5.27. MDAnalysis topology tables

The module contains static lookup tables for atom typing etc. The tables are dictionaries that are indexed by the element.

MDAnalysis.topology.tables.atomelements = {'AC': 'C', 'BC': 'C', 'BR': 'BR', 'C0': 'CA', 'CA2+': 'CA', 'CAL': 'CA', 'CES': 'CS', 'CL': 'CL', 'CL-': 'CL', 'CLA': 'CL', 'CLAL': 'CL', 'CS': 'CS', 'CS+': 'CS', 'CU': 'CU', 'FE': 'FE', 'FE2': 'FE', 'IOD': 'I', 'K': 'K', 'K+': 'K', 'LI': 'LI', 'LI+': 'LI', 'LIT': 'LI', 'MG': 'MG', 'MG2+': 'MG', 'MW': 'DUMMY', 'NA': 'NA', 'NA+': 'NA', 'POT': 'K', 'QC': 'CE', 'QK': 'K', 'QL': 'LI', 'QN': 'NA', 'QR': 'RB', 'RB': 'RB', 'SOD': 'NA', 'ZN': 'ZN'}

Dictionary with hard-coded special atom names, used for guessing atom types with MDAnalysis.topology.core.guess_atom_type().

MDAnalysis.topology.tables.masses = {'Ac': 227.028, 'Ag': 107.8682, 'Al': 26.981539, 'Am': 243.0, 'Ar': 39.948, 'As': 74.92159, 'At': 210.0, 'Au': 196.96654, 'B': 10.811, 'BR': 79.904, 'Ba': 137.327, 'Be': 9.012182, 'Bh': 262.0, 'Bi': 208.98037, 'Bk': 247.0, 'C': 12.011, 'CA': 40.08, 'CL': 35.45, 'CS': 132.9, 'CU': 63.546, 'Cd': 112.411, 'Ce': 140.116, 'Cf': 251.0, 'Cm': 247.0, 'Co': 58.9332, 'Cr': 51.9961, 'DUMMY': 0.0, 'Db': 262.0, 'Dy': 162.5, 'Er': 167.26, 'Es': 252.0, 'Eu': 151.965, 'F': 18.998, 'FE': 55.847, 'Fm': 257.0, 'Fr': 223.0, 'Ga': 69.723, 'Gd': 157.25, 'Ge': 72.61, 'H': 1.008, 'HE': 4.0026, 'Hf': 178.49, 'Hg': 200.59, 'Ho': 164.93032, 'Hs': 265.0, 'I': 126.9045, 'In': 114.82, 'Ir': 192.22, 'K': 39.102, 'Kr': 83.8, 'La': 138.9055, 'Li': 6.941, 'Lr': 262.0, 'Lu': 174.967, 'MG': 24.305, 'Md': 258.0, 'Mn': 54.93805, 'Mo': 95.94, 'Mt': 266.0, 'N': 14.007, 'NA': 22.98977, 'NE': 20.1797, 'Na': 22.989768, 'Nb': 92.90638, 'Nd': 144.24, 'Ni': 58.6934, 'No': 259.0, 'Np': 237.048, 'O': 15.999, 'Os': 190.2, 'P': 30.974, 'Pa': 231.0359, 'Pb': 207.2, 'Pd': 106.42, 'Pm': 145.0, 'Po': 209.0, 'Pr': 140.90765, 'Pt': 195.08, 'Pu': 244.0, 'RB': 85.4678, 'Ra': 226.025, 'Re': 186.207, 'Rf': 261.0, 'Rh': 102.9055, 'Rn': 222.0, 'Ru': 101.07, 'S': 32.06, 'Sb': 121.757, 'Sc': 44.95591, 'Se': 78.96, 'Sg': 263.0, 'Si': 28.0855, 'Sm': 150.36, 'Sn': 118.71, 'Sr': 87.62, 'Ta': 180.9479, 'Tb': 158.92534, 'Tc': 98.0, 'Te': 127.6, 'Th': 232.0381, 'Ti': 47.88, 'Tl': 204.3833, 'Tm': 168.93421, 'U': 238.0289, 'V': 50.9415, 'W': 183.85, 'Xe': 131.29, 'Y': 88.90585, 'Yb': 173.04, 'ZN': 65.37, 'Zr': 91.224}

Dictionary table with atomic masses in u, indexed by the element from atomelements.

