initial import

This commit is contained in:
Greg Landrum
2006-05-06 22:20:08 +00:00
commit 75a79b6327
2358 changed files with 578190 additions and 0 deletions

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Code/Catalogs/Catalog.cpp Executable file
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// $Id: Catalog.cpp 4942 2006-02-17 01:19:53Z glandrum $
//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
//
#include "Catalog.h"
namespace RDCatalog {
}

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Code/Catalogs/Catalog.h Executable file
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//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#ifndef __RD_CATALOG_H__
#define __RD_CATALOG_H__
// Boost graph stuff
#include <boost/graph/graph_traits.hpp>
#include <boost/graph/adjacency_list.hpp>
#include <boost/property_map.hpp>
// for some typedefs
#include <RDGeneral/types.h>
#include <RDGeneral/StreamOps.h>
namespace RDCatalog {
const int versionMajor=1;
const int versionMinor=0;
const int versionPatch=0;
const int endianId=0xDEADBEEF;
//-----------------------------------------------------------------------------
//! abstract base class for a catalog object
template <class entryType, class paramType>
class Catalog {
public:
//------------------------------------
Catalog() : d_fpLength(0), dp_cParams(0) {};
//------------------------------------
virtual ~Catalog(){
if (dp_cParams) {
delete dp_cParams;
}
}
//------------------------------------
//! return a serialized form of the Catalog as an std::string
virtual std::string Serialize() const = 0;
//------------------------------------
//! adds an entry to the catalog
/*!
\param entry the entry to be added
\param updateFPLength (optional) if this is true, our internal
fingerprint length will also be updated.
*/
virtual unsigned int addEntry(entryType *entry, bool updateFPLength = true) = 0;
//------------------------------------
//! returns a particular entry in the Catalog
virtual const entryType* getEntryWithIdx(unsigned int idx) const = 0;
//------------------------------------
//! returns the number of entries
virtual unsigned int getNumEntries() const = 0;
//------------------------------------
//! returns the length of our fingerprint
unsigned int getFPLength() const {return d_fpLength;}
//------------------------------------
//! sets our fingerprint length
void setFPLength(unsigned int val) {d_fpLength = val;}
//------------------------------------
//! sets our parameters by copying the \c params argument
void setCatalogParams(paramType *params) {
PRECONDITION(params,"bad parameter object");
//if we already have a paramter object throw an exception
PRECONDITION(!dp_cParams,"A parameter object already exists on the catalog" );
/*
if (dp_cParams) {
// we already have parameter object on the catalog
// can't overwrite it
PRECONDITION(0, "A parameter object already exist on the catalog");
}*/
dp_cParams = new paramType(*params);
}
//------------------------------------
//! returns a pointer to our parameters
const paramType *getCatalogParams() const { return dp_cParams;}
protected:
// this is the ID that will be assigned to the next entry
// added to the catalog - need not be same as the number of entries
// in the catalog and does not correspond with the
// id of the entry in the catalog.
// this is more along the lines of bitId
unsigned int d_fpLength; //!< the length of our fingerprint
paramType *dp_cParams; //!< our params object
};
//-----------------------------------------------------------------------------
//! A Catalog with a hierarchical structure
/*!
The entries of a HierarchCatalog are arranged in a directed graph
<b>The difference between <i>Indices</i> and <i>Bit Ids</i></b>
A HierarchCatalog may contain more entries than the user is actually
interested in. For example a HierarchCatalog constructed to contain
orders 5 through 8 may well contain information about orders 1-5,
in order to facilitate some search optimizations.
- <i>Bit Ids</i> refer to the "interesting" bits.
So, in the above example, Bit Id \c 0 will be the first entry
with order 5.
- <i>Indices</i> refer to the underlying structure of the catalog.
So, in the above example, the entry with index \c 0 will be
the first entry with order 1.
*/
template <class entryType, class paramType, class orderType>
class HierarchCatalog : public Catalog <entryType, paramType> {
// the entries in the catalog can be traversed using the edges
// in a desired order
public:
//! used by the BGL to set up the node properties in our graph
struct vertex_entry_t {
enum { num=1003 };
typedef boost::vertex_property_tag kind;
};
typedef boost::property<vertex_entry_t, entryType *> EntryProperty;
//! the type of the graph itself:
typedef boost::adjacency_list<boost::vecS,
boost::vecS, // FIX: should be using setS for edges so that parallel edges are never added (page 225 BGL book)
// but that seems result in compile errors
boost::bidirectionalS,
