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# Copyright 2001 by Katharine Lindner. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Martel based parser to read ECell formatted files.
This is a huge regular regular expression for Ecell, built using
the 'regular expressiona on steroids' capabilities of Martel.
#http://www.bioinformatics.org/ecell2/
Notes:
Just so I remember -- the new end of line syntax is:
New regexp syntax - \R
\R means "\n|\r\n?"
[\R] means "[\n\r]"
This helps us have endlines be consistent across platforms.
"""
# standard library
import string
"""Hold ECell data in a straightforward format.
classes:
o Record - All of the information in an ECell record.
"""
class Record:
"""Hold ECell information in a format similar to the original record.
"""
def __init__(self):
self.cell_dict = {}
self._max_dict = {}
self._duplicates = []
self._ecell_version = '0.9.4.6'
self._name = 'Ecell module'
self._version = ''
self.include_buf = ''
self.num_systems = 0
self.num_substances = 0
self.num_reactors = 0
self.include_block = ''
self.contains_concentration = 0
def __str__( self ):
output = '# this is ecell rule file for E-CELL' + self._ecell_version + '\n'
output = output + '# converted by %s %s\n\n' % ( self._name, self._version )
if( self.contains_concentration ):
output = output + 'include(qty.er)\n'
output = output + self.include_buf
system_output = self._print_systems()
substance_output = self._print_substances()
reactor_output = self._print_reactors( substance_output )
output = output + system_output + reactor_output
return output
def _print_systems( self ):
output = ''
for system in range( 1, self.num_systems + 1 ):
composite_key = 'system' + str( system ) + 'class0'
output = output + '\nsystem %s' % self.cell_dict[ composite_key ]
composite_key = 'system' + str( system ) + 'path0'
output = output + '(%s:' % self.cell_dict[ composite_key ]
composite_key = 'system' + str( system ) + 'id0'
output = output + '%s,' % self.cell_dict[ composite_key ]
composite_key = 'system' + str( system ) + 'name0'
output = output + '"%s")\n' % self.cell_dict[ composite_key ]
output = output + '{\n'
output = output + '\tStepper SlaveStepper;\n'
composite_key = 'system' + str( system ) + 'inside0'
if( self.cell_dict.has_key( composite_key ) ):
output = output + '\tInside %s;\n' % self.cell_dict[ composite_key ]
composite_key = 'system' + str( system ) + 'outside0'
if( self.cell_dict.has_key( composite_key ) ):
output = output + '\tOutside %s;\n' % self.cell_dict[ composite_key ]
composite_key = 'system' + str( system ) + 'volumeindex0'
if( self.cell_dict.has_key( composite_key ) ):
output = output + '\tVolumeIndex %s;\n' % self.cell_dict[ composite_key ]
output = output + '}\n'
return output
def _print_substances( self ):
output = ''
for substance in range( 1, self.num_substances + 1 ):
composite_key = 'substance' + str( substance ) + 'class0'
if( self.cell_dict.has_key( composite_key ) ):
output = output + 'substance %s' % self.cell_dict[ composite_key ]
composite_key = 'substance' + str( substance ) + 'path0'
output = output + '(%s:' % get_entry( self.cell_dict, composite_key )
composite_key = 'substance' + str( substance ) + 'id0'
output = output + '%s,' % get_entry( self.cell_dict, composite_key )
composite_key = 'substance' + str( substance ) + 'name0'
output = output + '"%s")\n' % get_entry( self.cell_dict, composite_key )
composite_key = 'substance' + str( substance ) + 'qty0'
output = output + '{\n\tQuantity %s;\n}\n' % get_entry( self.cell_dict, composite_key )
else:
composite_key = 'substance' + str( substance ) + 'path0'
output = output + 'substance %s:' % get_entry( self.cell_dict, composite_key )
composite_key = 'substance' + str( substance ) + 'id0'
output = output + '%s ' % get_entry( self.cell_dict, composite_key )
composite_key = 'substance' + str( substance ) + 'name0'
output = output + '"%s" ' % get_entry( self.cell_dict, composite_key )
composite_key = 'substance' + str( substance ) + 'qty0'
output = output + '%s;\n' % get_entry( self.cell_dict, composite_key )
qty_key = 'substance' + str( substance ) + 'qty1'
conc_key = 'substance' + str( substance ) + 'conc1'
if( get_entry( self.cell_dict, qty_key ).lower() == 'fix' ):
composite_key = 'substance' + str( substance ) + 'path0'
output = output + 'fix %s:' % get_entry( self.cell_dict, composite_key )
composite_key = 'substance' + str( substance ) + 'id0'
output = output + '%s;\n' % get_entry( self.cell_dict, composite_key )
elif( get_entry( self.cell_dict, conc_key ).lower() == 'fix' ):
composite_key = 'substance' + str( substance ) + 'path0'
output = output + 'fix %s:' % get_entry( self.cell_dict, composite_key )
composite_key = 'substance' + str( substance ) + 'id0'
output = output + '%s;\n' % get_entry( self.cell_dict, composite_key )
return output
def _print_reactors( self, output ):
volume_buf = '\n'
self._check_duplicates()
for reactor in range( 1, self.num_reactors + 1 ):
output = output + '\nreactor '
prefix = 'reactor' + str( reactor )
composite_key = prefix + 'class0'
output = output + self.cell_dict[ composite_key ]
composite_key = prefix + 'path0'
