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pharmarec.h
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pharmarec.h
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/*
Pharmer: Efficient and Exact 3D Pharmacophore Search
Copyright (C) 2011 David Ryan Koes and the University of Pittsburgh
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; either version 2
of the License, or (at your option) any later version.
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.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
/*
* pharmarec.h
*
* Created on: July 30, 2010
* Author: dkoes
*
* Routines for pharmacophore recognition.
*/
#ifndef PHARMAREC_H_
#define PHARMAREC_H_
#include <iostream>
#include <boost/unordered_map.hpp>
#include "boost/tuple/tuple.hpp"
#include <float.h>
#include <json/json.h>
#include <openbabel/mol.h>
#include <openbabel/math/vector3.h>
#include <openbabel/obconversion.h>
#include "CommandLine2/CommandLine.h"
using namespace std;
extern cl::opt<bool> DKoesTest;
//somewhat arbitrary numerical threshold for close enoughness
#define THRESHOLD (.0001)
//generate a vector corresponding to pharma point (hbonds, aromatic?)
struct PharmaPoint;
typedef void (*genPointVectorFn)(const vector<int>& atoms_indexes,
const OpenBabel::OBMol& mol, PharmaPoint& pnt);
//description of interaction features
struct PharmaInteract
{
unsigned complement; //index of interacting point
float maxDist; //max distance that a feature can be to still be considered interacting
unsigned minMatch; //minimum number of feature that must be close
PharmaInteract(unsigned c, float md, unsigned mm): complement(c), maxDist(md), minMatch(mm) {}
PharmaInteract(): complement(0), maxDist(0), minMatch(0) {}
};
//a description of a pharmacophore class
struct Pharma {
string name;
int atomic_number_label;
unsigned index; //position in pharmas array
vector<OpenBabel::OBSmartsPattern> smarts;
float defaultSearchRadius;
genPointVectorFn getVectors;
float clusterLimit;
Pharma(): atomic_number_label(0), index(-1), defaultSearchRadius(0), getVectors(NULL), clusterLimit(0)
{
}
Pharma(int indx, const char *n, const char** sm, int atomic, float r = .5, float cl = 0, unsigned nb =1, float trfr = 0):
name(n), atomic_number_label(atomic),
index(indx), defaultSearchRadius(r), getVectors(NULL), clusterLimit(cl){
//const char * smiles for easier initialization
if(sm != NULL)
{
while(*sm != NULL)
{
smarts.push_back(OpenBabel::OBSmartsPattern());
smarts.back().Init(*sm);
sm++;
}
}
setVectorFn();
}
Pharma(int indx, const string& n, const vector<string>& sm, int atomic, float r = .5, float cl = 0, unsigned nb =1, float trfr = 0):
name(n), atomic_number_label(atomic),
index(indx), defaultSearchRadius(r), getVectors(NULL), clusterLimit(cl) {
unsigned ns = sm.size();
smarts.resize(ns);
for(unsigned i = 0; i < ns; i++)
{
smarts[i].Init(sm[i]);
}
setVectorFn();
}
bool operator==(const Pharma& rhs) const;
bool operator!=(const Pharma& rhs) const { return !(*this == rhs); }
//function for determining vectors of a point; with no arguments
//uses built-in defaults
void setVectorFn(genPointVectorFn fn = NULL);
};
//a collection of pharmacophore descriptors
//PharmaPoints reference back to these descriptors so the creating Pharmas
//should not be allowed to go out of scope before the pharmapoints
class Pharmas
{
private:
//supporting copying operations is askign for trouble - there
//really should only be one instance of pharmas that is either programmatically
//initialized with a vector of Pharmas or by reading in pharmas from a file
Pharmas(const Pharmas&);
Pharmas& operator=(const Pharmas&);
protected:
Pharma *pharmas;
unsigned numPharmas;
boost::unordered_map<string, unsigned> nameLookup;
void initialize(const vector<Pharma>& ps);
