| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
|
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "restraints/MolecularRestraint.hpp" |
| 86 |
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|
| 87 |
|
Mat3x3d R(0.0); |
| 88 |
|
|
| 89 |
< |
for (int n = 0; n < struc.size(); n++){ |
| 89 |
> |
for (unsigned int n = 0; n < struc.size(); n++){ |
| 90 |
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|
| 91 |
|
/* |
| 92 |
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* correlation matrix R: |
| 138 |
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Vector3d eularAngles = A.toEulerAngles(); |
| 139 |
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|
| 140 |
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|
| 141 |
< |
RealType twistAngle, swingAngle; |
| 141 |
> |
RealType twistAngle; |
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Vector3d swingAxis; |
| 143 |
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|
| 144 |
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Quat4d quat = A.toQuaternion(); |
| 145 |
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|
| 146 |
< |
RealType tw, sx, sy, ttw, swingX, swingY; |
| 146 |
> |
RealType swingX, swingY; |
| 147 |
|
quat.toSwingTwist(swingX, swingY, twistAngle); |
| 148 |
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|
| 149 |
< |
RealType dVdtwist, dVdswing, dVdswingX, dVdswingY; |
| 150 |
< |
RealType dTwist, dSwing, dSwingX, dSwingY; |
| 149 |
> |
RealType dVdtwist, dVdswingX, dVdswingY; |
| 150 |
> |
RealType dTwist, dSwingX, dSwingY; |
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|
RealType p; |
| 152 |
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|
| 153 |
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if (restType_ & rtTwist){ |
| 190 |
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|
| 191 |
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Vector3d rLab, rBody, txr, fBody, fLab; |
| 192 |
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|
| 193 |
< |
for (int i = 0; i < struc.size(); i++) { |
| 193 |
> |
for (unsigned int i = 0; i < struc.size(); i++) { |
| 194 |
|
|
| 195 |
|
rLab = struc[i]; |
| 196 |
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rBody = A * rLab; |
