From dd59f5293369b0bdf2fa344c5c724a590e1f34c7 Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:33:36 +1100 Subject: [PATCH 01/14] Update getting_started.rst Heavy sigh --- docs/source/getting_started.rst | 74 +++++++++++++-------------------- 1 file changed, 30 insertions(+), 44 deletions(-) diff --git a/docs/source/getting_started.rst b/docs/source/getting_started.rst index 07ffcf5..b722986 100644 --- a/docs/source/getting_started.rst +++ b/docs/source/getting_started.rst @@ -1,31 +1,29 @@ -PolyConstruct +Getting Started with PolyConstruct =============== This page details how to get started with *PolyConstruct*. The design, testing, and validation of *PolyConstruct* is detailed in the manuscript *"PolyConstruct: adapting biomolecular simulation pipelines for polymers with PolyBuild, PolyConf and PolyTop"*, by -***Rangika Munaweera**, **Ada Quinn**, Luna Morrow, Richard A Morris, Megan L O’Mara* +**Rangika Munaweera**, **Ada Quinn**, Luna Morrow, Richard A Morris, and Megan L O’Mara* -Getting Started -=============== **Installing PolyConstruct:** -From your home directory, clone *PolyConstruct* from GitHub: +From your home directory, clone PolyConstruct from Git: .. code-block:: python cd ~ git clone https://github.com/OMaraLab/polyconstruct.git -Then navigate to `~/PolyConstruct`: +Then navigate to polyconstruct: .. code-block:: python cd polyconstruct -To setup an environment for *PolyConstruct*, run: +To setup an environment for polyconstruct, run: .. code-block:: python @@ -34,7 +32,7 @@ To setup an environment for *PolyConstruct*, run: pip install -r requirements.txt -Then, build the *PolyTop*, *PolyConf* and *PolyBuild* packages: +Then, build the PolyTop, PolyConf and PolyBuild packages: .. code-block:: python @@ -86,8 +84,8 @@ Monomer design For both *PolyBuild* and *PolyTop*, monomer parameters should include all monomer atoms that will be present in the simulation model of the final polymer, and dummy atoms correesponding to connectivity with adjacent monomers. The method for preparing monomer .itp depends on the choice of force field, and a number of suitable automated tools -exist for small molecule parameterization such as the `Automated Topology Builder `_, -`antechamber `_, and `LigParGen `_. +exist for small molecule parameterization such as the `Automated Topology Builder `, +`antechamber `, and `LigParGen https://zarbi.chem.yale.edu/ligpargen/`. Monomer coordinates and parameters used as inputs should be designed to reflect the state of the monomer in the mature polymer chain, rather than the isolated monomer molecule prior to polymerization. For example, @@ -98,8 +96,9 @@ and not the ammonium and carboxylate groups found in the precursor amino acids. Monomer parameters should be designed in a manner consistent with the desired force field. We recommend you do not combine monomer parameters from different force field families in a single polymer. + For *PolyConf* These coordinate files should represent a sensible monomer geometry as could be found in the final -polymer. These might be created using tools like `ChimeraX `_, with theoretical ideal bond lengths and +polymer. These might be created using tools like ChimeraX, with theoretical ideal bond lengths and angles, by geometry optimization, or generated by automated parameterization tools. Additionally, it is often convenient if the monomer is in a conformation where atoms corresponding to adjacent monomers are as far as possible from other atoms, and pointed away from other attachment points. @@ -112,8 +111,7 @@ Worked Examples PolyConf creates polymer coordinate files through the tiling and manipulation of monomer pdb files. There are several detailed examples of the use of PolyConf to create ensembles of starting -conformations for a series of increasingly complex polymer architectures. These are contained in the -*PolyConf* repository in the folder `polyconstruct/polyconf_examples/` contained in the +conformations for a series of increasingly complex polymer architectures. These are contained in the PolyConf repository in the folder 'polyconstruct/polyconf_examples/' contained in the Here is one simple example, showing the construction of a linear polyethylenimine 128-mer. @@ -190,31 +188,18 @@ Here is one simple example, showing the construction of a linear polyethylenimin # end of example script +**PolyBuild** +Example input itp files and the resulting rtp database entries are presented in the folder `polybuild_examples/RTP_entries` -**PolyTop** +RTP entries +**PolyTop** -.. note:: - The import path provided in the examples below is *different* to the path - in the examples contained within 'polyconstruct/data_paper_examples/', as - the path used to locate modules from within the package structure is - different. You must use the structure in the examples below for the module - import to be correctly resolved. Simple example - construction of a linear homopolymer: -.. note:: - Note that when more than one type of junction exists within a PolyTop polymer, - it is important that each junction type is given a unique name. In the case where - there exist multiple junctions in either molecule sharing the same name, the specific - junctions chosen will be randomly distributed among junctions with the same name, - allowing for stochastic extension of polymers. For repeatability it is therefore - necessary to use a consistent seed value (in python), and use PolyTop as a python - library rather than from the command line. If an exact structure is desired instead, - simply ensure that each junction type has a unique name that does not allow for any - discrepancy in exactly which junctions are joined and where. .. code-block:: python @@ -252,6 +237,9 @@ Simple example - construction of a linear homopolymer: Visualize.polymer(polymer,infer_bond_order=False).draw2D('data_paper_examples/pei_linear_polymer.png',(400,300)) +.. note:: + Note that when more than one type of junction exists within a PolyTop polymer, + it is important that each junction type is given a unique name. Complex example - construction of a 4-arm PEG star polymer from single monomeric units: @@ -266,9 +254,9 @@ Complex example - construction of a 4-arm PEG star polymer from single monomeric from polytop.Topology import Topology # Load in monomer topologies from ITP files - ethanol = Topology.from_ITP("data_paper_examples/extended_ethanol.itp") # main arm monomer - methane = Topology.from_ITP("data_paper_examples/extended_methane.itp") # terminal monomer - neopentane = Topology.from_ITP("data_paper_examples/extended_neopentane.itp") # central monomer + ethanol = Topology.from_ITP("polytop_examples/data/extended_ethanol.itp") # main arm monomer + methane = Topology.from_ITP("polytop_examples/data/extended_methane.itp") # terminal monomer + neopentane = Topology.from_ITP("polytop_examples/data/extended_neopentane.itp") # central monomer # Create junctions for each monomer with the bonding atom and then the leaving # atom specified, in that order, with a unique name. Note how each junction @@ -331,18 +319,16 @@ Complex example - construction of a 4-arm PEG star polymer from single monomeric four_polymer.topology.title = "four arm star polymer" # renames the ITP header and image # save the polymer to a file and visualise the structure with RDKit for an easy visual structure check - four_polymer.save_to_file('data_paper_examples/four_arm_star_overlapped_monomers.json') # text dump - four_polymer.topology.to_ITP('data_paper_examples/four_arm_star_overlapped_monomers.itp') - Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('data_paper_examples/four_arm_star_overlapped_monomers.png',(400,300)) + four_polymer.save_to_file('polytop_examples/data/four_arm_star.json') # text