Source Code for Module physical_constants

  1  ############################################################################### 
  2  #                                                                             # 
  3  # Copyright (C) 2007-2011 Edward d'Auvergne                                   # 
  4  #                                                                             # 
  5  # This file is part of the program relax.                                     # 
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 20  #                                                                             # 
 21  ############################################################################### 
 22   
 23  # Module docstring. 
 24  """Module containing all physical constants used in relax, as well as all associated functions.""" 
 25   
 26   
 27  # Python module imports. 
 28  from math import pi 
 29  from string import ascii_letters, digits, upper 
 30   
 31  # relax module imports. 
 32  from float import nan 
 33  from relax_errors import RelaxError 
 34   
 35   
 36  # Misc. constants. 
 37  ################## 
 38   
 39  h = 6.62606876 * 1e-34 
 40  """Planck's constant.""" 
 41   
 42  h_bar = h / (2.0 * pi) 
 43  """Dirac's constant.""" 
 44   
 45  mu0 = 4.0 * pi * 1e-7 
 46  """The magnetic constant or the permeability of vacuum.""" 
 47   
 48  kB = 1.380650424 * 1e-23 
 49  """Boltzmann's constant in SI units of J.K^-1 (the last 2 digits of '24' are within the measured error limits).""" 
 50   
 51   
 52  # CSA and bond lengths. 
 53  ####################### 
 54   
 55  N15_CSA = -172 * 1e-6 
 56  """The 15N CSA in the NH bond (default value).""" 
 57   
 58  NH_BOND_LENGTH = 1.02 * 1e-10 
 59  """The length of the NH bond (default value).""" 
 60   
 61  NH_BOND_LENGTH_RDC = 1.041 * 1e-10 
 62  """The length of the NH bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).""" 
 63   
 64  CA_HA_BOND_LENGTH_RDC = 1.118 * 1e-10 
 65  """The length of the C_alpha-H_alpha bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).""" 
 66   
 67  CA_C_BOND_LENGTH_RDC = 1.526 * 1e-10 
 68  """The length of the C_alpha-C_prime bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).""" 
 69   
 70  C_N_BOND_LENGTH_RDC = 1.329 * 1e-10 
 71  """The length of the C_prime-N bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).""" 
 72   
 73  C_HN_BOND_LENGTH_RDC = 2.067 * 1e-10 
 74  """The length of the C_prime-HN bond for RDCs (from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341).""" 
 75   
 76   
 77   
 78  # The dipolar constant. 
 79  ####################### 
 80   
 81 -def dipolar_constant(gx, gh, r): 
 82      """Calculate the dipolar constant. 
 83   
 84      The dipolar constant is defined as:: 
 85   
 86                mu0 gI.gS.h_bar 
 87          d = - --- ----------- , 
 88                4pi    r**3 
 89   
 90      where: 
 91          - mu0 is the permeability of free space, 
 92          - gI and gS are the gyromagnetic ratios of the I and S spins, 
 93          - h_bar is Dirac's constant which is equal to Planck's constant divided by 2pi, 
 94          - r is the distance between the two spins. 
 95   
 96   
 97      @param gx:  The gyromagnetic ratio of the heteronucleus (or first spin). 
 98      @type gx:   float 
 99      @param gh:  The gyromagnetic ratio of the proton (or second spin). 
100      @type gh:   float 
101      @param r:   The distance between the two nuclei. 
102      @type r:    float 
103      """ 
104   
105      # Catch zero bond lengths, returning NaN. 
106      if r == 0: 
107          return nan 
108   
109      # Calculate and return the value. 
110      return - mu0 / (4.0*pi) * gx * gh * h_bar / r**3 
111   
112   
113  # The pseudocontact shift constant. 
114  ################################### 
115   
116 -def pcs_constant(T, Bo, r): 
117      """Calculate the pseudocontact shift constant. 
118   
119      The pseudocontact shift constant is defined as:: 
120   
121              mu0 15kT   1 
122          d = --- ----- ---- , 
123              4pi Bo**2 r**3 
124   
125      where: 
126          - mu0 is the permeability of free space, 
127          - k is Boltzmann's constant, 
128          - T is the absolute temperature, 
129          - Bo is the magnetic field strength, 
130          - r is the distance between the paramagnetic centre (electron spin) and the nuclear spin. 
131   
132   
133      @param T:   The temperature in kelvin. 
134      @type T:    float 
135      @param Bo:  The magnetic field strength. 
136      @type Bo:   float 
137      @param r:   The distance between the two nuclei. 
138      @type r:    float 
139      """ 
140   
141      # Catch zero bond lengths, returning NaN. 
