# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""
MDAnalysis topology tables
==========================
The module contains static lookup tables for atom typing etc. The
tables are dictionaries that are indexed by the element.
.. autodata:: atomelements
.. autodata:: masses
.. autodata:: vdwradii
The original raw data are stored as multi-line strings that are
translated into dictionaries with :func:`kv2dict`. In the future,
these tables might be moved into external data files; see
:func:`kv2dict` for explanation of the file format.
.. autofunction:: kv2dict
The raw tables are stored in the strings
.. autodata:: TABLE_ATOMELEMENTS
.. autodata:: TABLE_MASSES
.. autodata:: TABLE_VDWRADII
"""
from typing import Any
[docs]
def kv2dict(s, convertor: Any = str):
"""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 :func:`str` but other
possibilities are :func:`int` (for integers) or :func:`float` for
floating point numbers.
"""
d = {}
lines = s.splitlines()
for line in lines:
line = line.lstrip()
values = line.split(None, 1)
if len(values) == 0 or line.startswith("#"):
continue
d[values[0]] = convertor(values[1])
return d
#: Table with hard-coded special atom names, used for guessing atom types
#: with :func:`MDAnalysis.topology.core.guess_atom_element`.
TABLE_ATOMELEMENTS = """
# translation of atomnames to types/element
# based on CHARMM and AMBER usage with a little bit of GROMOS (and PROPKA)
# NOTE: CL might be ambiguous and is interpreted as chloride!
# --------- ------------------
# atomname element
# --------- ------------------
# Bromide
BR BR
# Calcium
CAL CA
C0 CA
CA2+ CA
# Cesium
CES CS
# Chloride
CLA CL
CLAL CL
CL CL
CL- CL
# Iodide
IOD I
# Iron
FE FE
FE2 FE
# Lithium
LIT LI
LI LI
LI+ LI
QL LI
# Magnesium
MG MG
MG2+ MG
# Noble gases
## XXX collides with NE, HE in Arg XXX
## XXX so we remove the noble gases XXX
##HE HE
##NE NE
# Potassium
K K
POT K
K+ K
QK K
# Sodium
SOD NA
NA NA
NA+ NA
QN NA
# Zink
ZN ZN
# Copper
CU CU
# Cesium
CS CS
CS+ CS
CES CS
# Cerium??
QC CE
# Rubidium
RB RB
QR RB
# special carbons (Amber?)
BC C
AC C
# dummy atom types
MW DUMMY
# other types are guessed from the name; see
# topology.core.guess_atom_elements()
"""
#: Dictionary with hard-coded special atom names, used for guessing atom types
#: with :func:`MDAnalysis.topology.core.guess_atom_type`.
atomelements = kv2dict(TABLE_ATOMELEMENTS)
# fmt: off
elements = ['H',
'LI', 'BE', 'B', 'C', 'N', 'O', 'F',
'NA', 'MG', 'AL', 'P', 'SI', 'S', 'CL',
'K']
# fmt: on
#: Plain-text table with atomic masses in u.
TABLE_MASSES = """
# masses for elements in atomic units (u)
# (taken from CHARMM and Gromacs atommass.dat)
#------------ -----------
# atomtype mass
#------------ -----------
Ac 227.028
Al 26.981539
Am 243
Sb 121.757
Ar 39.948
As 74.92159
At 210
Ba 137.327
Bk 247
Be 9.012182
Bi 208.98037
Bh 264
B 10.811
BR 79.90400
Cd 112.411
CA 40.08000
Cf 251
C 12.01100
Ce 140.11600
CS 132.90000
CL 35.45000
Cr 51.9961
Co 58.9332
CU 63.54600
Cm 247
Db 262
Dy 162.5
Es 252
Er 167.26
Eu 151.965
Fm 257
F 18.99800
Fr 223
Gd 157.25
Ga 69.723
Ge 72.61
Au 196.96654
Hf 178.49
Hs 265
HE 4.00260
Ho 164.93032
H 1.00800
In 114.82
I 126.90450
Ir 192.22
FE 55.84700
Kr 83.8
La 138.9055
Lr 262
Pb 207.2
Li 6.941
Lu 174.967
MG 24.30500
Mn 54.93805
Mt 266
Md 258
Hg 200.59
Mo 95.94
N 14.00700
NA 22.98977
Nd 144.24
NE 20.17970
Np 237.048
Ni 58.6934
Nb 92.90638
No 259
Os 190.2
O 15.99900
Pd 106.42
P 30.97400
Pt 195.08
Pu 244
Po 209
K 39.10200
Pr 140.90765
Pm 145
Pa 231.0359
Ra 226.025
Rn 222
Re 186.207
Rh 102.9055
RB 85.46780
Ru 101.07
Rf 261
Sm 150.36
Sc 44.95591
Sg 263
Se 78.96
Si 28.0855
Ag 107.8682
Na 22.989768
Sr 87.62
S 32.06000
Ta 180.9479
Tc 98
Te 127.6
Tb 158.92534
Tl 204.3833
Th 232.0381
Tm 168.93421
Sn 118.71
Ti 47.88
W 183.85
U 238.0289
V 50.9415
Xe 131.29
Yb 173.04
Y 88.90585
ZN 65.37000
Zr 91.224
DUMMY 0.0
"""
#: Dictionary table with atomic masses in u, indexed by the element from
#: :data:`atomelements`.
masses = kv2dict(TABLE_MASSES, convertor=float)
#: Plain-text table with vdw radii.
