schrodinger.protein.analysis_params module

schrodinger.protein.analysis_params.sidechain_dihedral_atomnames = {' ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'A': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'ARG ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'ASN ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' OD1']], 'ASP ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' OD1']], 'CYS ': [[' N  ', ' CA ', ' CB ', ' SG ']], 'G': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'GLN ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'GLU ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'H': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'HID ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' ND1']], 'HIE ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' ND1']], 'HIP ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' ND1']], 'HIS ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' ND1']], 'ILE ': [[' N  ', ' CA ', ' CB ', ' CG1'], [' CA ', ' CB ', ' CG1', ' CD1']], 'L': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'LEU ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD1']], 'LYS ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'MET ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' SD ']], 'N': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'PHE ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD1']], 'PRO ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'R': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']], 'S': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' OD1']], 'SER ': [[' N  ', ' CA ', ' CB ', ' OG ']], 'THR ': [[' N  ', ' CA ', ' CB ', ' OG1']], 'TRP ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD1']], 'TYR ': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD1']], 'VAL ': [[' N  ', ' CA ', ' CB ', ' CG1']], 'Y': [[' N  ', ' CA ', ' CB ', ' CG '], [' CA ', ' CB ', ' CG ', ' CD ']]}

Dictionary containing atom names for amino acid sidechains, keys are residue names and values are lists of lists of atom names, one list for each sidechain. NOTE: only Chi1 and Chi2 atoms are included for each residue. Deprecated; use mmrotamer library function instead.

schrodinger.protein.analysis_params.backbone_dihedrals = {' ': {'-10.0,-70.0': 1.7e-05, '-10.0,100.0': 1.7e-05, '-10.0,110.0': 1.7e-05, '-100.0,-10.0': 0.00367, '-100.0,-100.0': 0.000121, '-100.0,-110.0': 1.7e-05, '-100.0,-120.0': 1.7e-05, '-100.0,-130.0': 1.7e-05, '-100.0,-140.0': 5.2e-05, '-100.0,-150.0': 5.2e-05, '-100.0,-160.0': 8.7e-05, '-100.0,-170.0': 0.000104, '-100.0,-20.0': 0.002822, '-100.0,-30.0': 0.002112, '-100.0,-40.0': 0.001558, '-100.0,-50.0': 0.000589, '-100.0,-60.0': 0.000173, '-100.0,-70.0': 0.000121, '-100.0,-80.0': 6.9e-05, '-100.0,-90.0': 3.5e-05, '-100.0,0.0': 0.005833, '-100.0,10.0': 0.005193, '-100.0,100.0': 0.001402, '-100.0,110.0': 0.003133, '-100.0,120.0': 0.006024, '-100.0,130.0': 0.007322, '-100.0,140.0': 0.005539, '-100.0,150.0': 0.0036, '-100.0,160.0': 0.002146, '-100.0,170.0': 0.001091, '-100.0,180.0': 