#705 SMARTS component-level grouping and stereo matching

[John May]

This builds on all other open patches. There's still more to fix in the SMARTS but these patches add a fair bit. It's probably best to apply other patches first and then see where it starts. Here's a summary of what has been added.

• nested recursion, previous SMARTS parser would only allow one level of recursive patterns. Extending the parsing to multiple matches actually makes it a lot simpler and is easier when we add component grouping / stereo.
• removes initialisation from recursive atom matches, these had to be set up separately but are now all done via a 'SMARTSInvariants' class. This was also need for the nest recursion to be clean.
• parse large ring numbers in SMARTS
• match component-level grouping, also meant an updated to the ConnectivityChecker. the component-level group is fundamental to SMIRKS... (maybe next weekend). the grouping also works in recursive patterns and fixes bug (#1312).
• match tetrahedral and geometric (double-bond) configurations in SMARTS. The matching is relative and tetrahedral chirality can use logical operators. the double-bond chemistry is more tricky, 'C/C=C/,\C' is technically valid but even DEPICTMATCH doesn't handle it correctly.

branch: master+

[John May]

• Description has changed:

Diff:

--- old
+++ new
@@ -1,4 +1,4 @@
-This builds on all other open commits. There's still more to fix in the SMARTS but these patches add a fair bit. It's probably best to apply those and then see where it starts. 
+This builds on all other open patches. There's still more to fix in the SMARTS but these patches add a fair bit. It's probably best to apply other patches first and then see where it starts. Here's a summary of what has been added. 

 - nested recursion, previous SMARTS parser would only allow one level of recursive patterns. Extending the parsing to multiple matches actually makes it a lot 
 - removes initialisation from recursive atom matches, these had to be set up separately but are now all done via a 'SMARTSInvariants' class. This was also need for the nest recursion to be clean.
 - parse large ring numbers in SMARTS

[John May]

• Description has changed:

Diff:

--- old
+++ new
@@ -1,5 +1,5 @@
 This builds on all other open patches. There's still more to fix in the SMARTS but these patches add a fair bit. It's probably best to apply other patches first and then see where it starts. Here's a summary of what has been added. 
-- nested recursion, previous SMARTS parser would only allow one level of recursive patterns. Extending the parsing to multiple matches actually makes it a lot 
+- nested recursion, previous SMARTS parser would only allow one level of recursive patterns. Extending the parsing to multiple matches actually makes it a lot simpler and is easier when we add component grouping / stereo.

 - removes initialisation from recursive atom matches, these had to be set up separately but are now all done via a 'SMARTSInvariants' class. This was also need for the nest recursion to be clean.
 - parse large ring numbers in SMARTS
 - match component-level grouping, also meant an updated to the ConnectivityChecker. the component-level group is fundamental to SMIRKS... (maybe next weekend). the grouping also works in recursive patterns and fixes bug (#1312).

[John May]

other parts on downnstream master+

• renderer updates, (alignment of labels, correct bounding box and improved the specification of general shapes)
• faster canonisation/symmetry perception
• Inchi numbers for labelling universal SMILES
• depiction of tetrahedral stereo chemistry (that is assignment of wedge/hatch bonds)
• correction of double bond stereo chemistry (that is adjusting layout coordinates such the representation is correct).

[John May]

Applied