ppafm.atomicUtils

ppafm.atomicUtils.ZsToElems(Zs)

Convert atomic numbers to element symbols.

ppafm.atomicUtils.countTypeBonds(atoms, ofAtoms, rcut)

ppafm.atomicUtils.findBonds(atoms, iZs, sc, ELEMENTS=[[1, 'H', 1, 1, 'S', 'Hydrogen', 0.365, 1.487, (255, 255, 255), 1], [2, 'He', 1, 0, '0', 'Helium', 0.32, 1.481, (217, 255, 255), 2], [3, 'Li', 2, 1, 'S', 'Lithium', 1.395, 2.0, (204, 128, 255), 1], [4, 'Be', 2, 2, 'S', 'Beryllium', 0.975, 2.0, (194, 255, 0), 2], [5, 'B', 2, 3, 'P', 'Boron', 0.835, 2.08, (255, 181, 181), 3], [6, 'C', 2, 4, 'P', 'Carbon', 0.735, 1.908, (144, 144, 144), 4], [7, 'N', 2, 5, 'P', 'Nitrogen', 0.7, 1.78, (48, 80, 248), 5], [8, 'O', 2, 6, 'P', 'Oxygen', 0.665, 1.661, (255, 13, 13), 6], [9, 'F', 2, 7, 'P', 'Fluorine', 0.605, 1.75, (144, 224, 80), 7], [10, 'Ne', 2, 0, '0', 'Neon', 0.69, 1.543, (179, 227, 245), 8], [11, 'Na', 3, 1, 'S', 'Sodium', 1.67, 2.77, (171, 92, 242), 1], [12, 'Mg', 3, 2, 'S', 'Magnesium', 1.4, 2.42, (138, 255, 0), 2], [13, 'Al', 3, 3, 'P', 'Aluminium', 1.215, 2.4, (191, 166, 166), 3], [14, 'Si', 3, 4, 'P', 'Silicon', 1.105, 1.9, (240, 200, 160), 4], [15, 'P', 3, 5, 'P', 'Phosphorus', 1.03, 2.1, (255, 128, 0), 5], [16, 'S', 3, 6, 'P', 'Sulfur', 1.01, 2.0, (255, 255, 48), 6], [17, 'Cl', 3, 7, 'P', 'Chlorine', 0.995, 1.948, (31, 240, 31), 7], [18, 'Ar', 3, 0, '0', 'Argon', 0.84, 1.88, (128, 209, 227), 8], [19, 'K', 4, 1, 'S', 'Potassium', 2.08, 3.02, (143, 64, 212), 1], [20, 'Ca', 4, 2, 'S', 'Calcium', 1.77, 2.78, (250, 150, 0), 2], [21, 'Sc', 4, 3, 'D', 'Scandium', 1.52, 2.62, (230, 230, 230), 3], [22, 'Ti', 4, 4, 'D', 'Titanium', 1.38, 2.44, (191, 194, 199), 4], [23, 'V', 4, 5, 'D', 'Vanadium', 1.3, 2.27, (166, 166, 171), 5], [24, 'Cr', 4, 6, 'D', 'Chromium', 1.335, 2.23, (138, 153, 199), 6], [25, 'Mn', 4, 7, 'D', 'Manganese', 1.395, 2.25, (156, 122, 199), 7], [26, 'Fe', 4, 8, 'D', 'Iron', 1.325, 2.27, (224, 102, 51), 8], [27, 'Co', 4, 9, 'D', 'Cobalt', 1.305, 2.25, (240, 144, 160), 9], [28, 'Ni', 4, 10, 'D', 'Nickel', 1.28, 2.23, (80, 208, 80), 0], [29, 'Cu', 4, 1, 'D', 'Copper', 1.365, 2.23, (200, 128, 51), 0], [30, 'Zn', 4, 2, 'D', 'Zinc', 1.33, 2.24, (125, 128, 176), 0], [31, 'Ga', 4, 3, 'P', 'Gallium', 1.28, 2.41, (194, 143, 143), 0], [32, 'Ge', 4, 4, 'P', 'Germanium', 1.235, 2.32, (102, 143, 143), 0], [33, 'As', 4, 5, 'P', 'Arsenic', 1.17, 2.25, (189, 128, 227), 0], [34, 'Se', 4, 6, 'P', 'Selenium', 1.155, 2.18, (255, 161, 0), 0], [35, 'Br', 4, 7, 'P', 'Bromine', 1.145, 2.22, (166, 41, 41), 0], [36, 'Kr', 4, 0, '0', 