From 25d70508bc4ca4e80e969060ba446efd3d18a1a3 Mon Sep 17 00:00:00 2001 From: ricalessandri Date: Sun, 27 Aug 2023 13:10:17 -0500 Subject: [PATCH] Add test for ibi_GBNO2/PTMA --- .../ibi_GBNO2/PTMA/polyply/PTMA.itp | 338 ++++++++++++++++++ .../ibi_GBNO2/PTMA/polyply/command | 1 + polyply/tests/test_lib_files.py | 1 + 3 files changed, 340 insertions(+) create mode 100644 polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/PTMA.itp create mode 100644 polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/command diff --git a/polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/PTMA.itp b/polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/PTMA.itp new file mode 100644 index 00000000..dac3162a --- /dev/null +++ b/polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/PTMA.itp @@ -0,0 +1,338 @@ +; /Users/alessandri/miniconda3/envs/polyplyRA/bin/polyply gen_params -lib ibi_GBNO2 -seq PTMA:10 -o PTMA.itp -name PTMA + +; Please cite the following papers: +; Grunewald, F; Alessandri, R; Kroon, P C; Monticelli, L; Souza, P C; Marrink, S J; Nature Communications 2022; 10.1038/s41467-021-27627-4 +; Alessandri, R; de Pablo, J J; Macromolecules 2023; 10.1021/acs.macromol.3c00141 + +[ moleculetype ] +PTMA 2 + +[ atoms ] + 1 VNL 1 PTMA VNL 1 0.0 71.099 + 2 EST 1 PTMA EST 2 0.0 29.018 + 3 C1 1 PTMA C1 3 0.0 56.108 + 4 U 1 PTMA NN 4 0.0 0.0 + 5 U 1 PTMA OO 5 0.0 0.0 + 6 C1 1 PTMA C2 6 0.0 56.108 + 7 NO 1 PTMA NO 7 0.0 30.006 + 8 VNL 2 PTMA VNL 8 0.0 71.099 + 9 EST 2 PTMA EST 9 0.0 29.018 +10 C1 2 PTMA C1 10 0.0 56.108 +11 U 2 PTMA NN 11 0.0 0.0 +12 U 2 PTMA OO 12 0.0 0.0 +13 C1 2 PTMA C2 13 0.0 56.108 +14 NO 2 PTMA NO 14 0.0 30.006 +15 VNL 3 PTMA VNL 15 0.0 71.099 +16 EST 3 PTMA EST 16 0.0 29.018 +17 C1 3 PTMA C1 17 0.0 56.108 +18 U 3 PTMA NN 18 0.0 0.0 +19 U 3 PTMA OO 19 0.0 0.0 +20 C1 3 PTMA C2 20 0.0 56.108 +21 NO 3 PTMA NO 21 0.0 30.006 +22 VNL 4 PTMA VNL 22 0.0 71.099 +23 EST 4 PTMA EST 23 0.0 29.018 +24 C1 4 PTMA C1 24 0.0 56.108 +25 U 4 PTMA NN 25 0.0 0.0 +26 U 4 PTMA OO 26 0.0 0.0 +27 C1 4 PTMA C2 27 0.0 56.108 +28 NO 4 PTMA NO 28 0.0 30.006 +29 VNL 5 PTMA VNL 29 0.0 71.099 +30 EST 5 PTMA EST 30 0.0 29.018 +31 C1 5 PTMA C1 31 0.0 56.108 +32 U 5 PTMA NN 32 0.0 0.0 +33 U 5 PTMA OO 33 0.0 0.0 +34 C1 5 PTMA C2 34 0.0 56.108 +35 NO 5 PTMA NO 35 0.0 30.006 +36 VNL 6 PTMA VNL 36 0.0 71.099 +37 EST 6 PTMA EST 37 0.0 29.018 +38 C1 6 PTMA C1 38 0.0 56.108 +39 U 6 PTMA NN 39 0.0 0.0 +40 U 6 PTMA OO 40 0.0 0.0 +41 C1 6 PTMA C2 41 0.0 56.108 +42 NO 6 PTMA NO 42 0.0 30.006 +43 VNL 7 PTMA VNL 43 0.0 71.099 +44 EST 7 PTMA EST 44 0.0 29.018 +45 C1 7 PTMA C1 45 0.0 56.108 +46 U 7 PTMA NN 46 0.0 0.0 +47 U 7 PTMA OO 47 0.0 0.0 +48 C1 7 PTMA C2 48 0.0 56.108 +49 NO 7 PTMA NO 49 0.0 30.006 +50 VNL 8 PTMA VNL 50 0.0 71.099 +51 EST 8 PTMA EST 51 0.0 29.018 +52 C1 8 PTMA C1 52 0.0 56.108 +53 U 8 PTMA NN 53 0.0 0.0 +54 U 8 PTMA OO 54 0.0 0.0 +55 C1 8 PTMA C2 55 0.0 56.108 +56 NO 8 PTMA NO 56 0.0 30.006 +57 VNL 9 PTMA VNL 57 0.0 71.099 +58 EST 9 PTMA EST 58 0.0 29.018 +59 C1 9 PTMA C1 59 0.0 56.108 +60 U 9 PTMA NN 60 0.0 0.0 +61 U 9 PTMA OO 61 0.0 0.0 +62 C1 9 PTMA C2 62 0.0 56.108 +63 NO 9 PTMA NO 63 0.0 30.006 +64 VNL 10 PTMA VNL 64 0.0 71.099 +65 EST 10 PTMA EST 65 0.0 29.018 +66 C1 10 PTMA C1 66 0.0 56.108 +67 U 10 PTMA NN 67 0.0 0.0 +68 U 10 PTMA OO 68 0.0 0.0 +69 C1 10 PTMA C2 69 0.0 56.108 +70 NO 10 PTMA NO 70 0.0 30.006 + +[ bonds ] + 1 2 1 0.35337 12500 + 2 3 1 0.32325 32000 + 2 6 1 0.32369 32000 + 3 6 1 0.38838 32000 + 8 9 1 0.35337 12500 + 9 10 1 0.32325 32000 + 9 13 1 0.32369 32000 +10 13 1 0.38838 32000 +15 16 1 0.35337 12500 +16 17 1 0.32325 32000 +16 20 1 0.32369 32000 +17 20 1 0.38838 32000 +22 23 1 0.35337 12500 +23 24 1 0.32325 32000 +23 27 1 0.32369 32000 +24 27 1 0.38838 32000 +29 30 1 0.35337 12500 +30 31 1 0.32325 32000 +30 34 1 0.32369 32000 +31 34 1 0.38838 32000 +36 37 1 0.35337 12500 +37 38 1 0.32325 32000 +37 41 1 0.32369 32000 +38 41 1 0.38838 32000 +43 44 1 0.35337 12500 +44 45 1 0.32325 32000 +44 48 1 0.32369 32000 +45 48 1 0.38838 32000 +50 51 1 0.35337 12500 +51 52 1 0.32325 32000 +51 55 1 0.32369 32000 +52 55 1 0.38838 32000 +57 58 1 0.35337 12500 +58 59 1 0.32325 32000 +58 62 1 0.32369 32000 +59 62 1 0.38838 32000 +64 65 1 0.35337 12500 +65 66 1 0.32325 32000 +65 69 1 0.32369 32000 +66 69 1 0.38838 32000 + +; vinyl backbone + 1 8 1 0.305 12000 + 8 15 1 0.305 12000 +15 22 1 0.305 12000 +22 29 1 0.305 12000 +29 36 1 0.305 12000 +36 43 1 0.305 12000 +43 50 1 0.305 12000 +50 57 1 0.305 12000 +57 64 1 0.305 12000 + +#ifdef FLEXIBLE + 3 7 1 0.23794 1000000 + 6 7 1 0.23793 1000000 +10 14 1 0.23794 