#! /usr/bin/python # parse_doxy_html.py """"Parse Doxygen-generated html files to get out stuff we want for Javadocs Most code here works on doxytext: this is text taken from Doxygen-generated html created by processing the C++ code. That html is viewed with Firefox and the appropriate pieces (now starting at "Detailed Descripted"are just copied and pasted into a text file. Note that some of the Doxygen-generated files don't have that section and for now this program can't handle them without some additional annotation by hand. """ from __future__ import print_function from BeautifulSoup import * import os import re def list_class_files(dir): return [ name for name in os.listdir(dir) if (name.startswith('class_') and (not name.endswith('png')) and name.find('-members') == -1) ] def get_detail(fname): bs = BeautifulSoup(open(fname).read()) det = bs.find(text='Detailed Description') return [bs, det] _example = \ """int RDKit::Atom::getPerturbationOrder ( INT_LIST probe ) const returns the perturbation order for a list of integers This value is associated with chirality. Parameters: probe a list of bond indices. This must be the same length as our number of incoming bonds (our degree). Returns: the number of swaps required to convert the ordering of the probe list to match the order of our incoming bonds: e.g. if our incoming bond order is: [0,1,2,3] getPerturbationOrder([1,0,2,3]) = 1 getPerturbationOrder([1,2,3,0]) = 3 getPerturbationOrder([1,2,0,3]) = 2 See the class documentation for a more detailed description of our representation of chirality. Usage ... molPtr is a const ROMol & ... ... atomPtr is a const Atom * ... ROMol::ADJ_ITER nbrIdx,endNbrs; boost::tie(nbrIdx,endNbrs) = molPtr.getAtomNeighbors(atomPtr); while(nbrIdx!=endNbrs){ const ATOM_SPTR at=molPtr[*nbrIdx]; ... do something with the Atom ... ++nbrIdx; } Notes: * requires an owning molecule """ _atom = '''Detailed Description The class for representing atoms. Notes: * many of the methods of Atom require that the Atom be associated with a molecule (an ROMol). * each Atom maintains a Dict of properties: o Each property is keyed by name and can store an arbitrary type. o Properties can be marked as calculated, in which case they will be cleared when the clearComputedProps() method is called. o Because they have no impact upon chemistry, all property operations are const, this allows extra flexibility for clients who need to store extra data on Atom objects. * Atom objects are lazy about computing their explicit and implicit valence values. These will not be computed until their values are requested. Chirality: The chirality of an Atom is determined by two things: * its chiralTag * the input order of its bonds (see note below for handling of implicit Hs) For tetrahedral coordination, the chiralTag tells you what direction you have to rotate to get from bond 2 to bond 3 while looking down bond 1. This is pretty much identical to the SMILES representation of chirality. NOTE: if an atom has an implicit H, the bond to that H is considered to be at the *end* of the list of other bonds. Member Enumeration Documentation enum RDKit::Atom::ChiralType store type of chirality Enumerator: CHI_UNSPECIFIED chirality that hasn't been specified CHI_TETRAHEDRAL_CW tetrahedral: clockwise rotation (SMILES @) CHI_TETRAHEDRAL_CCW tetrahedral: counter-clockwise rotation (SMILES @) CHI_OTHER some unrecognized type of chirality enum RDKit::Atom::HybridizationType store hybridization Enumerator: UNSPECIFIED hybridization that hasn't been specified OTHER unrecognized hybridization Member Function Documentation int RDKit::Atom::calcExplicitValence ( bool strict = true ) calculates and returns our explicit valence Notes: * requires an owning molecule int RDKit::Atom::calcImplicitValence ( bool strict = true ) calculates and returns our implicit valence Notes: * requires an owning molecule void RDKit::Atom::clearProp ( const std::string key ) const [inline] This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. void RDKit::Atom::clearProp ( const char * key ) const [inline] clears the value of a property Notes: * if no property with name key exists, a KeyErrorException will be thrown. * if the property is marked as computed, it will also be removed from our list of computedProperties Atom * RDKit::Atom::copy ( ) const [virtual] makes a copy of this Atom and returns a pointer to it. Note: the caller is responsible for deleteing the result Reimplemented in RDKit::QueryAtom. unsigned