Here is a list of all files with brief descriptions:

include
nuri
algo
crdgen.h
guess.h
optim.h
rings.h
core
container
bool_matrix.h
compact_map.h
container_ext.h
dumb_buffer.h
index_set.h
linear_queue.h
property_map.h
graph
adaptor.h
graph.h
subgraph.h
traits.h
vf2pp.h
element.h
geometry.h
molecule.h
desc
pcharge.h
surface.h
fmt
base.h
cif.h
mmcif.h
mol2.h
pdb.h
sdf.h
smiles.h
tools
chimera.h
galign.h
tm.h
eigen_config.h
iterator.h
meta.h
random.h
utils.h