'Krypton', 1.1, 2.0, (92, 184, 209), 0], [37, 'Rb', 5, 1, 'S', 'Rubidium', 2.23, 3.15, (112, 46, 176), 0], [38, 'Sr', 5, 2, 'S', 'Strontium', 1.96, 2.94, (0, 255, 0), 0], [39, 'Y', 5, 3, 'D', 'Yttrium', 1.71, 2.71, (148, 255, 255), 0], [40, 'Zr', 5, 4, 'D', 'Zirconium', 1.515, 2.57, (148, 224, 224), 0], [41, 'Nb', 5, 5, 'D', 'Niobium', 1.41, 2.46, (115, 194, 201), 0], [42, 'Mo', 5, 6, 'D', 'Molybdenum', 1.45, 2.39, (84, 181, 181), 0], [43, 'Tc', 5, 7, 'D', 'Technetium', 1.455, 2.37, (59, 158, 158), 0], [44, 'Ru', 5, 8, 'D', 'Ruthenium', 1.28, 2.35, (36, 143, 143), 0], [45, 'Rh', 5, 9, 'D', 'Rhodium', 1.35, 2.32, (10, 125, 140), 0], [46, 'Pd', 5, 10, 'D', 'Palladium', 1.355, 2.35, (0, 105, 133), 0], [47, 'Ag', 5, 1, 'D', 'Silver', 1.565, 2.37, (192, 192, 192), 0], [48, 'Cd', 5, 2, 'D', 'Cadmium', 1.515, 2.37, (255, 217, 143), 0], [49, 'In', 5, 3, 'P', 'Indium', 1.495, 2.53, (166, 117, 115), 0], [50, 'Sn', 5, 4, 'P', 'Tin', 1.43, 2.46, (102, 128, 128), 0], [51, 'Sb', 5, 5, 'P', 'Antimony', 1.415, 2.41, (158, 99, 181), 0], [52, 'Te', 5, 6, 'P', 'Tellurium', 1.375, 2.36, (212, 122, 0), 0], [53, 'I', 5, 7, 'P', 'Iodine', 1.365, 2.35, (148, 0, 148), 0], [54, 'Xe', 5, 0, '0', 'Xenon', 1.3, 2.181, (66, 158, 176), 0], [55, 'Cs', 6, 1, 'S', 'Caesium', 2.425, 3.3, (87, 23, 143), 0], [56, 'Ba', 6, 2, 'S', 'Barium', 2.065, 3.05, (0, 201, 0), 0], [57, 'La', 6, 3, 'F', 'Lanthanum', 1.82, 2.81, (112, 212, 255), 0], [58, 'Ce', 6, 4, 'F', 'Cerium', 1.85, 2.0, (255, 255, 199), 0], [59, 'Pr', 6, 5, 'F', 'Praseodymium', 1.85, 2.0, (217, 255, 199), 0], [60, 'Nd', 6, 6, 'F', 'Neodymium', 1.85, 2.0, (199, 255, 199), 0], [61, 'Pm', 6, 7, 'F', 'Promethium', 1.85, 2.0, (163, 255, 199), 0], [62, 'Sm', 6, 8, 'F', 'Samarium', 1.85, 2.0, (143, 255, 199), 0], [63, 'Eu', 6, 9, 'F', 'Europium', 1.85, 2.0, (97, 255, 199), 0], [64, 'Gd', 6, 10, 'F', 'Gadolinium', 1.8, 2.0, (69, 255, 199), 0], [65, 'Tb', 6, 11, 'F', 'Terbium', 1.75, 2.0, (48, 255, 199), 0], [66, 'Dy', 6, 12, 'F', 'Dysprosium', 1.75, 2.0, (31, 255, 199), 0], [67, 'Ho', 6, 13, 'F', 'Holmium', 1.75, 2.0, (0, 255, 156), 0], [68, 'Er', 6, 14, 'F', 'Erbium', 1.75, 2.0, (0, 230, 117), 0], [69, 'Tm', 6, 1, 'F', 'Thulium', 1.75, 2.0, (0, 212, 82), 0], [70, 'Yb', 6, 2, 'F', 'Ytterbium', 1.75, 2.0, (0, 191, 56), 0], [71, 'Lu', 6, 3, 'D', 'Lutetium', 1.675, 2.0, (0, 171, 36), 0], [72, 'Hf', 6, 4, 'D', 'Hafnium', 1.525, 2.52, (77, 194, 255), 0], [73, 'Ta', 6, 5, 'D', 'Tantalum', 1.415, 2.42, (77, 166, 255), 0], [74, 'W', 6, 6, 'D', 'Tungsten', 