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Develop ITP reader and writer methods (and corresponding tests) for other forcefields #52

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Merged
lunamorrow merged 14 commits into from
Feb 7, 2025
Merged

Develop ITP reader and writer methods (and corresponding tests) for other forcefields #52

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8ac8d8a
ITP reader for OPLS forcefield files developed and base tested
lunamorrow Jan 28, 2025
3925fe5
Modify 'from_ITP()' reader to use a new 'format' optional argument - …
lunamorrow Jan 28, 2025
e5e7959
Specify that the Topology to_ITP() function should only include '[ mo…
lunamorrow Jan 28, 2025
8ef299d
ITP writer now supportive of OPLS forcefield format developed and bas…
lunamorrow Jan 28, 2025
663dd86
ITP reader and writer now both supportive of CHARMM forcefield format…
lunamorrow Jan 29, 2025
df78a93
ITP reader and writer now supportive of AMBER forcefield format. Adde…
lunamorrow Feb 3, 2025
330f4f3
Large commit message below:
lunamorrow Feb 5, 2025
f165266
Update paper_worked_example.ipynb output files - no observable/major …
lunamorrow Feb 5, 2025
0f0eb2f
Add polymer extension test for polymer constructed from OPLS itp file…
lunamorrow Feb 5, 2025
215fce0
Merge branch 'main' of https://github.com/OMaraLab/polyconstruct into…
lunamorrow Feb 5, 2025
6b55f59
Merge branch 'main' of https://github.com/OMaraLab/polyconstruct into…
lunamorrow Feb 6, 2025
81e808f
Add polymer extension test for polymer constructed from AMBER itp fil…
lunamorrow Feb 6, 2025
c0db921
Update docstring in Polytop.Polymer.extend() to inform users that the…
lunamorrow Feb 6, 2025
142ea10
Add polymer extension test for polymer constructed from CHARMM itp fi…
lunamorrow Feb 7, 2025
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1,252 changes: 626 additions & 626 deletions data_paper_examples/ethylamine_dendrimer.itp
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2 changes: 1 addition & 1 deletion data_paper_examples/ethylamine_dendrimer.json
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342 changes: 171 additions & 171 deletions data_paper_examples/four_arm_star_overlapped_monomers.itp
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2 changes: 1 addition & 1 deletion data_paper_examples/four_arm_star_overlapped_monomers.json
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108 changes: 54 additions & 54 deletions data_paper_examples/pei_linear_polymer.itp
