lib.spectrum.sparky

1 ############################################################################### 2 # # 3 # Copyright (C) 2004-2013 Edward d'Auvergne # 4 # Copyright (C) 2008 Sebastien Morin # 5 # # 6 # This file is part of the program relax (http://www.nmr-relax.com). # 7 # # 8 # This program is free software: you can redistribute it and/or modify # 9 # it under the terms of the GNU General Public License as published by # 10 # the Free Software Foundation, either version 3 of the License, or # 11 # (at your option) any later version. # 12 # # 13 # This program is distributed in the hope that it will be useful, # 14 # but WITHOUT ANY WARRANTY; without even the implied warranty of # 15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # 16 # GNU General Public License for more details. # 17 # # 18 # You should have received a copy of the GNU General Public License # 19 # along with this program. If not, see <http://www.gnu.org/licenses/>. # 20 # # 21 ############################################################################### 22 23 # Module docstring. 24 """Module containing functions for handling Sparky files.""" 25 26 27 # Python module imports. 28 from re import split 29 30 # relax module imports. 31 from lib.errors import RelaxError 32 from lib.io import open_write_file, strip 33 34

35 -def read_list(peak_list=None, file_data=None):

36 """Extract the peak intensity information from the Sparky peak intensity file. 37 38 @keyword peak_list: The peak list object to place all data into. 39 @type peak_list: lib.spectrum.objects.Peak_list instance 40 @keyword file_data: The data extracted from the file converted into a list of lists. 41 @type file_data: list of lists of str 42 @raises RelaxError: When the expected peak intensity is not a float. 43 """ 44 45 # The number of header lines. 46 num = 0 47 if file_data[0][0] == 'Assignment': 48 num = num + 1 49 if file_data[1] == '': 50 num = num + 1 51 print("Number of header lines found: %s" % num) 52 53 # The columns according to the file. 54 w1_col = None 55 w2_col = None 56 w3_col = None 57 w4_col = None 58 int_col = None 59 for i in range(len(file_data[0])): 60 # The chemical shifts. 61 if file_data[0][i] == 'w1': 62 w1_col = i 63 elif file_data[0][i] == 'w2': 64 w2_col = i 65 elif file_data[0][i] == 'w3': 66 w3_col = i 67 elif file_data[0][i] == 'w4': 68 w4_col = i 69 70 # The peak height. 71 elif file_data[0][i] == 'Data' and file_data[0][i+1] == 'Height': 72 int_col = i 73 74 # The peak volume. 75 elif file_data[0][i] == 'Intensity': 76 int_col = i 77 78 # Remove the header. 79 file_data = file_data[num:] 80 81 # Strip the data. 82 file_data = strip(file_data) 83 84 # The dimensionality. 85 if w4_col != None: 86 dim = 4 87 elif w3_col != None: 88 dim = 3 89 elif w2_col != None: 90 dim = 2 91 elif w1_col != None: 92 dim = 1 93 else: 94 raise RelaxError("The dimensionality of the peak list cannot be determined.") 95 print("%sD peak list detected." % dim) 96 97 # Loop over the file data. 98 for line in file_data: 99 # Skip non-assigned peaks. 100 if line[0] == '?-?': 101 continue 102 103 # Split up the assignments. 104 if dim == 1: 105 assign1 = line[0] 106 elif dim == 2: 107 assign1, assign2 = split('-', line[0]) 108 elif dim == 3: 109 assign1, assign2, assign3 = split('-', line[0]) 110 elif dim == 4: 111 assign1, assign2, assign3, assign4 = split('-', line[0]) 112 113 # Process the assignment for each dimension. 114 if dim >= 1: 115 row1 = split('([a-zA-Z]+)', assign1) 116 name1 = row1[-2] + row1[-1] 117 if dim >= 2: 118 row2 = split('([a-zA-Z]+)', assign2) 119 name2 = row2[-2] + row2[-1] 120 if dim >= 3: 121 row3 = split('([a-zA-Z]+)', assign3) 122 name3 = row3[-2] + row3[-1] 123 if dim >= 4: 124 row4 = split('([a-zA-Z]+)', assign4) 125 name4 = row4[-2] + row4[-1] 126 127 # The residue number. 128 try: 129 res_num = int(row1[-3]) 130 except: 131 raise RelaxError("Improperly formatted Sparky file, cannot process the assignment '%s'." % line[0]) 132 133 # Chemical shifts. 134 w1 = None 135 w2 = None 136 w3 = None 137 w4 = None 138 if w1_col != None: 139 try: 140 w1 = float(line[w1_col]) 141 except ValueError: 142 raise RelaxError("The chemical shift from the line %s is invalid." % line) 143 if w2_col != None: 144 try: 145 w2 = float(line[w2_col]) 146 except ValueError: 147 raise RelaxError("The chemical shift from the line %s is invalid." % line) 148 if w3_col != None: 149 try: 150 w3 = float(line[w3_col]) 151 except ValueError: 152 raise RelaxError("The chemical shift from the line %s is invalid." % line) 153 if w4_col != None: 154 try: 155 w4 = float(line[w4_col]) 156 except ValueError: 157 raise RelaxError("The chemical shift from the line %s is invalid." % line) 158 159 # Intensity. 160 if int_col != None: 161 try: 162 intensity = float(line[int_col]) 163 except ValueError: 164 raise RelaxError("The peak intensity value from the line %s is invalid." % line) 165 166 # Add the assignment to the peak list object. 167 if dim == 1: 168 peak_list.add(res_nums=[res_num], spin_names=[name1], shifts=[w1], intensity=intensity) 169 elif dim == 2: 170 peak_list.add(res_nums=[res_num, res_num], spin_names=[name1, name2], shifts=[w1, w2], intensity=intensity) 171 elif dim == 3: 172 peak_list.add(res_nums=[res_num, res_num, res_num], spin_names=[name1, name2, name3], shifts=[w1, w2, w3], intensity=intensity) 173 elif dim == 4: 174 peak_list.add(res_nums=[res_num, res_num, res_num, res_num], spin_names=[name1, name2, name3, name4], shifts=[w1, w2, w3, w4], intensity=intensity)

