ccpnmodel.ccpncore.lib.assignment package

Module Documentation here

Submodules

ccpnmodel.ccpncore.lib.assignment.Assignment module

Assignment-related library functions at API (data storage) level

ccpnmodel.ccpncore.lib.assignment.Assignment.getConnectedAtoms(spectrum)[source]

ccpnmodel.ccpncore.lib.assignment.ChemicalShift module

Chemical shift-related library functions at API (data storage) level

ccpnmodel.ccpncore.lib.assignment.ChemicalShift.REFDB_SD_MEAN_LIST = {('protein', 'Ala'): [('C', (177.828848, 2.10968, 0.452147, None)), ('CA', (53.352984, 1.902676, 0.210713, 'HA')), ('CB', (19.222672, 1.746981, 0.258369, 'HB*')), ('H', (8.1982, 0.628909, 0.033675, 'N')), ('HA', (4.276693, 0.44626, 0.146317, 'CA')), ('HB*', (1.36408, 0.226681, 0.212091, 'CB')), ('N', (122.7087, 3.549744, 0.159512, 'H2'))], ('protein', 'Arg'): [('C', (176.476635, 1.985958, 0.496077, None)), ('CA', (56.956118, 2.286571, 0.23627, 'HA')), ('CB', (30.902098, 1.776631, 0.317743, 'HB2')), ('CD', (43.264272, 0.631, 0.568196, 'HD2')), ('CG', (27.332456, 1.047844, 0.581473, 'HG2')), ('CZ', (160.254836, 3.230362, 0.9828, None)), ('H', (8.251157, 0.626805, 0.038322, 'N')), ('HA', (4.312683, 0.477117, 0.133977, 'CA')), ('HB2', (1.79666, 0.261361, 0.24653, 'CB')), ('HB3', (1.770165, 0.267594, 0.301147, 'CB')), ('HD2', (3.124174, 0.221769, 0.361798, 'CD')), ('HD3', (3.10899, 0.23785, 0.419433, 'CD')), ('HE', (7.358268, 0.581758, 0.718769, 'NE')), ('HG2', (1.565723, 0.256262, 0.342788, 'CG')), ('HG3', (1.543494, 0.272259, 0.396198, 'CG')), ('HH11', (6.806578, 0.394752, 0.968618, 'NH1')), ('HH12', (6.804218, 0.413009, 0.973446, 'NH1')), ('HH21', (6.725168, 0.354246, 0.971032, 'NH2')), ('HH22', (6.729098, 0.436935, 0.971636, 'NH2')), ('N', (120.208274, 3.814534, 0.208509, 'H2')), ('NE', (91.403172, 13.311577, 0.865419, 'HE')), ('NH1', (76.300233, 12.184632, 0.99306, 'HH12')), ('NH2', (75.668286, 10.259347, 0.99306, 'HH21'))], ('protein', 'Asn'): [('C', (175.387335, 1.722342, 0.461435, None)), ('CA', (53.715068, 1.780935, 0.233736, 'HA')), ('CB', (38.88261, 1.63745, 0.291751, 'HB2')), ('CG', (176.82666, 1.209325, 0.911804, None)), ('H', (8.34926, 0.632518, 0.049966, 'N')), ('HA', (4.681485, 0.371691, 0.153253, 'CA')), ('HB2', (2.819383, 0.300069, 0.232059, 'CB')), ('HB3', (2.776859, 0.314775, 0.260899, 'CB')), ('HD21', (7.356185, 0.463488, 0.462441, 'ND2')), ('HD22', (7.141474, 0.456559, 0.466465, 'ND2')), ('N', (118.480741, 4.131918, 0.192153, 'H2')), ('ND2', (112.78409, 2.263417, 0.61603, 'HD21'))], ('protein', 'Asp'): [('C', (176.552707, 1.676911, 0.428646, None)), ('CA', (54.879282, 1.972805, 0.195573, 'HA')), ('CB', (41.08803, 1.475807, 0.253906, 'HB2')), ('CG', (179.515246, 1.549972, 0.978906, None)), ('H', (8.3159, 0.588151, 0.036198, 'N')), ('HA', (4.603843, 0.309474, 0.133594, 'CA')), ('HB2', (2.7264, 0.280057, 0.220312, 'CB')), ('HB3', (2.683034, 0.255266, 0.255729, 'CB')), ('N', (120.230927, 