': 1.0, 'VS': 0.322, 'VT': 0.305, 'VV': 0.0, 'VW': 0.472, 'VY': 0.31, 'WA': 0.658, 'WC': 0.56, 'WD': 1.0, 'WE': 0.931, 'WF': 0.196, 'WG': 0.829, 'WH': 0.678, 'WI': 0.305, 'WK': 0.892, 'WL': 0.304, 'WM': 0.344, 'WN': 0.631, 'WP': 0.555, 'WQ': 0.538, 'WR': 0.968, 'WS': 0.689, 'WT': 0.638, 'WV': 0.418, 'WW': 0.0, 'WY': 0.204, 'YA': 0.587, 'YC': 0.478, 'YD': 1.0, 'YE': 0.932, 'YF': 0.202, 'YG': 0.782, 'YH': 0.678, 'YI': 0.23, 'YK': 0.904, 'YL': 0.219, 'YM': 0.268, 'YN': 0.512, 'YP': 0.444, 'YQ': 0.404, 'YR': 0.995, 'YS': 0.612, 'YT': 0.557, 'YV': 0.328, 'YW': 0.244, 'YY': 0.0})[source]

Compute the sequence order coupling numbers from 1 to maxlag for a given protein sequence based on the Grantham chemical distance matrix.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger than maxlag
  • distancematrix (Dict[Any, Any]) – contains Schneider-Wrede physicochemical distance matrix
Returns:

Tau – contains all sequence order coupling numbers based on the Grantham chemical distance matrix

Return type:

Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetSequenceOrderCouplingNumberGrant(protein)
propy.QuasiSequenceOrder.GetSequenceOrderCouplingNumberSW(ProteinSequence: str, maxlag: int = 30, distancematrix={'AA': 0.0, 'AC': 0.112, 'AD': 0.819, 'AE': 0.827, 'AF': 0.54, 'AG': 0.208, 'AH': 0.696, 'AI': 0.407, 'AK': 0.891, 'AL': 0.406, 'AM': 0.379, 'AN': 0.318, 'AP': 0.191, 'AQ': 0.372, 'AR': 1.0, 'AS': 0.094, 'AT': 0.22, 'AV': 0.273, 'AW': 0.739, 'AY': 0.552, 'CA': 0.114, 'CC': 0.0, 'CD': 0.847, 'CE': 0.838, 'CF': 0.437, 'CG': 0.32, 'CH': 0.66, 'CI': 0.304, 'CK': 0.887, 'CL': 0.301, 'CM': 0.277, 'CN': 0.324, 'CP': 0.157, 'CQ': 0.341, 'CR': 1.0, 'CS': 0.176, 'CT': 0.233, 'CV': 0.167, 'CW': 0.639, 'CY': 0.457, 'DA': 0.729, 'DC': 0.742, 'DD': 0.0, 'DE': 0.124, 'DF': 0.924, 'DG': 0.697, 'DH': 0.435, 'DI': 0.847, 'DK': 0.249, 'DL': 0.841, 'DM': 0.819, 'DN': 0.56, 'DP': 0.657, 'DQ': 0.584, 'DR': 0.295, 'DS': 0.667, 'DT': 0.649, 'DV': 0.797, 'DW': 1.0, 'DY': 0.836, 'EA': 0.79, 'EC': 0.788, 'ED': 0.133, 'EE': 0.0, 'EF': 0.932, 'EG': 0.779, 'EH': 0.406, 'EI': 0.86, 'EK': 0.143, 'EL': 0.854, 'EM': 0.83, 'EN': 0.599, 'EP': 0.688, 'EQ': 0.598, 'ER': 0.234, 'ES': 0.726, 'ET': 0.682, 'EV': 0.824, 'EW': 1.0, 'EY': 0.837, 'FA': 0.508, 'FC': 0.405, 'FD': 0.977, 'FE': 0.918, 'FF': 0.0, 'FG': 0.69, 'FH': 0.663, 'FI': 0.128, 'FK': 0.903, 'FL': 0.131, 'FM': 0.169, 'FN': 0.541, 'FP': 0.42, 'FQ': 0.459, 'FR': 1.0, 'FS': 0.548, 'FT': 0.499, 'FV': 0.252, 'FW': 0.207, 'FY': 0.179, 'GA': 0.206, 'GC': 0.312, 'GD': 0.776, 'GE': 0.807, 'GF': 0.727, 'GG': 0.0, 'GH': 0.769, 'GI': 0.592, 'GK': 0.894, 'GL': 0.591, 'GM': 0.557, 'GN': 0.381, 'GP': 0.323, 'GQ': 0.467, 'GR': 1.0, 'GS': 0.158, 'GT': 0.272, 'GV': 0.464, 'GW': 0.923, 'GY': 0.728, 'HA': 0.896, 'HC': 0.836, 'HD': 0.629, 'HE': 0.547, 'HF': 0.907, 'HG': 1.0, 'HH': 0.0, 'HI': 0.848, 'HK': 0.566, 'HL': 0.842, 'HM': 0.825, 'HN': 0.754, 'HP': 0.777, 'HQ': 0.716, 'HR': 0.697, 'HS': 0.865, 'HT': 0.834, 'HV': 0.831, 'HW': 0.981, 'HY': 0.821, 'IA': 0.403, 'IC': 0.296, 'ID': 0.942, 'IE': 0.891, 'IF': 0.134, 'IG': 0.592, 'IH': 0.652, 'II': 0.0, 'IK': 0.892, 'IL': 0.013, 'IM': 0.057, 'IN': 0.457, 'IP': 0.311, 'IQ': 0.383, 'IR': 1.0, 'IS': 0.443, 'IT': 0.396, 'IV': 0.133, 'IW': 0.339, 'IY': 0.213, 'KA': 0.889, 'KC': 0.871, 'KD': 0.279, 'KE': 0.149, 'KF': 0.957, 'KG': 0.9, 'KH': 0.438, 'KI': 0.899, 'KK': 0.0, 'KL': 0.892, 'KM': 0.871, 'KN': 0.667, 'KP': 0.757, 'KQ': 0.639, 'KR': 0.154, 'KS': 0.825, 'KT': 0.759, 'KV': 0.882, 'KW': 1.0, 'KY': 0.848, 'LA': 0.405, 'LC': 0.296, 'LD': 0.944, 'LE': 0.892, 'LF': 0.139, 'LG': 0.596, 'LH': 0.653, 'LI': 0.013, 'LK': 0.893, 'LL': 0.0, 'LM': 0.062, 'LN': 0.452, 'LP': 0.309, 'LQ': 0.376, 'LR': 1.0, 'LS': 0.443, 'LT': 0.397, 'LV': 0.133, 'LW': 0.341, 'LY': 0.205, 'MA': 0.383, 'MC': 0.276, 'MD': 0.932, 'ME': 0.879, 'MF': 0.182, 'MG': 0.569, 'MH': 0.648, 'MI': 0.058, 'MK': 0.884, 'ML': 0.062, 'MM': 0.0, 'MN': 0.447, 'MP': 0.285, 'MQ': 0.372, 'MR': 1.0, 'MS': 0.417, 'MT': 0.358, 'MV': 0.12, 'MW': 0.391, 'MY': 0.255, 'NA': 0.424, 'NC': 0.425, 'ND': 0.838, 'NE': 0.835, 'NF': 0.766, 'NG': 0.512, 'NH': 0.78, 'NI': 0.615, 'NK': 0.891, 'NL': 0.603, 'NM': 0.588, 'NN': 0.0, 'NP': 0.266, 'NQ': 0.175, 'NR': 1.0, 'NS': 0.361, 'NT': 0.368, 'NV': 0.503, 'NW': 0.945, 'NY': 0.641, 'PA': 0.22, 'PC': 0.179, 'PD': 0.852, 'PE': 0.831, 'PF': 0.515, 'PG': 0.376, 'PH': 0.696, 'PI': 0.363, 'PK': 0.875, 'PL': 0.357, 'PM': 0.326, 'PN': 0.231, 'PP': 0.0, 'PQ': 0.228, 'PR': 1.0, 'PS': 0.196, 'PT': 0.161, 'PV': 0.244, 'PW': 0.72, 'PY': 0.481, 'QA': 0.512, 'QC': 0.462, 'QD': 0.903, 'QE': 0.861, 'QF': 0.671, 'QG': 0.648, 'QH': 0.765, 'QI': 0.532, 'QK': 0.881, 'QL': 0.518, 'QM': 0.505, 'QN': 0.181, 'QP': 0.272, 'QQ': 0.0, 'QR': 1.0, 'QS': 0.461, 'QT': 0.389, 'QV': 0.464, 'QW': 0.831, 'QY': 0.522, 'RA': 0.919, 'RC': 0.905, 'RD': 0.305, 'RE': 0.225, 'RF': 0.977, 'RG': 0.928, 'RH': 0.498, 'RI': 0.929, 'RK': 0.141, 'RL': 0.92, 'RM': 0.908, 'RN': 0.69, 'RP': 0.796, 'RQ': 0.668, 'RR': 0.0, 'RS': 0.86, 'RT': 0.808, 'RV': 0.914, 'RW': 1.0, 'RY': 0.859, 'SA': 0.1, 'SC': 0.185, 'SD': 0.801, 'SE': 0.812, 'SF': 0.622, 'SG': 0.17, 'SH': 0.718, 'SI': 0.478, 'SK': 0.883, 'SL': 0.474, 'SM': 0.44, 'SN': 0.289, 'SP': 0.181, 'SQ': 0.358, 'SR': 1.0, 'SS': 0.0, 'ST': 0.174, 'SV': 0.342, 'SW': 0.827, 'SY': 0.615, 'TA': 0.251, 'TC': 0.261, 'TD': 0.83, 'TE': 0.812, 'TF': 0.604, 'TG': 0.312, 'TH': 0.737, 'TI': 0.455, 'TK': 0.866, 'TL': 0.453, 'TM': 0.403, 'TN': 0.315, 'TP': 0.159, 'TQ': 0.322, 'TR': 1.0, 'TS': 0.185, 'TT': 0.0, 'TV': 0.345, 'TW': 0.816, 'TY': 0.596, 'VA': 0.275, 'VC': 0.165, 'VD': 0.9, 'VE': 0.867, 'VF': 0.269, 'VG': 0.471, 'VH': 0.649, 'VI': 0.135, 'VK': 0.889, 'VL': 0.134, 'VM': 0.12, 'VN': 0.38, 'VP': 0.212, 'VQ': 0.339, 'VR': 1.0, 'VS': 0.322, 'VT': 0.305, 'VV': 0.0, 'VW': 0.472, 'VY': 0.31, 'WA': 0.658, 'WC': 0.56, 'WD': 1.0, 'WE': 0.931, 'WF': 0.196, 'WG': 0.829, 'WH': 0.678, 'WI': 0.305, 'WK': 0.892, 'WL': 0.304, 'WM': 0.344, 'WN': 0.631, 'WP': 0.555, 'WQ': 0.538, 'WR': 0.968, 'WS': 0.689, 'WT': 0.638, 'WV': 0.418, 'WW': 0.0, 'WY': 0.204, 'YA': 0.587, 'YC': 0.478, 'YD': 1.0, 'YE': 0.932, 'YF': 0.202, 'YG': 0.782, 'YH': 0.678, 'YI': 0.23, 'YK': 0.904, 'YL': 0.219, 'YM': 0.268, 'YN': 0.512, 'YP': 0.444, 'YQ': 0.404, 'YR': 0.995, 'YS': 0.612, 'YT': 0.557, 'YV': 0.328, 'YW': 0.244, 'YY': 0.0})[source]

