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8efb4bd | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 | #ifndef DISTANCE_RESTRAINT_H
#define DISTANCE_RESTRAINT_H
#include <Vector3.h>
#include <RigidTrans3.h>
#include <vector>
#include <limits>
class DistanceRestraint {
public:
DistanceRestraint(const std::vector<Vector3>& p1,
const std::vector<Vector3>& p2,
float maxdist, float mindist = 0.0, float weight=1.0)
: p1_(p1), p2_(p2), mindist_(mindist), maxdist_(maxdist),
mindist2_(mindist*mindist), maxdist2_(maxdist*maxdist),
weight_(weight) {}
DistanceRestraint(const std::vector<Vector3>& p1,
const std::vector<Vector3>& p2,
const std::vector<std::pair<std::string, std::string>>& p1Info,
const std::vector<std::pair<std::string, std::string>>& p2Info,
float maxdist, float mindist = 0.0, float weight=1.0)
: DistanceRestraint(p1, p2, maxdist, mindist, weight) {
p1Info_ = p1Info;
p2Info_ = p2Info;
}
DistanceRestraint(const Vector3& p1, const Vector3& p2,
float maxdist, float mindist = 0.0, float weight=1.0)
: mindist_(mindist), maxdist_(maxdist),
mindist2_(mindist*mindist), maxdist2_(maxdist*maxdist),
weight_(weight)
{
p1_.push_back(p1);
p2_.push_back(p2);
}
DistanceRestraint() = default;
float getWeight() const { return weight_; }
float getMinDistance() const { return mindist_; }
float getMaxDistance() const { return maxdist_; }
const std::vector<Vector3>& getPoints1() const { return p1_; }
const std::vector<Vector3>& getPoints2() const { return p2_; }
bool isViolated() const {
// calculate the distance and compare to mindist_ and maxdist_
for(unsigned int i = 0; i < p1_.size(); i++) {
for(unsigned int j = 0; j < p2_.size(); j++) {
float dist2 = p1_[i].dist2(p2_[j]);
if(dist2 <= maxdist2_) return false; // found one in range
}
}
return true;
}
bool isViolated(const std::vector<RigidTrans3>& trans) const {
// calculate the distance and compare to mindist_ and maxdist_
for(unsigned int i = 0; i < p1_.size(); i++) {
for(unsigned int j = 0; j < p2_.size(); j++) {
float dist2 = p1_[i].dist2(trans[j]*p2_[j]);
if(dist2 <= maxdist2_) return false; // found one in range
}
}
return true;
}
bool isViolated(const std::vector<RigidTrans3>& trans1,
const std::vector<RigidTrans3>& trans2) const {
// calculate the distance and compare to mindist_ and maxdist_
for(unsigned int i = 0; i < p1_.size(); i++) {
Vector3 transP1 = trans1[i]*p1_[i];
for(unsigned int j = 0; j < p2_.size(); j++) {
float dist2 = transP1.dist2(trans2[j]*p2_[j]);
if(dist2 <= maxdist2_) return false; // found one in range
}
}
return true;
}
// backward compatability
bool isSatisfied() const { return !isViolated(); }
bool isSatisfied(const RigidTrans3& trans) const {
std::vector<RigidTrans3> t(p2_.size(), trans);
return !isViolated(t);
}
bool isSatisfied(const RigidTrans3& trans1,
const RigidTrans3& trans2) const {
std::vector<RigidTrans3> t1(p1_.size(), trans1);
std::vector<RigidTrans3> t2(p2_.size(), trans2);
return !isViolated(t1, t2);
}
//calculate violationDistance
float violationDistance() const {
float bestdist = distance();
if(bestdist > maxdist_) return bestdist - maxdist_;
return 0.0;
}
float violationDistance(const std::vector<RigidTrans3>& trans) const {
float bestdist = distance(trans);
if(bestdist > maxdist_) return bestdist - maxdist_;
return 0.0;
}
float violationDistance(const std::vector<RigidTrans3>& trans1,
const std::vector<RigidTrans3>& trans2) const {
float bestdist = distance(trans1, trans2);
if(bestdist > maxdist_) return bestdist - maxdist_;
return 0.0;
}
float distance2() const {
float bestdist2 = std::numeric_limits<float>::max();
for(unsigned int i = 0; i < p1_.size(); i++) {
for(unsigned int j = 0; j < p2_.size(); j++) {
float dist2 = p1_[i].dist2(p2_[j]);
if(dist2 < bestdist2) bestdist2 = dist2;
}
}
return bestdist2;
}
float distance() const { return sqrt(distance2()); }
float distance2(const std::vector<RigidTrans3>& trans) const {
float bestdist2 = std::numeric_limits<float>::max();
for(unsigned int i = 0; i < p1_.size(); i++) {
for(unsigned int j = 0; j < p2_.size(); j++) {
float dist2 = p1_[i].dist2(trans[j]*p2_[j]);
if(dist2 < bestdist2) bestdist2 = dist2;
}
}
return bestdist2;
}
float distance(const std::vector<RigidTrans3>& trans) const {
return sqrt(distance2(trans));
}
float distance(const RigidTrans3& trans) const {
std::vector<RigidTrans3> t(1, trans);
return distance(t);
}
float distance2(const std::vector<RigidTrans3>& trans1,
const std::vector<RigidTrans3>& trans2) const {
float bestdist2 = std::numeric_limits<float>::max();
for(unsigned int i = 0; i < p1_.size(); i++) {
Vector3 transP1 = trans1[i]*p1_[i];
for(unsigned int j = 0; j < p2_.size(); j++) {
float dist2 = transP1.dist2(trans2[j]*p2_[j]);
if(dist2 < bestdist2) bestdist2 = dist2;
}
}
return bestdist2;
}
float distance(const std::vector<RigidTrans3>& trans1,
const std::vector<RigidTrans3>& trans2) const {
return sqrt(distance2(trans1, trans2));
}
// TODO: add trans versions
float minDistanceIndices(unsigned int& index1, unsigned int& index2) const;
std::string getChimeraXPseudoBond() const;
bool operator < (const DistanceRestraint& d) const { return (maxdist_ < d.maxdist_); }
friend std::ostream& operator<<(std::ostream& s, const DistanceRestraint& d) {
// TODO
return s << d.p1_[0] << ' ' << d.p2_[0] << ' ' << d.mindist_ <<' ' << d.maxdist_;
}
private:
std::vector<Vector3> p1_; // end point1, vector for ambiguity
std::vector<Vector3> p2_; // end point2, vector for ambiguity
std::vector<std::pair<std::string, std::string>> p1Info_, p2Info_; // residueSequenceID and chain for p1 and p2 endpoints
float mindist_; // minimal distance threshold
float maxdist_; // maximal distance threshold
float mindist2_; // minimal distance threshold (squared)
float maxdist2_; // maximal distance threshold (squared)
float weight_;
};
#endif /* DISTANCE_RESTRAINT_H */
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