3.966225, 0.146615, 'H'))], ('protein', 'Cys'): [('C', (174.775094, 1.963682, 0.690521, None)), ('CA', (58.07139, 3.292878, 0.49592, 'HA')), ('CB', (28.6, 1.8, 0.549906, 'HB2')), ('H', (8.415828, 0.683783, 0.061519, 'N')), ('HA', (4.699157, 0.549761, 0.084118, 'CA')), ('HB2', (2.927206, 0.473968, 0.123038, 'CB')), ('HB3', (2.884519, 0.495915, 0.140615, 'CB')), ('HG', (2.539318, 2.428652, 0.998117, 'SG')), ('N', (119.339964, 4.450665, 0.438795, 'H'))], ('protein', 'Cyss'): [('C', (174.775094, 1.963682, 0.690521, None)), ('CA', (58.07139, 3.292878, 0.49592, 'HA')), ('CB', (41.8, 1.8, 0.549906, 'HB2')), ('H', (8.415828, 0.683783, 0.061519, 'N')), ('HA', (4.699157, 0.549761, 0.084118, 'CA')), ('HB2', (2.927206, 0.473968, 0.123038, 'CB')), ('HB3', (2.884519, 0.495915, 0.140615, 'CB')), ('N', (119.339964, 4.450665, 0.438795, 'H'))], ('protein', 'Gln'): [('C', (176.40403, 1.920946, 0.433155, None)), ('CA', (56.761798, 2.082327, 0.192157, 'HA')), ('CB', (29.358559, 1.772749, 0.260606, 'HB3')), ('CD', (179.827346, 1.026666, 0.926916, None)), ('CG', (33.876419, 0.89098, 0.516221, 'HG2')), ('H', (8.216737, 0.61244, 0.03779, 'N')), ('HA', (4.281435, 0.44826, 0.145811, 'CA')), ('HB2', (2.056673, 0.235446, 0.253476, 'CB')), ('HB3', (2.032193, 0.243198, 0.301604, 'CB')), ('HE21', (7.243197, 0.430273, 0.512656, 'NE2')), ('HE22', (7.014516, 0.403005, 0.512656, 'NE2')), ('HG2', (2.327917, 0.242786, 0.313369, 'CG')), ('HG3', (2.302919, 0.262972, 0.37861, 'CG')), ('N', (119.290354, 3.686866, 0.153298, 'H')), ('NE2', (111.88868, 1.758582, 0.612478, 'HE21'))], ('protein', 'Glu'): [('C', (177.019843, 1.91817, 0.41323, None)), ('CA', (57.531344, 2.064791, 0.179611, 'HA')), ('CB', (30.197538, 1.660817, 0.241365, 'HB2')), ('CD', (182.899624, 1.786294, 0.982834, None)), ('CG', (36.202941, 0.965699, 0.497593, 'HG3')), ('H', (8.34354, 0.613833, 0.030563, 'N')), ('HA', (4.26613, 0.434106, 0.131673, 'CA')), ('HB2', (2.031746, 0.198885, 0.230061, 'CB')), ('HB3', (2.009291, 0.202896, 0.284069, 'CB')), ('HG2', (2.279046, 0.202965, 0.311911, 'CG')), ('HG3', (2.260935, 0.206668, 0.364455, 'CG')), ('N', (120.173056, 3.592825, 0.139837, 'H2'))], ('protein', 'Gly'): [('C', (174.017069, 1.841177, 0.473382, None)), ('CA', (45.562676, 1.121685, 0.235463, 'HA3')), ('H', (8.33061, 0.673335, 0.04484, 'N')), ('HA2', (3.988405, 0.369611, 0.150491, 'CA')), ('HA3', (3.912364, 0.37351, 0.191237, 'CA')), ('N', (109.068021, 3.80918, 0.190418, 'H'))], ('protein', 'His'): [('C', (175.302898, 1.948641, 0.514085, None)), ('CA', (56.675864, 2.330521, 0.279577, 'HA')), ('CB', (30.475373, 2.009559, 0.33169, 'HB2')), ('CD2', (119.952558, 2.769141, 0.787324, 'HD2')), ('CE1', (137.238155, 2.346656, 0.840141, 'HE1')), ('CG', (132.303333, 3.787014, 0.992253, None)), ('H', (8.262735, 0.688922, 0.100704, 'N')), ('HA', (4.627289, 0.467128, 0.18662, 'CA')), ('HB2', (3.110051, 0.349972, 0.261972, 'CB')), ('HB3', (3.057166, 