code/test/Python/0034980_edr.py

'''Parser for gromacs edr'''
from .base import IOHandler
import numpy as np
import xdrlib
import difflib

class QuantityNotAvailable(Exception):
    pass

class EdrIO(IOHandler):
    '''EDR files store per-frame information for gromacs
    trajectories. Examples of properties obtainable from EDR files are::

    - temperature
    - pressure
    - density
    - potential energy
    - total energy
    - etc.
    
    To know which quantities are available in a certain edr file you
    can access the feature 'avail quantity'::
    
        >>> datafile('ener.edr').read('avail quantities')
        ['Temperature', 'Pressure', 'Potential', ...]
    
    To get the frame information for a certain quantity you may use
    the "quantity" property passing the quantity as additional
    argument, this will return two arrays, the first is an array of
    times in ps and the second are the corrisponding quantities::
    
        >>> time, temp = datafile('ener.edr').read('quantity', 'Temperature')
    
    **Features**

    .. method:: read("quantity", quant)
    
        Return an array of times in ps and the corresponding quantities
        at that times.
       
    .. method:: read("avail quantities")
    
        Return the available quantities in the file.
    
    .. method:: read("units")
    
        Return a dictionary where the keys are the quantities and
        the value are the units in which that quantity is expressed.
    
    .. method:: read("frames")
    
        Return a dictionary where the keys are the quantities and
        the value are the units in which that quantity is expressed.


    '''

    can_read = ['quantity', 'units', 'avail quantities']
    can_write = []
    
    def __init__(self, fd):
        super(EdrIO, self).__init__(fd)
        self.processed = False
        
    def read(self, feature, *args):
        self.check_feature(feature, 'read')
        
        if not self.processed:
            self.frames = frames = self.process_frames()        
            self.processed = True
        else:
            frames = self.frames
        
        if feature == 'quantity':
            if not args[0]:
                raise Exception('the method read("quantity", arg) requires a quantity to get')
                
            
            quant = args[0]
            
            if quant not in self.props:
                close = difflib.get_close_matches(quant, self.props)
                raise QuantityNotAvailable('Quantity %s not available. Close matches: %s'%
                                           (str(quant), str(close)))
                
            i = self.props.index(quant)
            ret = []
            for f in frames:
                ret.append(f[i][0])
            
            return np.array(self.times), np.array(ret)
            
        if feature == 'units':
            quant = args[0]
            i = self.props.index(quant)
            return self.units[i]
            
        if feature == 'avail quantities':
            return self.props

            
    def process_frames(self):
        
        f = self.fd.read()
        self.up = xdrlib.Unpacker(f)

        self.times = []
        self.dts = []
        self.frames = []

        self._unpack_start()
        fr = self._unpack_frame()
        self.frames.append(fr)
        
        
        while True:
            try:
                fr = self._unpack_frame()
            except EOFError:
                break
            self.frames.append(fr)

        return self.frames

    def _unpack_start(self):
        up = self.up
        magic = up.unpack_int()
        if  (magic != -55555):
            raise Exception('Format not supported: magic number -55555 not matching')

        self.version = up.unpack_int()
        
        # Number of properties
        self.nre = up.unpack_int()
        

        self.props = props = []
        self.units = units = []

        # Strings and units of quantities
        for i in range(self.nre):
            prop = up.unpack_string()
            unit = up.unpack_string()
            
            props.append(prop.decode('utf-8'))
            units.append(unit.decode('utf-8'))

    def _unpack_eheader(self):
        up = self.up
        first_real_to_check = -2e10

        # Checking the first real for format
        first_real = up.unpack_double()

        if (first_real != first_real_to_check):
            raise Exception('Format not supported, first real not matching.')


        magic = up.unpack_int()
        if  (magic != -7777777):
            raise Exception('Format not supported, magic number not matching -7777777')

        version = up.unpack_int()
        time = up.unpack_double()
        self.times.append(time)
        
        # This two should give us large int that represent the step number
        min = up.unpack_int()
        maj = up.unpack_int()

        self.nsum = up.unpack_int()

        # NSTEPS (again?)
        min = up.unpack_int()
        maj = up.unpack_int()

        # For version 5
        dt = up.unpack_double()
        self.dts.append(dt)

        # Number of properties?
        self.nre = up.unpack_int()
        
        dum = up.unpack_int()

        nblock = up.unpack_int() + 1

        # Block headers:
        id = up.unpack_int()
        nsubblocks = up.unpack_int()
        
        e_size = up.unpack_int()
        
        #dum = up.unpack_int()
        #dum = up.unpack_int()
        #up.unpack_int()

    def _unpack_frame(self):
        # Energies, averages and rmsd
        self._unpack_eheader()

        frame = []
        

        for i in range(self.nre):
            en = self.up.unpack_double()
            if self.nsum > 0:
                avg = self.up.unpack_double()
                rmsd = self.up.unpack_double()
            
                frame.append([en, avg, rmsd])
            else:
                frame.append([en, en, 0.0])
                
        return frame