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*/ |
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#include "primitives/Inversion.hpp" |
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– |
#include "fstream" |
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namespace oopse { |
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// is treated as atom *3* in a standard torsion form: |
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Vector3d pos1 = atom2_->getPos(); |
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< |
Vector3d pos2 = atom1_->getPos(); |
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< |
Vector3d pos3 = atom4_->getPos(); |
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< |
Vector3d pos4 = atom3_->getPos(); |
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> |
Vector3d pos2 = atom3_->getPos(); |
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> |
Vector3d pos3 = atom1_->getPos(); |
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> |
Vector3d pos4 = atom4_->getPos(); |
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/*std::ofstream myfile; |
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myfile.open("Inversion", std::ios::app); |
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<< atom4_->getType() << " - atom4; " |
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<< std::endl; |
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*/ |
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< |
Vector3d r21 = pos1 - pos2; |
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< |
Vector3d r32 = pos2 - pos3; |
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< |
Vector3d r42 = pos2 - pos4; |
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> |
Vector3d r31 = pos1 - pos3; |
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> |
Vector3d r23 = pos3 - pos2; |
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> |
Vector3d r43 = pos3 - pos4; |
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// Calculate the cross products and distances |
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< |
Vector3d A = cross(r21, r32); |
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> |
Vector3d A = cross(r31, r43); |
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RealType rA = A.length(); |
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< |
Vector3d B = cross(r32, r42); |
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> |
Vector3d B = cross(r43, r23); |
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RealType rB = B.length(); |
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//Vector3d C = cross(r23, A); |
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//RealType rC = C.length(); |
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Vector3d dcosdA = (cos_phi * A - B) /rA; |
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Vector3d dcosdB = (cos_phi * B - A) /rB; |
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| 105 |
< |
f1 = dVdcosPhi * cross(r32, dcosdA); |
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< |
f2 = dVdcosPhi * ( cross(r42, dcosdB) - cross(r21, dcosdA)); |
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< |
f3 = dVdcosPhi * cross(dcosdB, r32); |
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> |
f1 = dVdcosPhi * cross(r43, dcosdA); |
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> |
f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA)); |
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> |
f3 = dVdcosPhi * cross(dcosdB, r43); |
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// In OOPSE's version of an improper torsion, the central atom |
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// comes first. However, to get the planarity in a typical cosine |