0.355392, 0.291549, 'CB')), ('HD1', (8.265318, 2.399673, 0.943662, 'ND1')), ('HD2', (7.03722, 0.429625, 0.45493, 'CD2')), ('HE1', (8.013054, 0.520085, 0.517606, 'CE1')), ('HE2', (9.920824, 2.588519, 0.98169, 'NE2')), ('N', (119.109795, 4.192319, 0.235211, 'H')), ('ND1', (195.537424, 37.008263, 0.947183, 'HD1')), ('NE2', (177.698489, 16.243778, 0.952817, 'HE2'))], ('protein', 'Ile'): [('C', (175.86434, 1.82821, 0.422507, None)), ('CA', (61.705518, 2.600251, 0.188136, 'HA')), ('CB', (38.854432, 1.944834, 0.25269, 'HB')), ('CD1', (13.584336, 1.626539, 0.482408, 'HD1*')), ('CG1', (27.780248, 1.684249, 0.515848, 'HG13')), ('CG2', (17.636566, 1.237755, 0.469613, 'HG2*')), ('H', (8.308229, 0.703239, 0.032858, 'N')), ('HA', (4.224109, 0.580233, 0.132306, 'CA')), ('HB', (1.784957, 0.304183, 0.218377, 'CB')), ('HD1*', (0.685842, 0.282454, 0.294272, 'CD1')), ('HG12', (1.270219, 0.392634, 0.329165, 'CG1')), ('HG13', (1.216866, 0.399083, 0.364059, 'CG1')), ('HG2*', (0.789078, 0.258937, 0.281477, 'CG2')), ('N', (121.173088, 4.413042, 0.150044, 'H'))], ('protein', 'Leu'): [('C', (177.056361, 1.919039, 0.431646, None)), ('CA', (55.752106, 2.056969, 0.191568, 'HA')), ('CB', (42.540153, 1.789209, 0.255424, 'HB2')), ('CD1', (24.785797, 1.489808, 0.494267, 'HD1*')), ('CD2', (24.227473, 1.601505, 0.521609, 'HD2*')), ('CG', (26.875515, 0.996005, 0.543658, 'HG')), ('H', (8.238177, 0.674706, 0.033163, 'N')), ('HA', (4.346146, 0.491254, 0.154877, 'CA')), ('HB2', (1.616793, 0.329304, 0.261069, 'CB')), ('HB3', (1.534532, 0.346944, 0.302699, 'CB')), ('HD1*', (0.755018, 0.268818, 0.295114, 'CD1')), ('HD2*', (0.728231, 0.285852, 0.323337, 'CD2')), ('HG', (1.509274, 0.327438, 0.357559, 'CG')), ('N', (121.455301, 4.025737, 0.146587, 'H2'))], ('protein', 'Lys'): [('C', (176.775235, 1.906749, 0.452691, None)), ('CA', (57.154802, 2.135196, 0.229246, 'HA')), ('CB', (32.992345, 1.70047, 0.286857, 'HB3')), ('CD', (29.036786, 0.920116, 0.588718, 'HD2')), ('CE', (41.966911, 0.532535, 0.611722, 'HE2')), ('CG', (25.002996, 0.954247, 0.555511, 'HG3')), ('H', (8.190187, 0.62647, 0.036807, 'N')), ('HA', (4.283917, 0.449233, 0.134827, 'CA')), ('HB2', (1.788608, 0.231602, 0.230646, 'CB')), ('HB3', (1.765164, 0.240192, 0.286457, 'CB')), ('HD2', (1.606115, 0.230201, 0.433887, 'CD')), ('HD3', (1.597734, 0.235158, 0.490898, 'CD')), ('HE2', (2.924529, 0.170173, 0.447289, 'CE')), ('HE3', (2.919496, 0.175103, 0.516303, 'CE')), ('HG2', (1.380507, 0.240617, 0.340068, 'CG')), ('HG3', (1.370381, 0.245205, 0.40048, 'CG')), ('HZ*', (7.483198, 0.367244, 0.962393, 'NZ')), ('N', (120.486754, 3.843313, 0.179236, 'H')), ('NZ', (48.671163, 36.303503, 0.9982, 'HZ*'))], ('protein', 'Met'): [('C', (176.273626, 2.049059, 0.449133, None)), ('CA', (56.283714, 2.173536, 0.205727, 'HA')), ('CB', (33.259592, 2.202185, 0.269028, 'HB2')), ('CE', (17.113516, 1.14295, 0.691786, 'HE*')), ('CG', (32.098797, 1.057559, 0.567445, 