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When both comparison structures in RMSD come from the simulation,
the RMSD value returned was incorrect, as it was still calculated
on the assumption of fixedness of the first structure. Properties
of the first structure such as radius of gyration, used in the
RMSD calculation were calculated and stored at initialisation were
used throughout, even when the first structure was not a fixed
one from a PDB file.

The lines in the description of argparse are wrapped by default.
Since we want to use the formatted doc string, we have to add
`formatter_class=argparse.RawDescriptionHelpFormatter` as argument.

update_g, when called from ctest does not have an environment
where other programs like "prf", "mc_stats" are in PATH. It
therefore needs a special PATH set up for the subprocesses it
spawns.

Live generation of gpars.out was broken, as pointed out by Stefan
Wallin. The monte carlo statistics, such as visit counts to different
temperatures are now calculated in bunches, and the counters are
reset regularly. SimTempRun did not take that into account, and
hence generated g_T = 0 for all T randomly in the middle of a
run. The values in the file gpars.out were therefore completely
wrong eversince the statistics collection method was changed.
With this patch, we simply remove the live generation of gpars.out
file, and move that action to a post processing step. The user
is now supposed to run "prf simtemp update_g" after a simulated
tempering run to generate a new g parameters file, and replace
the gpars.in file consciously. There is more flexibility now,
as we can choose how much of the previous run should be used to
re-calculate the g-parameters after the run is finished and we
have inspected the "rt" files. For instance, to use cycles
starting from 200000 in the calculation of new g-parameters, we
can now do this "prf simtemp update_g --starting_cycle 200000".
See "prf simtemp update_g --help" for details.

It is possible to request xml output with -xml. It is possible to
pick a specific child node in the information tree with a -get
option, similar to how prfxml handles that option.

SimTemp will now write the g-parameters in the binary configuration
files, so that the parameters used in the simulation will always
be available for inspection along with the binary data. The
values will be visible using the runinfo system : "prf runinfo -m"

If we try to open a normal file with JoinedTextFileIstream,
it should emit an error, because all read operations will fail.
For now, non-existent files are handled separately.

We expand the "prf" script interface to add a few scripts to
manage simulated tempering runs. Eventually, there should be
some setup scripts, and may be simulated tempering specific
post-processing scripts here. For now, we have only the cover
script "prf simtemp" and "prf simtemp update_g". The later
calculates new g-parameters from input g-parameters and the
visit counts to different temperatures collected from a run.
This will now be the "official" way to update g-parameters.
The parameters as generated during a run are no longer correct
as they only take the visit counts in the latest "packet" in
the monte carlo statistics. The live generation of gpars.out
will be removed.

The user documentation that was included in the source code of the
corresponding classes was moved to reStructuredText files in the doc
directory. It is now available again when documentation is build, but
some cleanup is still needed.

Incremental update does not access elements of a zero sized
array anymore ObsExpression initializes its internal copy of
the incremental update. Observable gets new functions to
getPopulation(), as that can be used to selectively and
lazily initialize some.

When a new FF term is added after the force field
has been fully set up, the newly added term must be
given a population and initialized.

While harvesting possible disulphide bond sites, Seq(i) was previously
compared with C. For proteins with an N-terminal ligand,
Seq(i) would be offset by 1 compared to the index needed
for accessing the i'th amino acid. It's better to compare
AA(j)->OLC() with C. We also extend the search for the
participating Sulfur atom to both the labels " SG " and
"_SG_".

Some vestigial warning messages about the total number
of moved atoms and apparent misplacement of atoms discovered
during update_cells() were silenced.

A typo broke the message about the atoms involved in a disulphide bond,
writing out the id of the first atom twice. A logical operator, which
should have been "and" was mistakenly written as "or".

In prf::Wrap, because of copy-and-paste, post-increment and
post-decrement operators were incorrectly returning references,
leading to dangling references and SEGFAULTS.

GroupLibXML represents an XML node containing information about
entities available for simulation, presumably provided by the
force field class.

LittleParser header needed an include guard. It is now possible to
have a string with all the defined variables from the parser. It
is possible to query if an expression is definitely false. An
expression may be neither true or false, if information to determine
its truth value is not available. For instance, if we want to evaluate
"a < 10 and b > 0", and a = 2 and b is unknown, the expression is not
true, but it is also not false. Under the same circumstances,
"a < 10 or b > 0" will evaluate to true, because a<10 is sufficient
to determine the truth value even if b is unknown.

It is now possible to just query whether an attribute list has
an attribute of a given name.

Geometric information about all the amino acids is now in FF08.xml.
We have a new way to specify geometry of entities to be used to
construct molecules in ProFASi 2.0. The geometry is to be encoded
in the XML file specifying all possible interacting entities in
the model. So far, amino acids had very minimal information in the
XML format, and their geometry was directly encoded in their own
classes. Now, amino acid geometry is in a very easy extensible
form, and we can begin the work of removing the individual
amino acid classes.

LittleParser is likely to be updated a lot in the comming weeks. This
patch isolates the rest of ProFASi so that trivial changes in LittleParser
do not trigger a big recompilation. From the outside, we only see a
rudimentary interface: one can set variables to specific values, ask if
an expression, represented by a string is true. Details about the tree
structure of the expressions, how type information about variables is
stored etc. can be kept under wraps in the implementation. They have
currently no value to users of the LittleParser.

LittleParser now treats "&&" and "and" as interchangable signs for
the logical AND operation, and similarly for logical OR. An explicit
integer type was introduced to store values set as integers really
as integers, so that equality comparisons between them can not be
broken by rounding errors.

prf_assert_true does what prf_assert_throw also does, but the name
is more intuitive. prf_assert_false throws UNLESS the condition provided
is false.

find_any_of(i1, i2, j1, j2) takes an input range [i1, i2) and a token
range [j1, j2), and tries to find a location in the input range which
marks the start of any of the tokens found in [j1, j2). The token range
can be, for instance, ["&&", "and", "AND"]. The idea is to treat the
token range as equivalent, and find any entry in the range.
split_by_any_of(string, string_container) accepts a token range as
a string container and splits the input string by them, treating the
entries in the token range as synonymous, even if they contain different
number of characters.

Most matrix functions can be noexcept, so they were labeled accordingly. For fixed size
matrices, if they take more than 32 bytes they are aligned to 32 bytes, and if they are
more than 64 bytes, they are aligned to 64 bytes.

Clang 7 moved experimental filesystem objects from libc++experimental to libc++fs,
which requires that the choose_fslib had to be modified to adapt. GCC and Clang
required versions in the compiler specific CMake files were updated to reflect
what is stated in the installation.rst file. Options to enable aligned allocation
from C++17 when available were added for both GCC and Clang.