File: finger2.cpp

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/**********************************************************************
finger2.cpp: fingerprint2 definition and implementation.

Copyright (C) 2005 Chris Morley
 
This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>
 
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#include <openbabel/babelconfig.h>
#include <openbabel/mol.h>
#include <openbabel/fingerprint.h>
#include <set>
#include <vector>

/*
#ifdef _DEBUG
 #include "stdafx.h"
 #undef AddAtom
#endif
*/
using namespace std;
namespace OpenBabel
{
/// \brief Fingerprint based on linear fragments up to 7 atoms ID="FP2"
class fingerprint2 : public OBFingerprint
{
public:
	fingerprint2(const char* ID, bool IsDefault=false) 
		: OBFingerprint(ID, IsDefault){};

	virtual const char* Description()
	{ return "Indexes linear fragments up to 7 atoms.";};

	//Calculates the fingerprint 
	virtual bool GetFingerprint(OBBase* pOb, vector<unsigned int>&fp, int nbits=0);
private:
	typedef std::set<std::vector<int> > Fset;
	typedef std::set<std::vector<int> >::iterator SetItr;
	
	void getFragments(std::vector<int> levels, std::vector<int> curfrag, 
			int level, OBAtom* patom, OBBond* pbond);
	void DoReverses();
	void DoRings();

	unsigned int CalcHash(const std::vector<int>& frag);
	void PrintFpt(std::vector<int>& f, int hash=0);

	Fset fragset;
	Fset ringset;

};

//***********************************************
//Make a global instance
fingerprint2 thefingerprint2("FP2",true);
//***********************************************

/*! class fingerprint2
Similar to Fabien Fontain's fingerprint class, with a slightly improved
algorithm, but re-written using STL which makes it shorter.
 
A molecule structure is analysed to identify linear fragments of length
from one to Max_Fragment_Size = 7 atoms but single atom fragments of C,N,and O 
are ignored. A fragment is terminated when the atoms form a ring. 

For each of these fragments the atoms, bonding and whether
they constitute a complete ring is recorded and saved in a std::set
so that there is only one of each fragment type. Chemically identical versions,
i.e. ones with the atoms listed in reverse order and rings listed starting at 
different atoms, are identified and only a single canonical fragment is retained.

Each remaining fragment is assigned a hash number from 0 to 1020 which is used
to set a bit in a 1024 bit vector  
*/

bool fingerprint2::GetFingerprint(OBBase* pOb, vector<unsigned int>&fp, int nbits) 
{
	OBMol* pmol = dynamic_cast<OBMol*>(pOb);
	if(!pmol) return false;
	fp.resize(1024/Getbitsperint());
	fragset.clear();//needed because now only one instance of fp class
	ringset.clear();
	
	//identify fragments starting at every atom
	OBAtom *patom;
	vector<OBNodeBase*>::iterator i;
	for (patom = pmol->BeginAtom(i);patom;patom = pmol->NextAtom(i))
	{
		if(patom->IsHydrogen()) continue;
		vector<int> curfrag;
		vector<int> levels(pmol->NumAtoms());
		getFragments(levels, curfrag, 1, patom, NULL);
	}
	
//	TRACE("%s %d frags before; ",pmol->GetTitle(),fragset.size());

	//Ensure that each chemically identical fragment is present only in a single
	DoRings();
	DoReverses();

	SetItr itr;
	for(itr=fragset.begin();itr!=fragset.end();++itr)
	{	
		//Use hash of fragment to set a bit in the fingerprint
		int hash = CalcHash(*itr);
		SetBit(fp,hash);
		//PrintFpt(*itr,hash);
	}
	if(nbits)
		Fold(fp, nbits);

//	TRACE("%d after\n",fragset.size());
	return true;
}

//////////////////////////////////////////////////////////
void fingerprint2::getFragments(vector<int> levels, vector<int> curfrag, 
					int level, OBAtom* patom, OBBond* pbond)
{
	//Recursive routine to analyse schemical structure and populate fragset and ringset
	//Hydrogens,charges(except dative bonds), spinMultiplicity ignored
	const int Max_Fragment_Size = 7;
	int bo=0;
	if(pbond)
	{
		bo = pbond->IsAromatic() ? 5 : pbond->GetBO();