1.405, 2.36, (33, 148, 214), 0], [75, 'Re', 6, 7, 'D', 'Rhenium', 1.47, 2.35, (38, 125, 171), 0], [76, 'Os', 6, 8, 'D', 'Osmium', 1.29, 2.33, (38, 102, 150), 0], [77, 'Ir', 6, 9, 'D', 'Iridium', 1.36, 2.34, (23, 84, 135), 0], [78, 'Pt', 6, 10, 'D', 'Platinum', 1.315, 2.37, (208, 208, 224), 0], [79, 'Au', 6, 1, 'D', 'Gold', 1.395, 2.41, (255, 209, 35), 0], [80, 'Hg', 6, 2, 'D', 'Mercury', 1.495, 2.25, (184, 184, 208), 0], [81, 'Tl', 6, 3, 'P', 'Thallium', 1.69, 2.53, (166, 84, 77), 0], [82, 'Pb', 6, 4, 'P', 'Lead', 1.635, 2.53, (87, 89, 97), 0], [83, 'Bi', 6, 5, 'P', 'Bismuth', 1.53, 3.52, (158, 79, 181), 0], [84, 'Po', 6, 6, 'P', 'Polonium', 1.9, 2.0, (171, 92, 0), 0], [85, 'At', 6, 7, 'P', 'Astatine', 2.0, 2.0, (117, 79, 69), 0], [86, 'Rn', 6, 0, '0', 'Radon', 2.0, 2.0, (66, 130, 150), 0], [87, 'Fr', 7, 1, 'S', 'Francium', 2.0, 2.0, (66, 0, 102), 0], [88, 'Ra', 7, 2, 'S', 'Radium', 2.0, 2.0, (0, 125, 0), 0], [89, 'Ac', 7, 3, 'F', 'Actinium', 2.0, 2.0, (112, 171, 250), 0], [90, 'Th', 7, 4, 'F', 'Thorium', 2.0, 2.75, (0, 186, 255), 0], [91, 'Pa', 7, 5, 'F', 'Protactinium', 2.0, 2.0, (0, 161, 255), 0], [92, 'U', 7, 6, 'F', 'Uranium', 2.0, 2.65, (0, 143, 255), 0], [93, 'Np', 7, 7, 'F', 'Neptunium', 2.0, 2.0, (0, 128, 255), 0], [94, 'Pu', 7, 8, 'F', 'Plutonium', 2.0, 2.0, (0, 107, 255), 0], [95, 'Am', 7, 9, 'F', 'Americium', 2.0, 2.0, (84, 92, 242), 0], [96, 'Cm', 7, 10, 'F', 'Curium', 2.0, 2.0, (120, 92, 227), 0], [97, 'Bk', 7, 11, 'F', 'Berkelium', 2.0, 2.0, (138, 79, 227), 0], [98, 'Cf', 7, 12, 'F', 'Californium', 2.0, 2.0, (161, 54, 212), 0], [99, 'Es', 7, 13, 'F', 'Einsteinium', 2.0, 2.0, (179, 31, 212), 0], [100, 'Fm', 7, 14, 'F', 'Fermium', 2.0, 2.0, (179, 31, 186), 0], [101, 'Md', 7, 1, 'F', 'Mendelevium', 2.0, 2.0, (179, 13, 166), 0], [102, 'No', 7, 2, 'F', 'Nobelium', 2.0, 2.0, (189, 13, 135), 0], [103, 'Lr', 7, 3, 'D', 'Lawrencium', 2.0, 2.0, (199, 0, 102), 0], [104, 'Rf', 7, 4, 'D', 'Rutherfordium', 2.0, 2.0, (204, 0, 89), 0], [105, 'Db', 7, 5, 'D', 'Dubnium', 2.0, 2.0, (209, 0, 79), 0], [106, 'Sg', 7, 6, 'D', 'Seaborgium', 2.0, 2.0, (217, 0, 69), 0], [107, 'Bh', 7, 7, 'D', 'Bohrium', 2.0, 2.0, (224, 0, 56), 0], [108, 'Hs', 7, 8, 'D', 'Hassium', 2.0, 2.0, (230, 0, 46), 0], [109, 'Mt', 7, 9, 'D', 'Meitnerium', 2.0, 2.0, (235, 0, 38), 0], [110, 'Ds', 7, 10, 'D', 'Darmstadtium', 2.0, 2.0, (128, 128, 128), 0], [111, 'Rg', 7, 1, 'D', 'Roentgenium', 2.0, 2.0, (128, 128, 128), 0], [112, 'Uub', 7, 2, 'D', 'Ununbium', 2.0, 2.0, (128, 128, 128), 0]], FFparams=None)

