/usr/include/BALL/STRUCTURE/molecularSimilarity.h is in libball1.4-dev 1.4.3~beta1-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// $Maintainer: Marcel Schumann $
// $Authors: Marcel Schumann $
// ----------------------------------------------------
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#ifndef BALL_STRUCTURE_MOLECULARSIMILARITY_H
#define BALL_STRUCTURE_MOLECULARSIMILARITY_H
#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif
#include <BALL/STRUCTURE/smartsMatcher.h>
#include <BALL/KERNEL/system.h>
#ifdef BALL_HAS_OPENEYE
#include <oechem/mol.h>
#elif defined BALL_HAS_OPENBABEL
#include <openbabel/mol.h>
#endif
namespace BALL
{
class BALL_EXPORT MolecularSimilarity
{
public:
MolecularSimilarity(String smarts_file);
void generateFingerprints(System& molecules, vector<vector<Size> >& fingerprints);
void generateFingerprints(const list<Molecule*>& molecules, vector<vector<Size> >& fingerprints);
void generateFingerprint(Molecule& molecule, vector<Size>& fingerprint);
#ifdef BALL_HAS_OPENEYE
static OEChem::OEMol* createOEMol(const Molecule& mol, bool ignore_hydrogen=0);
void generateCanSmile(const Molecule& molecule, String& cansmile, OEChem::OEMol** output_oemol=0, bool ignore_hydrogen=0);
void generateFingerprint(OEChem::OEMol& mol, vector<Size>& fingerprint);
#elif defined BALL_HAS_OPENBABEL
/** create an Openbabel-molecule from a given BALL::Molecule
@param suppress_warning if set to true, warning about aromatic bonds of carboxyl- and guanidinium-groups being de-aromatized (which OpenBabel requires) will not be shown. */
static OpenBabel::OBMol* createOBMol(const Molecule& mol, bool ignore_hydrogen=0, bool suppress_warning=0);
/** create a BALL::Molecule from a given OpenBabel-molecule */
static Molecule* createMolecule(OpenBabel::OBMol& obmol, bool ignore_hydrogen=0);
void generateCanSmile(const Molecule& mol, String& cansmile, OpenBabel::OBMol** output_obmol=0, bool ignore_hydrogen=0);
void generateFingerprint(OpenBabel::OBMol& mol, vector<Size>& fingerprint);
#endif
#if (defined BALL_HAS_OPENEYE | defined BALL_HAS_OPENBABEL)
/** match the given SMARTS pattern to the supplied smile and return the number of matches.
@param max_matches the maximal number of SMART matches to be made; can be used as a speed-up. If this number of matches has been found, the SMARTS-matching algorithm will abort. Specifying zero will not set any such constraint.*/
void matchSmarts(const String& usmile, const String& smarts, Size& no_matches, Size max_matches=0);
#endif
void generatePathFingerprint(Molecule& mol, vector<bool>& fingerprint);
/** Calculate Tanimoto coefficient for two given binary fingerprints. */
float calculateSimilarity(vector<bool>& fingerprint1, vector<bool>& fingerprint2);
void filterRedundantMolecules(const list<Molecule*>& molecules, float similarity_threshold);
void filterRedundantMolecules(System& molecules, float similarity_threshold);
/** Calculate similarity between two fingerprints.\n
If stddev for function-group counts are specified, then the similarity of position i in the fingerprint-vectors is defined as zero if their absolute difference is larger than the the standard deviation, else as 1-abs(difference_i/stddev_i).
If no stddev for function-group counts are given, the calculated similarity-value is equal to Tanimoto. */
float calculateSimilarity(vector<Size>& fingerprint1, vector<Size>& fingerprint2, vector<float>* stddev);
/** Returns the names of the functional groups that have been read from the SMARTS-file */
const vector<String>& getFunctionalGroupNames();
protected:
vector<vector<Size> > fingerprints_;
vector<String> smarts_;
vector<String> smart_names_;
SmartsMatcher matcher_;
/** Generate a hash-ID for a given molecule-path. \n
This function was adapted from OpenBabel (finger2.cpp). */
void generatePathHash_(vector<Size>& path, Size& hash);
bool generatePathFingerprint_(const Atom* atom, std::vector<Size>& path, std::set<const Bond*>& path_bonds,
std::vector<bool>& fingerprint);
};
}
#endif
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