pipe_control.grace

1 ############################################################################### 2 # # 3 # Copyright (C) 2003-2014 Edward d'Auvergne # 4 # # 5 # This file is part of the program relax (http://www.nmr-relax.com). # 6 # # 7 # This program is free software: you can redistribute it and/or modify # 8 # it under the terms of the GNU General Public License as published by # 9 # the Free Software Foundation, either version 3 of the License, or # 10 # (at your option) any later version. # 11 # # 12 # This program is distributed in the hope that it will be useful, # 13 # but WITHOUT ANY WARRANTY; without even the implied warranty of # 14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # 15 # GNU General Public License for more details. # 16 # # 17 # You should have received a copy of the GNU General Public License # 18 # along with this program. If not, see <http://www.gnu.org/licenses/>. # 19 # # 20 ############################################################################### 21 22 # Module docstring. 23 """Module for interfacing with Grace (also known as Xmgrace, Xmgr, and ace).""" 24 25 # Python module imports. 26 from os import system 27 from warnings import warn 28 29 # relax module imports. 30 from lib.errors import RelaxError, RelaxNoSequenceError, RelaxNoSimError 31 from lib.io import get_file_path, open_write_file, test_binary 32 from lib.software.grace import write_xy_data, write_xy_header 33 from lib.warnings import RelaxWarning 34 from pipe_control.mol_res_spin import count_molecules, count_residues, count_spins, exists_mol_res_spin_data 35 from pipe_control import pipes 36 from pipe_control.result_files import add_result_file 37 from pipe_control.plotting import assemble_data 38 from specific_analyses.api import return_api 39 from status import Status; status = Status() 40 41

42 -def axis_setup(data_type=None, norm=True):

43 """Determine the axis information for relax data store specific data. 44 45 @keyword data_type: The axis data category (in the [X, Y] list format). 46 @type data_type: list of str 47 @keyword norm: The normalisation flag which if set to True will cause all graphs to be normalised to a starting value of 1. 48 @type norm: bool 49 @return: The axis information. This includes the sequence type, the list of lower bounds, the list of upper bounds, and the axis labels. 50 @rtype: list of str or None, list of int or None, list of int or None, list of str or None 51 """ 52 53 # Axis specific settings. 54 axes = ['x', 'y'] 55 seq_type = [None, None] 56 axis_labels = [None, None] 57 for i in range(2): 58 # Determine the sequence data type. 59 if data_type[i] == 'res_num': 60 seq_type[i] = 'res' 61 62 # Analysis specific methods for making labels. 63 analysis_spec = False 64 if pipes.cdp_name(): 65 # Flag for making labels. 66 analysis_spec = True 67 68 # The specific analysis API object. 69 api = return_api() 70 71 # Some axis default values for spin data. 72 if data_type[i] == 'res_num': 73 # Residue only data. 74 if seq_type[i] == 'res': 75 # X-axis label. 76 if not axis_labels[i]: 77 axis_labels[i] = "Residue number" 78 79 # Spin only data. 80 if seq_type[i] == 'spin': 81 # X-axis label. 82 if not axis_labels[i]: 83 axis_labels[i] = "Spin number" 84 85 # Mixed data. 86 if seq_type[i] == 'mixed': 87 # X-axis label. 88 if not axis_labels[i]: 89 axis_labels[i] = "Spin identification string" 90 91 # Some axis default values for other data types. 92 else: 93 # Label. 94 if analysis_spec and not axis_labels[i]: 95 # Get the units. 96 units = api.return_units(data_type[i]) 97 98 # Set the label. 99 axis_labels[i] = api.return_grace_string(data_type[i]) 100 101 # Add units. 102 if units: 103 axis_labels[i] = axis_labels[i] + "\\N (" + units + ")" 104 105 # Normalised data. 106 if norm and axes[i] == 'y': 107 axis_labels[i] = axis_labels[i] + " \\N\\q(normalised)\\Q" 108 109 # Return the data. 110 return seq_type, axis_labels

111 112

113 -def determine_seq_type(spin_id=None):

114 """Determine the spin sequence data type. 115 116 The purpose is to identify systems whereby only spins or only residues exist. 117 118 @keyword spin_id: The spin identification string. 119 @type spin_id: str 120 @return: The spin sequence data type. This can be one of 'spin', 'res,' or 'mixed'. 121 @rtype: str 122 """ 123 124 # Count the molecules, residues, and spins. 125 num_mol = count_molecules(spin_id) 126 num_res = count_residues(spin_id) 127 num_spin = count_spins(spin_id) 128 129 # Only residues. 130 if num_mol == 1 and num_spin == 1: 131 return 'res' 132 133 # Only spins. 134 if num_mol == 1 and num_res == 1: 135 return 'spin' 136 137 # Mixed. 138 return 'mixed'

139 140

141 -def get_data_types():