ppafm.atomicUtils.findBonds_(atoms, iZs, sc, ELEMENTS=[[1, 'H', 1, 1, 'S', 'Hydrogen', 0.365, 1.487, (255, 255, 255), 1], [2, 'He', 1, 0, '0', 'Helium', 0.32, 1.481, (217, 255, 255), 2], [3, 'Li', 2, 1, 'S', 'Lithium', 1.395, 2.0, (204, 128, 255), 1], [4, 'Be', 2, 2, 'S', 'Beryllium', 0.975, 2.0, (194, 255, 0), 2], [5, 'B', 2, 3, 'P', 'Boron', 0.835, 2.08, (255, 181, 181), 3], [6, 'C', 2, 4, 'P', 'Carbon', 0.735, 1.908, (144, 144, 144), 4], [7, 'N', 2, 5, 'P', 'Nitrogen', 0.7, 1.78, (48, 80, 248), 5], [8, 'O', 2, 6, 'P', 'Oxygen', 0.665, 1.661, (255, 13, 13), 6], [9, 'F', 2, 7, 'P', 'Fluorine', 0.605, 1.75, (144, 224, 80), 7], [10, 'Ne', 2, 0, '0', 'Neon', 0.69, 1.543, (179, 227, 245), 8], [11, 'Na', 3, 1, 'S', 'Sodium', 1.67, 2.77, (171, 92, 242), 1], [12, 'Mg', 3, 2, 'S', 'Magnesium', 1.4, 2.42, (138, 255, 0), 2], [13, 'Al', 3, 3, 'P', 'Aluminium', 1.215, 2.4, (191, 166, 166), 3], [14, 'Si', 3, 4, 'P', 'Silicon', 1.105, 1.9, (240, 200, 160), 4], [15, 'P', 3, 5, 'P', 'Phosphorus', 1.03, 2.1, (255, 128, 0), 5], [16, 'S', 3, 6, 'P', 'Sulfur', 1.01, 2.0, (255, 255, 48), 6], [17, 'Cl', 3, 7, 'P', 'Chlorine', 0.995, 1.948, (31, 240, 31), 7], [18, 'Ar', 3, 0, '0', 'Argon', 0.84, 1.88, (128, 209, 227), 8], [19, 'K', 4, 1, 'S', 'Potassium', 2.08, 3.02, (143, 64, 212), 1], [20, 'Ca', 4, 2, 'S', 'Calcium', 1.77, 2.78, (250, 150, 0), 2], [21, 'Sc', 4, 3, 'D', 'Scandium', 1.52, 2.62, (230, 230, 230), 3], [22, 'Ti', 4, 4, 'D', 'Titanium', 1.38, 2.44, (191, 194, 199), 4], [23, 'V', 4, 5, 'D', 'Vanadium', 1.3, 2.27, (166, 166, 171), 5], [24, 'Cr', 4, 6, 'D', 'Chromium', 1.335, 2.23, (138, 153, 199), 6], [25, 'Mn', 4, 7, 'D', 'Manganese', 1.395, 2.25, (156, 122, 199), 7], [26, 'Fe', 4, 8, 'D', 'Iron', 1.325, 2.27, (224, 102, 51), 8], [27, 'Co', 4, 9, 'D', 'Cobalt', 1.305, 2.25, (240, 144, 160), 9], [28, 'Ni', 4, 10, 'D', 'Nickel', 1.28, 2.23, (80, 208, 80), 0], [29, 'Cu', 4, 1, 'D', 'Copper', 1.365, 2.23, (200, 128, 51), 0], [30, 'Zn', 4, 2, 'D', 'Zinc', 1.33, 2.24, (125, 128, 176), 0], [31, 'Ga', 4, 3, 'P', 'Gallium', 1.28, 2.41, (194, 143, 143), 0], [32, 'Ge', 4, 4, 'P', 'Germanium', 1.235, 2.32, (102, 143, 143), 0], [33, 'As', 4, 5, 'P', 'Arsenic', 1.17, 2.25, (189, 128, 227), 0], [34, 'Se', 4, 6, 'P', 'Selenium', 1.155, 2.18, (255, 161, 0), 0], [35, 'Br', 4, 7, 'P', 'Bromine', 1.145, 2.22, (166, 41, 41), 0], [36, 'Kr', 4, 0, '0', 'Krypton', 1.1, 2.0, (92, 184, 209), 0], [37, 'Rb', 5, 1, 'S', 'Rubidium', 2.23, 3.15, (112, 46, 176), 0], [38, 'Sr', 5, 2, 'S', 'Strontium', 1.96, 2.94, (0, 255, 0), 0], [39, 'Y', 5, 3, 'D', 'Yttrium', 1.71, 2.71, (148, 255, 255), 0], [40, 'Zr', 5, 4, 'D', 'Zirconium', 1.515, 2.57, (148, 224, 224), 0], [41, 'Nb', 5, 5, 'D', 'Niobium', 1.41, 2.46, (115, 194, 201), 0], [42, 'Mo', 5, 6, 'D', 'Molybdenum', 1.45, 2.39, (84, 181, 181), 0], [43, 'Tc', 5, 7, 'D', 'Technetium', 1.455, 2.37, (59, 158, 158), 0], [44, 'Ru', 5, 8, 'D', 'Ruthenium', 1.28, 2.35, (36, 143, 143), 0], [45, 'Rh', 5, 9, 'D', 'Rhodium', 1.35, 2.32, (10, 125, 140), 0], [46, 'Pd', 5, 10, 'D', 'Palladium', 1.355, 2.35, (0, 105, 133), 0], [47, 'Ag', 5, 1, 'D', 'Silver', 1.565, 2.37, (192, 192, 192), 0], [48, 'Cd', 5, 2, 'D', 'Cadmium', 1.515, 2.37, (255, 217, 143), 0], [49, 'In', 5, 3, 'P', 'Indium', 1.495, 2.53, (166, 117, 115), 0], [50, 'Sn', 5, 4, 'P', 'Tin', 1.43, 2.46, (102, 128, 128), 0], [51, 'Sb', 5, 5, 'P', 'Antimony', 1.415, 2.41, (158, 99, 181), 0], [52, 'Te', 5, 6, 'P', 'Tellurium', 1.375, 2.36, (212, 122, 0), 0], [53, 'I', 5, 7, 'P', 'Iodine', 1.365, 2.35, (148, 0, 148), 0], [54, 'Xe', 5, 0, '0', 'Xenon', 1.3, 2.181, (66, 158, 176), 0], [55, 'Cs', 6, 1, 'S', 'Caesium', 2.425, 3.3, (87, 23, 143), 0], [56, 'Ba', 6, 2, 'S', 