Show re-orientation of view axis.

Graphic is the tree, which appears on top. Table appears below graphic and has 3 columns: Step; Action; and Stack.

This can be done in LaTeX:

% ...

\begin{tabular}{c}
    % the graphics
    \includegraphics[width=2in]{name.pdf}
\end{tabular}

\bigskip

\begin{tabular}{l L}
% the actual table
\end{tabular}

% ...

Again, use the graphical language rather than string syntax.

Example molecules with highlighted implicit hydrogen count. Include counter-intuitive cases.

Depict what's in the text.

A graphical method to indicate selected status would be nice.

Examples of compatible and incompatible pairings for left/right.

Figure 4, for example, is not.

Selected and unselected forms of a molecular tree are 100% equivalent to each other. So the passage should point out that the selection algorithm itself is an implementation detail only, provided that it produces DS with perfect matchings after pruning.

Earlier in the text, it is stated that:

A selected atom must use one of the following five elements: B; C; N; O; P; or S.

But later the selection production rule was defined without "b".

<selection> ::= "c" | "n" | "o" | "p" | "s"

See #33.

For example, the passage on selection algorithm notes: "A selection algorithm selects two or more nodes, thereby adding them to the DS." It should instead refer to atoms, because only atoms can be selected.

It should be possible to directly demonstrate the functionality of the grammar by running a test suite over test strings. Running this test suite as changes are made can prevent regressions and syntax errors in the grammar itself as well.

Candidates include:

• Ruby EBNF

Left, center, and right panels should be depicted.

Example molecules whose marked atoms would be selected gratuitously.

The symbols up arrow/down arrow might be helpful labels on the molecular tree.

Discussion in Syntax uses the variants Left and Right. Correct this and any other occurrences.

They are not currently. Table 3 lists the two atom parity variants as Clockwise and Counterclockwise. But under syntax, "... corresponding to the values Left and Right respectively."

Pick one pair of variants and use it consistently.

Example molecules whose marked atom should not use a configurational descriptor.

Might want to consult the reference implementation to see if this one still applies.

Current organization:

• Introduction
• Goals and Overall Design
• Molecular Tree
• Atoms and Bonds
• Electron Counting
• Delocalization Subgraph
• Valence and Subvalence
• Computing Implicit Hydrogen Count
• Conformation
• Configuration
• Syntax (might be broken down further)
  • Atom
  • Sequence
• Reading Strings
• Writing Strings
• Working with Molecular Graphs
• Compatibility
• Discussion
• Conclusion

These topics could be broken down more evenly like so:

• Introduction
• Goals
• Molecular Representation (starts with last paragraph of Goals...)
  • Molecular Tree
  • Atoms and Bonds
  • Electron Counting
  • Delocalization Subgraph
  • Valence and Subvalence
  • Computing Implicit Hydrogen Count
  • Conformation
  • Configuration
• Syntax
  • Grammar
  • Atom
  • Sequence
• Implementation
  • Reading Strings
  • Pruning
  • Writing Strings
  • Working with Molecular Graphs
• Compatibility
• Discussion
• Conclusion

Structure drawing of unrepresentable conformation.

Stack is defined twice (Reading and Writing). It should only be defined once.

To avoid any confusion. List each character together with its ASCII code.

<virtual_hydrogen at "The virtual hydrogen count is set to zero by omitting..." Correct similar mistakes.

Explain what this section is for. It's to guide implementation by answering specific questions likely to come up.

Is there any real example for such a pentavalent nitrogen center? There are about 550 examples of N atoms with a coordination number (= "valence") of five in the Cambridge Structural Database, but most of these are clusters with nitrogen bonded to small 1st or 2nd row metals such as lithium. A rare example which does not match this description is here:

Much more likely, you will find an ammonium cation:

Valence [= coordination number]: 1+1+1+1=4
Subvalence: 4-4 = 0
Implicit H: 0

The right-hand side of Figure 19 should place the H atom at the leftmost child position. The cyan atom should have a "[H]" next to it to indicate virtual hydrogen.

Example use of a stack to push/pop head atom as open/close parens are read.

It might be possible to re-purpose one already found on depth-first.com.

Illustrates the five transformations defined in the text.

Not defined at the level of syntax, but could be. Readers encountering unbalanced parentheses must report an error. Writers must not write such strings.

See #32 for one way to do this.

Put tree into graphic and put graphic at top of table. The table columns would be: Step; Character; Stack; and Action.

Intro gives 3 but Conclusion lists 4.

Maybe two examples, one of which selects gratuitously.

"C[NH4+]" should be "C[NH3+]". The graphical structure should also be fixed.

Highlight all of the bonds that participate in the system.

Show traversal order, including bridges and gaps.

A worked example based on text description.

An example molecule showing DIME and the corresponding molecular trees.

Paragraph starting with "Broader expansion..." uses the term.

Turns out they're required and some tools won't like it if they're missing.

How do you want to handle atoms which do not follow the octet rule?

Classical examples of 2nd row compounds are diborane (B2H6) and nitric oxide (NO). How do you want to make sure BALSA handles NO and HNO differently?

And more importantly, how to handle diborane with its 3c2e bonds, which cannot be expressed in terms of Lewis formulas?

https://en.wikipedia.org/wiki/Diborane
https://en.wikipedia.org/wiki/Nitric_oxide
https://en.wikipedia.org/wiki/Nitroxyl

This specification appears to be the most coherent and widely-supported of the "EBNF-like" notations.

Its main differences are the angle brackets around production rule names are not allowed, nor are semicolons at the end of rules.

Switching to W3C EBNF will make it possible to use parser generator tooling more easily.

As described, the procedure deducts double the electrons it should from the referenced atom.

The referenced atom's electron count will be deducted when it is added as a parent and then bonded to its own referenced atom.

It could be that the concept of referenced atom is no longer needed if this use is dropped.

It should illustrate exactly how index reuse works. Two levels deep should do it.

For example, node-order.pdf uses 2.5cm. It should be possible to make all widths \columnwidth.