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How to use

The explore-reactions subcommand is used to explore reactions between assemblies.

Syntax

nasapnet explore-reactions [OPTIONS] ASSEMBLIES COMPONENT_KINDS CONFIG OUTPUT

Info

If this raises an error command not found, you may need to use python -m nasap_net or python3 -m nasap_net instead of nasapnet. 

python -m nasap_net explore-reactions [OPTIONS] ASSEMBLIES COMPONENT_KINDS CONFIG OUTPUT

Positional Arguments

  1. ASSEMBLIES: Relative path to the assemblies file. (YAML format)
  2. COMPONENT_KINDS: Relative path to the component kinds file. (YAML format)
  3. CONFIG: Relative path to the config file. (YAML format)
  4. OUTPUT: Relative path to the output file. (CSV format)

Options

Options with single hyphen (-) are aliases for the corresponding options with double hyphen (--), e.g., -w is an alias for --wip-dir. Either of them can be used.

Command Alias Description Example
--overwrite -o Overwrite output file if it exists. nasapnet explore-reactions -o input.yaml output.yaml
--verbose -v Print feedback messages to the console. nasapnet explore-reactions -v input.yaml output.yaml
--help Show this message and exit. nasapnet explore-reactions --help

Reversible reactions not guaranteed

The explore-reactions command considers left-to-right and right-to-left reactions as separate reactions.

This means that the results may contain only one direction of a reversible reaction.

For example, if the config file is set up as follows: 

mle_kinds: 
    metal_kind: M
    leaving_kind: X
    reactant_kind: L
the results only include "X-to-L" reactions, NOT "L-to-X".

e.g., "MX4 + L -> MX3L + X" will be included, but the reverse "MX3L + X -> MX4 + L" will never be included.

If you want to include both directions, you can run the command twice with swapped reactant_kind and leaving_kind in the config file, e.g., 

mle_kinds: 
    metal_kind: M
    leaving_kind: L
    reactant_kind: X
This will include "L-to-X" reactions, such as "MX3L + X -> MX4 + L".

Then you can concatenate the two resulting CSV files.

Example

Directory structure before running the command: 

/
├── assemblies.yaml
├── component_kinds.yaml
└── config.yaml

Command: 

nasapnet explore-reactions assemblies.yaml component_kinds.yaml config.yaml output.csv

Directory structure after running the command: 

/
├── assemblies.yaml
├── component_kinds.yaml
├── config.yaml
└── output.csv

Input and output files are as follows:

Input File (1) assemblies.yaml
assemblies.yaml
0: !Assembly
  bonds:
  - [M1.a, X1.a]
  - [M1.b, X2.a]
  comp_id_to_kind: {M1: M, X1: X, X2: X}
1: !Assembly
  comp_id_to_kind: {L1: L}
2: !Assembly
  comp_id_to_kind: {X1: X}
3: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [M1.a, X0.a]
  comp_id_to_kind: {L1: L, M1: M, X0: X}
4: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [M1.a, X0.a]
  - [M2.b, X1.a]
  comp_id_to_kind: {L1: L, M1: M, M2: M, X0: X, X1: X}
5: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L4.b, M1.a]
  comp_id_to_kind: {L1: L, L4: L, M1: M}
6: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [M1.a, X0.a]
  comp_id_to_kind: {L1: L, L2: L, M1: M, M2: M, X0: X}
7: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [M1.a, X0.a]
  - [M3.b, X1.a]
  comp_id_to_kind: {L1: L, L2: L, M1: M, M2: M, M3: M, X0: X, X1: X}
8: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L4.b, M1.a]
  comp_id_to_kind: {L1: L, L2: L, L4: L, M1: M, M2: M}
9: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [M1.a, X0.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, M1: M, M2: M, M3: M, X0: X}
10: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [L3.b, M4.a]
  - [M1.a, X0.a]
  - [M4.b, X1.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, M1: M, M2: M, M3: M, M4: M, X0: X, X1: X}
11: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [L4.b, M1.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, L4: L, M1: M, M2: M, M3: M}
12: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [L3.b, M4.a]
  - [L4.a, M4.b]
  - [M1.a, X0.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, L4: L, M1: M, M2: M, M3: M, M4: M, X0: X}
13: !Assembly
  bonds:
  - [L1.a, M1.b]
  - [L1.b, M2.a]
  - [L2.a, M2.b]
  - [L2.b, M3.a]
  - [L3.a, M3.b]
  - [L3.b, M4.a]
  - [L4.a, M4.b]
  - [L4.b, M1.a]
  comp_id_to_kind: {L1: L, L2: L, L3: L, L4: L, M1: M, M2: M, M3: M, M4: M}
Input File (2) component_kinds.yaml
component_kinds.yaml
component_kinds:
  M: !Component
    binding_sites: [a, b]
  L: !Component
    binding_sites: [a, b]
  X: !Component
    binding_sites: [a]
Input File (3) config.yaml
config.yaml
mle_kinds:
  metal: M
  leaving: X
  entering: L
Output File

Warning

The output file only contains the X-to-L reactions, not the L-to-X reactions.

init_assem_id entering_assem_id product_assem_id leaving_assem_id metal_bs leaving_bs entering_bs duplicate_count
12 nan 13 2 M1.a X0.a L4.b 1
0 1 3 2 M1.a X1.a L1.a 4
0 3 4 2 M1.a X1.a L1.b 2
0 5 6 2 M1.a X1.a L1.b 4
0 6 7 2 M1.a X1.a L2.b 2
0 8 9 2 M1.a X1.a L2.b 4
0 9 10 2 M1.a X1.a L3.b 2
0 11 12 2 M1.a X1.a L3.b 4
3 1 5 2 M1.a X0.a L1.a 2
3 3 6 2 M1.a X0.a L1.b 2
3 5 8 2 M1.a X0.a L1.b 2
3 6 9 2 M1.a X0.a L2.b 1
3 8 11 2 M1.a X0.a L2.b 2
3 9 12 2 M1.a X0.a L3.b 1
4 1 6 2 M1.a X0.a L1.a 4
4 3 7 2 M1.a X0.a L1.b 2
4 5 9 2 M1.a X0.a L1.b 4
4 6 10 2 M1.a X0.a L2.b 2
4 8 12 2 M1.a X0.a L2.b 4
6 1 8 2 M1.a X0.a L1.a 2
6 3 9 2 M1.a X0.a L1.b 1
6 5 11 2 M1.a X0.a L1.b 2
6 6 12 2 M1.a X0.a L2.b 2
7 1 9 2 M1.a X0.a L1.a 4
7 3 10 2 M1.a X0.a L1.b 2
7 5 12 2 M1.a X0.a L1.b 4
9 1 11 2 M1.a X0.a L1.a 2
9 3 12 2 M1.a X0.a L1.b 1
10 1 12 2 M1.a X0.a L1.a 4