'Barium', 2.065, 3.05, (0, 201, 0), 0], [57, 'La', 6, 3, 'F', 'Lanthanum', 1.82, 2.81, (112, 212, 255), 0], [58, 'Ce', 6, 4, 'F', 'Cerium', 1.85, 2.0, (255, 255, 199), 0], [59, 'Pr', 6, 5, 'F', 'Praseodymium', 1.85, 2.0, (217, 255, 199), 0], [60, 'Nd', 6, 6, 'F', 'Neodymium', 1.85, 2.0, (199, 255, 199), 0], [61, 'Pm', 6, 7, 'F', 'Promethium', 1.85, 2.0, (163, 255, 199), 0], [62, 'Sm', 6, 8, 'F', 'Samarium', 1.85, 2.0, (143, 255, 199), 0], [63, 'Eu', 6, 9, 'F', 'Europium', 1.85, 2.0, (97, 255, 199), 0], [64, 'Gd', 6, 10, 'F', 'Gadolinium', 1.8, 2.0, (69, 255, 199), 0], [65, 'Tb', 6, 11, 'F', 'Terbium', 1.75, 2.0, (48, 255, 199), 0], [66, 'Dy', 6, 12, 'F', 'Dysprosium', 1.75, 2.0, (31, 255, 199), 0], [67, 'Ho', 6, 13, 'F', 'Holmium', 1.75, 2.0, (0, 255, 156), 0], [68, 'Er', 6, 14, 'F', 'Erbium', 1.75, 2.0, (0, 230, 117), 0], [69, 'Tm', 6, 1, 'F', 'Thulium', 1.75, 2.0, (0, 212, 82), 0], [70, 'Yb', 6, 2, 'F', 'Ytterbium', 1.75, 2.0, (0, 191, 56), 0], [71, 'Lu', 6, 3, 'D', 'Lutetium', 1.675, 2.0, (0, 171, 36), 0], [72, 'Hf', 6, 4, 'D', 'Hafnium', 1.525, 2.52, (77, 194, 255), 0], [73, 'Ta', 6, 5, 'D', 'Tantalum', 1.415, 2.42, (77, 166, 255), 0], [74, 'W', 6, 6, 'D', 'Tungsten', 1.405, 2.36, (33, 148, 214), 0], [75, 'Re', 6, 7, 'D', 'Rhenium', 1.47, 2.35, (38, 125, 171), 0], [76, 'Os', 6, 8, 'D', 'Osmium', 1.29, 2.33, (38, 102, 150), 0], [77, 'Ir', 6, 9, 'D', 'Iridium', 1.36, 2.34, (23, 84, 135), 0], [78, 'Pt', 6, 10, 'D', 'Platinum', 1.315, 2.37, (208, 208, 224), 0], [79, 'Au', 6, 1, 'D', 'Gold', 1.395, 2.41, (255, 209, 35), 0], [80, 'Hg', 6, 2, 'D', 'Mercury', 1.495, 2.25, (184, 184, 208), 0], [81, 'Tl', 6, 3, 'P', 'Thallium', 1.69, 2.53, (166, 84, 77), 0], [82, 'Pb', 6, 4, 'P', 'Lead', 1.635, 2.53, (87, 89, 97), 0], [83, 'Bi', 6, 5, 'P', 'Bismuth', 1.53, 3.52, (158, 79, 181), 0], [84, 'Po', 6, 6, 'P', 'Polonium', 1.9, 2.0, (171, 92, 0), 0], [85, 'At', 6, 7, 'P', 'Astatine', 2.0, 2.0, (117, 79, 69), 0], [86, 'Rn', 6, 0, '0', 'Radon', 2.0, 2.0, (66, 130, 150), 0], [87, 'Fr', 7, 1, 'S', 'Francium', 2.0, 2.0, (66, 0, 102), 0], [88, 'Ra', 7, 2, 'S', 'Radium', 2.0, 2.0, (0, 125, 0), 0], [89, 'Ac', 7, 3, 'F', 'Actinium', 2.0, 2.0, (112, 171, 250), 0], [90, 'Th', 7, 4, 'F', 'Thorium', 2.0, 2.75, (0, 186, 255), 0], [91, 'Pa', 7, 5, 'F', 'Protactinium', 2.0, 2.0, (0, 161, 255), 0], [92, 'U', 7, 6, 'F', 'Uranium', 2.0, 2.65, (0, 143, 255), 0], [93, 'Np', 7, 7, 'F', 'Neptunium', 2.0, 2.0, (0, 128, 255), 0], [94, 'Pu', 7, 8, 'F', 'Plutonium', 2.0, 2.0, (0, 107, 255), 0], [95, 'Am', 7, 9, 'F', 'Americium', 2.0, 2.0, (84, 92, 242), 0], [96, 'Cm', 7, 10, 'F', 'Curium', 2.0, 2.0, (120, 92, 227), 0], [97, 'Bk', 7, 11, 'F', 'Berkelium', 2.0, 2.0, (138, 79, 227), 0], [98, 'Cf', 7, 12, 'F', 'Californium', 2.0, 2.0, (161, 54, 212), 0], [99, 'Es', 7, 13, 'F', 'Einsteinium', 2.0, 2.0, (179, 31, 212), 0], [100, 'Fm', 7, 14, 'F', 'Fermium', 2.0, 2.0, (179, 31, 186), 0], [101, 'Md', 7, 1, 'F', 'Mendelevium', 2.0, 2.0, (179, 13, 166), 0], [102, 'No', 7, 2, 'F', 'Nobelium', 2.0, 2.0, (189, 13, 135), 0], [103, 'Lr', 7, 3, 'D', 'Lawrencium', 2.0, 2.0, (199, 0, 102), 0], [104, 'Rf', 7, 4, 'D', 'Rutherfordium', 2.0, 2.0, (204, 0, 89), 0], [105, 'Db', 7, 5, 'D', 'Dubnium', 2.0, 2.0, (209, 0, 79), 0], [106, 'Sg', 7, 6, 'D', 'Seaborgium', 2.0, 2.0, (217, 0, 69), 0], [107, 'Bh', 7, 7, 'D', 'Bohrium', 2.0, 2.0, (224, 0, 56), 0], [108, 'Hs', 7, 8, 'D', 'Hassium', 2.0, 2.0, (230, 0, 46), 0], [109, 'Mt', 7, 9, 'D', 'Meitnerium', 2.0, 2.0, (235, 0, 38), 0], [110, 'Ds', 7, 10, 'D', 'Darmstadtium', 2.0, 2.0, (128, 128, 128), 0], [111, 'Rg', 7, 1, 'D', 'Roentgenium', 2.0, 2.0, (128, 128, 128), 0], [112, 'Uub', 7, 2, 'D', 'Ununbium', 2.0, 2.0, (128, 128, 128), 0]])