EntryProperty> CatalogGraph;
typedef boost::graph_traits<CatalogGraph> CAT_GRAPH_TRAITS;
typedef typename CAT_GRAPH_TRAITS::vertex_iterator VER_ITER;
typedef std::pair<VER_ITER, VER_ITER> ENT_ITER_PAIR;
typedef typename CAT_GRAPH_TRAITS::adjacency_iterator DOWN_ENT_ITER;
typedef std::pair<DOWN_ENT_ITER, DOWN_ENT_ITER> DOWN_ENT_ITER_PAIR;
//------------------------------------
HierarchCatalog<entryType, paramType, orderType>() {};
//------------------------------------
//! Construct by making a copy of the input \c params object
HierarchCatalog<entryType, paramType, orderType>(paramType *params) : Catalog<entryType,paramType>() {
this->setCatalogParams(params);
}
//------------------------------------
//! Construct from a \c pickle (a serialized form of the HierarchCatalog)
HierarchCatalog<entryType, paramType, orderType>(const std::string &pickle) {
this->initFromString(pickle);
}
//------------------------------------
~HierarchCatalog() {
destroy();
}
//------------------------------------
//! serializes this object to a stream
void toStream(std::ostream &ss) const {
// the i/o header:
RDKit::streamWrite(ss,endianId);
RDKit::streamWrite(ss,versionMajor);
RDKit::streamWrite(ss,versionMinor);
RDKit::streamWrite(ss,versionPatch);
// information about the catalog itself:
int tmpUInt;
tmpUInt = this->getFPLength();
RDKit::streamWrite(ss,tmpUInt);
tmpUInt = this->getNumEntries();
RDKit::streamWrite(ss,tmpUInt);
//std::cout << ">>>>-------------------------------" << std::endl;
//std::cout << "\tlength: " << getFPLength() << " " << getNumEntries() << std::endl;
// add the params object:
this->getCatalogParams()->toStream(ss);
//std::cout << "\tparams: " << getCatalogParams()->getLowerFragLength();
//std::cout << " " << getCatalogParams()->getUpperFragLength();
//std::cout << " " << getCatalogParams()->getNumFuncGroups();
//std::cout << std::endl;
// write the entries in order:
for(unsigned int i=0;i<getNumEntries();i++){
this->getEntryWithIdx(i)->toStream(ss);
}
// finally the adjacency list:
for(unsigned int i=0;i<getNumEntries();i++){
RDKit::INT_VECT children=this->getDownEntryList(i);
tmpUInt = children.size();
RDKit::streamWrite(ss,tmpUInt);
for(RDKit::INT_VECT::const_iterator ivci=children.begin();
ivci!=children.end();
ivci++){
RDKit::streamWrite(ss,*ivci);
}
}
}
//------------------------------------
//! serializes this object and returns the resulting \c pickle
std::string Serialize() const {
std::stringstream ss(std::ios_base::binary|std::ios_base::out|std::ios_base::in);
this->toStream(ss);
return ss.str();
}
//------------------------------------
//! fills the contents of this object from a stream containing a \c pickle
void initFromStream(std::istream &ss) {
int tmpInt;
// FIX: at the moment we ignore the header info:
RDKit::streamRead(ss,tmpInt);
RDKit::streamRead(ss,tmpInt);
RDKit::streamRead(ss,tmpInt);
RDKit::streamRead(ss,tmpInt);
unsigned int tmpUInt;
RDKit::streamRead(ss,tmpUInt);// fp length
this->setFPLength(tmpUInt);
unsigned int numEntries;
RDKit::streamRead(ss,numEntries);
//std::cout << "<<<-------------------------------" << std::endl;
//std::cout << "\tlength: " << getFPLength() << " " << numEntries << std::endl;
// grab the params:
paramType *params = new paramType();
params->initFromStream(ss);
this->setCatalogParams(params);
//std::cout << "\tparams: " << getCatalogParams()->getLowerFragLength();
//std::cout << " " << getCatalogParams()->getUpperFragLength();
//std::cout << " " << getCatalogParams()->getNumFuncGroups();
//std::cout << std::endl;
// now all of the entries:
for(unsigned int i=0;i<numEntries;i++){
entryType *entry = new entryType();
entry->initFromStream(ss);
this->addEntry(entry,false);
}
// and, finally, the adjacency list:
for(unsigned int i=0;i<numEntries;i++){
unsigned int nNeighbors;
RDKit::streamRead(ss,nNeighbors);
for(unsigned int j=0;j<nNeighbors;j++){
RDKit::streamRead(ss,tmpInt);
this->addEdge(i,tmpInt);
}
}
}
//------------------------------------
unsigned int getNumEntries() const {
return boost::num_vertices(d_graph);
}
//------------------------------------
//! fills the contents of this object from a string containing a \c pickle
void initFromString(const std::string &text){
std::stringstream ss(std::ios_base::binary|std::ios_base::out|std::ios_base::in);
// initialize the stream:
ss.write(text.c_str(),text.length());
// now start reading out values:
this->initFromStream(ss);
}
//------------------------------------
//! add a new entry to the catalog
/*!
\param entry the entry to be added
\param updateFPLength (optional) if this is true, our internal
fingerprint length will also be updated.
*/
unsigned int addEntry(entryType *entry, bool updateFPLength = true){
PRECONDITION(entry,"bad arguments");
if (updateFPLength) {
unsigned int fpl = this->getFPLength();
entry->setBitId(fpl);
fpl++;
this->setFPLength(fpl);
}
unsigned int eid = boost::add_vertex(EntryProperty(entry), d_graph);
orderType etype = entry->getOrder();