'HG3')), ('H', (8.266266, 0.624249, 0.094951, 'N')), ('HA', (4.423979, 0.489446, 0.147702, 'CA')), ('HB2', (2.033462, 0.323993, 0.271289, 'CB')), ('HB3', (2.006533, 0.336088, 0.324039, 'CB')), ('HE*', (1.870402, 0.366566, 0.595328, 'CE')), ('HG2', (2.416216, 0.370668, 0.3685, 'CG')), ('HG3', (2.3767, 0.421305, 0.403919, 'CG')), ('N', (119.593417, 3.693716, 0.196684, 'H2'))], ('protein', 'Phe'): [('C', (175.565521, 1.948348, 0.445665, None)), ('CA', (58.305101, 2.55198, 0.217338, 'HA')), ('CB', (40.181708, 1.952764, 0.279609, 'HB2')), ('CD1', (131.626637, 1.261599, 0.746439, 'HD1')), ('CD2', (131.620012, 1.257999, 0.828246, 'HD2')), ('CE1', (130.696973, 1.484393, 0.782662, 'HE1')), ('CE2', (130.73114, 1.294712, 0.85348, 'HE2')), ('CD*', (131.620012, 1.257999, 0.828246, 'HD*')), ('CE*', (130.696973, 1.484393, 0.782662, 'HE*')), ('CG', (137.410725, 3.251523, 0.994302, None)), ('CZ', (129.222986, 1.622311, 0.835165, 'HZ')), ('H', (8.382242, 0.749659, 0.058201, 'N')), ('HA', (4.648786, 0.588854, 0.160765, 'CA')), ('HB2', (2.998135, 0.362851, 0.245828, 'CB')), ('HB3', (2.952455, 0.375443, 0.26862, 'CB')), ('HD1', (7.058833, 0.306262, 0.365893, 'CD1')), ('HD2', (7.06555, 0.304958, 0.494506, 'CD2')), ('HE1', (7.081438, 0.306502, 0.435083, 'CE1')), ('HE2', (7.084839, 0.303505, 0.541718, 'CE2')), ('HD*', (7.06555, 0.304958, 0.494506, 'CD*')), ('HE*', (7.081438, 0.306502, 0.435083, 'CE*')), ('HZ', (6.996208, 0.413472, 0.582418, 'CZ')), ('N', (120.085399, 4.232138, 0.169312, 'H3'))], ('protein', 'Pro'): [('C', (176.780325, 1.499687, 0.483755, None)), ('CA', (63.539193, 1.404973, 0.228159, 'HA')), ('CB', (31.977618, 1.011604, 0.292058, 'HB2')), ('CD', (50.448136, 0.757834, 0.560289, 'HD2')), ('CG', (27.3254, 0.9267, 0.57509, 'HG3')), ('HA', (4.408505, 0.329217, 0.180505, 'CA')), ('HB2', (2.077811, 0.327969, 0.25704, 'CB')), ('HB3', (2.029493, 0.322236, 0.275812, 'CB')), ('HD2', (3.665299, 0.3171, 0.331408, 'CD')), ('HD3', (3.643425, 0.3381, 0.362816, 'CD')), ('HG2', (1.944234, 0.266628, 0.361372, 'CG')), ('HG3', (1.920546, 0.282568, 0.404693, 'CG')), ('N', (131.085662, 9.209093, 0.979783, 'H3'))], ('protein', 'Ser'): [('C', (174.683288, 1.659248, 0.464592, None)), ('CA', (58.850778, 2.018005, 0.217349, 'HA')), ('CB', (63.993613, 1.384288, 0.300172, 'HB3')), ('H', (8.290302, 0.607958, 0.058564, 'N')), ('HA', (4.513436, 0.42012, 0.147023, 'CA')), ('HB2', (3.884335, 0.239598, 0.248714, 'CB')), ('HB3', (3.861902, 0.25007, 0.313159, 'CB')), ('HG', (5.575657, 1.195882, 0.988238, 'OG')), ('N', (115.813074, 3.723294, 0.185739, 'H3'))], ('protein', 'Thr'): [('C', (174.631688, 1.7074, 0.462333, None)), ('CA', (62.366001, 2.580251, 0.224368, 'HA')), ('CB', (69.886568, 1.524338, 0.292086, 'HB')), ('CG2', (21.649765, 0.95876, 0.519445, 'HG2*')), ('H', (8.264453, 0.646697, 0.039162, 'N')), ('HA', (4.487641, 0.495678, 0.153658, 'CA')), ('HB', (4.167755, 0.343464, 0.253196, 'CB')), ('HG1', (5.132804, 