dump + four_polymer.topology.to_ITP('polytop_examples/data/four_arm_star.itp') + Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('polytop_examples/data/four_arm_star.png',(800,600)) -All of the monomer ITP files used in the above two examples, and the resulting -polymer files, are also readily available at 'polyconstruct/data_paper_examples/'. +-------------------------------------------------------------------------------------- +Find the above and additional worked examples as executable Python scripts on the `PolyConstruct GitHub repository `_. --------------------------------------------------------------------------------------- +Examples for *PolyTop* are available at 'polyconstruct/polytop_examples/' + +Examples for *PolyConf* at 'polyconstruct/polyconf_examples/' -Find the above and additional worked examples as executable Python scripts or Jupyter -Notebooks on the `PolyConstruct GitHub repository `_. -Examples for PolyTop are available at 'polyconstruct/paper_worked_examples.ipynb' -and for PolyConf at 'polyconstruct/polyconf_examples/'; while instructions to -use the two PolyBuild scripts are included under the :ref:`PolyBuild` documentation. +Instructions to use *PolyBuild* are included under the :ref:`PolyBuild` documentation. From 3022afac125434750b8df2327072b4d9245e996b Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:35:12 +1100 Subject: [PATCH 02/14] Update .gitignore --- .gitignore | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.gitignore b/.gitignore index 842e969..82a96fc 100644 --- a/.gitignore +++ b/.gitignore @@ -146,3 +146,7 @@ polyconf_examples/PMMA_* polytop_examples/data/ethylamine_dendrimer.* polytop_examples/data/four_arm_star.* polytop_examples/data/pei_linear_polymer.* + +# OS X nonsense + +.DS_store From 6ddc92cba6955fb534fb551b10d8a43db64df92d Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:35:36 +1100 Subject: [PATCH 03/14] Delete .DS_Store --- .DS_Store | Bin 6148 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 .DS_Store diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index 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62, "atom_b": 56, "atom_c": 57, "atom_d": 58, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 66, "atom_b": 60, "atom_c": 61, "atom_d": 62, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 65, "atom_b": 66, "atom_c": 60, "atom_d": 61, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 70, "atom_b": 64, "atom_c": 65, "atom_d": 66, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 69, "atom_b": 70, "atom_c": 64, "atom_d": 65, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 73, "atom_b": 74, "atom_c": 68, "atom_d": 69, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 74, "atom_b": 68, "atom_c": 69, "atom_d": 70, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 79, "atom_b": 80, "atom_c": 72, "atom_d": 73, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 80, "atom_b": 72, "atom_c": 73, "atom_d": 74, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 86, "atom_b": 76, "atom_c": 78, "atom_d": 79, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 76, "atom_b": 78, "atom_c": 79, "atom_d": 80, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 81, "atom_b": 82, "atom_c": 83, "atom_d": 85, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 82, "atom_b": 83, "atom_c": 85, "atom_d": 86, "dihedral_type": 1, "phase_angle": 180.0, "force_constant": 1.0, "multiplicity": 6, "constants": []}, {"atom_a": 83, "atom_b": 85, "atom_c": 86, "atom_d": 76, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 3, "pair_type": 1}, {"atom_a": 2, "atom_b": 6, "pair_type": 1}, {"atom_a": 2, "atom_b": 5, "pair_type": 1}, {"atom_a": 10, "atom_b": 4, "pair_type": 1}, {"atom_a": 7, "atom_b": 9, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 15, "atom_b": 17, "pair_type": 1}, {"atom_a": 19, "atom_b": 21, "pair_type": 1}, {"atom_a": 23, "atom_b": 25, "pair_type": 1}, {"atom_a": 27, "atom_b": 29, "pair_type": 1}, {"atom_a": 31, "atom_b": 33, "pair_type": 1}, {"atom_a": 35, "atom_b": 37, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 43, "atom_b": 45, "pair_type": 1}, {"atom_a": 47, "atom_b": 49, "pair_type": 1}, {"atom_a": 51, "atom_b": 53, "pair_type": 1}, {"atom_a": 55, "atom_b": 57, "pair_type": 1}, {"atom_a": 59, "atom_b": 61, "pair_type": 1}, {"atom_a": 63, "atom_b": 65, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 71, "atom_b": 73, "pair_type": 1}, {"atom_a": 77, "atom_b": 79, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 82, "atom_b": 86, "pair_type": 1}, {"atom_a": 84, "atom_b": 86, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:05 on 2024-12-13 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : LHCU", "; Output : UNITED ATOM topology", ";\tUse in conjunction with the corresponding united atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1707355", "; ATB Topology Hash: f968d", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "LHCU", "nrexcl": 3}}, "junctions": [{"name": "to", "monomer_atom": "C5", "residue_atom": "N7"}, {"name": "from", "monomer_atom": "N71", "residue_atom": "C51"}]} \ No newline at end of file From 8d0fb2ee93d610704acbbad7857b4f537acfcd7e Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:39:27 +1100 Subject: [PATCH 07/14] Delete polytop_examples/data/pei_linear_polymer.itp --- polytop_examples/data/pei_linear_polymer.itp | 419 ------------------- 1 file changed, 419 deletions(-) delete mode 100644 polytop_examples/data/pei_linear_polymer.itp diff --git a/polytop_examples/data/pei_linear_polymer.itp b/polytop_examples/data/pei_linear_polymer.itp deleted file mode 100644 index 9e6bc1d..0000000 --- a/polytop_examples/data/pei_linear_polymer.itp +++ /dev/null @@ -1,419 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; pei polymer -; -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; None -; -; This file was generated at 14:05 on 2024-12-13 by -; -; Automatic Topology Builder -; -; REVISION 2024-11-20 12:06:25 -;--------------------------------------------------------------------------------------------------------------------------- -; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark -; -; Institute : Molecular Dynamics group, -; School of Chemistry and Molecular Biosciences (SCMB), -; The University of Queensland, QLD 4072, Australia -; URL : https://atb.uq.edu.au -; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. -; An Automated force field Topology Builder (ATB) and repository: version 1.0. -; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037. -; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE. -; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane. -; DOI:10.1021/acs.jctc.8b00768 -; -; Disclaimer : -; While every effort has been made to ensure the accuracy and validity of parameters provided below -; the assignment of parameters is being based on an automated procedure combining data provided by a -; given user as well as calculations performed using third party software. They are provided as a guide. -; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided -; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion -; and to perform additional validation tests for their specific application if required. Neither the authors -; of the ATB or The University of Queensland except any responsibly for how the parameters may be used. -; -; Release notes and warnings: -; (1) The topology is based on a set of atomic coordinates and other data provided by the user after -; after quantum mechanical optimization of the structure using different levels of theory depending on -; the nature of the molecule. -; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous. -; In these