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__init__.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-* 
#-* 
#-*
#Z* -------------------------------------------------------------------

try:
    import _champ
except ImportError:
    print " Error: unable to import architecture-dependent _champ module."

# okay, this module is going to take some planning, since Champ
# has the potential to evolve into a full-blown
# chemical informatics system 

# what do we need to be prepared to handle?
#
# - single structures
# - single patterns
# - lists of patterns
# - lists of compounds
# - dictionaries of compounds (key/value)
# - molecules in other class formats (chempy models, etc.)
# - subsets of protein structures
# - scripts which apply rules according to patterns
# - synchronized chempy models

# what does the architecture-dependent modules need to support?

# - Smiles/SMARTS/etc. conversion (bidirectional)
# - ChemPy model conversion (bidirectional)
# - modification recipe for extant chempy models?...

class Champ:

    def __init__(self):
        '''
        creates a new champ object, which contains
        a collect of comparable, searchable patterns 
        '''
        self._champ = _champ.new()

    def insert_pattern_string(self,pattern):
        '''
        adds a new pattern, and
        returns the index to this pattern
        '''
        (e,r) = _champ.insert_pattern_string(self._champ,str(pattern))
        if e: raise RuntimeError
        return r

    def pattern_free(self,index):
        '''
        frees a pattern
        '''
        (e,r) = _champ.pattern_free(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_clear_tags(self,index):
        '''
        resets a pattern\'s tags
        '''
        (e,r) = _champ.pattern_clear_tags(self._champ,int(index))
        if e: raise RuntimeError
        return r
        
    
    def pattern_get_string(self,index):
        '''
        retrieves the smiles string for a given pattern index
        '''
        (e,r) = _champ.pattern_get_string(self._champ,int(index),0)
        if e: raise RuntimeError
        return r

    def pattern_get_string_with_names(self,index):
        '''
        retrieves the smiles string for a given pattern index
        '''
        (e,r) = _champ.pattern_get_string(self._champ,int(index),1)
        if e: raise RuntimeError
        return r

    def insert_model(self,model):
        '''
        inserts the pattern from a ChemPy model pattern and returns the index
        '''
        (e,r) = _champ.insert_model(self._champ,model)
        if e: raise RuntimeError
        return r

    def list_prepend_pattern_strings(self,handle,pattern):
        '''
        adds pattern string to the top of a list
        '''
        (e,r) = _champ.list_prepend_pattern_strings(self._champ,int(handle),pattern)
        if e: raise RuntimeError
        return r

    def list_prepend_pattern_index(self,handle,index):
        '''
        adds pattern index to the top of a list
        '''
        (e,r) = _champ.list_prepend_pattern_index(self._champ,int(handle),int(index))
        if e: raise RuntimeError
        return r
    
    def list_new(self):
        '''
        returns a new list handle
        '''
        (e,r) = _champ.list_new(self._champ)
        if e: raise RuntimeError
        return r

    def list_free(self,handle,purge=1):
        '''
        destroys a list and associated patterns (if purge = 1)
        '''
        (e,r) = _champ.list_free(self._champ,int(handle),int(purge))
        if e: raise RuntimeError
        return r

    def list_get_pattern_indices(self,handle):
        '''
        returns pattern indices in a list as a list
        '''
        (e,r) = _champ.list_get_pattern_indices(self._champ,int(handle))
        if e: raise RuntimeError
        return r

    def list_get_pattern_strings(self,handle):
        '''
        returns list of smiles strings contained in a list
        '''
        (e,r) = _champ.list_get_pattern_strings(self._champ,int(handle))
        if e: raise RuntimeError
        return r

    def match_1v1_b(self,pattern,target): # boolean
        '''
        returns whether or not pattern can be found in target
        as a boolean result
        '''
        (e,r) = _champ.match_1v1_b(self._champ,
                                    int(pattern),int(target))
        if e: raise RuntimeError
        return r

    def match_1v1_n(self,pattern,target,limit,tag=0):
        '''
        returns tag list for single pattern on target
        '''
        (e,r) = _champ.match_1v1_n(self._champ,
                                    int(pattern),int(target),
                                            int(limit),int(tag))
        if e: raise RuntimeError
        return r

    def match_1v1_map(self,pattern,target,limit,tag=0): # boolean
        '''
        returns mappings (if any) between two patterns
        '''
        (e,r) = _champ.match_1v1_map(self._champ,
                                    int(pattern),int(target),int(limit),int(tag))
        if e: raise RuntimeError
        return r

    def match_Nv1_n(self,pattern,target,limit,tag):
        '''
        returns count of matches
        '''
        (e,r) = _champ.match_Nv1_n(self._champ,
                                    int(pattern),int(target),
                                            int(limit),int(tag))
        if e: raise RuntimeError
        return r

        
    def match_1vN_n(self,pattern,handle):
        '''
        returns count of how many times pattern occurs in list
        '''
        (e,r) = _champ.match_1vN_n(self._champ,
                                    int(pattern),int(handle))
        if e: raise RuntimeError
        return r

    def exact_1vN_n(self,pattern,handle):
        '''
        returns count of how many times exact compound occurs in list
        
        NOTE: should call generalize first as patterns are loaded...
                otherwise, equivalent aromatic bonds will be missed.
        '''
        (e,r) = _champ.exact_1vN_n(self._champ,
                                    int(pattern),int(handle))
        if e: raise RuntimeError
        return r
        
    def memory_dump(self):
        '''
        dump bulk memory information
        '''
        (e,r) = _champ.memory_dump(self._champ)
        if e: raise RuntimeError
        return r

    def pattern_get_cycle(self,index):
        '''
        debugging routine
        '''
        (e,r) = _champ.pattern_get_cycle(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_get_class(self,index):
        '''
        debugging routine
        '''
        (e,r) = _champ.pattern_get_class(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_get_codes(self,index):
        '''
        debugging routine
        '''
        (e,r) = _champ.pattern_get_codes(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_get_tag_masks(self,index):
        '''
        get tags as bit masks
        '''
        (e,r) = _champ.pattern_get_tag_masks(self._champ,int(index))
        if e: raise RuntimeError
        return r
    
    def pattern_get_tags(self,index):
        '''
        get tags (numeric lists)
        '''
        (e,r) = _champ.pattern_get_tags(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_get_ext_indices_with_tags(self,index):
        '''
        get tags (numeric lists)
        '''
        (e,r) = _champ.pattern_get_ext_indices_with_tags(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_get_atom_symbols(self,index):
        '''
        debugging routine
        '''
        (e,r) = _champ.pattern_get_atom_symbols(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_get_atom_names(self,index):
        '''
        debugging routine
        '''
        (e,r) = _champ.pattern_get_atom_names(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_dump(self,index):
        '''
        debugging routine
        '''
        (e,r) = _champ.pattern_dump(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_orient_bonds(self,index):
        '''
        experimental
        '''
        (e,r) = _champ.pattern_orient_bonds(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_detect_chirality(self,index):
        '''
        experimental
        '''
        (e,r) = _champ.pattern_detect_chirality(self._champ,int(index))
        if e: raise RuntimeError
        return r

    def pattern_generalize(self,index):
        '''
        experimental
        '''
        (e,r) = _champ.pattern_generalize(self._champ,int(index))
        if e: raise RuntimeError
        return r

        

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