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Original file line number Diff line number Diff line change
Expand Up @@ -212,8 +212,8 @@ LHCU 3
[ bonds ]
1 2 2 0.1530 7.1500e+06
2 3 2 0.1470 8.7100e+06
3 5 2 0.1470 8.7100e+06
3 4 2 0.1020 1.7782e+07
3 5 2 0.1470 8.7100e+06
5 6 2 0.1530 7.1500e+06
6 7 2 0.1470 8.7100e+06
7 9 2 0.1500 8.7100e+06
Expand All @@ -223,11 +223,11 @@ LHCU 3
10 11 2 0.1020 1.7782e+07
12 13 2 0.1530 7.1500e+06
13 14 2 0.1470 8.7100e+06
14 16 2 0.1500 8.7100e+06
14 15 2 0.1020 1.7782e+07
14 16 2 0.1500 7.1500e+06
16 17 2 0.1470 8.7100e+06
17 18 2 0.1020 1.7782e+07
17 19 2 0.1470 8.7100e+06
17 18 2 0.1020 1.7782e+07
19 20 2 0.1530 7.1500e+06
20 21 2 0.1470 8.7100e+06
21 22 2 0.1020 1.7782e+07
Expand All @@ -237,11 +237,11 @@ LHCU 3
24 26 2 0.1470 8.7100e+06
26 27 2 0.1530 7.1500e+06
27 28 2 0.1470 8.7100e+06
28 30 2 0.1500 8.7100e+06
28 29 2 0.1020 1.7782e+07
28 30 2 0.1500 8.7100e+06
30 31 2 0.1470 8.7100e+06
31 33 2 0.1470 8.7100e+06
31 32 2 0.1020 1.7782e+07
31 33 2 0.1470 8.7100e+06
33 34 2 0.1530 7.1500e+06
34 35 2 0.1470 8.7100e+06
35 37 2 0.1500 8.7100e+06
Expand All @@ -251,11 +251,11 @@ LHCU 3
38 40 2 0.1470 8.7100e+06
40 41 2 0.1530 7.1500e+06
41 42 2 0.1470 8.7100e+06
42 44 2 0.1500 8.7100e+06
42 43 2 0.1020 1.7782e+07
42 44 2 0.1500 8.7100e+06
44 45 2 0.1470 8.7100e+06
45 47 2 0.1470 8.7100e+06
45 46 2 0.1020 1.7782e+07
45 47 2 0.1470 8.7100e+06
47 48 2 0.1530 7.1500e+06
48 49 2 0.1470 8.7100e+06
49 51 2 0.1500 8.7100e+06
Expand All @@ -265,11 +265,11 @@ LHCU 3
52 54 2 0.1470 8.7100e+06
54 55 2 0.1530 7.1500e+06
55 56 2 0.1470 8.7100e+06
56 57 2 0.1020 1.7782e+07
56 58 2 0.1500 8.7100e+06
56 57 2 0.1020 1.7782e+07
58 59 2 0.1470 8.7100e+06
59 61 2 0.1470 8.7100e+06
59 60 2 0.1020 1.7782e+07
59 61 2 0.1470 8.7100e+06
61 62 2 0.1530 7.1500e+06
62 63 2 0.1470 8.7100e+06
63 65 2 0.1500 8.7100e+06
Expand All @@ -287,74 +287,74 @@ LHCU 3
75 76 2 0.1530 7.1500e+06
76 77 2 0.1470 8.7100e+06
77 78 2 0.1020 1.7782e+07
77 79 2 0.1500 7.1500e+06
77 79 2 0.1500 8.7100e+06
79 80 2 0.1470 8.7100e+06
80 81 2 0.1020 1.7782e+07
80 82 2 0.1470 8.7100e+06
82 83 2 0.1530 7.1500e+06
83 84 2 0.1470 8.7100e+06
84 86 2 0.1500 7.1500e+06
84 86 2 0.1500 8.7100e+06
84 85 2 0.1020 1.7782e+07
86 87 2 0.1470 8.7100e+06
87 89 2 0.1470 8.7100e+06
87 88 2 0.1020 1.7782e+07
89 90 2 0.1530 7.1500e+06
90 91 2 0.1470 8.7100e+06
91 93 2 0.1500 7.1500e+06
91 92 2 0.1020 1.7782e+07
91 93 2 0.1500 8.7100e+06
93 94 2 0.1470 8.7100e+06
94 96 2 0.1470 8.7100e+06
94 95 2 0.1020 1.7782e+07