ppafm.atomicUtils.findCOG(ps, byBox=False)

ppafm.atomicUtils.findNearest(p, ps, rcut=1000000000.0)

ppafm.atomicUtils.findPairs(select1, select2, atoms, Rcut=2.0)

ppafm.atomicUtils.findPairs_one(select1, atoms, Rcut=2.0)

ppafm.atomicUtils.findTypeNeigh(atoms, neighs, typ, neighTyps=[(1, 2, 2)])

ppafm.atomicUtils.getAllNeighsOfSelected(selected, neighs, atoms, typs={1})

ppafm.atomicUtils.getAtomColors(iZs, ELEMENTS=[[1, 'H', 1, 1, 'S', 'Hydrogen', 0.365, 1.487, (255, 255, 255), 1], [2, 'He', 1, 0, '0', 'Helium', 0.32, 1.481, (217, 255, 255), 2], [3, 'Li', 2, 1, 'S', 'Lithium', 1.395, 2.0, (204, 128, 255), 1], [4, 'Be', 2, 2, 'S', 'Beryllium', 0.975, 2.0, (194, 255, 0), 2], [5, 'B', 2, 3, 'P', 'Boron', 0.835, 2.08, (255, 181, 181), 3], [6, 'C', 2, 4, 'P', 'Carbon', 0.735, 1.908, (144, 144, 144), 4], [7, 'N', 2, 5, 'P', 'Nitrogen', 0.7, 1.78, (48, 80, 248), 5], [8, 'O', 2, 6, 'P', 'Oxygen', 0.665, 1.661, (255, 13, 13), 6], [9, 'F', 2, 7, 'P', 'Fluorine', 0.605, 1.75, (144, 224, 80), 7], [10, 'Ne', 2, 0, '0', 'Neon', 0.69, 1.543, (179, 227, 245), 8], [11, 'Na', 3, 1, 'S', 'Sodium', 1.67, 2.77, (171, 92, 242), 1], [12, 'Mg', 3, 2, 'S', 'Magnesium', 1.4, 2.42, (138, 255, 0), 2], [13, 'Al', 3, 3, 'P', 'Aluminium', 1.215, 2.4, (191, 166, 166), 3], [14, 'Si', 3, 4, 'P', 'Silicon', 1.105, 1.9, (240, 200, 160), 4], [15, 'P', 3, 5, 'P', 'Phosphorus', 1.03, 2.1, (255, 128, 0), 5], [16, 'S', 3, 6, 'P', 'Sulfur', 1.01, 2.0, (255, 255, 48), 6], [17, 'Cl', 3, 7, 'P', 'Chlorine', 0.995, 1.948, (31, 240, 31), 7], [18, 'Ar', 3, 0, '0', 'Argon', 0.84, 1.88, (128, 209, 227), 8], [19, 'K', 4, 1, 'S', 'Potassium', 2.08, 3.02, (143, 64, 212), 1], [20, 'Ca', 4, 2, 'S', 'Calcium', 1.77, 2.78, (250, 150, 0), 2], [21, 'Sc', 4, 3, 'D', 'Scandium', 1.52, 2.62, (230, 230, 230), 3], [22, 'Ti', 4, 4, 'D', 'Titanium', 1.38, 2.44, (191, 194, 199), 4], [23, 'V', 4, 5, 'D', 'Vanadium', 1.3, 2.27, (166, 166, 171), 5], [24, 'Cr', 4, 6, 'D', 'Chromium', 1.335, 2.23, (138, 153, 199), 6], [25, 'Mn', 4, 7, 'D', 'Manganese', 1.395, 2.25, (156, 122, 199), 7], [26, 'Fe', 4, 8, 'D', 'Iron', 1.325, 2.27, (224, 102, 51), 8], [27, 'Co', 4, 9, 'D', 'Cobalt', 1.305, 2.25, (240, 144, 160), 9], [28, 'Ni', 4, 10, 'D', 'Nickel', 1.28, 2.23, (80, 208, 80), 0], [29, 'Cu', 4, 1, 'D', 'Copper', 1.365, 2.23, (200, 128, 51), 0], [30, 'Zn', 4, 2, 'D', 'Zinc', 1.33, 2.24, (125, 128, 176), 0], [31, 'Ga', 4, 3, 'P', 'Gallium', 1.28, 2.41, (194, 143, 143), 0], [32, 'Ge', 4, 4, 'P', 'Germanium', 1.235, 2.32, (102, 143, 143), 0], [33, 'As', 4, 5, 'P', 'Arsenic', 1.17, 2.25, (189, 128, 227), 0], [34, 'Se', 4, 6, 'P', 'Selenium', 1.155, 2.18, (255, 161, 0), 0], [35, 'Br', 4, 7, 'P', 'Bromine', 1.145, 2.22, (166, 41, 41), 0], [36, 'Kr', 4, 0, '0', 'Krypton', 