142 """Get all of the data types to plot for the current data pipe. 143 144 @return: A list of lists of all the allowable data type descriptions and their values. 145 @rtype: list of list of str 146 """ 147 148 # The specific analysis API object. 149 api = return_api() 150 151 # Return an empty list if the required functions are absent. 152 if not hasattr(api, 'data_names') or not hasattr(api, 'return_data_desc'): 153 return [] 154 155 # The data names, if they exist. 156 names = api.data_names(set='params') 157 158 # Initialise the list and then add the sequence data. 159 data = [] 160 data.append(["Spin sequence", 'spin']) 161 162 # Loop over the parameters. 163 for name in (api.data_names(set='params') + api.data_names(set='generic') + api.data_names(set='min')): 164 # Get the description. 165 try: 166 desc = api.return_data_desc(name) 167 except: 168 return [] 169 170 # No description. 171 if not desc: 172 text = name 173 174 # The text. 175 else: 176 text = "'%s': %s" % (name, desc) 177 178 # Append the description. 179 data.append([text, name]) 180 181 # Return the data. 182 return data

183 184

185 -def view(file=None, dir=None, grace_exe='xmgrace'):

186 """Execute Grace. 187 188 @keyword file: The name of the file to open in Grace. 189 @type file: str 190 @keyword dir: The optional directory containing the file. 191 @type dir: str 192 @keyword grace_exe: The name of the Grace executable file. This should be located within the 193 system path. 194 @type grace_exe: str 195 """ 196 197 # Test the binary file string corresponds to a valid executable. 198 test_binary(grace_exe) 199 200 # File path. 201 file_path = get_file_path(file, dir) 202 203 # Run Grace. 204 system(grace_exe + " \"" + file_path + "\" &")

205 206

207 -def write(x_data_type='res_num', y_data_type=None, spin_id=None, plot_data='value', file=None, dir=None, force=False, norm=True):

208 """Writing data to a file. 209 210 @keyword x_data_type: The category of the X-axis data. 211 @type x_data_type: str 212 @keyword y_data_type: The category of the Y-axis data. 213 @type y_data_type: str 214 @keyword spin_id: The spin identification string. 215 @type spin_id: str 216 @keyword plot_data: The type of the plotted data, one of 'value', 'error', or 'sim'. 217 @type plot_data: str 218 @keyword file: The name of the Grace file to create. 219 @type file: str 220 @keyword dir: The optional directory to place the file into. 221 @type dir: str 222 @param force: Boolean argument which if True causes the file to be overwritten if it already exists. 223 @type force: bool 224 @keyword norm: The normalisation flag which if set to True will cause all graphs to be normalised to a starting value of 1. 225 @type norm: bool 226 """ 227 228 # Test if the current pipe exists. 229 pipes.test() 230 231 # Test if the sequence data is loaded. 232 if not exists_mol_res_spin_data(): 233 raise RelaxNoSequenceError 234 235 # Test if the plot_data argument is one of 'value', 'error', or 'sim'. 236 if plot_data not in ['value', 'error', 'sim']: 237 raise RelaxError("The plot data argument " + repr(plot_data) + " must be set to either 'value', 'error', 'sim'.") 238 239 # Test if the simulations exist. 240 if plot_data == 'sim' and not hasattr(cdp, 'sim_number'): 241 raise RelaxNoSimError 242 243 # Open the file for writing. 244 file_path = get_file_path(file, dir) 245 file = open_write_file(file, dir, force) 246 247 # Get the data. 248 data, set_names, graph_type = assemble_data(spin_id, x_data_name=x_data_type, y_data_name=y_data_type, plot_data=plot_data) 249 250 # Convert the graph type. 251 if graph_type == 'X,Y': 252 graph_type = 'xy' 253 elif graph_type == 'X,Y,dX': 254 graph_type = 'xydx' 255 elif graph_type == 'X,Y,dY': 256 graph_type = 'xydy' 257 elif graph_type == 'X,Y,dX,dY': 258 graph_type = 'xydxdy' 259 260 # No data, so close the empty file and exit. 261 if not len(data) or not len(data[0]) or not len(data[0][0]): 262 warn(RelaxWarning("No data could be found, creating an empty file.")) 263 file.close() 264 return 265 266 # Get the axis information. 267 data_type = [x_data_type, y_data_type] 268 seq_type, axis_labels = axis_setup(data_type=data_type, norm=norm) 269 270 # Write the header. 271 write_xy_header(file=file, data_type=data_type, seq_type=seq_type, sets=[len(data[0])], set_names=[set_names], axis_labels=[axis_labels], norm=[norm]) 272 273 # Write the data. 274 write_xy_data(data, file=file, graph_type=graph_type, norm=[norm]) 275 276 # Close the file. 277 file.close() 278 279 # Add the file to the results file list. 280 add_result_file(type='grace', label='Grace', file=file_path)

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Source Code for Module pipe_control.grace