94 96 2 0.1470 8.7100e+06
96 97 2 0.1530 7.1500e+06
97 98 2 0.1470 8.7100e+06
98 100 2 0.1500 7.1500e+06
98 99 2 0.1020 1.7782e+07
98 100 2 0.1500 8.7100e+06
100 101 2 0.1470 8.7100e+06
101 103 2 0.1470 8.7100e+06
101 102 2 0.1020 1.7782e+07
103 104 2 0.1530 7.1500e+06
104 105 2 0.1470 8.7100e+06
105 106 2 0.1020 1.7782e+07
105 107 2 0.1500 7.1500e+06
105 107 2 0.1500 8.7100e+06
107 108 2 0.1470 8.7100e+06
108 110 2 0.1470 8.7100e+06
108 109 2 0.1020 1.7782e+07
110 111 2 0.1530 7.1500e+06
111 112 2 0.1470 8.7100e+06
112 113 2 0.1020 1.7782e+07
112 114 2 0.1500 8.7100e+06
112 113 2 0.1020 1.7782e+07
114 115 2 0.1470 8.7100e+06
115 116 2 0.1020 1.7782e+07
115 117 2 0.1470 8.7100e+06
115 116 2 0.1020 1.7782e+07
117 118 2 0.1530 7.1500e+06
118 119 2 0.1470 8.7100e+06
119 120 2 0.1020 1.7782e+07
119 121 2 0.1500 7.1500e+06
119 121 2 0.1500 8.7100e+06
121 122 2 0.1470 8.7100e+06
122 124 2 0.1470 8.7100e+06
122 123 2 0.1020 1.7782e+07
122 124 2 0.1470 8.7100e+06
124 125 2 0.1530 7.1500e+06
125 126 2 0.1470 8.7100e+06
126 128 2 0.1500 7.1500e+06
126 128 2 0.1500 8.7100e+06
126 127 2 0.1020 1.7782e+07
128 129 2 0.1470 8.7100e+06
129 130 2 0.1020 1.7782e+07
129 131 2 0.1470 8.7100e+06
131 132 2 0.1530 7.1500e+06
132 133 2 0.1470 8.7100e+06
133 135 2 0.1500 7.1500e+06
133 135 2 0.1500 8.7100e+06
133 134 2 0.1020 1.7782e+07
135 136 2 0.1470 8.7100e+06
136 137 2 0.1020 1.7782e+07
136 138 2 0.1470 8.7100e+06
136 137 2 0.1020 1.7782e+07
138 139 2 0.1530 7.1500e+06
139 140 2 0.1470 8.7100e+06
140 141 2 0.1020 1.7782e+07
140 142 2 0.1470 8.7100e+06
140 141 2 0.1020 1.7782e+07

[ pairs ]
1 5 1
1 4 1
1 5 1
2 6 1
3 7 1
4 6 1
Expand Down Expand Up @@ -439,49 +439,49 @@ LHCU 3

[ angles ]
1 2 3 2 111.0000 5.3000e+02
2 3 4 2 109.5000 4.2500e+02
2 3 5 2 116.0000 6.2000e+02
2 3 4 2 109.5000 4.2500e+02
4 3 5 2 109.5000 4.2500e+02
3 5 6 2 111.0000 5.3000e+02
5 6 7 2 111.0000 5.3000e+02
6 7 8 2 109.5000 4.2500e+02
6 7 9 2 116.0000 6.2000e+02
7 9 10 2 111.0000 5.3000e+02
8 7 9 2 109.5000 4.2500e+02
9 10 12 2 116.0000 6.2000e+02
9 10 11 2 109.5000 4.2500e+02
9 10 12 2 116.0000 6.2000e+02
11 10 12 2 109.5000 4.2500e+02
10 12 13 2 111.0000 5.3000e+02
12 13 14 2 111.0000 5.3000e+02
13 14 16 2 116.0000 6.2000e+02
13 14 15 2 109.5000 4.2500e+02
15 14 16 2 109.5000 4.2500e+02
14 16 17 2 111.0000 5.3000e+02
16 17 19 2 116.0000 6.2000e+02
16 17 18 2 109.5000 4.2500e+02
18 17 19 2 109.5000 4.2500e+02
16 17 19 2 116.0000 6.2000e+02
17 19 20 2 111.0000 5.3000e+02
18 17 19 2 109.5000 4.2500e+02