cases alternative type codes are provided at the end of the line. -; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral -; type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard" -; or "uncertain" in comments. -; (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder -; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually -; before the file can be used. -;--------------------------------------------------------------------------------------------------------------------------- -; Input Structure : LHCU -; Output : UNITED ATOM topology -; Use in conjunction with the corresponding united atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 1707355 -; ATB Topology Hash: f968d -;--------------------------------------------------------------------------------------------------------------------------- -; Final Topology Generation was performed using: -; A B3LYP/6-31G* optimized geometry. -; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set. -; Initial charges were estimated using the ESP method of Merz-Kollman. -; Final charges and charge groups were generated by method described in the ATB paper. -; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory. -;--------------------------------------------------------------------------------------------------------------------------- -; -; - -[ moleculetype ] -LHCU 3 -[ atoms ] - 1 NOpt 1 LHCU N71 1 -0.698385 14.0067 - 2 HS14 1 LHCU H72 2 0.291615 1.0080 - 3 CH2 1 LHCU C61 3 0.197615 14.0270 - 4 CH2 1 LHCU C5 4 0.212615 14.0270 - 5 NOpt 1 LHCU N7 5 -0.711385 14.0067 - 6 HS14 1 LHCU H21 6 0.305615 1.0080 - 7 CH3 1 LHCU C6 7 0.197615 15.0350 - 8 NOpt 2 LHCU N71 8 -0.698962 14.0067 - 9 HS14 2 LHCU H72 9 0.291038 1.0080 - 10 CH2 2 LHCU C61 10 0.197038 14.0270 - 11 CH2 2 LHCU C5 11 0.212038 14.0270 - 12 NOpt 3 LHCU N71 12 -0.699192 14.0067 - 13 HS14 3 LHCU H72 13 0.290808 1.0080 - 14 CH2 3 LHCU C61 14 0.196808 14.0270 - 15 CH2 3 LHCU C5 15 0.211808 14.0270 - 16 NOpt 4 LHCU N71 16 -0.699238 14.0067 - 17 HS14 4 LHCU H72 17 0.290762 1.0080 - 18 CH2 4 LHCU C61 18 0.196762 14.0270 - 19 CH2 4 LHCU C5 19 0.211762 14.0270 - 20 NOpt 5 LHCU N71 20 -0.699248 14.0067 - 21 HS14 5 LHCU H72 21 0.290752 1.0080 - 22 CH2 5 LHCU C61 22 0.196752 14.0270 - 23 CH2 5 LHCU C5 23 0.211752 14.0270 - 24 NOpt 6 LHCU N71 24 -0.699250 14.0067 - 25 HS14 6 LHCU H72 25 0.290750 1.0080 - 26 CH2 6 LHCU C61 26 0.196750 14.0270 - 27 CH2 6 LHCU C5 27 0.211750 14.0270 - 28 NOpt 7 LHCU N71 28 -0.699250 14.0067 - 29 HS14 7 LHCU H72 29 0.290750 1.0080 - 30 CH2 7 LHCU C61 30 0.196750 14.0270 - 31 CH2 7 LHCU C5 31 0.211750 14.0270 - 32 NOpt 8 LHCU N71 32 -0.699250 14.0067 - 33 HS14 8 LHCU H72 33 0.290750 1.0080 - 34 CH2 8 LHCU C61 34 0.196750 14.0270 - 35 CH2 8 LHCU C5 35 0.211750 14.0270 - 36 NOpt 9 LHCU N71 36 -0.699250 14.0067 - 37 HS14 9 LHCU H72 37 0.290750 1.0080 - 38 CH2 9 LHCU C61 38 0.196750 14.0270 - 39 CH2 9 LHCU C5 39 0.211750 14.0270 - 40 NOpt 10 LHCU N71 40 -0.699250 14.0067 - 41 HS14 10 LHCU H72 41 0.290750 1.0080 - 42 CH2 10 LHCU C61 42 0.196750 14.0270 - 43 CH2 10 LHCU C5 43 0.211750 14.0270 - 44 NOpt 11 LHCU N71 44 -0.699250 14.0067 - 45 HS14 11 LHCU H72 45 0.290750 1.0080 - 46 CH2 11 LHCU C61 46 0.196750 14.0270 - 47 CH2 11 LHCU C5 47 0.211750 14.0270 - 48 NOpt 12 LHCU N71 48 -0.699250 14.0067 - 49 HS14 12 LHCU H72 49 0.290750 1.0080 - 50 CH2 12 LHCU C61 50 0.196750 14.0270 - 51 CH2 12 LHCU C5 51 0.211750 14.0270 - 52 NOpt 13 LHCU N71 52 -0.699250 14.0067 - 53 HS14 13 LHCU H72 53 0.290750 1.0080 - 54 CH2 13 LHCU C61 54 0.196750 14.0270 - 55 CH2 13 LHCU C5 55 0.211750 14.0270 - 56 NOpt 14 LHCU N71 56 -0.699250 14.0067 - 57 HS14 14 LHCU H72 57 0.290750 1.0080 - 58 CH2 14 LHCU C61 58 0.196750 14.0270 - 59 CH2 14 LHCU C5 59 0.211750 14.0270 - 60 NOpt 15 LHCU N71 60 -0.699250 14.0067 - 61 HS14 15 LHCU H72 61 0.290750 1.0080 - 62 CH2 15 LHCU C61 62 0.196750 14.0270 - 63 CH2 15 LHCU C5 63 0.211750 14.0270 - 64 NOpt 16 LHCU N71 64 -0.699250 14.0067 - 65 HS14 16 LHCU H72 65 0.290750 1.0080 - 66 CH2 16 LHCU C61 66 0.196750 14.0270 - 67 CH2 16 LHCU C5 67 0.211750 14.0270 - 68 NOpt 17 LHCU N71 68 -0.699250 14.0067 - 69 HS14 17 LHCU H72 69 0.290750 1.0080 - 70 CH2 17 LHCU C61 70 0.196750 14.0270 - 71 CH2 17 LHCU C5 71 0.211750 14.0270 - 72 NOpt 18 LHCU N71 72 -0.699250 14.0067 - 73 HS14 18 LHCU H72 73 0.290750 1.0080 - 74 CH2 18 LHCU C61 74 0.196750 14.0270 - 75 CH2 18 LHCU C5 75 0.211750 14.0270 - 76 NOpt 19 LHCU N71 76 -0.699250 14.0067 - 77 HS14 19 LHCU H72 77 0.290750 1.0080 - 78 CH2 19 LHCU C61 78 0.196750 14.0270 - 79 CH2 19 LHCU C5 79 0.211750 14.0270 - 80 CH3 20 LHCU C62 80 0.000375 15.0350 - 81 CH2 20 LHCU C51 81 0.200375 14.0270 - 82 NOpt 20 LHCU N71 82 -0.698625 14.0067 - 83 HS14 20 LHCU H72 83 0.291375 1.0080 - 84 CH2 20 LHCU C61 84 0.197375 14.0270 - 85 CH2 20 LHCU C5 85 0.212375 14.0270 - -[ bonds ] - 1 2 2 0.1020 1.7782e+07 - 1 11 2 0.1470 8.7100e+06 - 1 3 2 0.1470 8.7100e+06 - 3 4 2 0.1530 7.1500e+06 - 4 5 2 0.1470 8.7100e+06 - 5 6 2 0.1020 1.7782e+07 - 5 7 2 0.1470 8.7100e+06 - 8 15 2 0.1470 8.7100e+06 - 8 9 2 0.1020 1.7782e+07 - 8 10 2 0.1470 8.7100e+06 - 10 11 2 0.1530 7.1500e+06 - 12 13 2 0.1020 1.7782e+07 - 12 19 2 0.1470 8.7100e+06 - 12 14 2 0.1470 8.7100e+06 - 14 15 2 0.1530 7.1500e+06 - 16 23 2 0.1470 8.7100e+06 - 16 17 2 0.1020 1.7782e+07 - 16 18 2 0.1470 8.7100e+06 - 18 19 2 0.1530 7.1500e+06 - 20 21 2 0.1020 1.7782e+07 - 20 22 2 0.1470 8.7100e+06 - 20 27 2 0.1470 8.7100e+06 - 22 23 2 0.1530 7.1500e+06 - 24 26 2 0.1470 8.7100e+06 - 24 25 2 0.1020 1.7782e+07 - 24 31 2 0.1470 8.7100e+06 - 26 27 2 0.1530 7.1500e+06 - 28 35 2 0.1470 8.7100e+06 - 28 30 2 0.1470 8.7100e+06 - 28 29 2 0.1020 1.7782e+07 - 30 31 2 0.1530 7.1500e+06 - 32 34 2 0.1470 8.7100e+06 - 32 39 2 0.1470 8.7100e+06 - 32 33 2 0.1020 1.7782e+07 - 34 35 2 0.1530 7.1500e+06 - 36 37 2 0.1020 1.7782e+07 - 36 43 2 0.1470 8.7100e+06 - 36 38 2 0.1470 8.7100e+06 - 38 39 2 0.1530 7.1500e+06 - 40 42 2 0.1470 8.7100e+06 - 40 41 2 0.1020 1.7782e+07 - 40 47 2 0.1470 8.7100e+06 - 42 43 2 0.1530 7.1500e+06 - 44 45 2 0.1020 1.7782e+07 - 44 51 2 0.1470 8.7100e+06 - 44 46 2 0.1470 8.7100e+06 - 46 47 2 0.1530 7.1500e+06 - 48 55 2 0.1470 8.7100e+06 - 48 50 2 0.1470 8.7100e+06 - 48 49 2 0.1020 1.7782e+07 - 50 51 2 0.1530 7.1500e+06 - 52 53 2 0.1020 1.7782e+07 - 52 59 2 0.1470 8.7100e+06 - 52 54 2 0.1470 8.7100e+06 - 54 55 2 0.1530 7.1500e+06 - 56 58 2 0.1470 8.7100e+06 - 56 63 2 0.1470 8.7100e+06 - 56 57 2 0.1020 1.7782e+07 - 58 59 2 0.1530 7.1500e+06 - 60 62 2 0.1470 8.7100e+06 - 60 61 2 0.1020 1.7782e+07 - 60 67 2 0.1470 8.7100e+06 - 62 63 2 0.1530 7.1500e+06 - 64 71 2 0.1470 8.7100e+06 - 64 66 2 0.1470 8.7100e+06 - 64 65 2 0.1020 1.7782e+07 - 66 67 2 0.1530 7.1500e+06 - 68 70 2 0.1470 8.7100e+06 - 68 75 2 0.1470 8.7100e+06 - 68 69 2 0.1020 1.7782e+07 - 70 71 2 0.1530 7.1500e+06 - 72 74 2 0.1470 8.7100e+06 - 72 79 2 0.1470 8.7100e+06 - 72 73 2 0.1020 1.7782e+07 - 74 75 2 0.1530 7.1500e+06 - 76 85 2 0.1470 8.7100e+06 - 76 77 2 0.1020 1.7782e+07 - 76 78 2 0.1470 8.7100e+06 - 78 79 2 0.1530 7.1500e+06 - 80 81 2 0.1530 7.1500e+06 - 81 82 2 0.1470 8.7100e+06 - 82 84 2 0.1470 8.7100e+06 - 82 83 2 0.1020 1.7782e+07 - 84 85 2 0.1530 7.1500e+06 - -[ pairs ] - 1 5 1 - 2 4 1 - 3 7 1 - 3 6 1 - 9 11 1 - 13 15 1 - 17 19 1 - 21 23 1 - 25 27 1 - 29 31 1 - 33 35 1 - 37 39 1 - 41 43 1 - 45 47 1 - 49 51 1 - 53 55 1 - 57 59 1 - 61 63 1 - 65 67 1 - 69 71 1 - 73 75 1 - 77 79 1 - 80 84 1 - 80 83 1 - 81 85 1 - 83 85 1 - -[ angles ] - 2 1 11 2 109.5000 4.2500e+02 - 2 1 3 2 109.5000 4.2500e+02 - 1 11 10 2 111.0000 5.3000e+02 - 3 1 11 2 116.0000 6.2000e+02 - 1 3 4 2 111.0000 5.3000e+02 - 3 4 5 2 111.0000 5.3000e+02 - 4 5 6 2 109.5000 4.2500e+02 - 4 5 7 2 116.0000 6.2000e+02 - 6 5 7 2 109.5000 4.2500e+02 - 8 15 14 2 111.0000 