// REVIEW: this initialization is not required: the STL map, in
// theory, will create a new object when operator[] is called
// for a new item
if (d_orderMap.find(etype) == d_orderMap.end()) {
RDKit::INT_VECT nets;
d_orderMap[etype] = nets;
}
d_orderMap[etype].push_back(eid);
return eid;
}
//------------------------------------
//! adds an edge between two entries in the catalog
/*!
Since we are using a bidirectional graph - the order in
which the ids are supplied here makes a difference
\param id1 index of the edge's beginning
\param id2 index of the edge's end
*/
void addEdge(unsigned int id1, unsigned int id2) {
unsigned int nents = getNumEntries();
RANGE_CHECK(0, id1, nents-1);
RANGE_CHECK(0, id2, nents-1);
// FIX: if we boost::setS for the edgeList BGL will
// do the checking for duplicity (parallel edges)
// But for reasons unknown setS results in compile
// errors while using adjacent_vertices.
typename CAT_GRAPH_TRAITS::edge_descriptor edge;
bool found;
boost::tie(edge,found) = boost::edge(boost::vertex(id1,d_graph),
boost::vertex(id2,d_graph),
d_graph);
if (!found) {
boost::add_edge(id1, id2, d_graph);
}
}
//------------------------------------
//! returns a pointer to our entry with a particular index
const entryType *getEntryWithIdx(unsigned int idx) const {
RANGE_CHECK(0,idx,getNumEntries()-1);
int vd = boost::vertex(idx, d_graph);
typename boost::property_map < CatalogGraph, vertex_entry_t>::const_type
pMap = boost::get(vertex_entry_t(), d_graph);
return pMap[vd];
}
//------------------------------------
//! returns a pointer to our entry with a particular bit ID
const entryType *getEntryWithBitId(unsigned int idx) const {
RANGE_CHECK(0,idx,this->getFPLength()-1);
typename boost::property_map < CatalogGraph, vertex_entry_t>::const_type
pMap = boost::get(vertex_entry_t(), d_graph);
const entryType *res=NULL;
for(unsigned int i=idx;i<this->getNumEntries();i++){
const entryType *e=pMap[i];
if(e->getBitId()==idx){
res=e;
break;
}
}
return res;
}
//------------------------------------
//! returns the index of the entry with a particular bit ID
int getIdOfEntryWithBitId(unsigned int idx) const {
RANGE_CHECK(0,idx,this->getFPLength()-1);
typename boost::property_map < CatalogGraph, vertex_entry_t>::const_type
pMap = boost::get(vertex_entry_t(), d_graph);
int res=-1;
for(unsigned int i=idx;i<this->getNumEntries();i++){
const entryType *e=pMap[i];
if(e->getBitId()==idx){
res=i;
break;
}
}
return res;
}
//------------------------------------
//! returns a list of the indices of entries below the one passed in
RDKit::INT_VECT getDownEntryList(unsigned int idx) const {
RDKit::INT_VECT res;
DOWN_ENT_ITER nbrIdx, endIdx;
boost::tie(nbrIdx, endIdx) = boost::adjacent_vertices(idx, d_graph);
while (nbrIdx != endIdx) {
res.push_back(*nbrIdx);
nbrIdx++;
}
//std::cout << res.size() << "\n";
return res;
}
//------------------------------------
//! returns a list of the indices that have a particular order
const RDKit::INT_VECT &getEntriesOfOrder(orderType ord) {
return d_orderMap[ord];
}
//------------------------------------
//! returns a list of the indices that have a particular order
/*!
\overload
*/
const RDKit::INT_VECT &getEntriesOfOrder(orderType ord) const {
typename std::map<orderType, RDKit::INT_VECT>::const_iterator elem;
elem = d_orderMap.find(ord);
CHECK_INVARIANT(elem!=d_orderMap.end()," catalog does not contain any entries of the order specified");
return elem->second;
}
private:
// graphs that store the entries in the catalog in a hierachical manner
CatalogGraph d_graph;
// a map that maps the order type of entries in the catalog to
// a vector of vertex indices in the graphs above
// e.g. for a catalog with molecular fragments, the order of a fragment can
// simply be the number of bond in it. The list this oder maps to is all the
// vertex ids of these fragment in the catalog that have this many bonds in them
std::map<orderType, RDKit::INT_VECT> d_orderMap;
//------------------------------------
//! clear any memory that we've used
void destroy() {
ENT_ITER_PAIR entItP = boost::vertices(d_graph);
typename boost::property_map < CatalogGraph, vertex_entry_t>::type
pMap = boost::get(vertex_entry_t(), d_graph);
while (entItP.first != entItP.second) {
delete pMap[*(entItP.first++)];
}
}
};
//-----------------------------------------------------------------------------
//! a linear Catalog (analogous to an std::vector)
/*!
Here there is no particular hierarchy, simply a
collection of entries.
*/
template <class entryType, class orderType>
class LinearCatalog : public Catalog <entryType, orderType> {
// here there is no particular hierarchy of entries
// we simply model it as a vector of entries
// FIX: for retrieval purposes a better model map be std::map
public:
std::string Serialize();
unsigned int addEntry(entryType *entry, bool updateFPLength = true);
const entryType *getEntryWithIdx(unsigned int idx) const;
private:
std::vector<entryType*> d_vector;
};
}
#endif

