Here chemical shift calculation is done. An iteration over every Hydrogen in proton_list_ is started. For each of these Hydrogens an iteration is started over every effector bounds in eff_list_. c_atom is assigned the first atom of effector bond and o_atom is the second. If the actual proton is in another residue then c_atom calculation is started. The next bounded carbonate atom of c_atom is stored in x_atom. Now we have three atoms with their positions stored in c_pos , o_pos and x_pos.
We then build a cartesian coordinate system with these vectors.
vz = o_pos - c_pos and vz is normalized. vy is the vectorproduct of vz and the difference vector of x_pos and c_pos and is normalized. vx is the vectorproduct of vz and vy and is normalized. Then the center cen of the effector bound is set to
c_pos + 1.1 * vz.
Next three vectors are calculated : v1 is the difference vector of the actual hydrogen and cen. v2 is the vectorproduct of v1 and vy. v3 is the vectorproduct of v2 and vx. abstand is assigned the length of vector v1. Then stheta is assigned the sinus of the angle between v1 and vy. The sinus of the angle between v2 and vx is assigned to sgamma. Now preparations have finished and we can start the real shift calculation.
dX1 and dX2 are some constant floats. If the actual Hydrogens name is "H" the constant floats dXN1 and dXN2 are used instead.
If eff_list_ has finished C=O anisotropy for actual Hydrogen is done and iteration over all C=N anisotropy effector bounds of eff_list_2_ is started.
This calculation is very similar with just some differences : We got three position vectors called: c_poso_pos position of n_pos position of the Nitrogen bonded to Carbonate.
The cartesion coordinate system is built on vz = n_pos - c_pos
vy is the vectorproduct of vz and the difference vector of o_pos and c_pos
vx is the vectorproduct of vz and vy.
The center of the effector bond is set to:
cen = c_pos + ( vz * ( 0.85 * length of vz ) )
The final calculation is just the same as above, except the use of different constants. Use ndX1 and ndX2 instead of dX1 and dX2 and ndXN1 and ndXN2 intead of dXN1 and dXN2. Finally C=N anisotropy has finished and gs is added to the actual hydrogens shift. Then iteration goes on with the next hydrogen.
eff_list_ that contains all effectors of C=O anisotropy and
eff_list_2_ that contains all effectors of C=N anisotropy. Effectors of C=O anisotropy are all bounds between atoms named "C" and "O", as well as bounds between atoms named "CG" and "OD1" in residues called "ASP" or "ASN, and finally bounds between atoms named "CD" and "OE1" in residues called "GLU" and "GLN". Effectors of C=N anisotropy are all bounds between atoms named "C" and "N".
