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recombinatrix merged 2 commits into from
Feb 24, 2025
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Adjustments #86

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43cc0e9
upload simulation data, final documentation update
recombinatrix Feb 24, 2025
2803e4d
remove videos
recombinatrix Feb 24, 2025
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6 changes: 3 additions & 3 deletions .github/CODEOWNERS
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* @lunamorrow @khiron @recombinatrix @RangikaM

/polyconf/ @lunamorrow @recombinatrix
/polytop/ @lunamorrow @khiron
/polybuild/ @lunamorrow @RangikaM
/polytop/ @lunamorrow @khiron @recombinatrix
/polybuild/ @lunamorrow @RangikaM @recombinatrix

# information on how to adjust the code owners can be found here:
# https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
10 changes: 5 additions & 5 deletions README.md
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*PolyConstruct* contains three python tools for generating polymer coordinate and topolgy files for molecular dynamics simulations.

*PolyConf* is a tool for generating ensembles of polymer conformations by combining monomer coordinate files.
* *PolyConf* is a tool for generating ensembles of polymer conformations by combining monomer coordinate files.

*PolyBuild* is a tool for generating polymer topology files for simulaton from polymer coordinate files, leveraging the functionality of the gromacs tool pdb2gmx.
* *PolyBuild* is a tool for generating polymer topology files for simulaton from polymer coordinate files, leveraging the functionality of the gromacs tool pdb2gmx.

*PolyTop* is a tool for generating polymer topology files from monomer topology files.
* *PolyTop* is a tool for generating polymer topology files from monomer topology files.

*PolyConstruct* was published in the paper *PolyConstruct: adapting biomolecular simulation pipelines for polymers with PolyBuild, PolyConf and PolyTop*.

## Getting started

Detailed documentation is available at the [PolyConstruct ReadTheDocs](https://polyconstruct.readthedocs.io/en/latest/index.html). This includes installation instructions, tutorials and worked examples, and api documentation for all polyconstruct methods.
Detailed documentation is available at the [PolyConstruct ReadTheDocs](https://polyconstruct.readthedocs.io/en/latest/index.html). This includes installation instructions, tutorials and worked examples, and api documentation for all *PolyConstruct* methods.

There are also detailed tutorials for PolyConf in the folder [polyconf_examples](https://github.com/OMaraLab/polyconstruct/tree/main/polyconf_examples), and detailed tutorials for PolyTop in the folder [polytop_examples](https://github.com/OMaraLab/polyconstruct/tree/main/polytop_examples)
There is a series of detailed tutorials for *PolyConf* in the folder [polyconf_examples](https://github.com/OMaraLab/polyconstruct/tree/main/polyconf_examples), and for *PolyTop* in the folder [polytop_examples](https://github.com/OMaraLab/polyconstruct/tree/main/polytop_examples). A set of example input and output files for *PolyBuild* are presented in the folder [polybuild_examples/RTP_entries](https://github.com/OMaraLab/polyconstruct/tree/main/polybuild_examples/RTP_entries)

## Quick and dirty installation

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6 changes: 3 additions & 3 deletions docs/CODEOWNERS
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* @lunamorrow @khiron @recombinatrix @RangikaM

/polyconf/ @lunamorrow @recombinatrix
/polytop/ @lunamorrow @khiron
/polybuild/ @lunamorrow @RangikaM
/polytop/ @lunamorrow @khiron @recombinatrix
/polybuild/ @lunamorrow @RangikaM @recombinatrix

# information on how to adjust the code owners can be found here:
# https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
8 changes: 4 additions & 4 deletions docs/source/conf.py
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# -- Project information -----------------------------------------------------

project = "polyconstruct"
project = "PolyConstruct"
copyright = (
"2024, Luna Morrow. "
"2024, Rangika Munaweera, Ada Quinn, Luna Morrow, Megan O'Mara. "
"A Python library for constructing polymer topologies and coordinates"
)
author = "Luna Morrow"
author = "Rangika Munaweera, Ada Quinn, Luna Morrow, Megan O'Mara"
add_module_names = False

# The short X.Y version
Expand Down Expand Up @@ -195,7 +195,7 @@
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, "polyconstruct", "PolyConstruct Documentation",
author, "polyconstruct", "A group of packages to construct polymer topologies and coordinates for molecular dynamics simulation with GROMACS",
author, "polyconstruct", "A python library to generate polymer topology and coordinate files for molecular dynamics simulation with GROMACS",
"Miscellaneous"),
]