1000000 +13 14 1 0.23793 1000000 +17 21 1 0.23794 1000000 +20 21 1 0.23793 1000000 +24 28 1 0.23794 1000000 +27 28 1 0.23793 1000000 +31 35 1 0.23794 1000000 +34 35 1 0.23793 1000000 +38 42 1 0.23794 1000000 +41 42 1 0.23793 1000000 +45 49 1 0.23794 1000000 +48 49 1 0.23793 1000000 +52 56 1 0.23794 1000000 +55 56 1 0.23793 1000000 +59 63 1 0.23794 1000000 +62 63 1 0.23793 1000000 +66 70 1 0.23794 1000000 +69 70 1 0.23793 1000000 +#endif + +[ constraints ] +#ifndef FLEXIBLE + 3 7 1 0.23794 + 6 7 1 0.23793 +10 14 1 0.23794 +13 14 1 0.23793 +17 21 1 0.23794 +20 21 1 0.23793 +24 28 1 0.23794 +27 28 1 0.23793 +31 35 1 0.23794 +34 35 1 0.23793 +38 42 1 0.23794 +41 42 1 0.23793 +45 49 1 0.23794 +48 49 1 0.23793 +52 56 1 0.23794 +55 56 1 0.23793 +59 63 1 0.23794 +62 63 1 0.23793 +66 70 1 0.23794 +69 70 1 0.23793 +#endif + +[ angles ] + 1 2 3 2 130.000 90 + 1 2 6 2 130.000 75 + 8 9 10 2 130.000 90 + 8 9 13 2 130.000 75 +15 16 17 2 130.000 90 +15 16 20 2 130.000 75 +22 23 24 2 130.000 90 +22 23 27 2 130.000 75 +29 30 31 2 130.000 90 +29 30 34 2 130.000 75 +36 37 38 2 130.000 90 +36 37 41 2 130.000 75 +43 44 45 2 130.000 90 +43 44 48 2 130.000 75 +50 51 52 2 130.000 90 +50 51 55 2 130.000 75 +57 58 59 2 130.000 90 +57 58 62 2 130.000 75 +64 65 66 2 130.000 90 +64 65 69 2 130.000 75 + 2 1 8 2 90 20 + 9 8 15 2 90 20 +16 15 22 2 90 20 +23 22 29 2 90 20 +30 29 36 2 90 20 +37 36 43 2 90 20 +44 43 50 2 90 20 +51 50 57 2 90 20 +58 57 64 2 90 20 + +; vinyl backbone + 1 8 15 2 126 40 + 8 15 22 2 126 40 +15 22 29 2 126 40 +22 29 36 2 126 40 +29 36 43 2 126 40 +36 43 50 2 126 40 +43 50 57 2 126 40 +50 57 64 2 126 40 + +[ dihedrals ] + 1 3 6 7 2 165.98 50 + 2 3 6 7 2 179.20 80 + 3 7 5 6 2 170.723 50 + 8 10 13 14 2 165.98 50 + 9 10 13 14 2 179.20 80 +10 14 12 13 2 170.723 50 +15 17 20 21 2 165.98 50 +16 17 20 21 2 179.20 80 +17 21 19 20 2 170.723 50 +22 24 27 28 2 165.98 50 +23 24 27 28 2 179.20 80 +24 28 26 27 2 170.723 50 +29 31 34 35 2 165.98 50 +30 31 34 35 2 179.20 80 +31 35 33 34 2 170.723 50 +36 38 41 42 2 165.98 50 +37 38 41 42 2 179.20 80 +38 42 40 41 2 170.723 50 +43 45 48 49 2 165.98 50 +44 45 48 49 2 179.20 80 +45 49 47 48 2 170.723 50 +50 52 55 56 2 165.98 50 +51 52 55 56 2 179.20 80 +52 56 54 55 2 170.723 50 +57 59 62 63 2 165.98 50 +58 59 62 63 2 179.20 80 +59 63 61 62 