int RDKit::Atom::getDegree ( ) const returns the explicit degree of the Atom (number of bonded neighbors in the graph) Notes: * requires an owning molecule int RDKit::Atom::getImplicitValence ( ) const returns the implicit valence for this Atom Notes: * requires an owning molecule unsigned int RDKit::Atom::getNumImplicitHs ( ) const returns the number of implicit Hs this Atom is bound to Notes: * requires an owning molecule unsigned int RDKit::Atom::getNumRadicalElectrons ( ) const [inline] returns the number of radical electrons for this Atom Notes: * requires an owning molecule int RDKit::Atom::getPerturbationOrder ( INT_LIST probe ) const returns the perturbation order for a list of integers This value is associated with chirality. Parameters: probe a list of bond indices. This must be the same length as our number of incoming bonds (our degree). Returns: the number of swaps required to convert the ordering of the probe list to match the order of our incoming bonds: e.g. if our incoming bond order is: [0,1,2,3] getPerturbationOrder([1,0,2,3]) = 1 getPerturbationOrder([1,2,3,0]) = 3 getPerturbationOrder([1,2,0,3]) = 2 See the class documentation for a more detailed description of our representation of chirality. Notes: * requires an owning molecule template void RDKit::Atom::getProp ( const std::string key, T & res ) const [inline] This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. template void RDKit::Atom::getProp ( const char * key, T & res ) const [inline] allows retrieval of a particular property value Parameters: key the name under which the property should be stored. If a property is already stored under this name, it will be replaced. res a reference to the storage location for the value. Notes: * if no property with name key exists, a KeyErrorException will be thrown. * the boost::lexical_cast machinery is used to attempt type conversions. If this fails, a boost::bad_lexical_cast exception will be thrown. unsigned int RDKit::Atom::getTotalDegree ( ) const returns the total degree of the Atom (number of bonded neighbors + number of Hs) Notes: * requires an owning molecule unsigned int RDKit::Atom::getTotalNumHs ( bool includeNeighbors = false ) const returns the total number of Hs (implicit and explicit) that this Atom is bound to Notes: * requires an owning molecule bool RDKit::Atom::hasProp ( const std::string key ) const [inline] This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. bool RDKit::Atom::Match ( const ATOM_SPTR what ) const [virtual] This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. Reimplemented in RDKit::QueryAtom. bool RDKit::Atom::Match ( Atom const * what ) const [virtual] returns whether or not we match the argument Notes: * for Atom objects, "match" means that atomic numbers are the same. Reimplemented in RDKit::QueryAtom. void RDKit::Atom::setIdx ( unsigned int index ) [inline] sets our index within the ROMol Notes: * this makes no sense if we do not have an owning molecule * the index should be < this->getOwningMol()->getNumAtoms() template void RDKit::Atom::setProp ( const std::string key, T val, bool computed = false ) const [inline] This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. template void RDKit::Atom::setProp ( const char * key, T val, bool computed = false ) const [inline] sets a property value Parameters: key the name under which the property should be stored. If a property is already stored under this name, it will be replaced. val the value to be stored computed (optional) allows the property to be flagged computed. void RDKit::Atom::updatePropertyCache ( bool strict = true ) calculates any of our lazy properties Notes: * requires an owning molecule * the current lazy properties are implicit and explicit valence ''' _renote = re.compile('^\w*(Notes?[:]?)(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL)) _reparam = re.compile('^\w*(Param(?:eter)?s?[:]?)(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL)) _rereturn = re.compile('^\w*(Returns[:])(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL)) _rereturn2 = re.compile('^\w*(Returns)\s+(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL)) _reusage = re.compile('^\w*(Usage[:]?)(?:.*?$)(.*?)((^\w)|\Z)', flags=(re.M | re.I | re.DOTALL)) def make_method_doc(doxy_method_text, class_name): for f in (do_usage, do_note, do_param, do_return): doxy_method_text = f(doxy_method_text) # Create paragraphs doxy_method_text = doxy_method_text.replace('\n\n', '\n