MDAnalysis.topology.tables.vdwradii = {'AA': 1.85, 'AG': 1.72, 'AL': 1.84, 'AR': 1.88, 'AT': 2.02, 'AU': 1.66, 'B': 1.92, 'BA': 2.68, 'BE': 1.53, 'BI': 2.07, 'BR': 1.85, 'C': 1.7, 'CA': 2.31, 'CD': 1.58, 'CL': 1.75, 'CS': 3.43, 'CU': 1.4, 'F': 1.47, 'FR': 3.48, 'GA': 1.87, 'GE': 2.11, 'H': 1.1, 'HE': 1.4, 'HH': 1.55, 'I': 1.98, 'IN': 1.93, 'K': 2.75, 'KR': 2.02, 'LI': 1.82, 'MG': 1.73, 'N': 1.55, 'NA': 2.27, 'NE': 1.54, 'NI': 1.63, 'O': 1.52, 'P': 1.8, 'PB': 2.02, 'PD': 1.63, 'PO': 1.97, 'PT': 1.75, 'RA': 2.83, 'RN': 2.2, 'RR': 3.03, 'S': 1.8, 'SB': 2.06, 'SE': 1.9, 'SI': 2.1, 'SN': 2.17, 'SR': 2.49, 'TE': 2.06, 'TL': 1.96, 'U': 1.86, 'XE': 2.16, 'ZN': 1.39}

Dictionary table with vdw radii, indexed by the element from atomelements. .. SeeAlso:: MDAnalysis.topology.core.guess_bonds()

The original raw data are stored as multi-line strings that are translated into dictionaries with kv2dict(). In the future, these tables might be moved into external data files; see kv2dict() for explanation of the file format.

MDAnalysis.topology.tables.kv2dict(s, convertor=<class 'str'>)[source]

Primitive ad-hoc parser of a key-value record list.

  • The string s should contain each key-value pair on a separate line (separated by newline). The first white space after the key separates key and value.

  • Empty lines are allowed.

  • Comment lines (starting with #) are allowed.

  • Leading whitespace is ignored.

The convertor is a function that converts its single argument to a valid Python type. The default is str() but other possibilities are int() (for integers) or float() for floating point numbers.

The raw tables are stored in the strings

MDAnalysis.topology.tables.TABLE_ATOMELEMENTS = '\n# translation of atomnames to types/element\n# based on CHARMM and AMBER usage with a little bit of GROMOS (and PROPKA)\n# NOTE: CL might be ambiguous and is interpreted as chloride!\n\n# --------- ------------------\n# atomname   element\n# --------- ------------------\n\n# Bromide\nBR           BR\n\n# Calcium\nCAL          CA\nC0           CA\nCA2+         CA\n\n# Cesium\nCES          CS\n\n# Chloride\nCLA          CL\nCLAL         CL\nCL           CL\nCL-          CL\n\n# Iodide\nIOD          I\n\n# Iron\nFE           FE\nFE2          FE\n\n# Lithium\nLIT          LI\nLI           LI\nLI+          LI\nQL           LI\n\n# Magnesium\nMG           MG\nMG2+         MG\n\n# Noble gases\n## XXX collides with NE, HE in Arg  XXX\n## XXX so we remove the noble gases XXX\n##HE           HE\n##NE           NE\n\n# Potassium\nK            K\nPOT          K\nK+           K\nQK           K\n\n# Sodium\nSOD          NA\nNA           NA\nNA+          NA\nQN           NA\n\n# Zink\nZN           ZN\n\n# Copper\nCU           CU\n\n# Cesium\nCS           CS\nCS+          CS\nCES          CS\n\n# Cerium??\nQC           CE\n\n# Rubidium\nRB           RB\nQR           RB\n\n# special carbons (Amber?)\nBC           C\nAC           C\n\n# dummy atom types\nMW           DUMMY\n\n# other types are guessed from the name; see\n# topology.core.guess_atom_elements()\n'

Table with hard-coded special atom names, used for guessing atom types with MDAnalysis.topology.core.guess_atom_element().

