gromacs.analysis.plugins.stripwater

48 """StripWater worker class.""" 49

50 - def __init__(self,**kwargs):

51 """Set up StripWater 52 53 :Arguments: 54 *force* 55 ``True`` will always regenerate trajectories even if they 56 already exist, ``False`` raises an exception, ``None`` 57 does the sensible thing in most cases (i.e. notify and 58 then move on). 59 *dt* : float or list of floats 60 only write every dt timestep (in ps); if a list of floats is 61 supplied, write multiple trajectories, one for each dt. 62 *compact* : bool 63 write a compact representation 64 *fit* 65 Create an additional trajectory from the stripped one in which 66 the Protein group is rms-fitted to the initial structure. See 67 :meth:`gromacs.cbook.Transformer.fit` for details. Useful 68 values: 69 - "xy" : perform a rot+trans fit in the x-y plane 70 - "all": rot+trans 71 - ``None``: no fitting 72 If *fit* is not supplied then the constructore-default is used 73 (:attr:`_StripWater.parameters.fit`). 74 *resn* 75 name of the residues that are stripped (typically it is 76 safe to leave this at the default 'SOL') 77 """ 78 # specific arguments: take them before calling the super class that 79 # does not know what to do with them 80 _fitvalues = ("xy", "all", None) 81 parameters = {} 82 parameters['fit'] = kwargs.pop('fit',None) # fitting algorithm 83 if not parameters['fit'] in _fitvalues: 84 raise ValueError("StripWater: *fit* must be one of %(_fitvalues)r, not %(fit)r." % vars()) 85 parameters['compact'] = kwargs.pop('compact', False) # compact+centered ? 86 parameters['resn'] = kwargs.pop('resn', 'SOL') # residue name to be stripped 87 parameters['dt'] = kwargs.pop('dt', None) 88 parameters['force'] = kwargs.pop('force', None) 89 90 # super class init: do this before doing anything else 91 # (also sets up self.parameters and self.results) 92 super(_StripWater, self).__init__(**kwargs) 93 94 # self.parameters is set up by the base Worker class... 95 self.parameters.filenames = AttributeDict() 96 self.parameters.update(parameters) 97 98 # self.simulation might have been set by the super class 99 # already; just leave this snippet at the end. Do all 100 # initialization that requires the simulation class in the 101 # _register_hook() method. 102 if not self.simulation is None: 103 self._register_hook()

104

105 - def _register_hook(self, **kwargs):

106 """Run when registering; requires simulation.""" 107 108 super(_StripWater, self)._register_hook(**kwargs) 109 assert not self.simulation is None 110 111 trjdir = os.path.dirname(self.simulation.tpr) 112 self.transformer = gromacs.cbook.Transformer(dirname=trjdir, 113 s=self.simulation.tpr, f=self.simulation.xtc, n=self.simulation.ndx)

114 115 # override 'API' methods of base class 116

117 - def run(self, **kwargs):

118 """Write new trajectory with water index group stripped. 119 120 kwargs are passed to 121 :meth:`gromacs.cbook.Transformer.strip_water`. Important 122 parameters: 123 124 :Keywords: 125 *force* 126 ``True`` will always regenerate trajectories even if they 127 already exist, ``False`` raises an exception, ``None`` 128 does the sensible thing in most cases (i.e. notify and 129 then move on). 130 *dt* : float or list of floats 131 only write every dt timestep (in ps); if a list of floats is 132 supplied, write multiple trajectories, one for each dt. 133 *compact* : bool 134 write a compact representation 135 *fit* 136 Create an additional trajectory from the stripped one in which 137 the Protein group is rms-fitted to the initial structure. See 138 :meth:`gromacs.cbook.Transformer.fit` for details. Useful 139 values: 140 - "xy" : perform a rot+trans fit in the x-y plane 141 - "all": rot+trans 142 - ``None``: no fitting 143 If *fit* is not supplied then the constructore-default is used 144 (:attr:`_StripWater.parameters.fit`). 145 *resn* 146 name of the residues that are stripped (typically it is 147 safe to leave this at the default 'SOL') 148 149 .. Note:: If set, *dt* is only applied to a fit step; the 150 no-water trajectory is always generated for all time 151 steps of the input. 152 """ 153 dt = kwargs.pop('dt', self.parameters.dt) 154 fit = kwargs.pop('fit', self.parameters.fit) 155 156 kwargs.setdefault('compact', self.parameters.compact) 157 kwargs.setdefault('resn', self.parameters.resn) 158 kwargs.setdefault('force', self.parameters.force) 159 160 newfiles = self.transformer.strip_water(**kwargs) 161 self.parameters.filenames.update(newfiles) 162 163 if fit != None: 164 if self.parameters.fit == "xy": 165 xy = True 166 else: 167 xy = False 168 transformer_nowater = self.transformer.nowater.values()[0] 169 for delta_t in asiterable(dt): 170 transformer_nowater.fit(xy=xy, dt=delta_t, force=kwargs['force'])

171

172 - def analyze(self,**kwargs):

173 """No postprocessing.""" 174 pass

175 176

177 - def plot(self, **kwargs):

178 """No plotting.""" 179 pass

Source Code for Module gromacs.analysis.plugins.stripwater