0.000346, '-100.0,20.0': 0.001679, '-100.0,30.0': 0.000675, '-100.0,40.0': 0.000156, '-100.0,50.0': 0.000121, '-100.0,60.0': 8.7e-05, '-100.0,70.0': 0.000312, '-100.0,80.0': 0.000225, '-100.0,90.0': 0.000537, '-110.0,-10.0': 0.00225, '-110.0,-100.0': 3.5e-05, '-110.0,-110.0': 3.5e-05, '-110.0,-130.0': 3.5e-05, '-110.0,-140.0': 5.2e-05, '-110.0,-150.0': 1.7e-05, '-110.0,-160.0': 6.9e-05, '-110.0,-170.0': 0.000138, '-110.0,-20.0': 0.001973, '-110.0,-30.0': 0.001385, '-110.0,-40.0': 0.001073, '-110.0,-50.0': 0.000537, '-110.0,-60.0': 0.000173, '-110.0,-70.0': 0.000104, '-110.0,-80.0': 6.9e-05, '-110.0,-90.0': 3.5e-05, '-110.0,0.0': 0.003652, '-110.0,10.0': 0.003704, '-110.0,100.0': 0.001212, '-110.0,110.0': 0.003081, '-110.0,120.0': 0.005228, '-110.0,130.0': 0.009105, '-110.0,140.0': 0.006768, '-110.0,150.0': 0.004656, '-110.0,160.0': 0.002804, '-110.0,170.0': 0.001073, '-110.0,180.0': 0.00026, '-110.0,20.0': 0.002925, '-110.0,30.0': 0.001021, '-110.0,40.0': 0.000208, '-110.0,50.0': 0.000121, '-110.0,60.0': 8.7e-05, '-110.0,70.0': 0.00019, '-110.0,80.0': 0.00019, '-110.0,90.0': 0.000398, '-120.0,-10.0': 0.001714, '-120.0,-100.0': 5.2e-05, '-120.0,-110.0': 0.000138, '-120.0,-120.0': 3.5e-05, '-120.0,-130.0': 8.7e-05, '-120.0,-140.0': 6.9e-05, '-120.0,-150.0': 5.2e-05, '-120.0,-160.0': 3.5e-05, '-120.0,-170.0': 0.000156, '-120.0,-20.0': 0.001367, '-120.0,-30.0': 0.00116, '-120.0,-40.0': 0.000727, '-120.0,-50.0': 0.000294, '-120.0,-60.0': 0.000277, '-120.0,-70.0': 3.5e-05, '-120.0,-80.0': 3.5e-05, '-120.0,-90.0': 3.5e-05, '-120.0,0.0': 0.001593, '-120.0,10.0': 0.002268, '-120.0,100.0': 0.001367, '-120.0,110.0': 0.002579, '-120.0,120.0': 0.005816, '-120.0,130.0': 0.008551, '-120.0,140.0': 0.009174, '-120.0,150.0': 0.00798, '-120.0,160.0': 0.004206, '-120.0,170.0': 0.001316, '-120.0,180.0': 0.000364, '-120.0,20.0': 0.002216, '-120.0,30.0': 0.001229, '-120.0,40.0': 0.000398, '-120.0,50.0': 0.000242, '-120.0,60.0': 0.000173, '-120.0,70.0': 0.000675, '-120.0,80.0': 0.000658, '-120.0,90.0': 0.000848, '-130.0,-10.0': 0.000692, '-130.0,-100.0': 1.7e-05, '-130.0,-110.0': 6.9e-05, '-130.0,-120.0': 3.5e-05, '-130.0,-130.0': 1.7e-05, '-130.0,-140.0': 3.5e-05, '-130.0,-150.0': 1.7e-05, '-130.0,-160.0': 0.000138, '-130.0,-170.0': 0.000173, '-130.0,-20.0': 0.000623, '-130.0,-30.0': 0.000398, '-130.0,-40.0': 0.000381, '-130.0,-50.0': 0.000242, '-130.0,-60.0': 0.000225, '-130.0,-70.0': 3.5e-05, '-130.0,-90.0': 3.5e-05, '-130.0,0.0': 0.000935, '-130.0,10.0': 0.001039, '-130.0,100.0': 0.001056, '-130.0,110.0': 0.002008, '-130.0,120.0': 0.004933, '-130.0,130.0': 0.008655, '-130.0,140.0': 0.011096, '-130.0,150.0': 0.01113, '-130.0,160.0': 0.007218, '-130.0,170.0': 0.002458, '-130.0,180.0': 0.000675, '-130.0,20.0': 0.000935, '-130.0,30.0': 0.000917, '-130.0,40.0': 0.000744, '-130.0,50.0': 0.000571, '-130.0,60.0': 0.000796, '-130.0,70.0': 0.001523, '-130.0,80.0': 0.001108, '-130.0,90.0': 0.000796, '-140.0,-10.0': 0.000156, '-140.0,-110.0': 1.7e-05, '-140.0,-120.0': 1.7e-05, '-140.0,-150.0': 1.7e-05, '-140.0,-160.0': 3.5e-05, '-140.0,-170.0': 