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Code/Catalogs/CatalogEntry.cpp Executable file
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// $Id: CatalogEntry.cpp 4942 2006-02-17 01:19:53Z glandrum $
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#include "CatalogEntry.h"
namespace RDCatalog {
CatalogEntry::~CatalogEntry() {}
}

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Code/Catalogs/CatalogEntry.h Executable file
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//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#ifndef __RD_CATALOGENTRY_H__
#define __RD_CATALOGENTRY_H__
#include <iostream>
#include <string>
namespace RDCatalog {
//! Abstract base class to be used to represent an entry in a Catalog
class CatalogEntry {
public:
virtual ~CatalogEntry() = 0;
//! sets our bit Id
void setBitId(int bid) {d_bitId = bid;};
//! returns our bit Id
int getBitId() const {return d_bitId;};
//! returns a text description of this entry
virtual std::string getDescription() const = 0;
//! serializes (pickles) to a stream
virtual void toStream(std::ostream &ss) const = 0;
//! returns a string with a serialized (pickled) representation
virtual std::string Serialize() const = 0;
//! initializes from a stream pickle
virtual void initFromStream(std::istream &ss) = 0;
//! initializes from a string pickle
virtual void initFromString(const std::string &text) = 0;
private:
int d_bitId; //!< our bit Id. This needs to be signed so that we can mark uninitialized entries.
};
}
#endif

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Code/Catalogs/CatalogParams.cpp Executable file
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// $Id: CatalogParams.cpp 4942 2006-02-17 01:19:53Z glandrum $
//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#include "CatalogParams.h"
namespace RDCatalog {
CatalogParams::~CatalogParams() {};
}

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Code/Catalogs/CatalogParams.h Executable file
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//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
//
#ifndef __RD_CATALOGPARAMS_H__
#define __RD_CATALOGPARAMS_H__
#include <string>
namespace RDCatalog {
//! abstract base class for the container used to create a catalog
class CatalogParams {
public:
virtual ~CatalogParams() = 0;
//! returns our type string
std::string getTypeStr() const { return d_typeStr; };
//! sets our type string
void setTypeStr(const std::string &typeStr) { d_typeStr=typeStr; };
//! serializes (pickles) to a stream
virtual void toStream(std::ostream &) const = 0;
//! returns a string with a serialized (pickled) representation
virtual std::string Serialize() const = 0;
//! initializes from a stream pickle
virtual void initFromStream(std::istream &ss) = 0;
//! initializes from a string pickle
virtual void initFromString(const std::string &text) = 0;
protected:
std::string d_typeStr; //!< our type string
};
}
#endif

