correct handling of amide distances for macrocycles

[hjuinj]

This PR is a patch to the previous PR I submitted for macrocycle conformer generation in order to get the trans preference behaviour when sampling amides in macrocycles.

In the previous PR, I only forced trans configuration of amides when the three consecutive bonds are all ring bonds (in the function _setMacrocycleAllInSameRing14Bounds).

However, another enforcing is needed when faced with two consecutive ring bonds(in the function _setMacrocycleTwoInSameRing14Bounds), which was included during my code development and I (carelessly) neglected to add in that PR.

This PR adds two more variants of the checkAmideEster14, please see illustration in the comment section above each of the two functions to understand the need for them.

In addition I also included:

• a test case for checking trans amide sampling when using macrocycle conformer generation (ETKDGv3)
• additional argument (useMacrocycle14config) when getting the bounds matrix of a molecule, which is needed when trying to set custom bounds matrix in order to bias sampling of macrocycles with amides

[greglandrum]

@sriniker : have you looked through (and approved) this already? Knowing that you have would save me a lot of effort. :-)

[sriniker]

@greglandrum: Yes, Shuzhe and I have discussed the implementation and gone through the code together.

[greglandrum]

Thanks @hjuinj !