Make index

The make_ndx tool creates and edits index files (.ndx) used throughout DROPPS analysis modules. It provides an interactive environment—similar to GROMACS make_ndx—allowing you to list groups, create new groups, combine groups, select atoms by rules, and finally save an .ndx file.

This tool is implemented in make_ndx.py.

Overview

Index files are a core part of the DROPPS analysis system, allowing the user to define arbitrary groups of atoms, residues, or chains. These groups are used by tools such as:

• cmap (contact maps)

• gyrate (radius of gyration)

• density (density profiles)

• idist and odist (distance metrics)

• any tool requiring chain-wise splitting (splitch)

dps make_ndx provides:

1. Load topology directly from a TPR file

2. Optionally load an existing NDX file

3. Enter a fully interactive prompt for editing groups

4. Use powerful commands from the indexGroups engine

5. Save results to a new index file when the user quits

Usage

dps make_ndx -s run.tpr -o index.ndx

Load an existing file before editing:

dps make_ndx -s run.tpr -n old.ndx -o new.ndx

Arguments

-s, --run-input TPR

Required. TPR file providing the topology, atom/residue information, and chain definitions.

-n, --index NDX

Optional. Load an existing index file before entering the interactive session.

-o, --output FILE

Required. Path to the output .ndx file that will be written when exiting.

Program Flow

1. Read TPR file

tpr = read_tpr(args.run_input)

If reading fails, the program prints:

ERROR: Cannot open tpr file ...

and exits.

2. Initialize index engine

index = indexGroups(tpr.mdtopology, tpr.itp_list)

This object provides:

• built-in groups

• atom/residue/chain metadata

• group combination engine

• command processor

• help menu

• .ndx writer

3. Load existing index (optional)

index.load_ndx(args.index)

Errors result in:

ERROR: Cannot open index file ...

4. Print initial groups

The command:

index.command('p')

prints all current groups.

5. Interactive prompt

A loop begins:

> <your command>

Supported actions include:

• p — print all groups

• q — write ndx & quit

• a <expr> — select atoms by rule

• r <expr> — select residues

• chain <expr> — select chain(s)

• name <pattern> — match atom names

• Boolean operations: - | union - & intersection - ! complement

• Numeric selection by group ID

• Combining groups (a 5 | 7, !4, etc.)

All helpers are provided through:

index.showhelp()

6. Quit and save

Typing q saves the final groups:

index.write_ndx(args.output)

and exits immediately.

Interactive Commands

The indexing engine exposes powerful commands (actual commands depend on indexGroups, but typical examples include):

Selecting atoms:

a 1-100
a name CA
a resname GLY

Selecting residues:

r 5-30

Chain operations:

chain 0
chain A B C

Set operations:

3 | 5         # union
2 & !4        # intersection with complement
7 - 1         # difference

Create new groups:

name backbone
a name N CA C O

Re-print groups:

p

Example Session

Typical interactive workflow:

$ dps make_ndx -s run.tpr -o mygroups.ndx
## Loading topology from run.tpr.
Loading index entries from file None.
> p
0 System
1 Protein
2 Water
...

> a name CA
> a name CB
> 10 | 11          # combine groups
> p
12 Combined_CA_CB

> q
## Writing ndx to mygroups.ndx
## Finished.

Error Messages

“ERROR: Cannot open tpr file …” Given TPR file cannot be read.

“ERROR: Cannot open index file …” Existing index file specified by --index is invalid.

Other errors (invalid command syntax, unknown group, etc.) are printed by the indexGroups engine.

Summary

dps make_ndx is a compact yet powerful interactive tool for building index files that feed into all analysis operations in the DROPPS ecosystem. Features:

• direct topology loading

• optional merging with existing ndx files

• robust expression engine for atom/residue/chain selection

• full interactive editing environment

• easy saving to a new index file

This tool is essential for preparing customized groups used by the DROPPS analysis modules.