142      if r == 0: 
143          return nan 
144   
145      # Calculate and return the value. 
146      return mu0 / (4.0*pi) * 15.0 * kB * T / Bo**2 / r**3 
147   
148   
149   
150  # Gyromagnetic ratios. 
151  ###################### 
152   
153  g13C = 6.728 * 1e7 
154  """The 13C gyromagnetic ratio.""" 
155   
156  g1H = 26.7522212 * 1e7 
157  """The 1H gyromagnetic ratio.""" 
158  # Pales:  2.675198e+8 
159   
160  g15N = -2.7126 * 1e7 
161  """The 15N gyromagnetic ratio.""" 
162  # Pales:  -2.7116e+7 
163   
164  g17O = -3.628 * 1e7 
165  """The 17O gyromagnetic ratio.""" 
166   
167  g31P = 10.841 * 1e7 
168  """The 31P gyromagnetic ratio.""" 
169   
170  # Function for returning the desired gyromagnetic ratio. 
171 -def return_gyromagnetic_ratio(nucleus=None): 
172      """Return the gyromagnetic ratio for the given nucleus type. 
173   
174      @keyword nucleus:   The nucleus type. 
175      @type nucleus:      str 
176      @raises RelaxError: If the nucleus type is unknown. 
177      @returns:           The desired gyromagnetic ratio. 
178      @rtype:             float 
179      """ 
180   
181      # Matching loop. 
182      if nucleus == '13C': 
183          return g13C 
184      elif nucleus == '1H': 
185          return g1H 
186      elif nucleus == '15N': 
187          return g15N 
188      elif nucleus == '17O': 
189          return g17O 
190      elif nucleus == '31P': 
191          return g31P 
192      else: 
193          raise RelaxError("The nucleus type " + repr(nucleus) + " is unknown.") 
194   
195   
196  # Relative atomic masses. 
197  ######################### 
198   
199  ArH = 1.00794 
200  """Proton atomic mass.""" 
201   
202  ArC = 12.0107 
203  """Carbon atomic mass.""" 
204   
205  ArN = 14.0067 
206  """Nitrogen atomic mass.""" 
207   
208  ArO = 15.9994 
209  """Oxygen atomic mass.""" 
210   
211  ArS = 32.065 
212  """Sulphur atomic mass.""" 
213   
214  ArCa = 40.078 
215  """Calcium atomic mass.""" 
216   
217   
218  # Function for returning the desired atomic mass. 
219 -def return_atomic_mass(element=None): 
220      """Return the atomic mass for the given element type. 
221   
222      @keyword element:   The element type. 
223      @type element:      str 
224      @raises RelaxError: If the element type is unknown. 
225      @returns:           The desired atomic mass. 
226      @rtype:             float 
227      """ 
228   
229      # Protons, deuterons. 
230      if element == 'H': 
231          return ArH 
232      if element == '1H': 
233          return 1.0 
234      if element == '2H': 
235          return 2.0 
236   
237      # Carbons. 
238      if element == 'C': 
239          return ArC 
240      if element == '12C': 
241          return 12.0 
242      if element == '13C': 
243          return 13.0 
244   
245      # Nitrogens. 
246      if element == 'N': 
247          return ArN 
248      if element == '14N': 
249          return 14.0 
250      if element == '15N': 
251          return 15.0 
252   
253      # Oxygens. 
254      if element == 'O': 
255          return ArO 
256      if element == '16O': 
257          return 16.0 
258      if element == '17O': 
259          return 17.0 
260   
261      # Sulphurs. 
262      if element == 'S': 
263          return ArS 
264   
265      # Calcium. 
266      if upper(element) == 'CA': 
267          return ArCa 
268   
269      # Unknown mass. 
270      raise RelaxError("The mass of the element " + repr(element) + " has not yet been programmed into relax.") 
271   
272   
273   
274  # Element info. 
275  ############### 
276   
277 -def element_from_isotope(isotope): 
278      """Determine and return the element name for the given isotope. 
279   
280      @param isotope: The isotope name, such as '1H', '15N'. 
281      @type isotope:  str 
282      @return:        The element name. 
283      @rtype:         str 
284      """ 
285   
286      # Remove the digit characters. 
287      return isotope.strip(digits) 
288   
289   
290 -def number_from_isotope(isotope): 
291      """Determine and return the isotope number for the given isotope. 
292   
293      @param isotope: The isotope name, such as '1H', '15N'. 
294      @type isotope:  str 
295      @return:        The isotope number. 
296      @rtype:         int 
297      """ 
298   
299      # Remove the digit characters. 
300      return int(isotope.strip(ascii_letters)) 
301