2 170.723 50 +64 66 69 70 2 165.98 50 +65 66 69 70 2 179.20 80 +66 70 68 69 2 170.723 50 + +[ virtual_sites3 ] + 4 3 2 7 2 0.834 0.210 + 5 3 2 7 2 1.180 0.276 +11 10 9 14 2 0.834 0.210 +12 10 9 14 2 1.180 0.276 +18 17 16 21 2 0.834 0.210 +19 17 16 21 2 1.180 0.276 +25 24 23 28 2 0.834 0.210 +26 24 23 28 2 1.180 0.276 +32 31 30 35 2 0.834 0.210 +33 31 30 35 2 1.180 0.276 +39 38 37 42 2 0.834 0.210 +40 38 37 42 2 1.180 0.276 +46 45 44 49 2 0.834 0.210 +47 45 44 49 2 1.180 0.276 +53 52 51 56 2 0.834 0.210 +54 52 51 56 2 1.180 0.276 +60 59 58 63 2 0.834 0.210 +61 59 58 63 2 1.180 0.276 +67 66 65 70 2 0.834 0.210 +68 66 65 70 2 1.180 0.276 + +[ exclusions ] + 1 2 3 4 5 6 7 + 2 3 4 5 6 7 + 3 4 5 6 7 + 4 5 6 7 + 5 6 7 + 6 7 + 8 9 10 11 12 13 14 + 9 10 11 12 13 14 +10 11 12 13 14 +11 12 13 14 +12 13 14 +13 14 +15 16 17 18 19 20 21 +16 17 18 19 20 21 +17 18 19 20 21 +18 19 20 21 +19 20 21 +20 21 +22 23 24 25 26 27 28 +23 24 25 26 27 28 +24 25 26 27 28 +25 26 27 28 +26 27 28 +27 28 +29 30 31 32 33 34 35 +30 31 32 33 34 35 +31 32 33 34 35 +32 33 34 35 +33 34 35 +34 35 +36 37 38 39 40 41 42 +37 38 39 40 41 42 +38 39 40 41 42 +39 40 41 42 +40 41 42 +41 42 +43 44 45 46 47 48 49 +44 45 46 47 48 49 +45 46 47 48 49 +46 47 48 49 +47 48 49 +48 49 +50 51 52 53 54 55 56 +51 52 53 54 55 56 +52 53 54 55 56 +53 54 55 56 +54 55 56 +55 56 +57 58 59 60 61 62 63 +58 59 60 61 62 63 +59 60 61 62 63 +60 61 62 63 +61 62 63 +62 63 +64 65 66 67 68 69 70 +65 66 67 68 69 70 +66 67 68 69 70 +67 68 69 70 +68 69 70 +69 70 + diff --git a/polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/command b/polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/command new file mode 100644 index 00000000..1d930ddd --- /dev/null +++ b/polyply/tests/test_data/library_tests/ibi_GBNO2/PTMA/polyply/command @@ -0,0 +1 @@ +polyply gen_params -lib ibi_GBNO2 -seq PTMA:10 -o PTMA.itp -name PTMA diff --git a/polyply/tests/test_lib_files.py b/polyply/tests/test_lib_files.py index 98d748eb..f9209424 100644 --- a/polyply/tests/test_lib_files.py +++ b/polyply/tests/test_lib_files.py @@ -188,6 +188,7 @@ def _interaction_equal(interaction1, interaction2, inter_type): ['martini3', 'P3HT'], ['martini3', 'PPE'], ['martini3', 'PTMA'], + ['ibi_GBNO2','PTMA'], ['martini2', 'PEO'], ['martini2', 'PS'], ['martini2', 'PEL'],