19 20 21 2 111.0000 5.3000e+02
20 21 23 2 116.0000 6.2000e+02
20 21 22 2 109.5000 4.2500e+02
20 21 23 2 116.0000 6.2000e+02
22 21 23 2 109.5000 4.2500e+02
21 23 24 2 111.0000 5.3000e+02
23 24 26 2 116.0000 6.2000e+02
23 24 25 2 109.5000 4.2500e+02
23 24 26 2 116.0000 6.2000e+02
25 24 26 2 109.5000 4.2500e+02
24 26 27 2 111.0000 5.3000e+02
26 27 28 2 111.0000 5.3000e+02
27 28 30 2 116.0000 6.2000e+02
27 28 29 2 109.5000 4.2500e+02
28 30 31 2 111.0000 5.3000e+02
29 28 30 2 109.5000 4.2500e+02
30 31 33 2 116.0000 6.2000e+02
28 30 31 2 111.0000 5.3000e+02
30 31 32 2 109.5000 4.2500e+02
30 31 33 2 116.0000 6.2000e+02
32 31 33 2 109.5000 4.2500e+02
31 33 34 2 111.0000 5.3000e+02
33 34 35 2 111.0000 5.3000e+02
34 35 36 2 109.5000 4.2500e+02
34 35 37 2 116.0000 6.2000e+02
34 35 36 2 109.5000 4.2500e+02
36 35 37 2 109.5000 4.2500e+02
35 37 38 2 111.0000 5.3000e+02
37 38 39 2 109.5000 4.2500e+02
Expand All @@ -493,35 +493,35 @@ LHCU 3
41 42 43 2 109.5000 4.2500e+02
43 42 44 2 109.5000 4.2500e+02
42 44 45 2 111.0000 5.3000e+02
44 45 46 2 109.5000 4.2500e+02
44 45 47 2 116.0000 6.2000e+02
45 47 48 2 111.0000 5.3000e+02
44 45 46 2 109.5000 4.2500e+02
46 45 47 2 109.5000 4.2500e+02
45 47 48 2 111.0000 5.3000e+02
47 48 49 2 111.0000 5.3000e+02
48 49 50 2 109.5000 4.2500e+02
48 49 51 2 116.0000 6.2000e+02
50 49 51 2 109.5000 4.2500e+02
48 49 50 2 109.5000 4.2500e+02
49 51 52 2 111.0000 5.3000e+02
50 49 51 2 109.5000 4.2500e+02
51 52 53 2 109.5000 4.2500e+02
51 52 54 2 116.0000 6.2000e+02
53 52 54 2 109.5000 4.2500e+02
52 54 55 2 111.0000 5.3000e+02
54 55 56 2 111.0000 5.3000e+02
55 56 57 2 109.5000 4.2500e+02
55 56 58 2 116.0000 6.2000e+02
57 56 58 2 109.5000 4.2500e+02
56 58 59 2 111.0000 5.3000e+02
57 56 58 2 109.5000 4.2500e+02
58 59 61 2 116.0000 6.2000e+02
58 59 60 2 109.5000 4.2500e+02
59 61 62 2 111.0000 5.3000e+02
60 59 61 2 109.5000 4.2500e+02
59 61 62 2 111.0000 5.3000e+02
61 62 63 2 111.0000 5.3000e+02
62 63 64 2 109.5000 4.2500e+02
62 63 65 2 116.0000 6.2000e+02
62 63 64 2 109.5000 4.2500e+02
64 63 65 2 109.5000 4.2500e+02
63 65 66 2 111.0000 5.3000e+02
65 66 68 2 116.0000 6.2000e+02
65 66 67 2 109.5000 4.2500e+02
65 66 68 2 116.0000 6.2000e+02
67 66 68 2 109.5000 4.2500e+02
66 68 69 2 111.0000 5.3000e+02
68 69 70 2 111.0000 5.3000e+02
Expand All @@ -543,28 +543,28 @@ LHCU 3
81 80 82 2 109.5000 4.2500e+02
80 82 83 2 111.0000 5.3000e+02
82 83 84 2 111.0000 5.3000e+02
83 84 86 2 116.0000 6.2000e+02
83 84 85 2 109.5000 4.2500e+02
84 86 87 2 111.0000 5.3000e+02
83 84 86 2 116.0000 6.2000e+02