5.3000e+02 - 10 8 15 2 116.0000 6.2000e+02 - 9 8 15 2 109.5000 4.2500e+02 - 9 8 10 2 109.5000 4.2500e+02 - 8 10 11 2 111.0000 5.3000e+02 - 13 12 19 2 109.5000 4.2500e+02 - 13 12 14 2 109.5000 4.2500e+02 - 14 12 19 2 116.0000 6.2000e+02 - 12 19 18 2 111.0000 5.3000e+02 - 12 14 15 2 111.0000 5.3000e+02 - 17 16 23 2 109.5000 4.2500e+02 - 18 16 23 2 116.0000 6.2000e+02 - 16 23 22 2 111.0000 5.3000e+02 - 17 16 18 2 109.5000 4.2500e+02 - 16 18 19 2 111.0000 5.3000e+02 - 21 20 27 2 109.5000 4.2500e+02 - 21 20 22 2 109.5000 4.2500e+02 - 22 20 27 2 116.0000 6.2000e+02 - 20 22 23 2 111.0000 5.3000e+02 - 20 27 26 2 111.0000 5.3000e+02 - 24 26 27 2 111.0000 5.3000e+02 - 25 24 26 2 109.5000 4.2500e+02 - 26 24 31 2 116.0000 6.2000e+02 - 25 24 31 2 109.5000 4.2500e+02 - 24 31 30 2 111.0000 5.3000e+02 - 28 35 34 2 111.0000 5.3000e+02 - 30 28 35 2 116.0000 6.2000e+02 - 29 28 35 2 109.5000 4.2500e+02 - 28 30 31 2 111.0000 5.3000e+02 - 29 28 30 2 109.5000 4.2500e+02 - 33 32 34 2 109.5000 4.2500e+02 - 34 32 39 2 116.0000 6.2000e+02 - 32 34 35 2 111.0000 5.3000e+02 - 33 32 39 2 109.5000 4.2500e+02 - 32 39 38 2 111.0000 5.3000e+02 - 37 36 38 2 109.5000 4.2500e+02 - 37 36 43 2 109.5000 4.2500e+02 - 36 43 42 2 111.0000 5.3000e+02 - 38 36 43 2 116.0000 6.2000e+02 - 36 38 39 2 111.0000 5.3000e+02 - 42 40 47 2 116.0000 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180.0000 1.0000e+00 6 - 19 12 14 15 1 180.0000 1.0000e+00 6 - 16 18 19 12 1 0.0000 5.9200e+00 3 - 23 16 18 19 1 180.0000 1.0000e+00 6 - 20 22 23 16 1 0.0000 5.9200e+00 3 - 27 20 22 23 1 180.0000 1.0000e+00 6 - 24 26 27 20 1 0.0000 5.9200e+00 3 - 31 24 26 27 1 180.0000 1.0000e+00 6 - 28 30 31 24 1 0.0000 5.9200e+00 3 - 32 34 35 28 1 0.0000 5.9200e+00 3 - 35 28 30 31 1 180.0000 1.0000e+00 6 - 39 32 34 35 1 180.0000 1.0000e+00 6 - 36 38 39 32 1 0.0000 5.9200e+00 3 - 40 42 43 36 1 0.0000 5.9200e+00 3 - 43 36 38 39 1 180.0000 1.0000e+00 6 - 47 40 42 43 1 180.0000 1.0000e+00 6 - 44 46 47 40 1 0.0000 5.9200e+00 3 - 51 44 46 47 1 180.0000 1.0000e+00 6 - 48 50 51 44 1 0.0000 5.9200e+00 3 - 55 48 50 51 1 180.0000 1.0000e+00 6 - 52 54 55 48 1 0.0000 5.9200e+00 3 - 59 52 54 55 1 180.0000 1.0000e+00 6 - 56 58 59 52 1 0.0000 5.9200e+00 3 - 63 56 58 59 1 180.0000 1.0000e+00 6 - 60 62 63 56 1 0.0000 5.9200e+00 3 - 67 60 62 63 1 180.0000 1.0000e+00 6 - 64 66 67 60 1 0.0000 5.9200e+00 3 - 68 70 71 64 1 0.0000 5.9200e+00 3 - 71 64 66 67 1 180.0000 1.0000e+00 6 - 75 68 70 71 1 180.0000 1.0000e+00 6 - 72 74 75 68 1 0.0000 5.9200e+00 3 - 79 72 74 75 1 180.0000 1.0000e+00 6 - 76 78 79 72 1 0.0000 5.9200e+00 3 - 85 76 78 79 1 180.0000 1.0000e+00 6 - 82 84 85 76 1 0.0000 5.9200e+00 3 - 80 81 82 84 1 180.0000 1.0000e+00 6 - 81 82 84 85 1 180.0000 1.0000e+00 6 - -[ exclusions ] From f8da4741b46ef31eaa24665787b935f4888e0842 Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:39:37 +1100 Subject: [PATCH 08/14] Delete polytop_examples/data/four_arm_star.png --- polytop_examples/data/four_arm_star.png | Bin 13685 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 polytop_examples/data/four_arm_star.png diff --git a/polytop_examples/data/four_arm_star.png b/polytop_examples/data/four_arm_star.png deleted file mode 100644 index f5beba208d400fbb0ca5c99880b5e158bd2466a3..0000000000000000000000000000000000000000 GIT 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"phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 44, "atom_b": 12, "atom_c": 15, "atom_d": 16, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 43, "atom_b": 44, "atom_c": 12, "atom_d": 15, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 50, "atom_b": 51, "atom_c": 19, "atom_d": 22, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 51, "atom_b": 19, "atom_c": 22, "atom_d": 23, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 58, "atom_b": 26, "atom_c": 29, "atom_d": 30, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 57, "atom_b": 58, "atom_c": 26, "atom_d": 29, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 65, "atom_b": 33, "atom_c": 36, "atom_d": 37, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 64, "atom_b": 65, "atom_c": 33, "atom_d": 36, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 72, "atom_b": 40, "atom_c": 43, "atom_d": 44, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 71, "atom_b": 72, "atom_c": 40, "atom_d": 43, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 79, "atom_b": 47, "atom_c": 50, "atom_d": 51, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 78, "atom_b": 79, "atom_c": 47, "atom_d": 50, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 85, "atom_b": 86, "atom_c": 54, "atom_d": 57, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 86, "atom_b": 54, "atom_c": 57, "atom_d": 58, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 94, "atom_b": 95, "atom_c": 61, "atom_d": 64, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 95, "atom_b": 61, "atom_c": 64, "atom_d": 65, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 96, "atom_b": 68, "atom_c": 71, "atom_d": 72, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 97, "atom_b": 96, "atom_c": 68, "atom_d": 71, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 101, "atom_b": 75, "atom_c": 78, "atom_d": 79, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 102, "atom_b": 101, "atom_c": 75, "atom_d": 78, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 107, "atom_b": 106, "atom_c": 82, "atom_d": 85, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 106, "atom_b": 82, "atom_c": 85, "atom_d": 86, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}, {"atom_a": 112, "atom_b": 88, "atom_c": 91, "atom_d": 94, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 5.92, "multiplicity": 3, "constants": []}, {"atom_a": 88, "atom_b": 91, "atom_c": 94, "atom_d": 95, "dihedral_type": 1, "phase_angle": 0.0, "force_constant": 1.26, "multiplicity": 3, "constants": []}], "pairs": [{"atom_a": 1, "atom_b": 23, "pair_type": 1}, {"atom_a": 1, "atom_b": 16, "pair_type": 1}, {"atom_a": 1, "atom_b": 30, "pair_type": 1}, {"atom_a": 2, "atom_b": 30, "pair_type": 1}, {"atom_a": 2, "atom_b": 16, "pair_type": 1}, {"atom_a": 2, "atom_b": 23, "pair_type": 1}, {"atom_a": 4, "atom_b": 23, "pair_type": 1}, {"atom_a": 4, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 4, "pair_type": 1}, {"atom_a": 5, "atom_b": 23, "pair_type": 1}, {"atom_a": 5, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 5, "pair_type": 1}, {"atom_a": 37, "atom_b": 6, "pair_type": 1}, {"atom_a": 16, "atom_b": 6, "pair_type": 1}, {"atom_a": 6, "atom_b": 30, "pair_type": 1}, {"atom_a": 16, "atom_b": 7, "pair_type": 1}, {"atom_a": 37, "atom_b": 7, "pair_type": 1}, {"atom_a": 7, "atom_b": 30, "pair_type": 1}, {"atom_a": 37, "atom_b": 8, "pair_type": 1}, {"atom_a": 23, "atom_b": 8, "pair_type": 1}, {"atom_a": 16, "atom_b": 8, "pair_type": 1}, {"atom_a": 37, "atom_b": 9, "pair_type": 1}, {"atom_a": 23, "atom_b": 9, "pair_type": 1}, {"atom_a": 16, "atom_b": 9, "pair_type": 1}, {"atom_a": 10, "atom_b": 13, "pair_type": 1}, {"atom_a": 10, "atom_b": 15, "pair_type": 1}, {"atom_a": 10, "atom_b": 14, "pair_type": 1}, {"atom_a": 11, "atom_b": 13, "pair_type": 1}, {"atom_a": 11, "atom_b": 15, "pair_type": 1}, {"atom_a": 11, "atom_b": 14, "pair_type": 1}, {"atom_a": 17, "atom_b": 21, "pair_type": 1}, {"atom_a": 17, "atom_b": 22, "pair_type": 1}, {"atom_a": 17, "atom_b": 20, "pair_type": 1}, {"atom_a": 18, "atom_b": 21, "pair_type": 1}, {"atom_a": 18, "atom_b": 22, "pair_type": 1}, {"atom_a": 18, "atom_b": 20, "pair_type": 1}, {"atom_a": 24, "atom_b": 29, "pair_type": 1}, {"atom_a": 24, "atom_b": 27, "pair_type": 1}, {"atom_a": 24, "atom_b": 28, "pair_type": 1}, {"atom_a": 25, "atom_b": 28, "pair_type": 1}, {"atom_a": 