output = output + '(%s:' % self.cell_dict[ composite_key ]
composite_key = prefix + 'id0'
output = output + '%s,' % self.cell_dict[ composite_key ]
composite_key = prefix + 'name0'
output = output + '"%s")\n' % self.cell_dict[ composite_key ]
composite_key = 's_' + str( reactor )
num_substrates = get_entry( self._max_dict, composite_key )
output = output + '{\n'
for substrate in range( 1, num_substrates + 1 ):
output = output + '\tSubstrate '
composite_key = prefix + 's_path' + str( substrate )
output = output + get_entry( self.cell_dict, composite_key )
composite_key = prefix + 's_id' + str( substrate )
output = output + ':%s ' % get_entry( self.cell_dict, composite_key )
composite_key = prefix + 's_coeff' + str( substrate )
output = output + '%s' % get_entry( self.cell_dict, composite_key )
output = output + ';\n'
composite_key = 'p_' + str( reactor )
num_products = get_entry( self._max_dict, composite_key )
for product in range( 1, num_products + 1 ):
output = output + '\tProduct '
composite_key = prefix + 'p_path' + str( product )
output = output + get_entry( self.cell_dict, composite_key )
composite_key = prefix + 'p_id' + str( product )
output = output + ':%s ' % get_entry( self.cell_dict, composite_key )
composite_key = prefix + 'p_coeff' + str( product )
output = output + '%s' % get_entry( self.cell_dict, composite_key )
output = output + ';\n'
composite_key = 'c_' + str( reactor )
num_catalysts = get_entry( self._max_dict, composite_key )
for catalyst in range( 1, num_catalysts + 1 ):
output = output + '\tCatalyst '
composite_key = prefix + 'c_path' + str( catalyst )
output = output + get_entry( self.cell_dict, composite_key )
composite_key = prefix + 'c_id' + str( catalyst )
output = output + ':%s' % get_entry( self.cell_dict, composite_key )
output = output + ';\n'
composite_key = 'e_' + str( reactor )
num_effectors = get_entry( self._max_dict, composite_key )
for effector in range( 1, num_effectors + 1 ):
output = output + '\tEffector '
composite_key = prefix + 'e_path' + str( effector )
output = output + get_entry( self.cell_dict, composite_key )
composite_key = prefix + 'e_id' + str( effector )
output = output + ':%s ' % get_entry( self.cell_dict, composite_key )
composite_key = prefix + 'e_coeff' + str( effector )
output = output + '%s;\n' % get_entry( self.cell_dict, composite_key )
output = output + ';\n'
composite_key = 'o_' + str( reactor )
num_options = get_entry( self._max_dict, composite_key )
for option in range( 1, num_options + 1 ):
composite_key = prefix + 'o_type' + str( option )
output = output + '\t%s ' % get_entry( self.cell_dict, composite_key )
composite_key = prefix + 'o_path' + str( option )
output = output + get_entry( self.cell_dict, composite_key )
composite_key = prefix + 'o_id' + str( option )
output = output + ':%s ' % get_entry( self.cell_dict, composite_key )
composite_key = prefix + 'o_coeff' + str( option )
output = output + '%s;\n' % get_entry( self.cell_dict, composite_key )
output = output + ';\n'
composite_key = 'arg_tag' + str( reactor )
num_args = get_entry( self._max_dict, composite_key )
for arg in range( 1, num_args + 1 ):
composite_key = prefix + 'arg_tag' + str( arg )
output = output + '\t%s ' % get_entry( self.cell_dict, composite_key )
composite_key = prefix + 'arg_coeff' + str( arg )
output = output + '%s;\n' % get_entry( self.cell_dict, composite_key )
for system in range( 1, self.num_systems + 1 ):
path_key = prefix + 'path0'
id_key = prefix + 'id0'
reactor_path = get_entry( self.cell_dict, path_key )
reactor_id = get_entry( self.cell_dict, id_key )
path_id = '%s:%s' % ( reactor_path, reactor_id )
volume_key = 'system' + str( system ) + 'volumeindex0'
volume_index = get_entry( self.cell_dict, volume_key )
if( path_id == volume_index ):
output = output + '\tInitialActivity '
init_act_key = prefix + 'init_act0'
init_act0 = get_entry( self.cell_dict, init_act_key )
if( init_act0 == '' ):
init_act0 = get_entry( self.cell_dict, prefix + 'init_act1' )
output = output + '%s;\n' % init_act0
if( not ( system in self._duplicates ) ):
volume_buf = volume_buf + R'_SETVOLUME('
volume_buf = volume_buf + '%s,%s)\n' % ( reactor_path, init_act0 )
volume_buf = volume_buf.replace( r'//', '\/' )
output = output + '}\n'
if( self.contains_concentration ):
output = volume_buf + output
return output
def _check_duplicates( self ):
self._duplicates = []
for system in range( 1, self.num_systems + 1 ):
target_path_key = 'system' + str( system ) + 'path0'
target_id_key = 'system' + str( system ) + 'id0'
for other in range( 1, system ):
match_path_key = 'system' + str( other ) + 'path0'
match_id_key = 'system' + str( other ) + 'id0'
if( self.cell_dict.has_key( target_path_key ) and \
self.cell_dict.has_key( target_id_key ) ):
if self._match_cell_dict_entry( target_path_key, match_path_key ):
if self._match_cell_dict_entry( target_id_key, match_id_key ):
self._duplicates.append( system )
def _match_cell_dict_entry( self, key, other_key ):
if( get_entry( self.cell_dict, key ) == get_entry( self.cell_dict, other_key ) ):
return 1
return 0
def get_entry( dict, key ):
try:
entry = dict[ key ]
except KeyError:
entry = ''
return entry
|