public:
Pharmas(): pharmas(NULL), numPharmas(0) {}
//note that ps gets copied: pointers don't stay the same
Pharmas(const vector<Pharma>& ps): pharmas(NULL), numPharmas(0)
{
initialize(ps);
}
virtual ~Pharmas()
{
delete [] pharmas;
}
const Pharma* operator[](unsigned i) const { return &pharmas[i]; }
bool operator==(const Pharmas& rhs) const;
bool operator!=(const Pharmas& rhs) const { return !(*this == rhs); }
unsigned size() const { return numPharmas; }
const Pharma* pharmaFromName(const string& name) const;
bool read(istream& in);
void write(ostream& out) const;
};
extern const vector<Pharma> defaultPharmaVec;
//a single pharmacophore point
struct PharmaPoint {
double x;
double y;
double z;
vector<OpenBabel::vector3> vecs; //directionality, can have multiple
unsigned size;
const Pharma *pharma; //pharmacophore descriptor
//query attributes
double radius;
float vecpivot;
enum PointRequirements {Required, Optional, NotPresent};
PointRequirements requirements;
unsigned minSize;
unsigned maxSize;
PharmaPoint() :
x(0), y(0), z(0), size(0), pharma(NULL), radius(0), vecpivot(0), requirements(Required), minSize(0), maxSize(0) {
}
PharmaPoint(const Pharma* p) :
x(0), y(0), z(0), size(0), pharma(p), radius(p->defaultSearchRadius), vecpivot(0), requirements(Required), minSize(0), maxSize(0) {
}
PharmaPoint(double xc, double yc, double zc, const Pharma* p) :
x(xc), y(yc), z(zc), size(),pharma(p), radius(p->defaultSearchRadius), vecpivot(0), requirements(Required), minSize(0), maxSize(0) {
}
double radiusWeight() const
{
return 1.0/(radius*radius);
}
//essentially in the same spot
bool sameLocation(const PharmaPoint& rhs) const {
if (fabs(x - rhs.x) > THRESHOLD)
return false;
if (fabs(y - rhs.y) > THRESHOLD)
return false;
if (fabs(z - rhs.z) > THRESHOLD)
return false;
return true;
}
const char* requirementStr() const
{
switch(requirements)
{
case Required:
return "required";
case Optional:
return "optional";
case NotPresent:
return "notpresent";
}
return NULL;
}
#define SQR(x) ((x)*(x))
//return distance between a and b
static double pharmaDist(const PharmaPoint& a, const PharmaPoint& b) {
return sqrt(SQR(a.x-b.x) + SQR(a.y-b.y) + SQR(a.z-b.z));
}
friend ostream& operator<<(ostream &stream, const PharmaPoint& obj);
bool read(const Pharmas& pharmas, istream &in);
};
//read from a json formatted stream
extern bool readPharmaPointsJSON(const Pharmas& pharma, Json::Value& data, vector<PharmaPoint>& points);
//special case - identify pharmagist output
bool isPharmaGist(const Pharmas& pharmas, const string& mol, vector<PharmaPoint>& points);
//identify all pharma points in mol
extern void getPharmaPoints(const Pharmas& pharmas, OpenBabel::OBMol& mol, vector<PharmaPoint>& points);
//identify all pharma points in a multi-conformer molecule
extern void getPharmaPointsMC(const Pharmas& pharmas, OpenBabel::OBMol& mol, vector< vector<PharmaPoint> >& points);
//accelerated pharma point recognition for proteins
extern void getProteinPharmaPoints(const Pharmas& pharmas, OpenBabel::OBMol& protein, vector<PharmaPoint>& points);
extern void getInteractionPoints(const Pharmas& pharmas, OpenBabel::OBMol& receptor, OpenBabel::OBMol& ligand,
vector<PharmaPoint>& points, vector<PharmaPoint>& screenedout);
//translate a point vector into json
extern bool convertPharmaJson(Json::Value& root, const vector<PharmaPoint>& points);
//add artificial pharma "atoms" to mol
extern void addPharmaPoints(OpenBabel::OBMol& mol, vector<PharmaPoint>& points);
//extract pharmacophore points into json from moldata in format
extern bool jsonPharmaQuery(const Pharmas& pharmas, Json::Value& root,
const string& moldata, OpenBabel::OBFormat *format, const string& recdata, OpenBabel::OBFormat *rformat);
#endif /* PHARMAREC_H_ */