1.738798, 0.975524, 'OG1')), ('HG2*', (1.144699, 0.201156, 0.278216, 'CG2')), ('N', (115.081474, 4.991324, 0.158009, 'H'))], ('protein', 'Trp'): [('C', (176.218157, 1.939642, 0.518771, None)), ('CA', (57.833198, 2.50792, 0.324232, 'HA')), ('CB', (30.290294, 1.875868, 0.369738, 'HB2')), ('CD1', (126.600126, 1.837343, 0.715586, 'HD1')), ('CD2', (128.065, 2.873504, 0.990899, None)), ('CE2', (137.984074, 9.322232, 0.98066, None)), ('CE3', (120.52884, 1.591558, 0.786121, 'HE3')), ('CG', (111.433182, 0.972309, 0.987486, None)), ('CH2', (123.90205, 1.477779, 0.773606, 'HH2')), ('CZ2', (114.407511, 1.382949, 0.754266, 'HZ2')), ('CZ3', (121.530652, 1.444072, 0.78157, 'HZ3')), ('H', (8.287413, 0.81469, 0.110353, 'N')), ('HA', (4.708245, 0.556373, 0.196815, 'CA')), ('HB2', (3.173023, 0.343723, 0.266212, 'CB')), ('HB3', (3.134429, 0.352943, 0.299204, 'CB')), ('HD1', (7.138713, 0.340667, 0.357224, 'CD1')), ('HE1', (10.116375, 0.537535, 0.356086, 'NE1')), ('HE3', (7.305717, 0.382677, 0.411832, 'CE3')), ('HH2', (6.964333, 0.346475, 0.420933, 'CH2')), ('HZ2', (7.286362, 0.324283, 0.379977, 'CZ2')), ('HZ3', (6.871129, 0.368175, 0.431172, 'CZ3')), ('N', (121.285471, 4.389069, 0.2719, 'H2')), ('NE1', (129.398739, 2.021644, 0.547213, 'HE1'))], ('protein', 'Tyr'): [('C', (175.491657, 1.900925, 0.48777, None)), ('CA', (58.281804, 2.475766, 0.264346, 'HA')), ('CB', (39.616805, 2.081812, 0.337723, 'HB3')), ('CD1', (132.791984, 1.567221, 0.745532, 'HD1')), ('CD2', (132.624189, 2.080215, 0.835842, 'HD2')), ('CE1', (118.05756, 1.375306, 0.740828, 'HE1')), ('CE2', (118.004726, 1.152713, 0.83396, 'HE2')), ('CD*', (132.624189, 2.080215, 0.835842, 'HD*')), ('CE*', (118.05756, 1.375306, 0.740828, 'HE*')), ('CG', (129.98507, 2.882228, 0.988241, None)), ('CZ', (157.562708, 1.371867, 0.992004, None)), ('H', (8.325909, 0.750383, 0.062088, 'N')), ('HA', (4.645483, 0.583003, 0.161336, 'CA')), ('HB2', (2.903203, 0.37181, 0.248824, 'CB')), ('HB3', (2.849544, 0.377313, 0.265757, 'CB')), ('HD1', (6.937622, 0.279576, 0.331609, 'CD1')), ('HD2', (6.935375, 0.28204, 0.447789, 'CD2')), ('HE1', (6.704741, 0.220055, 0.355597, 'CE1')), ('HE2', (6.705084, 0.218493, 0.468956, 'CE2')), ('HD*', (6.935375, 0.28204, 0.447789, 'CD*')), ('HE*', (6.704741, 0.220055, 0.355597, 'CE*')), ('HH', (9.149362, 1.563879, 0.984478, 'OH')), ('N', (120.200602, 4.345637, 0.224365, 'H'))], ('protein', 'Val'): [('C', (175.732054, 1.819574, 0.437803, None)), ('CA', (62.6319, 2.794401, 0.199169, 'HA')), ('CB', (32.935144, 1.675944, 0.260559, 'HB')), ('CG1', (21.586062, 1.243471, 0.47796, 'HG1*')), ('CG2', (21.43703, 1.431185, 0.509808, 'HG2*')), ('H', (8.307943, 0.704303, 0.039465, 'N')), ('HA', (4.204042, 0.59615, 0.14378, 'CA')), ('HB', (1.992687, 0.286555, 0.228479, 'CB')), ('HG1*', (0.832713, 0.242229, 0.252943, 'CG1')), ('HG2*', (0.810046, 0.266148, 0.27579, 'CG2')), ('N', (120.724161, 4.673536, 0.144242, 'H'))]}