1.1, 2.0, (92, 184, 209), 0], [37, 'Rb', 5, 1, 'S', 'Rubidium', 2.23, 3.15, (112, 46, 176), 0], [38, 'Sr', 5, 2, 'S', 'Strontium', 1.96, 2.94, (0, 255, 0), 0], [39, 'Y', 5, 3, 'D', 'Yttrium', 1.71, 2.71, (148, 255, 255), 0], [40, 'Zr', 5, 4, 'D', 'Zirconium', 1.515, 2.57, (148, 224, 224), 0], [41, 'Nb', 5, 5, 'D', 'Niobium', 1.41, 2.46, (115, 194, 201), 0], [42, 'Mo', 5, 6, 'D', 'Molybdenum', 1.45, 2.39, (84, 181, 181), 0], [43, 'Tc', 5, 7, 'D', 'Technetium', 1.455, 2.37, (59, 158, 158), 0], [44, 'Ru', 5, 8, 'D', 'Ruthenium', 1.28, 2.35, (36, 143, 143), 0], [45, 'Rh', 5, 9, 'D', 'Rhodium', 1.35, 2.32, (10, 125, 140), 0], [46, 'Pd', 5, 10, 'D', 'Palladium', 1.355, 2.35, (0, 105, 133), 0], [47, 'Ag', 5, 1, 'D', 'Silver', 1.565, 2.37, (192, 192, 192), 0], [48, 'Cd', 5, 2, 'D', 'Cadmium', 1.515, 2.37, (255, 217, 143), 0], [49, 'In', 5, 3, 'P', 'Indium', 1.495, 2.53, (166, 117, 115), 0], [50, 'Sn', 5, 4, 'P', 'Tin', 1.43, 2.46, (102, 128, 128), 0], [51, 'Sb', 5, 5, 'P', 'Antimony', 1.415, 2.41, (158, 99, 181), 0], [52, 'Te', 5, 6, 'P', 'Tellurium', 1.375, 2.36, (212, 122, 0), 0], [53, 'I', 5, 7, 'P', 'Iodine', 1.365, 2.35, (148, 0, 148), 0], [54, 'Xe', 5, 0, '0', 'Xenon', 1.3, 2.181, (66, 158, 176), 0], [55, 'Cs', 6, 1, 'S', 'Caesium', 2.425, 3.3, (87, 23, 143), 0], [56, 'Ba', 6, 2, 'S', 'Barium', 2.065, 3.05, (0, 201, 0), 0], [57, 'La', 6, 3, 'F', 'Lanthanum', 1.82, 2.81, (112, 212, 255), 0], [58, 'Ce', 6, 4, 'F', 'Cerium', 1.85, 2.0, (255, 255, 199), 0], [59, 'Pr', 6, 5, 'F', 'Praseodymium', 1.85, 2.0, (217, 255, 199), 0], [60, 'Nd', 6, 6, 'F', 'Neodymium', 1.85, 2.0, (199, 255, 199), 0], [61, 'Pm', 6, 7, 'F', 'Promethium', 1.85, 2.0, (163, 255, 199), 0], [62, 'Sm', 6, 8, 'F', 'Samarium', 1.85, 2.0, (143, 255, 199), 0], [63, 'Eu', 6, 9, 'F', 'Europium', 1.85, 2.0, (97, 255, 199), 0], [64, 'Gd', 6, 10, 'F', 'Gadolinium', 1.8, 2.0, (69, 255, 199), 0], [65, 'Tb', 6, 11, 'F', 'Terbium', 1.75, 2.0, (48, 255, 199), 0], [66, 'Dy', 6, 12, 'F', 'Dysprosium', 1.75, 2.0, (31, 255, 199), 0], [67, 'Ho', 6, 13, 'F', 'Holmium', 1.75, 2.0, (0, 255, 156), 0], [68, 'Er', 6, 14, 'F', 'Erbium', 1.75, 2.0, (0, 230, 117), 0], [69, 'Tm', 6, 1, 'F', 'Thulium', 1.75, 2.0, (0, 212, 82), 0], [70, 'Yb', 6, 2, 'F', 'Ytterbium', 1.75, 2.0, (0, 191, 56), 0], [71, 'Lu', 6, 3, 'D', 'Lutetium', 1.675, 2.0, (0, 171, 36), 0], [72, 'Hf', 6, 4, 'D', 'Hafnium', 1.525, 2.52, (77, 194, 255), 0], [73, 'Ta', 6, 5, 'D', 'Tantalum', 1.415, 2.42, (77, 166, 255), 0], [74, 'W', 6, 6, 'D', 'Tungsten', 1.405, 2.36, (33, 148, 214), 0], [75, 'Re', 6, 7, 'D', 'Rhenium', 1.47, 2.35, (38, 125, 171), 0], [76, 'Os', 6, 8, 'D', 'Osmium', 1.29, 2.33, (38, 102, 150), 0], [77, 'Ir', 6, 9, 'D', 'Iridium', 1.36, 2.34, (23, 84, 135), 0], [78, 'Pt', 6, 10, 'D', 