25, "atom_b": 27, "pair_type": 1}, {"atom_a": 25, "atom_b": 29, "pair_type": 1}, {"atom_a": 31, "atom_b": 35, "pair_type": 1}, {"atom_a": 31, "atom_b": 36, "pair_type": 1}, {"atom_a": 31, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 35, "pair_type": 1}, {"atom_a": 32, "atom_b": 34, "pair_type": 1}, {"atom_a": 32, "atom_b": 36, "pair_type": 1}, {"atom_a": 38, "atom_b": 42, "pair_type": 1}, {"atom_a": 38, "atom_b": 41, "pair_type": 1}, {"atom_a": 38, "atom_b": 43, "pair_type": 1}, {"atom_a": 39, "atom_b": 41, "pair_type": 1}, {"atom_a": 39, "atom_b": 42, "pair_type": 1}, {"atom_a": 39, "atom_b": 43, "pair_type": 1}, {"atom_a": 45, "atom_b": 50, "pair_type": 1}, {"atom_a": 45, "atom_b": 48, "pair_type": 1}, {"atom_a": 45, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 49, "pair_type": 1}, {"atom_a": 46, "atom_b": 50, "pair_type": 1}, {"atom_a": 46, "atom_b": 48, "pair_type": 1}, {"atom_a": 52, "atom_b": 56, "pair_type": 1}, {"atom_a": 52, "atom_b": 55, "pair_type": 1}, {"atom_a": 52, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 56, "pair_type": 1}, {"atom_a": 53, "atom_b": 57, "pair_type": 1}, {"atom_a": 53, "atom_b": 55, "pair_type": 1}, {"atom_a": 59, "atom_b": 63, "pair_type": 1}, {"atom_a": 59, "atom_b": 62, "pair_type": 1}, {"atom_a": 59, "atom_b": 64, "pair_type": 1}, {"atom_a": 60, "atom_b": 62, "pair_type": 1}, {"atom_a": 60, "atom_b": 63, "pair_type": 1}, {"atom_a": 60, "atom_b": 64, "pair_type": 1}, {"atom_a": 66, "atom_b": 70, "pair_type": 1}, {"atom_a": 66, "atom_b": 71, "pair_type": 1}, {"atom_a": 66, "atom_b": 69, "pair_type": 1}, {"atom_a": 67, "atom_b": 71, "pair_type": 1}, {"atom_a": 67, "atom_b": 70, "pair_type": 1}, {"atom_a": 67, "atom_b": 69, "pair_type": 1}, {"atom_a": 73, "atom_b": 76, "pair_type": 1}, {"atom_a": 73, "atom_b": 77, "pair_type": 1}, {"atom_a": 73, "atom_b": 78, "pair_type": 1}, {"atom_a": 74, "atom_b": 77, "pair_type": 1}, {"atom_a": 74, "atom_b": 76, "pair_type": 1}, {"atom_a": 74, "atom_b": 78, "pair_type": 1}, {"atom_a": 80, "atom_b": 83, "pair_type": 1}, {"atom_a": 80, "atom_b": 84, "pair_type": 1}, {"atom_a": 80, "atom_b": 85, "pair_type": 1}, {"atom_a": 81, "atom_b": 84, "pair_type": 1}, {"atom_a": 81, "atom_b": 83, "pair_type": 1}, {"atom_a": 81, "atom_b": 85, "pair_type": 1}, {"atom_a": 89, "atom_b": 92, "pair_type": 1}, {"atom_a": 89, "atom_b": 94, "pair_type": 1}, {"atom_a": 89, "atom_b": 93, "pair_type": 1}, {"atom_a": 90, "atom_b": 94, "pair_type": 1}, {"atom_a": 90, "atom_b": 92, "pair_type": 1}, {"atom_a": 90, "atom_b": 93, "pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Pentaerythritol", ";", "; This file was generated at 13:37 on 2024-11-22 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 8WDY", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 39051", "; ATB Topology Hash: 07f0b", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "8WDY", "nrexcl": 3}}, "junctions": []} \ No newline at end of file From cfdd14047e89ec530922359e2515d71db165a76f Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:39:53 +1100 Subject: [PATCH 10/14] Delete polytop_examples/data/four_arm_star.itp --- polytop_examples/data/four_arm_star.itp | 637 ------------------------ 1 file changed, 637 deletions(-) delete mode 100644 polytop_examples/data/four_arm_star.itp diff --git a/polytop_examples/data/four_arm_star.itp b/polytop_examples/data/four_arm_star.itp deleted file mode 100644 index 4fa0280..0000000 --- a/polytop_examples/data/four_arm_star.itp +++ /dev/null @@ -1,637 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; four arm star polymer -; -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; Pentaerythritol -; -; This file was generated at 13:37 on 2024-11-22 by -; -; Automatic Topology Builder -; -; REVISION 2024-11-20 12:06:25 -;--------------------------------------------------------------------------------------------------------------------------- -; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark -; -; Institute : Molecular Dynamics group, -; School of Chemistry and Molecular Biosciences (SCMB), -; The University of Queensland, QLD 4072, Australia -; URL : https://atb.uq.edu.au -; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. -; An Automated force field Topology Builder (ATB) and repository: version 1.0. -; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037. -; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE. -; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane. -; DOI:10.1021/acs.jctc.8b00768 -; -; Disclaimer : -; While every effort has been made to ensure the accuracy and validity of parameters provided below -; the assignment of parameters is being based on an automated procedure combining data provided by a -; given user as well as calculations performed using third party software. They are provided as a guide. -; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided -; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion -; and to perform additional validation tests for their specific application if required. Neither the authors -; of the ATB or The University of Queensland except any responsibly for how the parameters may be used. -; -; Release notes and warnings: -; (1) The topology is based on a set of atomic coordinates and other data provided by the user after -; after quantum mechanical optimization of the structure using different levels of theory depending on -; the nature of the molecule. -; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous. -; In these cases alternative type codes are provided at the end of the line. -; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral -; type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard" -; or "uncertain" in comments. -; (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder -; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually -; before the file can be used. -;--------------------------------------------------------------------------------------------------------------------------- -; Input Structure : 8WDY -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 39051 -; ATB Topology Hash: 07f0b -;--------------------------------------------------------------------------------------------------------------------------- -; Final Topology Generation was performed using: -; A B3LYP/6-31G* optimized geometry. -; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set. -; Initial charges were estimated using the ESP method of Merz-Kollman. -; Final charges and charge groups were generated by method described in the ATB paper. -; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory. -;--------------------------------------------------------------------------------------------------------------------------- -; -; - -[ moleculetype ] -8WDY 3 -[ atoms ] - 1 CPos 1 8WDY C5 1 0.231500 12.0110 - 2 HC 1 8WDY H10 2 0.010500 1.0080 - 3 HC 1 8WDY H11 3 0.010500 1.0080 - 4 C 1 8WDY C2 4 -0.014500 12.0110 - 5 CPos 1 8WDY C1 5 0.231500 12.0110 - 6 HC 1 8WDY H2 6 0.010500 1.0080 - 7 HC 1 8WDY H3 7 0.010500 1.0080 - 8 CPos 1 8WDY C3 8 0.231500 12.0110 - 9 HC 1 8WDY H4 9 0.010500 1.0080 - 10 HC 1 8WDY H5 10 0.010500 1.0080 - 11 CPos 1 8WDY C4 11 0.231500 12.0110 - 12 HC 1 8WDY H7 12 0.010500 1.0080 - 13 HC 1 8WDY H8 13 0.010500 1.0080 - 14 CPos 2 4Y3B C3 14 0.212333 12.0110 - 15 HC 2 4Y3B H6 15 0.006333 1.0080 - 16 HC 2 4Y3B H7 16 0.006333 1.0080 - 17 CPos 2 4Y3B C2 17 0.167333 12.0110 - 18 HC 2 4Y3B H4 18 0.036333 1.0080 - 19 HC 2 4Y3B H5 19 0.036333 1.0080 - 20 OE 2 4Y3B O1 20 -0.440667 15.9994 - 21 CPos 3 4Y3B C3 21 0.210667 12.0110 - 22 HC 3 4Y3B H6 22 0.004667 1.0080 - 23 HC 3 4Y3B H7 23 0.004667 1.0080 - 24 CPos 3 4Y3B C2 24 0.165667 12.0110 - 25 HC 3 4Y3B H4 25 0.034667 1.0080 - 26 HC 3 4Y3B H5 26 0.034667 