Compute the sequence order coupling numbers from 1 to maxlag for a given protein sequence based on the Schneider-Wrede physicochemical distance matrix.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger than maxlag
  • distancematrix (Dict[Any, Any]) – contains Schneider-Wrede physicochemical distance matrix
Returns:

Tau – contains all sequence order coupling numbers based on the Schneider-Wrede physicochemical distance matrix

Return type:

Dict[Any, Any]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetSequenceOrderCouplingNumberSW(protein)
propy.QuasiSequenceOrder.GetSequenceOrderCouplingNumberTotal(ProteinSequence: str, maxlag: int = 30) → Dict[Any, Any][source]

Compute the sequence order coupling numbers from 1 to maxlag for a given protein sequence.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger
Returns:

result – contains all sequence order coupling numbers

Return type:

Dict

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetSequenceOrderCouplingNumberTotal(protein)
propy.QuasiSequenceOrder.GetSequenceOrderCouplingNumberp(ProteinSequence: str, maxlag: int = 30, distancematrix: Dict[Any, Any] = None)[source]

Compute the sequence order coupling numbers from 1 to maxlag for a given protein sequence based on the user-defined property.

Parameters:
  • ProteinSequence (str) – a pure protein sequence
  • maxlag (int, optional (default: 30)) – the maximum lag and the length of the protein should be larger than maxlag.
  • distancematrix (Dict[Any, Any]) – contains 400 distance values
Returns:

Tau – contains all sequence order coupling numbers based on the given property

Return type:

Dict[str]

Examples

>>> from propy.GetProteinFromUniprot import GetProteinSequence
>>> protein = GetProteinSequence(ProteinID="Q9NQ39")
>>> result = GetSequenceOrderCouplingNumberp(protein)