Dates can be NULL in the current database schema. We never use them
anyways (ie they are not read back from the database when compounds are
loaded) so it is safe to skip them if they are missing.

Reading the BIRD data from prd-all.cif.gz which doesn't contain any
compound would result in a compound lib filled with dummy compounds and
atoms, containing no useful data. This commit skips compounds with no
_chem_comp.id (key data item) and non-loop atoms without an
_chem_comp_atom.atom_id, with a warning.
The result of reading prd-all.cif.gz is now an empty compound lib.

This avoids ignoring issues in optimized builds and hard to read errors in
unoptimized builds.

The breadcrumbs now correctly indicate the module hierarchy and can be
used to determine imports. All the documentation for ost.* is now rooted
on the base `ost` module for more clarity.

Before it just complained that the compound library was created with
an unsupported version of OST while in fact it could have been an empty or
even random file. Now it says:
Exception: Could not read OST version from loaded SQLITE DB - no valid
CompoundLib

Reduces insane amount of compiler warnings. Inheritance from std::iterator
template was used to define traits of an iterator. Cool people define these
traits directly nowadays.

This fixes test_complib.py on mac

Xavier Robin authored 1 year ago and Xavier Robin committed 1 year ago

An overflow would happen when the residue contains unknown atoms that
are not in the compound, and can prevent bonds from being properly
created in ConnectAtomsOfResidue.

An overflow would happen when the residue contains unknown atoms that
are not in the compound, and can prevent bonds from being properly
created in ConnectAtomsOfResidue.

Test behavior when no results and of invalid "by"

This replaces the awkward FindCompound(... by=) which would return
a single arbitrary compound.

This allows preferentially picking a non-obsolete compound
in FindCompound by="smiles/inchi"