1.0080 - 27 OE 3 4Y3B O1 27 -0.442333 15.9994 - 28 CPos 4 4Y3B C3 28 0.210667 12.0110 - 29 HC 4 4Y3B H6 29 0.004667 1.0080 - 30 HC 4 4Y3B H7 30 0.004667 1.0080 - 31 CPos 4 4Y3B C2 31 0.165667 12.0110 - 32 HC 4 4Y3B H4 32 0.034667 1.0080 - 33 HC 4 4Y3B H5 33 0.034667 1.0080 - 34 OE 4 4Y3B O1 34 -0.442333 15.9994 - 35 CPos 5 4Y3B C3 35 0.210148 12.0110 - 36 HC 5 4Y3B H6 36 0.004148 1.0080 - 37 HC 5 4Y3B H7 37 0.004148 1.0080 - 38 CPos 5 4Y3B C2 38 0.165148 12.0110 - 39 HC 5 4Y3B H4 39 0.034148 1.0080 - 40 HC 5 4Y3B H5 40 0.034148 1.0080 - 41 OE 5 4Y3B O1 41 -0.442852 15.9994 - 42 CPos 6 4Y3B C3 42 0.209444 12.0110 - 43 HC 6 4Y3B H6 43 0.003444 1.0080 - 44 HC 6 4Y3B H7 44 0.003444 1.0080 - 45 CPos 6 4Y3B C2 45 0.164444 12.0110 - 46 HC 6 4Y3B H4 46 0.033444 1.0080 - 47 HC 6 4Y3B H5 47 0.033444 1.0080 - 48 OE 6 4Y3B O1 48 -0.443556 15.9994 - 49 CPos 7 4Y3B C3 49 0.209259 12.0110 - 50 HC 7 4Y3B H6 50 0.003259 1.0080 - 51 HC 7 4Y3B H7 51 0.003259 1.0080 - 52 CPos 7 4Y3B C2 52 0.164259 12.0110 - 53 HC 7 4Y3B H4 53 0.033259 1.0080 - 54 HC 7 4Y3B H5 54 0.033259 1.0080 - 55 OE 7 4Y3B O1 55 -0.443741 15.9994 - 56 CPos 8 4Y3B C3 56 0.209202 12.0110 - 57 HC 8 4Y3B H6 57 0.003202 1.0080 - 58 HC 8 4Y3B H7 58 0.003202 1.0080 - 59 CPos 8 4Y3B C2 59 0.164202 12.0110 - 60 HC 8 4Y3B H4 60 0.033202 1.0080 - 61 HC 8 4Y3B H5 61 0.033202 1.0080 - 62 OE 8 4Y3B O1 62 -0.443798 15.9994 - 63 CPos 9 4Y3B C3 63 0.209066 12.0110 - 64 HC 9 4Y3B H6 64 0.003066 1.0080 - 65 HC 9 4Y3B H7 65 0.003066 1.0080 - 66 CPos 9 4Y3B C2 66 0.164066 12.0110 - 67 HC 9 4Y3B H4 67 0.033066 1.0080 - 68 HC 9 4Y3B H5 68 0.033066 1.0080 - 69 OE 9 4Y3B O1 69 -0.443934 15.9994 - 70 CPos 10 4Y3B C3 70 0.208967 12.0110 - 71 HC 10 4Y3B H6 71 0.002967 1.0080 - 72 HC 10 4Y3B H7 72 0.002967 1.0080 - 73 CPos 10 4Y3B C2 73 0.163967 12.0110 - 74 HC 10 4Y3B H4 74 0.032967 1.0080 - 75 HC 10 4Y3B H5 75 0.032967 1.0080 - 76 OE 10 4Y3B O1 76 -0.444033 15.9994 - 77 CPos 11 4Y3B C3 77 0.208940 12.0110 - 78 HC 11 4Y3B H6 78 0.002940 1.0080 - 79 HC 11 4Y3B H7 79 0.002940 1.0080 - 80 CPos 11 4Y3B C2 80 0.163940 12.0110 - 81 HC 11 4Y3B H4 81 0.032940 1.0080 - 82 HC 11 4Y3B H5 82 0.032940 1.0080 - 83 OE 11 4Y3B O1 83 -0.444060 15.9994 - 84 CPos 12 4Y3B C3 84 0.208919 12.0110 - 85 HC 12 4Y3B H6 85 0.002919 1.0080 - 86 HC 12 4Y3B H7 86 0.002919 1.0080 - 87 CPos 12 4Y3B C2 87 0.163919 12.0110 - 88 HC 12 4Y3B H4 88 0.032919 1.0080 - 89 HC 12 4Y3B H5 89 0.032919 1.0080 - 90 OE 12 4Y3B O1 90 -0.444081 15.9994 - 91 CPos 13 4Y3B C3 91 0.174485 12.0110 - 92 HC 13 4Y3B H6 92 -0.031515 1.0080 - 93 HC 13 4Y3B H7 93 -0.031515 1.0080 - 94 CPos 13 4Y3B C2 94 0.129485 12.0110 - 95 HC 13 4Y3B H4 95 -0.001515 1.0080 - 96 HC 13 4Y3B H5 96 -0.001515 1.0080 - 97 OE 13 4Y3B O1 97 -0.478515 15.9994 - 98 CPos 14 45ZJ C1 98 0.071393 12.0110 - 99 HC 14 45ZJ H1 99 -0.083607 1.0080 - 100 HC 14 45ZJ H2 100 -0.083607 1.0080 - 101 HC 14 45ZJ H3 101 -0.083607 1.0080 - 102 CPos 15 45ZJ C1 102 0.046715 12.0110 - 103 HC 15 45ZJ H1 103 -0.108285 1.0080 - 104 HC 15 45ZJ H2 104 -0.108285 1.0080 - 105 HC 15 45ZJ H3 105 -0.108285 1.0080 - 106 CPos 16 45ZJ C1 106 0.038101 12.0110 - 107 HC 16 45ZJ H1 107 -0.116899 1.0080 - 108 HC 16 45ZJ H2 108 -0.116899 1.0080 - 109 HC 16 45ZJ H3 109 -0.116899 1.0080 - 110 CPos 17 45ZJ C1 110 0.102246 12.0110 - 111 HC 17 45ZJ H1 111 -0.052754 1.0080 - 112 HC 17 45ZJ H2 112 -0.052754 1.0080 - 113 HC 17 45ZJ H3 113 -0.052754 1.0080 - -[ bonds ] - 1 3 2 0.1090 1.2300e+07 - 1 41 2 0.1430 8.1800e+06 - 1 4 2 0.1540 4.0057e+06 - 1 2 2 0.1090 1.2300e+07 - 4 5 2 0.1540 4.0057e+06 - 4 8 2 0.1540 4.0057e+06 - 4 11 2 0.1540 4.0057e+06 - 5 20 2 0.1430 8.1800e+06 - 5 7 2 0.1090 1.2300e+07 - 5 6 2 0.1090 1.2300e+07 - 8 10 2 0.1090 1.2300e+07 - 8 27 2 0.1430 8.1800e+06 - 8 9 2 0.1090 1.2300e+07 - 11 12 2 0.1090 1.2300e+07 - 11 13 2 0.1090 1.2300e+07 - 11 34 2 0.1430 8.1800e+06 - 14 15 2 0.1090 1.2300e+07 - 14 16 2 0.1090 1.2300e+07 - 14 17 2 0.1530 7.1500e+06 - 14 48 2 0.1430 8.1800e+06 - 17 20 2 0.1430 8.1800e+06 - 17 18 2 0.1090 1.2300e+07 - 17 19 2 0.1090 1.2300e+07 - 21 23 2 0.1090 1.2300e+07 - 21 24 2 0.1530 7.1500e+06 - 21 55 2 0.1430 8.1800e+06 - 21 22 2 0.1090 1.2300e+07 - 24 26 2 0.1090 1.2300e+07 - 24 27 2 0.1430 8.1800e+06 - 24 25 2 0.1090 1.2300e+07 - 28 31 2 0.1530 7.1500e+06 - 28 29 2 0.1090 1.2300e+07 - 28 30 2 0.1090 1.2300e+07 - 28 62 2 0.1430 8.1800e+06 - 31 34 2 0.1430 8.1800e+06 - 31 33 2 0.1090 1.2300e+07 - 31 32 2 0.1090 1.2300e+07 - 35 37 2 0.1090 1.2300e+07 - 35 36 2 0.1090 1.2300e+07 - 35 69 2 0.1430 8.1800e+06 - 35 38 2 0.1530 7.1500e+06 - 38 40 2 0.1090 1.2300e+07 - 38 41 2 0.1430 8.1800e+06 - 38 39 2 0.1090 1.2300e+07 - 42 43 2 0.1090 1.2300e+07 - 42 44 2 0.1090 1.2300e+07 - 42 45 2 0.1530 7.1500e+06 - 42 76 2 0.1430 8.1800e+06 - 45 48 2 0.1430 8.1800e+06 - 45 46 2 0.1090 1.2300e+07 - 45 47 2 0.1090 1.2300e+07 - 49 52 2 0.1530 7.1500e+06 - 49 51 2 0.1090 1.2300e+07 - 49 50 2 0.1090 1.2300e+07 - 49 83 2 0.1430 8.1800e+06 - 52 53 2 0.1090 1.2300e+07 - 52 55 2 0.1430 8.1800e+06 - 52 54 2 0.1090 1.2300e+07 - 56 90 2 0.1430 8.1800e+06 - 56 58 2 0.1090 1.2300e+07 - 56 59 2 0.1530 7.1500e+06 - 56 57 2 0.1090 1.2300e+07 - 59 60 2 0.1090 1.2300e+07 - 59 61 2 0.1090 1.2300e+07 - 59 62 2 0.1430 8.1800e+06 - 63 97 2 0.1430 8.1800e+06 - 63 65 2 0.1090 1.2300e+07 - 63 66 2 0.1530 7.1500e+06 - 63 64 2 0.1090 1.2300e+07 - 66 68 2 0.1090 1.2300e+07 - 66 69 2 0.1430 8.1800e+06 - 66 67 2 0.1090 1.2300e+07 - 70 71 2 0.1090 1.2300e+07 - 70 72 2 0.1090 1.2300e+07 - 70 98 2 0.1430 8.1800e+06 - 70 73 2 0.1530 7.1500e+06 - 73 76 2 0.1430 8.1800e+06 - 73 74 2 0.1090 1.2300e+07 - 73 75 2 0.1090 1.2300e+07 - 77 102 2 0.1430 8.1800e+06 - 77 79 2 0.1090 1.2300e+07 - 77 80 2 0.1530 7.1500e+06 - 77 78 2 0.1090 1.2300e+07 - 80 82 2 0.1090 1.2300e+07 - 80 83 2 0.1430 8.1800e+06 - 80 81 2 0.1090 1.2300e+07 - 84 106 2 0.1430 8.1800e+06 - 84 85 2 0.1090 1.2300e+07 - 84 86 2 0.1090 1.2300e+07 - 84 87 2 0.1530 7.1500e+06 - 87 89 2 0.1090 1.2300e+07 - 87 90 2 0.1430 8.1800e+06 - 87 88 2 0.1090 1.2300e+07 - 91 94 2 0.1530 7.1500e+06 - 91 110 2 0.1430 8.1800e+06 - 91 92 2 0.1090 1.2300e+07 - 91 93 2 0.1090 1.2300e+07 - 94 96 2 0.1090 1.2300e+07 - 94 95 2 0.1090 1.2300e+07 - 94 97 2 0.1430 8.1800e+06 - 98 99 2 0.1090 1.2300e+07 - 98 101 2 0.1090 1.2300e+07 - 98 100 2 0.1090 1.2300e+07 - 102 104 2 0.1090 1.2300e+07 - 102 103 2 0.1090 1.2300e+07 - 102 105 2 0.1090 1.2300e+07 - 106 107 2 0.1090 1.2300e+07 - 106 109 2 0.1090 1.2300e+07 - 106 108 2 0.1090 1.2300e+07 - 110 113 2 0.1090 1.2300e+07 - 110 111 2 0.1090 1.2300e+07 - 110 112 2 0.1090 1.2300e+07 - -[ pairs ] - 1 12 1 - 1 13 1 - 1 6 1 - 1 10 1 - 1 7 1 - 1 9 1 - 2 8 1 - 2 5 1 - 2 11 1 - 3 11 1 - 3 5 1 - 3 8 1 - 5 9 1 - 5 12 1 - 5 10 1 - 5 13 1 - 6 8 1 - 6 11 1 - 7 8 1 - 7 11 1 - 8 12 1 - 8 13 1 - 9 11 1 - 10 11 1 - 15 18 1 - 15 20 1 - 15 19 1 - 16 18 1 - 16 20 1 - 16 19 1 - 22 26 1 - 22 27 1 - 22 25 1 - 23 26 1 - 23 27 1 - 23 25 1 - 29 34 1 - 29 32 1 - 29 33 1 - 30 33 1 - 30 32 1 - 30 34 1 - 36 40 1 - 36 41 1 - 36 39 1 - 37 40 1 - 37 39 1 - 37 41 1 - 43 47 1 - 43 46 1 - 43 48 1 - 44 46 1 - 44 47 1 - 44 48 1 - 50 55 1 - 50 53 1 - 50 54 1 - 51 54 1 - 51 55 1 - 51 53 1 - 57 61 1 - 57 60 1 - 57 62 1 - 58 61 1 - 58 62 1 - 58 60 1 - 64 68 1 - 64 67 1 - 64 69 1 - 65 67 1 - 65 68 1 - 65 69 1 - 71 75 1 - 71 76 1 - 71 74 1 - 72 76 1 - 72 75 1 - 72 74 1 - 78 81 1 - 78 82 1 - 78 83 1 - 79 82 1 - 79 81 1 - 79 83 1 - 85 88 1 - 85 89 1 - 85 90 1 - 86 89 1 - 86 88 1 - 86 90 1 - 92 95 1 - 92 97 1 - 92 96 1 - 93 97 1 - 93 95 1 - 93 96 1 - -[ angles ] - 2 1 3 2 107.5700 4.8400e+02 - 3 1 4 2 109.5000 4.4800e+02 - 3 1 41 2 109.6000 4.5000e+02 - 1 41 38 2 109.5000 4.5000e+02 - 2 1 41 2 109.6000 4.5000e+02 - 4 1 41 2 115.0000 6.1000e+02 - 1 4 5 2 109.5000 5.2000e+02 - 