'Platinum', 1.315, 2.37, (208, 208, 224), 0], [79, 'Au', 6, 1, 'D', 'Gold', 1.395, 2.41, (255, 209, 35), 0], [80, 'Hg', 6, 2, 'D', 'Mercury', 1.495, 2.25, (184, 184, 208), 0], [81, 'Tl', 6, 3, 'P', 'Thallium', 1.69, 2.53, (166, 84, 77), 0], [82, 'Pb', 6, 4, 'P', 'Lead', 1.635, 2.53, (87, 89, 97), 0], [83, 'Bi', 6, 5, 'P', 'Bismuth', 1.53, 3.52, (158, 79, 181), 0], [84, 'Po', 6, 6, 'P', 'Polonium', 1.9, 2.0, (171, 92, 0), 0], [85, 'At', 6, 7, 'P', 'Astatine', 2.0, 2.0, (117, 79, 69), 0], [86, 'Rn', 6, 0, '0', 'Radon', 2.0, 2.0, (66, 130, 150), 0], [87, 'Fr', 7, 1, 'S', 'Francium', 2.0, 2.0, (66, 0, 102), 0], [88, 'Ra', 7, 2, 'S', 'Radium', 2.0, 2.0, (0, 125, 0), 0], [89, 'Ac', 7, 3, 'F', 'Actinium', 2.0, 2.0, (112, 171, 250), 0], [90, 'Th', 7, 4, 'F', 'Thorium', 2.0, 2.75, (0, 186, 255), 0], [91, 'Pa', 7, 5, 'F', 'Protactinium', 2.0, 2.0, (0, 161, 255), 0], [92, 'U', 7, 6, 'F', 'Uranium', 2.0, 2.65, (0, 143, 255), 0], [93, 'Np', 7, 7, 'F', 'Neptunium', 2.0, 2.0, (0, 128, 255), 0], [94, 'Pu', 7, 8, 'F', 'Plutonium', 2.0, 2.0, (0, 107, 255), 0], [95, 'Am', 7, 9, 'F', 'Americium', 2.0, 2.0, (84, 92, 242), 0], [96, 'Cm', 7, 10, 'F', 'Curium', 2.0, 2.0, (120, 92, 227), 0], [97, 'Bk', 7, 11, 'F', 'Berkelium', 2.0, 2.0, (138, 79, 227), 0], [98, 'Cf', 7, 12, 'F', 'Californium', 2.0, 2.0, (161, 54, 212), 0], [99, 'Es', 7, 13, 'F', 'Einsteinium', 2.0, 2.0, (179, 31, 212), 0], [100, 'Fm', 7, 14, 'F', 'Fermium', 2.0, 2.0, (179, 31, 186), 0], [101, 'Md', 7, 1, 'F', 'Mendelevium', 2.0, 2.0, (179, 13, 166), 0], [102, 'No', 7, 2, 'F', 'Nobelium', 2.0, 2.0, (189, 13, 135), 0], [103, 'Lr', 7, 3, 'D', 'Lawrencium', 2.0, 2.0, (199, 0, 102), 0], [104, 'Rf', 7, 4, 'D', 'Rutherfordium', 2.0, 2.0, (204, 0, 89), 0], [105, 'Db', 7, 5, 'D', 'Dubnium', 2.0, 2.0, (209, 0, 79), 0], [106, 'Sg', 7, 6, 'D', 'Seaborgium', 2.0, 2.0, (217, 0, 69), 0], [107, 'Bh', 7, 7, 'D', 'Bohrium', 2.0, 2.0, (224, 0, 56), 0], [108, 'Hs', 7, 8, 'D', 'Hassium', 2.0, 2.0, (230, 0, 46), 0], [109, 'Mt', 7, 9, 'D', 'Meitnerium', 2.0, 2.0, (235, 0, 38), 0], [110, 'Ds', 7, 10, 'D', 'Darmstadtium', 2.0, 2.0, (128, 128, 128), 0], [111, 'Rg', 7, 1, 'D', 'Roentgenium', 2.0, 2.0, (128, 128, 128), 0], [112, 'Uub', 7, 2, 'D', 'Ununbium', 2.0, 2.0, (128, 128, 128), 0]], FFparams=None)

ppafm.atomicUtils.groupToPair(p1, p2, group, up, up_by_cog=False)

ppafm.atomicUtils.histR(ps, dbin=None, Rmax=None, weights=None)

ppafm.atomicUtils.loadCoefs(characters=['s'])

ppafm.atomicUtils.makeRotMat(fw, up)

ppafm.atomicUtils.neighs(natoms, bonds)

ppafm.atomicUtils.pairsNotShareNeigh(pairs, neighs)

ppafm.atomicUtils.replace(atoms, found, to=17, bond_length=2.0, radial=0.0, prob=0.75)

ppafm.atomicUtils.replacePairs(pairs, atoms, group, up_vec=(array([0., 0., 0.]), 1))