//		OBAtom* pprevat = pbond->GetNbrAtom(patom);
//		if(patom->GetFormalCharge() && (patom->GetFormalCharge() == -pprevat->GetFormalCharge()))
//			++bo; //coordinate (dative) bond eg C[N+]([O-])=O is seen as CN(=O)=O
	}
	curfrag.push_back(bo);
	curfrag.push_back(patom->GetAtomicNum());
	levels[patom->GetIdx()-1] = level;

	vector<OBEdgeBase*>::iterator itr;
	OBBond *pnewbond;
//	PrintFpt(curfrag,(int)patom);
	for (pnewbond = patom->BeginBond(itr);pnewbond;pnewbond = patom->NextBond(itr))
	{		
		if(pnewbond==pbond) continue; //don't retrace steps
		OBAtom* pnxtat = pnewbond->GetNbrAtom(patom);
		if(pnxtat->IsHydrogen()) continue;

		int atlevel = levels[pnxtat->GetIdx()-1];
		if(atlevel) //ring
		{
			if(atlevel==1)
			{
				//If complete ring (last bond is back to starting atom) add bond at front
				//and save in ringset
				curfrag[0] = bo;
				ringset.insert(curfrag);
			}
		}
		else //no ring
		{
			if(level<Max_Fragment_Size)
			{
//				TRACE("level=%d size=%d %p frag[0]=%p\n",level, curfrag.size(),&curfrag, &(curfrag[0])); 
				//Do the next atom; levels, curfrag are passed by value and hence copied
				getFragments(levels, curfrag, level+1, pnxtat, pnewbond);
			}
		}
	}

	//do not save C,N,O single atom fragments
	if(curfrag[0]==0 &&
		(level>1 || patom->GetAtomicNum()>8  || patom->GetAtomicNum()<6))
	{
		fragset.insert(curfrag); //curfrag ignored if an identical fragment already present
//		PrintFpt(curfrag,level);
	}
}

///////////////////////////////////////////////////
void fingerprint2::DoReverses()
{
	SetItr itr;
	for(itr=fragset.begin();itr!=fragset.end();)
	{
		//Reverse the order of the atoms, add the smallest fragment and remove the larger
		SetItr titr = itr++; //Ensure have valid next iterator in case current one is erased
		vector<int> t1(*titr); //temporary copy
		reverse(t1.begin()+1, t1.end()); //(leave 0 at front alone)
		if(t1!=*titr)
		{
			//Add the larger fragment and delete the smaller
			if(t1>*titr)
			{
				fragset.erase(titr);
				fragset.insert(t1);
			}
			else
				fragset.erase(t1);
		}
	}
}
///////////////////////////////////////////////////
void fingerprint2::DoRings()
{
	//For each complete ring fragment, find its largest chemically identical representation
	//by rotating and reversing, and insert into the main set of fragments
	SetItr itr;
	for(itr=ringset.begin();itr!=ringset.end();++itr)
	{
		vector<int> t1(*itr); //temporary copy
		vector<int> maxring(*itr); //the current largest vector
		unsigned int i;
		for(i=0;i<t1.size()/2;++i)
		{
			//rotate atoms in ring
			rotate(t1.begin(),t1.begin()+2,t1.end());
			if(t1>maxring)
				maxring=t1;
			
			//Add the non-ring form of all ring rotations 
			int tmp = t1[0];
			t1[0] = 0;
			fragset.insert(t1);
			t1[0] = tmp;
			
			//reverse the direction around ring
			vector<int> t2(t1);
			reverse(t2.begin()+1, t2.end());
			if(t2>maxring)
				maxring=t2;
		}
		fragset.insert(maxring);
		//PrintFpt(maxring,0);
	}
}

//////////////////////////////////////////////////////////
unsigned int fingerprint2::CalcHash(const vector<int>& frag)
{
	//Something like... whole of fragment treated as a binary number modulus 1021
	const int MODINT = 108; //2^32 % 1021 
	unsigned int hash=0;
	for(unsigned i=0;i<frag.size();++i)
		hash= (hash*MODINT + (frag[i] % 1021)) % 1021;
	return hash;
}

void fingerprint2::PrintFpt(vector<int>& f, int hash)
{
	unsigned int i;
	for(i=0;i<f.size();++i)
//		TRACE("%d ",f[i]);
//	TRACE("<%d>\n",hash);
		cerr << f[i] << " ";
	cerr << "<" << hash << ">" << endl;
}

/* Structure of a fragment (vector<int>)
   For a complete ring: last atom bonded to first atom
    bo(0)(n), atno(1), bo(1)(2), atno(2), bo(2)(3),...atno(n)

 For the rest, even when stopped by encountering atoms already visited
       0    , atno(1), bo(1)(2), atno(2), bo(2)(3),...atno(n) 
*/

} //namespace OpenBabel

//! \file finger2.cpp
//! \brief fingerprint2 definition and implementation