#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by <NAME> 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:
    from . 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

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by <NAME> 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:
    from . 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

#A* ------------------------------------------------------------------- #B* This file contains source code for the PyMOL computer program #C* copyright 1998-2000 by <NAME> 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* ------------------------------------------------------------------- # 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?... creates a new champ object, which contains         a collect of comparable, searchable patterns adds a new pattern, and         returns the index to this pattern frees a pattern resets a pattern\'s tags retrieves the smiles string for a given pattern index retrieves the smiles string for a given pattern index inserts the pattern from a ChemPy model pattern and returns the index adds pattern string to the top of a list adds pattern index to the top of a list returns a new list handle destroys a list and associated patterns (if purge = 1) returns pattern indices in a list as a list returns list of smiles strings contained in a list # boolean returns whether or not pattern can be found in target         as a boolean result returns tag list for single pattern on target # boolean returns mappings (if any) between two patterns returns count of matches returns count of how many times pattern occurs in list 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. dump bulk memory information debugging routine debugging routine debugging routine get tags as bit masks get tags (numeric lists) get tags (numeric lists) debugging routine debugging routine debugging routine experimental experimental experimental