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0 polybuild/RTP_entries/EBPB.rtp → polybuild_examples/RTP_entries/EBPB.rtp
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0 polybuild/RTP_entries/ELNR.rtp → polybuild_examples/RTP_entries/ELNR.rtp
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0 polybuild/RTP_entries/ELPR.rtp → polybuild_examples/RTP_entries/ELPR.rtp
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0 polybuild/RTP_entries/ELPS.rtp → polybuild_examples/RTP_entries/ELPS.rtp
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0 polybuild/RTP_entries/EPBP.rtp → polybuild_examples/RTP_entries/EPBP.rtp
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0 polybuild/RTP_entries/PEAD.rtp → polybuild_examples/RTP_entries/PEAD.rtp
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0 polybuild/RTP_entries/PEMD.rtp → polybuild_examples/RTP_entries/PEMD.rtp
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301 changes: 301 additions & 0 deletions polybuild_examples/RTP_entries/PNIPAM_monomer.itp
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@@ -0,0 +1,301 @@
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_800 1 UNK C00 1 -0.2389 12.0110
2 opls_801 1 UNK C01 1 -0.1779 12.0110
3 opls_802 1 UNK C02 1 -0.1660 12.0110
4 opls_803 1 UNK C03 1 -0.1329 12.0110
5 opls_804 1 UNK C04 1 -0.1639 12.0110
6 opls_805 1 UNK C05 1 -0.2400 12.0110
7 opls_806 1 UNK C06 1 0.6111 12.0110
8 opls_807 1 UNK O07 1 -0.4483 15.9990
9 opls_808 1 UNK N08 1 -1.1135 14.0070
10 opls_809 1 UNK C09 1 0.2101 12.0110
11 opls_810 1 UNK C0A 1 -0.2525 12.0110
12 opls_811 1 UNK C0B 1 -0.2621 12.0110
13 opls_812 1 UNK H0C 1 0.0828 1.0080
14 opls_813 1 UNK H0D 1 0.0828 1.0080
15 opls_814 1 UNK H0E 1 0.0828 1.0080
16 opls_815 1 UNK H0F 1 0.0871 1.0080
17 opls_816 1 UNK H0G 1 0.0871 1.0080
18 opls_817 1 UNK H0H 1 0.1074 1.0080
19 opls_818 1 UNK H0I 1 0.1074 1.0080
20 opls_819 1 UNK H0J 1 0.1054 1.0080
21 opls_820 1 UNK H0K 1 0.0888 1.0080
22 opls_821 1 UNK H0M 1 0.0888 1.0080
23 opls_822 1 UNK H0N 1 0.0886 1.0080
24 opls_823 1 UNK H0O 1 0.0886 1.0080
25 opls_824 1 UNK H0P 1 0.0886 1.0080
26 opls_825 1 UNK H0Q 1 0.5084 1.0080
27 opls_826 1 UNK H0R 1 0.1356 1.0080
28 opls_827 1 UNK H0S 1 0.0906 1.0080
29 opls_828 1 UNK H0T 1 0.0906 1.0080
30 opls_829 1 UNK H0U 1 0.0906 1.0080
31 opls_830 1 UNK H0V 1 0.0908 1.0080
32 opls_831 1 UNK H0W 1 0.0908 1.0080
33 opls_832 1 UNK H0X 2 0.0908 1.0080
[ bonds ]
2 1 1 0.1529 224262.400
3 2 1 0.1529 224262.400
4 3 1 0.1529 224262.400
5 4 1 0.1529 224262.400
6 5 1 0.1529 224262.400
7 4 1 0.1522 265265.600
8 7 1 0.1229 476976.000
9 7 1 0.1335 410032.000
10 9 1 0.1449 282001.600
11 10 1 0.1529 224262.400
12 10 1 0.1529 224262.400
13 1 1 0.1090 284512.000
14 1 1 0.1090 284512.000
15 1 1 0.1090 284512.000
16 2 1 0.1090 284512.000
17 2 1 0.1090 284512.000
18 3 1 0.1090 284512.000
19 3 1 0.1090 284512.000
20 4 1 0.1090 284512.000
21 5 1 0.1090 284512.000
22 5 1 0.1090 284512.000
23 6 1 0.1090 284512.000
24 6 1 0.1090 284512.000
25 6 1 0.1090 284512.000
26 9 1 0.1010 363171.200
27 10 1 0.1090 284512.000
28 11 1 0.1090 284512.000
29 11 1 0.1090 284512.000
30 11 1 0.1090 284512.000
31 12 1 0.1090 284512.000
32 12 1 0.1090 284512.000
33 12 1 0.1090 284512.000