TABLE_VDWRADII = r"""
# Van der Waals radii taken from
# [1] Bondi, A. (1964). "Van der Waals Volumes and Radii".
# J. Phys. Chem. 68 (3): 441-451. doi:10.1021/j100785a001.
# [2] Rowland and Taylor (1996). "Intermolecular Nonbonded Contact Distances in Organic Crystal Structures:
# Comparison with Distances Expected from van der Waals Radii".
# J. Phys. Chem., 1996, 100 (18), 7384.7391. doi:10.1021/jp953141+.
# [3] Mantina, et al. (2009). "Consistent van der Waals Radii for the Whole Main Group".
# J. Phys. Chem. A, 2009, 113 (19), 5806-5812. doi:10.1021/jp8111556.
#------------ -----------
# atomtype r_vdw
#------------ -----------
H 1.10
HE 1.40
LI 1.82
BE 1.53
B 1.92
C 1.70
N 1.55
O 1.52
F 1.47
NE 1.54
NA 2.27
MG 1.73
AL 1.84
SI 2.10
P 1.80
S 1.80
CL 1.75
AR 1.88
K 2.75
CA 2.31
NI 1.63
CU 1.40
ZN 1.39
GA 1.87
GE 2.11
AA 1.85
SE 1.90
BR 1.85
KR 2.02
RR 3.03
SR 2.49
PD 1.63
AG 1.72
CD 1.58
IN 1.93
SN 2.17
SB 2.06
TE 2.06
I 1.98
XE 2.16
CS 3.43
BA 2.68
PT 1.75
AU 1.66
HH 1.55
TL 1.96
PB 2.02
BI 2.07
PO 1.97
AT 2.02
RN 2.20
FR 3.48
RA 2.83
U 1.86
"""
#: Dictionary table with vdw radii, indexed by the element from
#: :data:`atomelements`.
#: .. SeeAlso:: :func:`MDAnalysis.topology.core.guess_bonds`
vdwradii = kv2dict(TABLE_VDWRADII, convertor=float)
# fmt: off
Z2SYMB = {1: 'H', 2: 'He',
3: 'Li', 4: 'Be', 5: 'B', 6: 'C', 7: 'N', 8: 'O', 9: 'F', 10: 'Ne',
11: 'Na', 12: 'Mg', 13: 'Al', 14: 'Si', 15: 'P', 16: 'S', 17: 'Cl', 18: 'Ar',
19: 'K', 20: 'Ca', 21: 'Sc', 22: 'Ti', 23: 'V', 24: 'Cr', 25: 'Mn', 26: 'Fe',
27: 'Co', 28: 'Ni', 29: 'Cu', 30: 'Zn', 31: 'Ga', 32: 'Ge', 33: 'As', 34: 'Se',
35: 'Br', 36: 'Kr', 37: 'Rb', 38: 'Sr', 39: 'Y', 40: 'Zr', 41: 'Nb', 42: 'Mo',
43: 'Tc', 44: 'Ru', 45: 'Rh', 46: 'Pd', 47: 'Ag', 48: 'Cd', 49: 'In', 50: 'Sn',
51: 'Sb', 52: 'Te', 53: 'I', 54: 'Xe', 55: 'Cs', 56: 'Ba', 57: 'La', 58: 'Ce',
59: 'Pr', 60: 'Nd', 61: 'Pm', 62: 'Sm', 63: 'Eu', 64: 'Gd', 65: 'Tb', 66: 'Dy',
67: 'Ho', 68: 'Er', 69: 'Tm', 70: 'Yb', 71: 'Lu', 72: 'Hf', 73: 'Ta', 74: 'W',
75: 'Re', 76: 'Os', 77: 'Ir', 78: 'Pt', 79: 'Au', 80: 'Hg', 81: 'Tl', 82: 'Pb',
83: 'Bi', 84: 'Po', 85: 'At', 86: 'Rn', 87: 'Fr', 88: 'Ra', 89: 'Ac', 90: 'Th',
91: 'Pa', 92: 'U', 93: 'Np', 94: 'Pu', 95: 'Am', 96: 'Cm', 97: 'Bk', 98: 'Cf',
99: 'Es', 100: 'Fm', 101: 'Md', 102: 'No', 103: 'Lr', 104: 'Rf', 105: 'Db',
106: 'Sg', 107: 'Bh', 108: 'Hs', 109: 'Mt', 110: 'Ds', 111: 'Rg', 112: 'Cn',
113: 'Nh', 114: 'Fl', 115: 'Mc', 116: 'Lv', 117: 'Ts', 118: 'Og'}
# fmt: on
SYMB2Z = {v: k for k, v in Z2SYMB.items()}
# Conversion between SYBYL atom types and corresponding elements
# Tripos MOL2 file format:
# https://web.archive.org/web/*/http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
# fmt: off
SYBYL2SYMB = {
"H": "H", "H.spc": "H", "H.t3p": "H",
"C.3": "C", "C.2": "C", "C.1": "C", "C.ar": "C", "C.cat": "C",
"N.3": "N", "N.2": "N", "N.1": "N", "N.ar": "N",
"N.am": "N", "N.pl3": "N", "N.4": "N",
"O.3": "O", "O.2": "O", "O.co2": "O", "O.spc": "O", "O.t3p": "O",
"S.3": "S", "S.2": "S", "S.O": "S", "S.O2": "S",
"S.o": "S", "S.o2": "S", # Non-standard but often found in the wild...
"P.3": "P",
"F": "F",
"Li": "Li",
"Na": "Na",
"Mg": "Mg",
"Al": "Al",
"Si": "Si",
"K": "K",
"Ca": "Ca",
"Cr.th": "Cr",
"Cr.oh": "Cr",
"Mn": "Mn",
"Fe": "Fe",
"Co.oh": "Co",
"Cu": "Cu",
"Cl": "Cl",
"Br": "Br",
"I": "I",
"Zn": "Zn",
"Se": "Se",
"Mo": "Mo",
"Sn": "Sn",
}
# fmt: on