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Code/Catalogs/Catalogs.dsp Executable file
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BSC32=bscmake.exe
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# ADD BASE LIB32 /nologo
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# Name "Catalogs - Win32 Debug"
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Code/Catalogs/Catalogs.vcproj Executable file
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<?xml version="1.0" encoding="Windows-1252"?>
<VisualStudioProject
ProjectType="Visual C++"
Version="7.10"
Name="libCatalogs"
SccProjectName=""
SccLocalPath="">
<Platforms>
<Platform
Name="Win32"/>
</Platforms>
<Configurations>
<Configuration
Name="Release|Win32"
OutputDirectory=".\Catalogs___Win32_Release"
IntermediateDirectory=".\Catalogs___Win32_Release"
ConfigurationType="4"
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ATLMinimizesCRunTimeLibraryUsage="FALSE"
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<Tool
Name="VCPreLinkEventTool"/>
<Tool
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PreprocessorDefinitions="NDEBUG"
Culture="1033"/>
<Tool
Name="VCWebServiceProxyGeneratorTool"/>
<Tool
Name="VCXMLDataGeneratorTool"/>
<Tool
Name="VCManagedWrapperGeneratorTool"/>
<Tool
Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
</Configuration>
<Configuration
Name="Debug|Win32"
OutputDirectory=".\Catalogs___Win32_Debug0"
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ConfigurationType="4"
UseOfMFC="0"
ATLMinimizesCRunTimeLibraryUsage="FALSE"
CharacterSet="2">
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Name="VCXMLDataGeneratorTool"/>
<Tool
Name="VCManagedWrapperGeneratorTool"/>
<Tool
Name="VCAuxiliaryManagedWrapperGeneratorTool"/>
</Configuration>
</Configurations>
<References>
</References>
<Files>
<Filter
Name="Source Files"
Filter="cpp;c;cxx;rc;def;r;odl;idl;hpj;bat">
<File
RelativePath="Catalog.cpp">
<FileConfiguration
Name="Release|Win32">
<Tool
Name="VCCLCompilerTool"
Optimization="2"
AdditionalIncludeDirectories=""
PreprocessorDefinitions=""/>
</FileConfiguration>
<FileConfiguration
Name="Debug|Win32">
<Tool
Name="VCCLCompilerTool"
Optimization="0"
AdditionalIncludeDirectories=""
PreprocessorDefinitions=""
BasicRuntimeChecks="3"/>
</FileConfiguration>
</File>
<File
RelativePath="CatalogEntry.cpp">
<FileConfiguration
Name="Release|Win32">
<Tool
Name="VCCLCompilerTool"
Optimization="2"
AdditionalIncludeDirectories=""
PreprocessorDefinitions=""/>
</FileConfiguration>
<FileConfiguration
Name="Debug|Win32">
<Tool
Name="VCCLCompilerTool"
Optimization="0"
AdditionalIncludeDirectories=""
PreprocessorDefinitions=""
BasicRuntimeChecks="3"/>
</FileConfiguration>
</File>
<File
RelativePath="CatalogParams.cpp">
<FileConfiguration
Name="Release|Win32">
<Tool
Name="VCCLCompilerTool"
Optimization="2"
AdditionalIncludeDirectories=""
PreprocessorDefinitions=""/>
</FileConfiguration>
<FileConfiguration
Name="Debug|Win32">
<Tool
Name="VCCLCompilerTool"
Optimization="0"
AdditionalIncludeDirectories=""
PreprocessorDefinitions=""
BasicRuntimeChecks="3"/>
</FileConfiguration>
</File>
</Filter>
<Filter
Name="Header Files"
Filter="h;hpp;hxx;hm;inl">
<File
RelativePath="Catalog.h">
</File>
<File
RelativePath="CatalogEntry.h">
</File>
<File
RelativePath="CatalogParams.h">
</File>
</Filter>
<File
RelativePath=".\VTune\Catalogs.vpj">
</File>
</Files>
<Globals>
</Globals>
</VisualStudioProject>

14
Code/Catalogs/Makefile Executable file
View File

@@ -0,0 +1,14 @@
include $(RDBASE)/Code/rdvars.make
include $(RDBASE)/Code/rdrules.make
CXXFLAGS=$(BASECXXFLAGS) $(VFLIBINC)
SOURCES=Catalog.cpp CatalogParams.cpp CatalogEntry.cpp
LIB=$(RDCATALOGLIB)
$(LIB): $(OBJS)
ar -rv $@ $?
clean:
rm -f $(OBJS) $(LIB) $(DEPENDS)
include $(DEPENDS)