85 84 86 2 109.5000 4.2500e+02
86 87 89 2 116.0000 6.2000e+02
84 86 87 2 111.0000 5.3000e+02
86 87 88 2 109.5000 4.2500e+02
86 87 89 2 116.0000 6.2000e+02
88 87 89 2 109.5000 4.2500e+02
87 89 90 2 111.0000 5.3000e+02
89 90 91 2 111.0000 5.3000e+02
90 91 92 2 109.5000 4.2500e+02
90 91 93 2 116.0000 6.2000e+02
91 93 94 2 111.0000 5.3000e+02
92 91 93 2 109.5000 4.2500e+02
93 94 95 2 109.5000 4.2500e+02
91 93 94 2 111.0000 5.3000e+02
93 94 96 2 116.0000 6.2000e+02
94 96 97 2 111.0000 5.3000e+02
93 94 95 2 109.5000 4.2500e+02
95 94 96 2 109.5000 4.2500e+02
94 96 97 2 111.0000 5.3000e+02
96 97 98 2 111.0000 5.3000e+02
97 98 99 2 109.5000 4.2500e+02
97 98 100 2 116.0000 6.2000e+02
98 100 101 2 111.0000 5.3000e+02
99 98 100 2 109.5000 4.2500e+02
98 100 101 2 111.0000 5.3000e+02
100 101 102 2 109.5000 4.2500e+02
100 101 103 2 116.0000 6.2000e+02
102 101 103 2 109.5000 4.2500e+02
Expand All @@ -574,13 +574,13 @@ LHCU 3
104 105 107 2 116.0000 6.2000e+02
106 105 107 2 109.5000 4.2500e+02
105 107 108 2 111.0000 5.3000e+02
107 108 109 2 109.5000 4.2500e+02
107 108 110 2 116.0000 6.2000e+02
107 108 109 2 109.5000 4.2500e+02
109 108 110 2 109.5000 4.2500e+02
108 110 111 2 111.0000 5.3000e+02
110 111 112 2 111.0000 5.3000e+02
111 112 114 2 116.0000 6.2000e+02
111 112 113 2 109.5000 4.2500e+02
111 112 114 2 116.0000 6.2000e+02
113 112 114 2 109.5000 4.2500e+02
112 114 115 2 111.0000 5.3000e+02
114 115 116 2 109.5000 4.2500e+02
Expand All @@ -592,13 +592,13 @@ LHCU 3
118 119 121 2 116.0000 6.2000e+02
120 119 121 2 109.5000 4.2500e+02
119 121 122 2 111.0000 5.3000e+02
121 122 124 2 116.0000 6.2000e+02
121 122 123 2 109.5000 4.2500e+02
122 124 125 2 111.0000 5.3000e+02
121 122 124 2 116.0000 6.2000e+02
123 122 124 2 109.5000 4.2500e+02
122 124 125 2 111.0000 5.3000e+02
124 125 126 2 111.0000 5.3000e+02
125 126 127 2 109.5000 4.2500e+02
125 126 128 2 116.0000 6.2000e+02
125 126 127 2 109.5000 4.2500e+02
126 128 129 2 111.0000 5.3000e+02
127 126 128 2 109.5000 4.2500e+02
128 129 131 2 116.0000 6.2000e+02
Expand All @@ -610,8 +610,8 @@ LHCU 3
132 133 134 2 109.5000 4.2500e+02
133 135 136 2 111.0000 5.3000e+02
134 133 135 2 109.5000 4.2500e+02
135 136 138 2 116.0000 6.2000e+02
135 136 137 2 109.5000 4.2500e+02
135 136 138 2 116.0000 6.2000e+02
137 136 138 2 109.5000 4.2500e+02
136 138 139 2 111.0000 5.3000e+02
138 139 140 2 111.0000 5.3000e+02
Expand Down
2 changes: 1 addition & 1 deletion data_paper_examples/pei_linear_polymer.json
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