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make_mat modification for cmdata compatibility #495

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merged 5 commits into from
Dec 3, 2024
Merged

make_mat modification for cmdata compatibility #495

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153d55e
new make mat: --mode as cmdata
brunostega Nov 29, 2024
f3d0d9f
code cleaning and modified test command to new make_mat
brunostega Nov 29, 2024
8ac6e8f
code cleaning
brunostega Nov 29, 2024
f87eda6
fixed README and formatting
brunostega Dec 3, 2024
c1f9580
last formating and cleaning
brunostega Dec 3, 2024
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5 changes: 2 additions & 3 deletions test/run_make_mat.sh
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Expand Up @@ -4,12 +4,11 @@ set -e
set -o pipefail

tar -zxf test_inputs/make_mat_ttr/hh.tgz -C test_inputs/make_mat_ttr/
python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat_ttr/hh.tgz --target_top test_inputs/make_mat_ttr/topol_md.top --mego_top test_inputs/make_mat_ttr/topol_ref.top --cutoff 0.75 --inter --out test_inputs/make_mat_ttr/ --tar
python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat_ttr/histo --target_top test_inputs/make_mat_ttr/topol_md.top --mego_top test_inputs/make_mat_ttr/topol_ref.top --cutoff 0.75 --out test_inputs/make_mat_ttr/
python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat_ttr/hh.tgz --target_top test_inputs/make_mat_ttr/topol_md.top --mego_top test_inputs/make_mat_ttr/topol_ref.top --cutoff 0.75 --mode intra+same --out test_inputs/make_mat_ttr/ --tar
diff <(gzip -dc test_inputs/make_mat_ttr/intramat_1_1.ndx.gz) <(gzip -dc test_outputs/make_mat_ttr/intramat_1_1.ndx.gz)
diff <(gzip -dc test_inputs/make_mat_ttr/intermat_1_1.ndx.gz) <(gzip -dc test_outputs/make_mat_ttr/intermat_1_1.ndx.gz)

tar -zxf test_inputs/make_mat_popc/hh.tgz -C test_inputs/make_mat_popc/
python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat_popc/histo --target_top test_inputs/make_mat_popc/topol_md.top --mego_top test_inputs/make_mat_popc/topol_ref.top --cutoff 0.75 --out test_inputs/make_mat_popc/
python ../tools/make_mat/make_mat.py --histo test_inputs/make_mat_popc/histo --target_top test_inputs/make_mat_popc/topol_md.top --mego_top test_inputs/make_mat_popc/topol_ref.top --cutoff 0.75 --mode intra --out test_inputs/make_mat_popc/
diff <(gzip -dc test_inputs/make_mat_popc/intramat_1_1.ndx.gz) <(gzip -dc test_outputs/make_mat_popc/intramat_1_1.ndx.gz)

6 changes: 4 additions & 2 deletions tools/make_mat/README.md
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Expand Up @@ -17,17 +17,19 @@ Parameters:

`--mego_top`: Path to the standard multi-eGO topology of the system generated by pdb2gmx.

`--inter`: Flag to indicate that the calculation is adapted to intermolecular histograms. If not provided, intramolecular calculations are assumed.
`--mode`: modality of the histogram analysis. Can be intra,same or cross (intramolecular, itermolecular same and intermolecular cross) or any combination by "+", e.g --mode intra+cross, --mode same+cross. If not provided all of them will be calculated --mode intra+same+cross.

-`-out`: Optional parameter to set the output path. Default is the current directory.

`--out_name`: Optional parameter to set the output name of files. It will be added to the default one.
Example: intermat_<out_name>_mi_mj.ndx or intramat_<out_name>_mi_mj.ndx

`--proc`: Optional parameter to set the number of processes to perform the calculation. Default is 1.
`--num_threads`: Optional parameter to set the number of processes to perform the calculation. Default is 1.

`--cutoff`: The maximum cutoff used for the accumulation of the histograms.

`--zero`: Optional flag returning 0 distances and 0 probability matrices with the correct cutoff values and indeces.

## ndx2HDF5.py

This scripts convert a text or a text.gz matrix in HDF5 format, this is usefull for large system because it is much faster to process.
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