\n') # But no paragraph markers just before tag doxy_method_text = doxy_method_text.replace('

@', '

\n@') # Get rid of double quotes -- note that this causes an error with initialized string parameters doxy_method_text = doxy_method_text.replace('"', "'") # Get lines lines = doxy_method_text.split('\n') # Build header -- don't want type there header = lines[0][lines[0].find(class_name):] start = 1 while (header.find(')') < 0): start += 1 header += ' ' + lines[start - 1] ## print header # Or [] annotation header = header.replace('[inline]', '') header = header.replace('[virtual]', '') header = header.replace('[protected]', '') header = header.replace('[explicit]', '') header = '%javamethodmodifiers ' + header + '"\n/**\n' return header + '\n'.join(lines[start:]) + '\n*/\npublic";\n' def make_class_doc(doxy_text, class_name): for f in (do_usage, do_note): doxy_text = f(doxy_text) # Create paragraphs doxy_text = doxy_text.replace('\n\n', '\n

\n') # But no paragraph markers just before tag doxy_text = doxy_text.replace('

@', '

\n@') # Get rid of double quotes doxy_text = doxy_text.replace('"', "'") # Get lines lines = doxy_text.split('\n') # Build header -- don't want type there header = '%typemap(javaimports) ' + class_name + ' "\n/** ' return header + '\n'.join(lines) + ' */"\n' def do_note(doxy_text): m1 = _renote.search(doxy_text) if m1 != None: repl = m1.group(0) if repl[-1] != '\n': repl = repl[:-1] new_text = '

@notes\n' for line in m1.group(2).split('\n'): line = line.strip() if len(line) > 0: if line.startswith('*'): line = line[1:].strip() new_text = new_text + '

  • ' + line + '\n' doxy_text = doxy_text.replace(repl, new_text) return doxy_text def do_param(doxy_text): m1 = _reparam.search(doxy_text) if m1 != None: repl = m1.group(0) if repl[-1] != '\n': repl = repl[:-1] new_text = '

    @param\n' for line in m1.group(2).split('\n'): line = line.strip() if len(line) > 0: new_text = new_text + line + '\n' doxy_text = doxy_text.replace(repl, new_text) return doxy_text def do_return(doxy_text): m1 = _rereturn.search(doxy_text) if m1 == None: m1 = _rereturn2.search(doxy_text) if m1 != None: repl = m1.group(0) if repl[-1] != '\n': repl = repl[:-1] new_text = '

    @return\n' for line in m1.group(2).split('\n'): line = line.strip() if len(line) > 0: new_text = new_text + line + '\n' doxy_text = doxy_text.replace(repl, new_text) return doxy_text def do_usage(doxy_text): m1 = _reusage.search(doxy_text) if m1 != None: repl = m1.group(0) if repl[-1] != '\n': repl = repl[:-1] new_text = '

    @example\n

    \n'
    for line in m1.group(2).split('\n'):
      new_text = new_text + line + '\n'
    ## doxy_text = _reusage.sub(new_text,  doxy_text) + '
    \n' new_text += '\n' doxy_text = doxy_text.replace(repl, new_text) return doxy_text def do_methods(doxy_text, class_name): methods = [] method_lines = [] in_method_region = False for line in doxy_text.split('\n'): if line.find('Function Documentation') >= 0: in_method_region = True elif in_method_region: if line.find(class_name) >= 0 or line.find('Member Data') >= 0: if len(method_lines) > 0: methods.append(make_method_doc('\n'.join(method_lines), class_name)) if line.find('Member Data') >= 0: in_method_region = False else: method_lines = [line] else: method_lines.append(line) if len(method_lines) > 0: methods.append(make_method_doc('\n'.join(method_lines), class_name)) method_lines = [line] return methods def do_class(doxy_text, class_name): in_class_region = False class_doc = '' for line in doxy_text.split('\n'): if line.find('Detailed Description') >= 0: in_class_region = True class_lines = [] elif in_class_region: if line.strip().endswith('Documentation'): if len(class_lines) > 0: class_doc = make_class_doc('\n'.join(class_lines), class_name) in_class_region = False else: class_lines.append(line) return class_doc if __name__ == '__main__': import sys text = open(sys.argv[1]).read() class_name = sys.argv[2] print(do_class(text, class_name)) docs = do_methods(text, class_name) for doc in docs: print(doc)