merge

Combine multiple .pta files produced from the same topology into a single aggregated artifact. The standard use case is pooling independent replicate runs before plotting or exporting.

Before merging, Pharmacon requires that all inputs share the same command and subcommand — this is a hard requirement and mismatched files are refused. It also compares each file’s blueprint (a deterministic hash of the run inputs — topology, selections, flags); a differing blueprint (e.g. a different topology) is reported as a warning and, under the default zero-warning budget (-mw 0), aborts the merge.

Merged files replace per-frame datasets with aggregate summary tables stored under modes_merged/. The is_merged root attribute is set to True.

merge results 

Merge two or more .pta files into one aggregated artifact.

Arguments

Flag	Required	Description
`-i / --input`	Yes	Two or more input `.pta` files (space-separated)
`-o / --output`	Yes	Output merged `.pta` file
`--overwrite`	No	Overwrite an existing output file
`-mw / --max-warnings`	No	Maximum number of coercion warnings to tolerate
`-l / --log`	No	Log file (default: `merge_results.log`)
`-fl / --file-logging-level`	No	File log verbosity (default: `DEBUG`)
`-tl / --terminal-logging-level`	No	Terminal log verbosity (default: `INFO`)

Examples

Merge two RMSD files from consecutive trajectory segments:

pharmacon merge results \
    -i seg1/rmsd.pta seg2/rmsd.pta \
    -o merged_rmsd.pta

Merge three replicate interaction files:

pharmacon merge results \
    -i rep1/pli.pta rep2/pli.pta rep3/pli.pta \
    -o pli_merged.pta

Merge and overwrite an existing output:

pharmacon merge results \
    -i rep1/pli.pta rep2/pli.pta rep3/pli.pta \
    -o pli_merged.pta \
    --overwrite

Typical replicate workflow (analyse → merge → plot):

# Step 1 — run each replicate
for rep in rep1 rep2 rep3; do
  pharmacon trajectory pl-interactions \
      -p $rep/topol.tpr -x $rep/traj.xtc \
      -prt "protein" -lig "resname LIG" \
      -w  "resname WAT" \
      -o  $rep/pli.pta
done

# Step 2 — merge
pharmacon merge results \
    -i rep1/pli.pta rep2/pli.pta rep3/pli.pta \
    -o pli_merged.pta

# Step 3 — plot
pharmacon plot pta \
    -i pli_merged.pta \
    -o plots/merged/ \
    --overwrite

merge

merge results

merge results 