CLI task recipes¶

These commands target an installed MolOP environment and all start with molop parse PATTERN.

Summarize final frames¶

Bash

molop -q parse "results/*.log" \
  to-summary-df --full --out summary.csv

Result: summary.csv is created in the current directory with one row per successfully parsed file and columns such as Status.IsNormal and Energy.total_energy.hartree.

With the bundled water_mp2.out example, the terminal reports:

Terminal output

Text Only

Summary written to summary.csv

Created file:

Text Only

summary.csv

Summarize every frame¶

Bash

molop -q parse "results/*.log" \
  to-summary-df --frame all --full --out trajectory.csv

Result: trajectory.csv contains one row per frame and General.FrameID identifies each frame.

Created file

Text Only

trajectory.csv

Keep normal optimized results¶

Bash

molop -q parse "results/*.log" \
  filter-state --state normal \
  filter-state --state opt \
  to-summary-df --full --out optimized.csv

Result: optimized.csv contains only files that pass both filters.

Created file

Text Only

optimized.csv

Select ORCA outputs¶

Bash

molop -q parse "results/*" \
  filter-by-codec --codec-id orcaout \
  to-summary-df --out orca.csv

filter-by-codec uses the actual reader ID rather than the extension string.

Created file

Text Only

orca.csv

Export final XYZ files¶

Bash

molop -q parse "results/*.out" \
  filter-state --state normal \
  format-transform --format xyz --output-dir structures

Result: .xyz files named from their sources are written under structures/. The CLI creates a missing output directory.

Created files

Text Only

structures/
  water_mp2.xyz

Preview without writing¶

Bash

molop -q parse "water_mp2.out" \
  format-transform --format xyz --no-write

The terminal displays the source path and rendered XYZ text. No .xyz file is created.

For the shared example, the rendered content is:

Rendered XYZ

Text Only

3
comment charge 0 multiplicity 1
O               1.7849140000      1.2624220000      0.5119850000
H               2.6482370000      1.0729290000      0.1316310000
H               1.1831680000      1.2568160000     -0.2388350000

Produce JSON¶

Bash

molop -q parse "water_mp2.out" --output-format json \
  filter-state --state normal \
  sample --n 1 --seed 1

Output is a path array. The path is absolute and depends on the environment; the stable shape is shown below rather than a machine-specific prefix:

JSON output shape

JSON

[
  "<absolute-path-to-working-directory>/water_mp2.out"
]

Rules¶

Operations run in written order.
filter-state, filter-value, filter-by-codec, and sample can be chained further.
to-summary-df, format-transform, copy-to, move-to, groupby, and draw-grid-image are terminal operations; no business operation may follow them.
Use molop parse --help for the operation list and a specific operation’s --help for options.

See the CLI command reference for exact constraints.