MDAnalysis.topology.tables.TABLE_MASSES = '\n# masses for elements in atomic units (u)\n# (taken from CHARMM and Gromacs atommass.dat)\n\n#------------ -----------\n# atomtype    mass\n#------------ -----------\nAc    227.028\nAl    26.981539\nAm    243\nSb    121.757\nAr    39.948\nAs    74.92159\nAt    210\nBa    137.327\nBk    247\nBe    9.012182\nBi    208.98037\nBh    262\nB     10.811\nBR    79.90400\nCd    112.411\nCA    40.08000\nCf    251\nC     12.01100\nCe    140.11600\nCS    132.90000\nCL    35.45000\nCr    51.9961\nCo    58.9332\nCU    63.54600\nCm    247\nDb    262\nDy    162.5\nEs    252\nEr    167.26\nEu    151.965\nFm    257\nF     18.99800\nFr    223\nGd    157.25\nGa    69.723\nGe    72.61\nAu    196.96654\nHf    178.49\nHs    265\nHE    4.00260\nHo    164.93032\nH     1.00800\nIn    114.82\nI     126.90450\nIr    192.22\nFE    55.84700\nKr    83.8\nLa    138.9055\nLr    262\nPb    207.2\nLi    6.941\nLu    174.967\nMG    24.30500\nMn    54.93805\nMt    266\nMd    258\nHg    200.59\nMo    95.94\nN     14.00700\nNA    22.98977\nNd    144.24\nNE    20.17970\nNp    237.048\nNi    58.6934\nNb    92.90638\nNo    259\nOs    190.2\nO     15.99900\nPd    106.42\nP     30.97400\nPt    195.08\nPu    244\nPo    209\nK     39.10200\nPr    140.90765\nPm    145\nPa    231.0359\nRa    226.025\nRn    222\nRe    186.207\nRh    102.9055\nRB    85.46780\nRu    101.07\nRf    261\nSm    150.36\nSc    44.95591\nSg    263\nSe    78.96\nSi    28.0855\nAg    107.8682\nNa    22.989768\nSr    87.62\nS     32.06000\nTa    180.9479\nTc    98\nTe    127.6\nTb    158.92534\nTl    204.3833\nTh    232.0381\nTm    168.93421\nSn    118.71\nTi    47.88\nW     183.85\nU     238.0289\nV     50.9415\nXe    131.29\nYb    173.04\nY     88.90585\nZN    65.37000\nZr    91.224\nDUMMY 0.0\n'

Plain-text table with atomic masses in u.

MDAnalysis.topology.tables.TABLE_VDWRADII = '\n# Van der Waals radii taken from\n# [1] Bondi, A. (1964). "Van der Waals Volumes and Radii".\n#     J. Phys. Chem. 68 (3): 441-451. doi:10.1021/j100785a001.\n# [2] Rowland and Taylor (1996). "Intermolecular Nonbonded Contact Distances in Organic Crystal Structures:\n#                                 Comparison with Distances Expected from van der Waals Radii".\n#     J. Phys. Chem., 1996, 100 (18), 7384.7391. doi:10.1021/jp953141+.\n# [3] Mantina, et al. (2009). "Consistent van der Waals Radii for the Whole Main Group".\n#     J. Phys. Chem. A, 2009, 113 (19), 5806-5812. doi:10.1021/jp8111556.\n#------------ -----------\n# atomtype    r_vdw\n#------------ -----------\nH    1.10\nHE   1.40\nLI   1.82\nBE   1.53\nB    1.92\nC    1.70\nN    1.55\nO    1.52\nF    1.47\nNE   1.54\nNA   2.27\nMG   1.73\nAL   1.84\nSI   2.10\nP    1.80\nS    1.80\nCL   1.75\nAR   1.88\nK    2.75\nCA   2.31\nNI   1.63\nCU   1.40\nZN   1.39\nGA   1.87\nGE   2.11\nAA   1.85\nSE   1.90\nBR   1.85\nKR   2.02\nRR   3.03\nSR   2.49\nPD   1.63\nAG   1.72\nCD   1.58\nIN   1.93\nSN   2.17\nSB   2.06\nTE   2.06\nI    1.98\nXE   2.16\nCS   3.43\nBA   2.68\nPT   1.75\nAU   1.66\nHH   1.55\nTL   1.96\nPB   2.02\nBI   2.07\nPO   1.97\nAT   2.02\nRN   2.20\nFR   3.48\nRA   2.83\nU    1.86\n'

Plain-text table with vdw radii.