175 176

177 -def write_list(file_prefix=None, dir=None, res_names=None, res_nums=None, atom1_names=None, atom2_names=None, w1=None, w2=None, data_height=None, force=True):

178 """Create a Sparky .list file. 179 180 @keyword file_prefix: The base part of the file name without the .list extension. 181 @type file_prefix: str 182 @keyword dir: The directory to place the file in. 183 @type dir: str or None 184 @keyword res_names: The residue name list for each peak entry. 185 @type res_names: list of str 186 @keyword res_nums: The residue number list for each peak entry. 187 @type res_nums: list of int 188 @keyword atom1_names: The atom name list for w1 for each peak entry. 189 @type atom1_names: list of str 190 @keyword atom2_names: The atom name list for w2 for each peak entry. 191 @type atom2_names: list of str 192 @keyword w1: The w1 chemical shift list in ppm for each peak entry. 193 @type w1: list of float 194 @keyword w2: The w2 chemical shift list in ppm for each peak entry. 195 @type w2: list of float 196 @keyword data_height: The optional data height list for each peak entry. 197 @type data_height: None or list of float 198 @keyword force: A flag which if True will cause any pre-existing files to be overwritten. 199 @type force: bool 200 """ 201 202 # Checks. 203 N = len(w1) 204 if len(res_names) != N: 205 raise RelaxError("The %s residue names does not match the %s number of entries." % (len(res_names), N)) 206 if len(res_nums) != N: 207 raise RelaxError("The %s residue numbers does not match the %s number of entries." % (len(res_nums), N)) 208 if len(atom1_names) != N: 209 raise RelaxError("The %s w1 atom names does not match the %s number of entries." % (len(atom1_names), N)) 210 if len(atom2_names) != N: 211 raise RelaxError("The %s w2 atom names does not match the %s number of entries." % (len(atom2_names), N)) 212 if len(w1) != N: 213 raise RelaxError("The %s w1 chemical shifts does not match the %s number of entries." % (len(w1), N)) 214 if len(w2) != N: 215 raise RelaxError("The %s w2 chemical shifts does not match the %s number of entries." % (len(w2), N)) 216 if data_height and len(data_height) != N: 217 raise RelaxError("The %s data heights does not match the %s number of entries." % (len(data_height), N)) 218 219 # Printout. 220 print("Creating the Sparky list file.") 221 222 # Open the file. 223 if isinstance(file_prefix, str): 224 file = open_write_file(file_name=file_prefix+".list", dir=dir, force=force) 225 else: 226 file = file_prefix 227 228 # The header. 229 file.write("%17s %10s %10s" % ("Assignment ", "w1 ", "w2 ")) 230 if data_height != None: 231 file.write(" %12s" % "Data Height") 232 file.write("\n\n") 233 234 # The data. 235 for i in range(N): 236 # Generate the assignment. 237 assign = "%s%i%s-%s" % (res_names[i], res_nums[i], atom1_names[i], atom2_names[i]) 238 239 # Write out the line. 240 file.write("%17s %10.3f %10.3f" % (assign, w1[i], w2[i])) 241 if data_height != None: 242 file.write(" %12i" % data_height[i]) 243 file.write("\n")

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Source Code for Module lib.spectrum.sparky