8.7e-05, '-140.0,-20.0': 8.7e-05, '-140.0,-30.0': 8.7e-05, '-140.0,-40.0': 0.000104, '-140.0,-50.0': 0.000156, '-140.0,-60.0': 0.000104, '-140.0,-70.0': 3.5e-05, '-140.0,-90.0': 1.7e-05, '-140.0,0.0': 0.000173, '-140.0,10.0': 0.000381, '-140.0,100.0': 0.000519, '-140.0,110.0': 0.000883, '-140.0,120.0': 0.002718, '-140.0,130.0': 0.005591, '-140.0,140.0': 0.009036, '-140.0,150.0': 0.010317, '-140.0,160.0': 0.008482, '-140.0,170.0': 0.002614, '-140.0,180.0': 0.000467, '-140.0,20.0': 0.000329, '-140.0,30.0': 0.000467, '-140.0,40.0': 0.000225, '-140.0,50.0': 0.000346, '-140.0,60.0': 0.000606, '-140.0,70.0': 0.000796, '-140.0,80.0': 0.000415, '-140.0,90.0': 0.000398, '-150.0,-10.0': 1.7e-05, '-150.0,-160.0': 3.5e-05, '-150.0,-170.0': 0.000138, '-150.0,-30.0': 3.5e-05, '-150.0,-40.0': 1.7e-05, '-150.0,-50.0': 1.7e-05, '-150.0,-60.0': 3.5e-05, '-150.0,0.0': 1.7e-05, '-150.0,10.0': 8.7e-05, '-150.0,100.0': 0.00026, '-150.0,110.0': 0.000502, '-150.0,120.0': 0.001194, '-150.0,130.0': 0.002441, '-150.0,140.0': 0.004535, '-150.0,150.0': 0.005539, '-150.0,160.0': 0.006266, '-150.0,170.0': 0.00277, '-150.0,180.0': 0.000589, '-150.0,20.0': 6.9e-05, '-150.0,30.0': 6.9e-05, '-150.0,40.0': 3.5e-05, '-150.0,50.0': 3.5e-05, '-150.0,60.0': 0.000208, '-150.0,70.0': 0.00026, '-150.0,80.0': 0.000156, '-150.0,90.0': 0.000121, '-160.0,-10.0': 1.7e-05, '-160.0,-100.0': 1.7e-05, '-160.0,-140.0': 1.7e-05, '-160.0,-160.0': 1.7e-05, '-160.0,-170.0': 6.9e-05, '-160.0,-40.0': 1.7e-05, '-160.0,0.0': 1.7e-05, '-160.0,10.0': 3.5e-05, '-160.0,100.0': 5.2e-05, '-160.0,110.0': 0.000156, '-160.0,120.0': 0.000364, '-160.0,130.0': 0.000762, '-160.0,140.0': 0.002337, '-160.0,150.0': 0.002475, '-160.0,160.0': 0.004881, '-160.0,170.0': 0.002943, '-160.0,180.0': 0.000606, '-160.0,30.0': 1.7e-05, '-160.0,40.0': 5.2e-05, '-160.0,50.0': 3.5e-05, '-160.0,60.0': 3.5e-05, '-160.0,70.0': 6.9e-05, '-160.0,80.0': 0.000121, '-160.0,90.0': 5.2e-05, '-170.0,-150.0': 1.7e-05, '-170.0,-170.0': 0.000138, '-170.0,-30.0': 1.7e-05, '-170.0,10.0': 1.7e-05, '-170.0,100.0': 1.7e-05, '-170.0,110.0': 3.5e-05, '-170.0,120.0': 0.000104, '-170.0,130.0': 0.000156, '-170.0,140.0': 0.000346, '-170.0,150.0': 0.000866, '-170.0,160.0': 0.001714, '-170.0,170.0': 0.001402, '-170.0,180.0': 0.000138, '-170.0,80.0': 1.7e-05, '-170.0,90.0': 1.7e-05, '-20.0,110.0': 3.5e-05, '-20.0,130.0': 1.7e-05, '-30.0,-30.0': 1.7e-05, '-30.0,-40.0': 1.7e-05, '-30.0,-50.0': 1.7e-05, '-30.0,-60.0': 3.5e-05, '-30.0,-70.0': 1.7e-05, '-30.0,110.0': 1.7e-05, '-30.0,120.0': 5.2e-05, '-30.0,140.0': 1.7e-05, '-40.0,-30.0': 1.7e-05, '-40.0,-40.0': 0.000364, '-40.0,-50.0': 0.000848, '-40.0,-60.0': 0.000208, '-40.0,-70.0': 1.7e-05, '-40.0,-80.0': 3.5e-05, '-40.0,100.0': 1.7e-05, '-40.0,110.0': 3.5e-05, '-40.0,120.0': 6.9e-05, '-40.0,130.0': 0.000485, '-40.0,140.0': 0.000104, '-40.0,90.0': 1.7e-05, '-50.0,-20.0': 0.000104, '-50.0,-30.0': 0.002648, '-50.0,-40.0': 0.012307, '-50.0,-50.0': 0.012688, '-50.0,-60.0': 0.000606, '-50.0,100.0': 1.7e-05, '-50.0,110.0': 3.5e-05, '-50.0,120.0': 0.000779, '-50.0,130.0': 