[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1 112.700 488.273
2 3 4 1 112.700 488.273
3 4 5 1 112.700 488.273
4 5 6 1 112.700 488.273
3 4 7 1 111.100 527.184
4 7 8 1 120.400 669.440
4 7 9 1 116.600 585.760
7 9 10 1 121.900 418.400
9 10 11 1 109.700 669.440
9 10 12 1 109.700 669.440
2 1 13 1 110.700 313.800
2 1 14 1 110.700 313.800
2 1 15 1 110.700 313.800
1 2 16 1 110.700 313.800
1 2 17 1 110.700 313.800
2 3 18 1 110.700 313.800
2 3 19 1 110.700 313.800
3 4 20 1 110.700 313.800
4 5 21 1 110.700 313.800
4 5 22 1 110.700 313.800
5 6 23 1 110.700 313.800
5 6 24 1 110.700 313.800
5 6 25 1 110.700 313.800
7 9 26 1 119.800 292.880
9 10 27 1 109.500 292.880
10 11 28 1 110.700 313.800
10 11 29 1 110.700 313.800
10 11 30 1 110.700 313.800
10 12 31 1 110.700 313.800
10 12 32 1 110.700 313.800
10 12 33 1 110.700 313.800
11 10 12 1 112.700 488.273
11 10 27 1 110.700 313.800
31 12 33 1 107.800 276.144
13 1 14 1 107.800 276.144
5 4 7 1 111.100 527.184
31 12 32 1 107.800 276.144
6 5 22 1 110.700 313.800
21 5 22 1 107.800 276.144
3 2 17 1 110.700 313.800
12 10 27 1 110.700 313.800
28 11 29 1 107.800 276.144
4 3 19 1 110.700 313.800
29 11 30 1 107.800 276.144
8 7 9 1 122.900 669.440
7 4 20 1 109.500 292.880
28 11 30 1 107.800 276.144
32 12 33 1 107.800 276.144
3 2 16 1 110.700 313.800
18 3 19 1 107.800 276.144
4 3 18 1 110.700 313.800
16 2 17 1 107.800 276.144
14 1 15 1 107.800 276.144
23 6 24 1 107.800 276.144
6 5 21 1 110.700 313.800
5 4 20 1 110.700 313.800
10 9 26 1 118.400 317.984
24 6 25 1 107.800 276.144
23 6 25 1 107.800 276.144
13 1 15 1 107.800 276.144

[ dihedrals ]
; IMPROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1 c2 c3 c4 c5
26 9 7 10 4 180.000 10.460 2
9 7 4 8 4 180.000 43.932 2

