feat(output): add optional timed molecule output

docs/guide/report.md

@@ -23,7 +23,7 @@ You can load it through the <a href="../report.html" target="_blank">web page lo
 suffix: `.species`
 
 This text file stores the number of each species in each time step.
-One can read this file thorugh the Python method {meth}`reacnetgenerator.tools.read_species <reacnetgenerator.tools.read_species>`.
+One can read this file through the Python method {meth}`reacnetgenerator.tools.read_species <reacnetgenerator.tools.read_species>`.
 Note that when [HMM](hmm.md) is enabled, information in this file may not be accurate.
 
 ## Molecule file
@@ -34,6 +34,25 @@ This file contains information of each molecule.
 In each line, the first column is its SMILES.
 The second column is the atomic index (starts from 0) of atoms.
 The last column shows all the bonds in the molecule.
+This file always keeps the historical three-column format.
+
+## Molecule timeline file
+
+suffix: `.molecules.csv`
+
+This optional CSV file is written when `--show-molecule-time`,
+`--molecule-frame`, or `--molecule-timestep` is enabled. It contains one row per
+molecule occurrence in an analyzed frame, with the following columns:
+
+```text
+Timestep,Species,AtomIDs,BondIDs
+```
+
+Rows are sorted by `Timestep`. `Timestep` is the original timestep value from
+the input trajectory. `AtomIDs` and `BondIDs` are semicolon-separated lists.
+Bond IDs use `atom1-atom2-order` labels. The
+`--molecule-frame` and `--molecule-timestep` filters limit the CSV rows to
+selected frames or timesteps.
 
 ## Route file
 
@@ -51,9 +70,24 @@ Atom {idx}: {time} {SMILES} -> {time} {SMILES} -> ...
 suffix: `.reaction`, `.reactionabcd`
 
 `.reaction` shows the frequency of the reaction $\ce{A -> B}$ while `.reactionabcd` shows the frequency of the reaction $\ce{A + B -> C + D}$.
-One can read this file thorugh the Python method {meth}`reacnetgenerator.tools.read_reactions <reacnetgenerator.tools.read_reactions>`.
+One can read these files through the Python method {meth}`reacnetgenerator.tools.read_reactions <reacnetgenerator.tools.read_reactions>`.
 Note that $\ce{A + B -> C + D}$ information may be not accurate when [HMM](hmm.md) is enabled.
 
+## Reaction event file
+
+suffix: `.reactionevent.csv`
+
+This optional CSV file is written when `--reaction-event` is enabled. It contains
+one row per reaction event detected between two adjacent analyzed frames:
+
+```text
+Timestep_Index,Reactant,Product
+```
+
+`Timestep_Index` is the analyzed transition index. A value of `0` means the
+reaction was detected between analyzed frames 0 and 1. `Reactant` and `Product`
+use the same species names as the reaction summary files.
+
 ## Reaction matrix file
 
 suffix: `.table`