0.00315, '-50.0,140.0': 0.002233, '-50.0,150.0': 0.000692, '-50.0,160.0': 0.000173, '-50.0,170.0': 1.7e-05, '-50.0,90.0': 1.7e-05, '-60.0,-10.0': 0.001142, '-60.0,-20.0': 0.012255, '-60.0,-30.0': 0.034395, '-60.0,-40.0': 0.144729, '-60.0,-50.0': 0.063407, '-60.0,-60.0': 0.0009, '-60.0,-70.0': 5.2e-05, '-60.0,0.0': 6.9e-05, '-60.0,10.0': 1.7e-05, '-60.0,100.0': 1.7e-05, '-60.0,110.0': 8.7e-05, '-60.0,120.0': 0.001818, '-60.0,130.0': 0.008568, '-60.0,140.0': 0.01068, '-60.0,150.0': 0.006041, '-60.0,160.0': 0.001523, '-60.0,170.0': 0.000121, '-60.0,180.0': 1.7e-05, '-70.0,-10.0': 0.009642, '-70.0,-170.0': 1.7e-05, '-70.0,-20.0': 0.018279, '-70.0,-30.0': 0.03121, '-70.0,-40.0': 0.070833, '-70.0,-50.0': 0.013086, '-70.0,-60.0': 0.000606, '-70.0,-70.0': 6.9e-05, '-70.0,0.0': 0.000969, '-70.0,10.0': 6.9e-05, '-70.0,100.0': 0.000121, '-70.0,110.0': 0.000554, '-70.0,120.0': 0.002545, '-70.0,130.0': 0.008136, '-70.0,140.0': 0.010819, '-70.0,150.0': 0.008863, '-70.0,160.0': 0.004985, '-70.0,170.0': 0.001073, '-70.0,180.0': 0.000173, '-70.0,20.0': 1.7e-05, '-70.0,30.0': 1.7e-05, '-70.0,40.0': 1.7e-05, '-70.0,70.0': 1.7e-05, '-70.0,80.0': 3.5e-05, '-70.0,90.0': 3.5e-05, '-80.0,-10.0': 0.009469, '-80.0,-150.0': 1.7e-05, '-80.0,-160.0': 6.9e-05, '-80.0,-170.0': 3.5e-05, '-80.0,-20.0': 0.007478, '-80.0,-30.0': 0.007114, '-80.0,-40.0': 0.007097, '-80.0,-50.0': 0.001852, '-80.0,-60.0': 0.00064, '-80.0,-70.0': 6.9e-05, '-80.0,-80.0': 1.7e-05, '-80.0,0.0': 0.004812, '-80.0,10.0': 0.000727, '-80.0,100.0': 0.000779, '-80.0,110.0': 0.002146, '-80.0,120.0': 0.004293, '-80.0,130.0': 0.008343, '-80.0,140.0': 0.007893, '-80.0,150.0': 0.005937, '-80.0,160.0': 0.003895, '-80.0,170.0': 0.001835, '-80.0,180.0': 0.000277, '-80.0,40.0': 3.5e-05, '-80.0,50.0': 5.2e-05, '-80.0,60.0': 0.00026, '-80.0,70.0': 0.00071, '-80.0,80.0': 0.000744, '-80.0,90.0': 0.000606, '-90.0,-10.0': 0.006907, '-90.0,-100.0': 1.7e-05, '-90.0,-130.0': 1.7e-05, '-90.0,-140.0': 1.7e-05, '-90.0,-150.0': 1.7e-05, '-90.0,-160.0': 1.7e-05, '-90.0,-170.0': 6.9e-05, '-90.0,-20.0': 0.004379, '-90.0,-30.0': 0.003272, '-90.0,-40.0': 0.00206, '-90.0,-50.0': 0.000658, '-90.0,-60.0': 0.00045, '-90.0,-70.0': 6.9e-05, '-90.0,-80.0': 6.9e-05, '-90.0,0.0': 0.007755, '-90.0,10.0': 0.003999, '-90.0,100.0': 0.000935, '-90.0,110.0': 0.003168, '-90.0,120.0': 0.005574, '-90.0,130.0': 0.006578, '-90.0,140.0': 0.005712, '-90.0,150.0': 0.004102, '-90.0,160.0': 0.002718, '-90.0,170.0': 0.001316, '-90.0,180.0': 0.000433, '-90.0,20.0': 0.000415, '-90.0,30.0': 0.000121, '-90.0,40.0': 8.7e-05, '-90.0,50.0': 0.000156, '-90.0,60.0': 0.000883, '-90.0,70.0': 0.001125, '-90.0,80.0': 0.000727, '-90.0,90.0': 0.000762, '10.0,-50.0': 1.7e-05, '100.0,-50.0': 1.7e-05, '100.0,120.0': 1.7e-05, '120.0,-100.0': 1.7e-05, '140.0,130.0': 1.7e-05, '140.0,140.0': 1.7e-05, '140.0,150.0': 1.7e-05, '150.0,180.0': 1.7e-05, '160.0,150.0': 1.7e-05, '170.0,110.0': 1.7e-05, '170.0,160.0': 1.7e-05, '170.0,20.0': 1.7e-05, '170.0,30.0': 1.7e-05, '180.0,-170.0': 1.7e-05, 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