[ dihedrals ]
; PROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1 c2 c3 c4 c5
7 4 5 6 3 -4.960 6.286 1.310 -2.636 -0.000 0.000
7 4 3 2 3 -4.960 6.286 1.310 -2.636 -0.000 0.000
4 3 2 1 3 2.301 -1.464 0.837 -1.674 -0.000 0.000
5 4 3 2 3 2.301 -1.464 0.837 -1.674 -0.000 0.000
6 5 4 3 3 2.301 -1.464 0.837 -1.674 -0.000 0.000
11 10 9 7 3 1.933 0.000 -1.933 -0.000 -0.000 0.000
12 10 9 7 3 1.933 0.000 -1.933 -0.000 -0.000 0.000
10 9 7 4 3 30.288 -4.812 -25.476 -0.000 -0.000 0.000
10 9 7 8 3 25.476 0.000 -25.476 -0.000 -0.000 0.000
26 9 7 4 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
26 9 7 8 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
26 9 10 11 3 0.000 0.000 0.000 -0.000 -0.000 0.000
26 9 10 12 3 0.000 0.000 0.000 -0.000 -0.000 0.000
20 4 7 9 3 0.000 0.000 0.000 -0.000 -0.000 0.000
20 4 7 8 3 0.000 0.000 0.000 -0.000 -0.000 0.000
22 5 4 7 3 -0.209 -0.628 0.000 0.837 -0.000 0.000
19 3 4 7 3 -0.209 -0.628 0.000 0.837 -0.000 0.000
18 3 4 7 3 -0.209 -0.628 0.000 0.837 -0.000 0.000
21 5 4 7 3 -0.209 -0.628 0.000 0.837 -0.000 0.000
30 11 10 12 3 0.628 1.883 0.000 -2.510 -0.000 0.000
15 1 2 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000
29 11 10 12 3 0.628 1.883 0.000 -2.510 -0.000 0.000
22 5 4 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000
24 6 5 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000
32 12 10 11 3 0.628 1.883 0.000 -2.510 -0.000 0.000
14 1 2 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000
31 12 10 11 3 0.628 1.883 0.000 -2.510 -0.000 0.000
20 4 5 6 3 0.628 1.883 0.000 -2.510 -0.000 0.000
17 2 3 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000
19 3 4 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000
19 3 2 1 3 0.628 1.883 0.000 -2.510 -0.000 0.000
20 4 3 2 3 0.628 1.883 0.000 -2.510 -0.000 0.000
33 12 10 11 3 0.628 1.883 0.000 -2.510 -0.000 0.000
18 3 4 5 3 0.628 1.883 0.000 -2.510 -0.000 0.000
23 6 5 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000
18 3 2 1 3 0.628 1.883 0.000 -2.510 -0.000 0.000
13 1 2 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000
21 5 4 3 3 0.628 1.883 0.000 -2.510 -0.000 0.000
28 11 10 12 3 0.628 1.883 0.000 -2.510 -0.000 0.000
16 2 3 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000
25 6 5 4 3 0.628 1.883 0.000 -2.510 -0.000 0.000
29 11 10 27 3 0.628 1.883 0.000 -2.510 -0.000 0.000
25 6 5 21 3 0.628 1.883 0.000 -2.510 -0.000 0.000
18 3 2 17 3 0.628 1.883 0.000 -2.510 -0.000 0.000
19 3 2 16 3 0.628 1.883 0.000 -2.510 -0.000 0.000
20 4 3 19 3 0.628 1.883 0.000 -2.510 -0.000 0.000
18 3 2 16 3 0.628 1.883 0.000 -2.510 -0.000 0.000
33 12 10 27 3 0.628 1.883 0.000 -2.510 -0.000 0.000
31 12 10 27 3 0.628 1.883 0.000 -2.510 -0.000 0.000
16 2 1 15 3 0.628 1.883 0.000 -2.510 -0.000 0.000
17 2 1 14 3 0.628 1.883 0.000 -2.510 -0.000 0.000
16 2 1 14 3 0.628 1.883 0.000 -2.510 -0.000 0.000
17 2 1 13 3 0.628 1.883 0.000 -2.510 -0.000 0.000
25 6 5 22 3 0.628 1.883 0.000 -2.510 -0.000 0.000
24 6 5 21 3 0.628 1.883 0.000 -2.510 -0.000 0.000
28 11 10 27 3 0.628 1.883 0.000 -2.510 -0.000 0.000
23 6 5 22 3 0.628 1.883 0.000 -2.510 -0.000 0.000
30 11 10 27 3 0.628 1.883 0.000 -2.510 -0.000 0.000
21 5 4 20 3 0.628 1.883 0.000 -2.510 -0.000 0.000
19 3 2 17 3 0.628 1.883 0.000 -2.510 -0.000 0.000
20 4 3 18 3 0.628 1.883 0.000 -2.510 -0.000 0.000
23 6 5 21 3 0.628 1.883 0.000 -2.510 -0.000 0.000
22 5 4 20 3 0.628 1.883 0.000 -2.510 -0.000 0.000
24 6 5 22 3 0.628 1.883 0.000 -2.510 -0.000 0.000
17 2 1 15 3 0.628 1.883 0.000 -2.510 -0.000 0.000
16 2 1 13 3 0.628 1.883 0.000 -2.510 -0.000 0.000
32 12 10 27 3 0.628 1.883 0.000 -2.510 -0.000 0.000
33 12 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000
31 12 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000
28 11 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000
32 12 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000
29 11 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000
30 11 10 9 3 0.971 2.912 0.000 -3.883 -0.000 0.000
27 10 9 7 3 0.000 0.000 0.000 -0.000 -0.000 0.000
27 10 9 26 3 0.000 0.000 0.000 -0.000 -0.000 0.000
9 7 4 3 3 0.734 -9.985 -0.791 10.042 -0.000 0.000
9 7 4 5 3 0.734 -9.985 -0.791 10.042 -0.000 0.000
8 7 4 5 3 0.000 0.000 0.000 -0.000 -0.000 0.000
8 7 4 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000

[ pairs ]
1 4 1
2 5 1
3 6 1
2 7 1
3 8 1
3 9 1
6 7 1
5 8 1
5 9 1
4 10 1
3 13 1
3 14 1
8 10 1
7 11 1
3 15 1
7 12 1
1 18 1
4 16 1
1 19 1
4 17 1
2 20 1
5 18 1
5 19 1
3 21 1
7 18 1
3 22 1
7 19 1
6 20 1
4 23 1
8 20 1
7 21 1
4 24 1
13 16 1
9 20 1
7 22 1
4 25 1
14 16 1
13 17 1
4 26 1
15 16 1
14 17 1
15 17 1
16 18 1
8 26 1
7 27 1
17 18 1
16 19 1
17 19 1
11 26 1
9 28 1
18 20 1
12 26 1
9 29 1
19 20 1
9 30 1
12 28 1
9 31 1
20 21 1
12 29 1
9 32 1
20 22 1
12 30 1
11 31 1
9 33 1
11 32 1
21 23 1
11 33 1
22 23 1
21 24 1
22 24 1
21 25 1
22 25 1
26 27 1
27 28 1
27 29 1
27 30 1
27 31 1
27 32 1
27 33 1
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