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|
#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* -------------------------------------------------------------------
from __future__ import print_function
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
|
