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/*
Contributors: Nicola Zonta
Copyright Schrodinger, LLC. All rights reserved
*/
#pragma once
#include "CoordgenConfig.hpp"
#include <cstddef>
#include <vector>
class sketcherMinimizerFragment;
class sketcherMinimizerMolecule;
class sketcherMinimizerBond;
class sketcherMinimizerRing;
class sketcherMinimizerAtom;
/*
class to divide a molecule into rigid fragments
*/
class EXPORT_COORDGEN CoordgenFragmenter
{
public:
/*
divide the molecule into rigid fragments
*/
static void splitIntoFragments(sketcherMinimizerMolecule* molecule);
private:
/*
put all atoms and bonds of fragment2 into fragment1 and delete it
*/
static void
joinFragments(sketcherMinimizerFragment* fragment1,
sketcherMinimizerFragment* fragment2,
std::vector<sketcherMinimizerFragment*>& fragments);
/*
process bond between two fragments
*/
static void processInterFragmentBond(
sketcherMinimizerBond* bond,
std::vector<sketcherMinimizerFragment*>& fragments);
/*
process bond internal a fragment
*/
static void processBondInternalToFragment(
sketcherMinimizerBond* bond,
std::vector<sketcherMinimizerFragment*>& fragments);
/*
initialize info from bond
*/
static void addBondInformation(sketcherMinimizerBond* bond);
/*
initialize info from ring
*/
static void addRingInformation(sketcherMinimizerRing* ring);
/*
initialize info of molecule
*/
static void
initializeInformation(std::vector<sketcherMinimizerFragment*> fragments,
sketcherMinimizerMolecule* molecule);
/*
compare two fragments for priority (e.g. to find the main fragment)
*/
static bool hasPriority(const sketcherMinimizerFragment* fragment1,
const sketcherMinimizerFragment* fragment2);
/*
get the score of a particular descriptor for the given fragment (used to
assign priorities)
*/
static size_t getValueOfCheck(const sketcherMinimizerFragment* fragment,
int checkN, bool& checkNoMore);
/*
find the main fragment
*/
static sketcherMinimizerFragment*
findMainFragment(const std::vector<sketcherMinimizerFragment*>& fragments);
/*
if molecule has a long enough chain return the start of the chain as main
fragment instead
*/
static sketcherMinimizerFragment*
considerChains(const std::vector<sketcherMinimizerFragment*>& fragments,
sketcherMinimizerFragment* mainFragment);
/* empirical minimum length of zigzag chain of fragments
that makes the chain get priority over the main fragment
in determining the molecule's layout
*/
static unsigned int
acceptableChainLength(sketcherMinimizerFragment* mainFragment);
/*
find the longest chain of connected fragments
*/
static std::vector<sketcherMinimizerFragment*>
findLongestChain(const std::vector<sketcherMinimizerFragment*>& fragments);
/*
initialize parent-child info of bound fragments
*/
static void addParentRelationsToFragments(
sketcherMinimizerFragment* mainFragment,
const std::vector<sketcherMinimizerFragment*>& fragments);
/*
order the vector of fragments so that bound fragments are consecutive,
starting from the main fragment
*/
static void
orderFragments(std::vector<sketcherMinimizerFragment*>& fragments,
sketcherMinimizerFragment* mainFragment);
};
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