Below values from ftp://ftp.cbs.cnrs.fr/pub/RESCUE2

For reference see:

J Biomol NMR. 2004 Sep;30(1:47-60 From NMR chemical shifts to amino acid types: investigation of the predictive power carried by nuclei. Marin A, Malliavin TE, Nicolas P, Delsuc MA.

ccpnmodel.ccpncore.lib.assignment.ChemicalShift.getAtomProbability(ccpCode, atomName, shiftValue, molType='protein')[source]
ccpnmodel.ccpncore.lib.assignment.ChemicalShift.getCcpCodeData(nmrProject, ccpCode, molType=None, atomType=None)[source]
ccpnmodel.ccpncore.lib.assignment.ChemicalShift.getCcpCodes(chain)[source]
ccpnmodel.ccpncore.lib.assignment.ChemicalShift.getChainResTypesPriors(chain)[source]
ccpnmodel.ccpncore.lib.assignment.ChemicalShift.getChainResidueCodes(chain)[source]
ccpnmodel.ccpncore.lib.assignment.ChemicalShift.getResidueAtoms(ccpCode, molType='protein')[source]
ccpnmodel.ccpncore.lib.assignment.ChemicalShift.getSpinSystemChainProbabilities(spinSystem, chain, shiftList, resShifts)[source]
ccpnmodel.ccpncore.lib.assignment.ChemicalShift.getSpinSystemResidueProbability(spinSystem, shiftList, ccpCode, prior=0.05, molType='protein', resShifts=())[source]

Get probability that Spin system matches molType and ccpCode NB to avoid rejection all atom names must be either unassigned (default) or correct!

ccpnmodel.ccpncore.lib.assignment.ChemicalShift.getSpinSystemScore(spinSystem, resShifts, chain, shiftList)[source]