2 1 4 2 109.5000 4.4800e+02 - 1 4 11 2 109.5000 5.2000e+02 - 1 4 8 2 109.5000 5.2000e+02 - 5 4 8 2 109.5000 5.2000e+02 - 5 4 11 2 109.5000 5.2000e+02 - 4 5 6 2 109.5000 4.4800e+02 - 4 5 20 2 115.0000 6.1000e+02 - 4 5 7 2 109.5000 4.4800e+02 - 8 4 11 2 109.5000 5.2000e+02 - 4 8 10 2 109.5000 4.4800e+02 - 4 8 27 2 115.0000 6.1000e+02 - 4 8 9 2 109.5000 4.4800e+02 - 4 11 13 2 109.5000 4.4800e+02 - 4 11 12 2 109.5000 4.4800e+02 - 4 11 34 2 115.0000 6.1000e+02 - 7 5 20 2 109.6000 4.5000e+02 - 6 5 20 2 109.6000 4.5000e+02 - 5 20 17 2 109.5000 4.5000e+02 - 6 5 7 2 107.5700 4.8400e+02 - 9 8 10 2 107.5700 4.8400e+02 - 10 8 27 2 109.6000 4.5000e+02 - 8 27 24 2 109.5000 4.5000e+02 - 9 8 27 2 109.6000 4.5000e+02 - 12 11 13 2 107.5700 4.8400e+02 - 12 11 34 2 109.6000 4.5000e+02 - 13 11 34 2 109.6000 4.5000e+02 - 11 34 31 2 109.5000 4.5000e+02 - 15 14 16 2 107.6000 5.0700e+02 - 15 14 17 2 110.3000 5.2400e+02 - 15 14 48 2 111.0000 5.3000e+02 - 16 14 48 2 111.0000 5.3000e+02 - 16 14 17 2 110.3000 5.2400e+02 - 17 14 48 2 109.5000 5.2000e+02 - 14 17 18 2 109.6000 4.5000e+02 - 14 17 19 2 109.6000 4.5000e+02 - 14 17 20 2 111.0000 5.3000e+02 - 14 48 45 2 109.5000 4.5000e+02 - 18 17 20 2 111.0000 5.3000e+02 - 19 17 20 2 111.0000 5.3000e+02 - 18 17 19 2 108.0000 4.6500e+02 - 22 21 23 2 107.6000 5.0700e+02 - 23 21 24 2 110.3000 5.2400e+02 - 23 21 55 2 111.0000 5.3000e+02 - 24 21 55 2 109.5000 5.2000e+02 - 21 24 25 2 109.6000 4.5000e+02 - 21 24 26 2 109.6000 4.5000e+02 - 21 24 27 2 111.0000 5.3000e+02 - 22 21 24 2 110.3000 5.2400e+02 - 21 55 52 2 109.5000 4.5000e+02 - 22 21 55 2 111.0000 5.3000e+02 - 25 24 26 2 108.0000 4.6500e+02 - 26 24 27 2 111.0000 5.3000e+02 - 25 24 27 2 111.0000 5.3000e+02 - 29 28 31 2 110.3000 5.2400e+02 - 28 31 32 2 109.6000 4.5000e+02 - 28 31 34 2 111.0000 5.3000e+02 - 31 28 62 2 109.5000 5.2000e+02 - 30 28 31 2 110.3000 5.2400e+02 - 28 31 33 2 109.6000 4.5000e+02 - 29 28 30 2 107.6000 5.0700e+02 - 29 28 62 2 111.0000 5.3000e+02 - 30 28 62 2 111.0000 5.3000e+02 - 28 62 59 2 109.5000 4.5000e+02 - 32 31 34 2 111.0000 5.3000e+02 - 33 31 34 2 111.0000 5.3000e+02 - 32 31 33 2 108.0000 4.6500e+02 - 36 35 37 2 107.6000 5.0700e+02 - 37 35 69 2 111.0000 5.3000e+02 - 37 35 38 2 110.3000 5.2400e+02 - 36 35 38 2 110.3000 5.2400e+02 - 36 35 69 2 111.0000 5.3000e+02 - 35 69 66 2 109.5000 4.5000e+02 - 38 35 69 2 109.5000 5.2000e+02 - 35 38 39 2 109.6000 4.5000e+02 - 35 38 40 2 109.6000 4.5000e+02 - 35 38 41 2 111.0000 5.3000e+02 - 39 38 40 2 108.0000 4.6500e+02 - 40 38 41 2 111.0000 5.3000e+02 - 39 38 41 2 111.0000 5.3000e+02 - 43 42 44 2 107.6000 5.0700e+02 - 43 42 45 2 110.3000 5.2400e+02 - 43 42 76 2 111.0000 5.3000e+02 - 44 42 76 2 111.0000 5.3000e+02 - 44 42 45 2 110.3000 5.2400e+02 - 45 42 76 2 109.5000 5.2000e+02 - 42 45 46 2 109.6000 4.5000e+02 - 42 45 47 2 109.6000 4.5000e+02 - 42 45 48 2 111.0000 5.3000e+02 - 42 76 73 2 109.5000 4.5000e+02 - 47 45 48 2 111.0000 5.3000e+02 - 46 45 48 2 111.0000 5.3000e+02 - 46 45 47 2 108.0000 4.6500e+02 - 51 49 52 2 110.3000 5.2400e+02 - 50 49 52 2 110.3000 5.2400e+02 - 49 52 53 2 109.6000 4.5000e+02 - 49 52 55 2 111.0000 5.3000e+02 - 52 49 83 2 109.5000 5.2000e+02 - 49 52 54 2 109.6000 4.5000e+02 - 50 49 51 2 107.6000 5.0700e+02 - 51 49 83 2 111.0000 5.3000e+02 - 50 49 83 2 111.0000 5.3000e+02 - 49 83 80 2 109.5000 4.5000e+02 - 53 52 55 2 111.0000 5.3000e+02 - 53 52 54 2 108.0000 4.6500e+02 - 54 52 55 2 111.0000 5.3000e+02 - 59 56 90 2 109.5000 5.2000e+02 - 58 56 90 2 111.0000 5.3000e+02 - 56 90 87 2 109.5000 4.5000e+02 - 57 56 90 2 111.0000 5.3000e+02 - 58 56 59 2 110.3000 5.2400e+02 - 57 56 58 2 107.6000 5.0700e+02 - 56 59 60 2 109.6000 4.5000e+02 - 56 59 61 2 109.6000 4.5000e+02 - 56 59 62 2 111.0000 5.3000e+02 - 57 56 59 2 110.3000 5.2400e+02 - 60 59 61 2 108.0000 4.6500e+02 - 60 59 62 2 111.0000 5.3000e+02 - 61 59 62 2 111.0000 5.3000e+02 - 66 63 97 2 109.5000 5.2000e+02 - 65 63 97 2 111.0000 5.3000e+02 - 64 63 97 2 111.0000 5.3000e+02 - 63 97 94 2 109.5000 4.5000e+02 - 64 63 65 2 107.6000 5.0700e+02 - 65 63 66 2 110.3000 5.2400e+02 - 63 66 67 2 109.6000 4.5000e+02 - 63 66 68 2 109.6000 4.5000e+02 - 63 66 69 2 111.0000 5.3000e+02 - 64 63 66 2 110.3000 5.2400e+02 - 68 66 69 2 111.0000 5.3000e+02 - 67 66 68 2 108.0000 4.6500e+02 - 67 66 69 2 111.0000 5.3000e+02 - 71 70 72 2 107.6000 5.0700e+02 - 71 70 73 2 110.3000 5.2400e+02 - 71 70 98 2 111.0000 5.3000e+02 - 72 70 98 2 111.0000 5.3000e+02 - 72 70 73 2 110.3000 5.2400e+02 - 70 98 101 2 106.7500 5.0300e+02 - 70 98 99 2 106.7500 5.0300e+02 - 73 70 98 2 109.5000 5.2000e+02 - 70 98 100 2 106.7500 5.0300e+02 - 70 73 75 2 109.6000 4.5000e+02 - 70 73 76 2 111.0000 5.3000e+02 - 70 73 74 2 109.6000 4.5000e+02 - 75 73 76 2 111.0000 5.3000e+02 - 74 73 76 2 111.0000 5.3000e+02 - 74 73 75 2 108.0000 4.6500e+02 - 78 77 102 2 111.0000 5.3000e+02 - 79 77 102 2 111.0000 5.3000e+02 - 77 102 104 2 106.7500 5.0300e+02 - 80 77 102 2 109.5000 5.2000e+02 - 77 102 103 2 106.7500 5.0300e+02 - 77 102 105 2 106.7500 5.0300e+02 - 78 77 79 2 107.6000 5.0700e+02 - 79 77 80 2 110.3000 5.2400e+02 - 77 80 81 2 109.6000 4.5000e+02 - 77 80 82 2 109.6000 4.5000e+02 - 77 80 83 2 111.0000 5.3000e+02 - 78 77 80 2 110.3000 5.2400e+02 - 82 80 83 2 111.0000 5.3000e+02 - 81 80 82 2 108.0000 4.6500e+02 - 81 80 83 2 111.0000 5.3000e+02 - 84 106 107 2 106.7500 5.0300e+02 - 84 106 109 2 106.7500 5.0300e+02 - 87 84 106 2 109.5000 5.2000e+02 - 85 84 106 2 111.0000 5.3000e+02 - 84 106 108 2 106.7500 5.0300e+02 - 86 84 106 2 111.0000 5.3000e+02 - 85 84 86 2 107.6000 5.0700e+02 - 85 84 87 2 110.3000 5.2400e+02 - 86 84 87 2 110.3000 5.2400e+02 - 84 87 88 2 109.6000 4.5000e+02 - 84 87 89 2 109.6000 4.5000e+02 - 84 87 90 2 111.0000 5.3000e+02 - 88 87 89 2 108.0000 4.6500e+02 - 89 87 90 2 111.0000 5.3000e+02 - 88 87 90 2 111.0000 5.3000e+02 - 91 94 95 2 109.6000 4.5000e+02 - 94 91 110 2 109.5000 5.2000e+02 - 92 91 94 2 110.3000 5.2400e+02 - 91 94 96 2 109.6000 4.5000e+02 - 91 94 97 2 111.0000 5.3000e+02 - 93 91 94 2 110.3000 5.2400e+02 - 92 91 110 2 111.0000 5.3000e+02 - 91 110 112 2 106.7500 5.0300e+02 - 91 110 111 2 106.7500 5.0300e+02 - 93 91 110 2 111.0000 5.3000e+02 - 91 110 113 2 106.7500 5.0300e+02 - 92 91 93 2 107.6000 5.0700e+02 - 96 94 97 2 111.0000 5.3000e+02 - 95 94 96 2 108.0000 4.6500e+02 - 95 94 97 2 111.0000 5.3000e+02 - 99 98 101 2 108.5300 4.4300e+02 - 99 98 100 2 108.5300 4.4300e+02 - 100 98 101 2 108.5300 4.4300e+02 - 103 102 104 2 108.5300 4.4300e+02 - 104 102 105 2 108.5300 4.4300e+02 - 103 102 105 2 108.5300 4.4300e+02 - 107 106 108 2 108.5300 4.4300e+02 - 107 106 109 2 108.5300 4.4300e+02 - 108 106 109 2 108.5300 4.4300e+02 - 112 110 113 2 108.5300 4.4300e+02 - 111 110 113 2 108.5300 4.4300e+02 - 111 110 112 2 108.5300 4.4300e+02 - -[ dihedrals ] - 35 38 41 1 1 0.0000 1.2600e+00 3 - 41 1 4 5 1 0.0000 5.9200e+00 3 - 5 4 8 27 1 0.0000 5.9200e+00 3 - 8 4 5 20 1 0.0000 5.9200e+00 3 - 5 4 11 34 1 0.0000 5.9200e+00 3 - 14 17 20 5 1 0.0000 1.2600e+00 3 - 21 24 27 8 1 0.0000 1.2600e+00 3 - 28 31 34 11 1 0.0000 1.2600e+00 3 - 48 14 17 20 1 0.0000 5.9200e+00 3 - 42 45 48 14 1 0.0000 1.2600e+00 3 - 55 21 24 27 1 0.0000 5.9200e+00 3 - 49 52 55 21 1 0.0000 1.2600e+00 3 - 62 28 31 34 1 0.0000 5.9200e+00 3 - 56 59 62 28 1 0.0000 1.2600e+00 3 - 63 66 69 35 1 0.0000 1.2600e+00 3 - 69 35 38 41 1 0.0000 5.9200e+00 3 - 76 42 45 48 1 0.0000 5.9200e+00 3 - 70 73 76 42 1 0.0000 1.2600e+00 3 - 83 49 52 55 1 0.0000 5.9200e+00 3 - 77 80 83 49 1 0.0000 1.2600e+00 3 - 90 56 59 62 1 0.0000 5.9200e+00 3 - 84 87 90 56 1 0.0000 1.2600e+00 3 - 97 63 66 69 1 0.0000 5.9200e+00 3 - 91 94 97 63 1 0.0000 1.2600e+00 3 - 98 70 73 76 1 0.0000 5.9200e+00 3 - 102 77 80 83 1 0.0000 5.9200e+00 3 - 106 84 87 90 1 0.0000 5.9200e+00 3 - 110 91 94 97 1 0.0000 5.9200e+00 3 - -[ exclusions ] From b6807bf7c5b4b6e5a9887d93c815df62c18d799f Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:40:06 +1100 Subject: [PATCH 11/14] Delete polytop_examples/data/ethylamine_dendrimer.itp --- .../data/ethylamine_dendrimer.itp | 1319 ----------------- 1 file changed, 1319 deletions(-) delete mode 100644 polytop_examples/data/ethylamine_dendrimer.itp diff --git a/polytop_examples/data/ethylamine_dendrimer.itp b/polytop_examples/data/ethylamine_dendrimer.itp deleted file mode 100644 index 1865814..0000000 --- a/polytop_examples/data/ethylamine_dendrimer.itp +++ /dev/null @@ -1,1319 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; None -; -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; None -; -; This file was generated at 14:09 on 2024-12-06 by -; -; Automatic Topology Builder -; -; REVISION 2024-11-20 12:06:25 -;--------------------------------------------------------------------------------------------------------------------------- -; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark -; -; Institute : Molecular Dynamics group, -; School of Chemistry and Molecular Biosciences (SCMB), -; The University of Queensland, QLD 4072, Australia -; URL : https://atb.uq.edu.au -; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE. -; An Automated force field Topology Builder (ATB) and repository: version 1.0. -; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037. -; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE. -; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane. -; DOI:10.1021/acs.jctc.8b00768 -; -; Disclaimer : -; While every effort has been made to ensure the accuracy and validity of parameters provided below -; the assignment of parameters is being based on an automated procedure combining data provided by a -; given user as well as calculations performed using third party software. They are provided as a guide. -; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided -; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion -; and to perform additional validation tests for their specific application if required. Neither the authors -; of the ATB or The University of Queensland except any responsibly for how the parameters may be used. -; -; Release notes and warnings: -; (1) The topology is based on a set of atomic coordinates and other data provided by the user after -; after quantum mechanical optimization of the structure using different levels of theory depending on -; the nature of the molecule. -; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous. -; In these cases alternative type codes are provided at the end of the line. -; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral -; type code may be incorporated in cases where an exact match could not be found. These are marked as "non-standard" -; or "uncertain" in comments. -; (4) In some cases it is not possible to assign an appropriate parameter automatically. "%%" is used as a place holder -; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually -; before the file can be used. -;--------------------------------------------------------------------------------------------------------------------------- -; Input Structure : 6HTJ -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 1746623 -; ATB Topology Hash: f4741 -;--------------------------------------------------------------------------------------------------------------------------- -; Final Topology Generation was performed using: -; A B3LYP/6-31G* optimized geometry. -; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set. -; Initial charges were estimated using the ESP method of Merz-Kollman. -; Final charges and charge groups were generated by method described in the ATB paper. -; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory. -;--------------------------------------------------------------------------------------------------------------------------- -; -; - -[ moleculetype ] -6HTJ 3 -[ atoms ] - 1 NTer 1 6HTJ N2 1 -0.554160 14.0067 - 2 CPos 1 6HTJ C6 2 0.021840 12.0110 - 3 HC 1 6HTJ H13 3 0.078840 1.0080 - 4 HC 1 6HTJ H14 4 0.078840 1.0080 - 5 CPos 1 6HTJ C5 5 0.021840 12.0110 - 6 HC 1 6HTJ H11 6 0.078840 1.0080 - 7 HC 1 6HTJ H12 7 0.078840 1.0080 - 8 NTer 1 6HTJ N1 8 -0.554160 14.0067 - 9 CPos 2 BB6C C6 9 -0.138020 12.0110 - 10 HC 2 BB6C H13 10 0.115980 1.0080 - 11 HC 2 BB6C H14 11 0.115980 1.0080 - 12 CPos 2 BB6C C5 12 0.141980 12.0110 - 13 HC 2 BB6C H11 13 0.059980 1.0080 - 14 HC 2 BB6C H12 14 0.059980 1.0080 - 15 NTer 2 BB6C N1 15 -0.591020 14.0067 - 16 CPos 3 BB6C C6 16 -0.137720 12.0110 - 17 HC 3 BB6C H13 17 0.116280 1.0080 - 18 HC 3 BB6C H14 18 0.116280 1.0080 - 19 CPos 3 BB6C C5 19 0.142280 12.0110 - 20 HC 3 BB6C H11 20 0.060280 1.0080 - 21 HC 3 BB6C H12 21 0.060280 1.0080 - 22 NTer 3 BB6C N1 22 -0.590720 14.0067 - 23 CPos 4 BB6C C6 23 -0.137720 12.0110 - 24 HC 4 BB6C H13 24 0.116280 1.0080 - 25 HC 4 BB6C H14 25 0.116280 1.0080 - 26 CPos 4 BB6C C5 26 0.142280 12.0110 - 27 HC 4 BB6C H11 27 0.060280 1.0080 - 28 HC 4 BB6C H12 28 0.060280 1.0080 - 29 NTer 4 BB6C N1 29 -0.590720 14.0067 - 30 CPos 5 BB6C C6 30 -0.137266 12.0110 - 31 HC 5 BB6C H13 31 0.116734 1.0080 - 32 HC 5 BB6C H14 32 0.116734 1.0080 - 33 CPos 5 BB6C C5 33 0.142734 12.0110 - 34 HC 5 BB6C H11 34 0.060734 1.0080 - 35 HC 5 BB6C H12 35 0.060734 1.0080 - 36 NTer 5 BB6C N1 36 -0.590266 14.0067 - 37 CPos 6 BB6C C6 37 -0.136736 12.0110 - 38 HC 6 BB6C H13 38 0.117264 1.0080 - 39 HC 6 BB6C H14 39 0.117264 1.0080 - 40 CPos 6 BB6C C5 40 0.143264 12.0110 - 41 HC 6 BB6C H11 41 0.061264 1.0080 - 42 HC 6 BB6C H12 42 0.061264 1.0080 - 43 NTer 6 BB6C N1 43 -0.589736 14.0067 - 44 CPos 7 BB6C C6 44 -0.136786 12.0110 - 45 HC 7 BB6C H13 45 0.117214 1.0080 - 46 HC 7 BB6C H14 46 0.117214 1.0080 - 47 CPos 7 BB6C C5 47 0.143214 12.0110 - 48 HC 7 BB6C H11 48 0.061214 1.0080 - 49 HC 7 BB6C H12 49 0.061214 1.0080 - 50 NTer 7 BB6C N1 50 -0.589786 14.0067 - 51 CPos 8 BB6C C6 51 -0.136861 12.0110 - 52 HC 8 BB6C H13 52 0.117139 1.0080 - 53 HC 8 BB6C H14 53 0.117139 1.0080 - 54 CPos 8 BB6C C5 54 0.143139 12.0110 - 55 HC 8 BB6C H11 55 0.061139 1.0080 - 56 HC 8 BB6C H12 56 0.061139 1.0080 - 57 NTer 8 BB6C N1 57 -0.589861 14.0067 - 58 CPos 9 BB6C C6 58 -0.136736 12.0110 - 59 HC 9 BB6C H13 59 0.117264 1.0080 - 60 HC 9 BB6C H14 60 0.117264 1.0080 - 61 CPos 9 BB6C C5 61 0.143264 12.0110 - 62 HC 9 BB6C H11 62 0.061264 1.0080 - 63 HC 9 BB6C H12 63 0.061264 1.0080 - 64 NTer 9 BB6C N1 64 -0.589736 14.0067 - 65 CPos 10 BB6C C6 65 -0.136786 12.0110 - 66 HC 10 BB6C H13 66 0.117214 1.0080 - 67 HC 10 BB6C H14 67 0.117214 1.0080 - 68 CPos 10 BB6C C5 68 0.143214 12.0110 - 69 HC 10 BB6C H11 69 0.061214 1.0080 - 70 HC 10 BB6C H12 70 0.061214 1.0080 - 71 NTer 10 BB6C N1 71 -0.589786 14.0067 - 72 CPos 11 BB6C C6 72 -0.136861 12.0110 - 73 HC 11 BB6C H13 73 0.117139 1.0080 - 74 HC 11 BB6C H14 74 0.117139 1.0080 - 75 CPos 11 BB6C C5 75 0.143139 12.0110 - 76 HC 11 BB6C H11 76 0.061139 1.0080 - 77 HC 11 BB6C H12 77 0.061139 1.0080 - 78 NTer 11 BB6C N1 78 -0.589861 14.0067 - 79 CPos 12 BB6C C6 79 -0.136811 12.0110 - 80 HC 12 BB6C H13 80 0.117189 1.0080 - 81 HC 12 BB6C H14 81 0.117189 1.0080 - 82 CPos 12 BB6C C5 82 0.143189 12.0110 - 83 HC 12 BB6C H11 83 0.061189 1.0080 - 84 HC 12 BB6C H12 84 0.061189 1.0080 - 85 NTer 12 BB6C N1 85 -0.589811 14.0067 - 86 CPos 13 BB6C C6 86 -0.137307 12.0110 - 87 HC 13 BB6C H13 87 0.116693 1.0080 - 88 HC 13 BB6C H14 88 0.116693 1.0080 - 89 CPos 13 BB6C C5 89 0.142693 12.0110 - 90 HC 13 BB6C H11 90 0.060693 1.0080 - 91 HC 13 BB6C H12 91 0.060693 1.0080 - 92 NTer 13 BB6C N1 92 -0.590307 14.0067 - 93 HS14 14 PHGY H12 93 0.376960 1.0080 - 94 NPri 14 PHGY N2 94 -1.037040 14.0067 - 95 HS14 14 PHGY H11 95 0.376960 1.0080 - 96 CPos 14 PHGY C2 96 0.353960 12.0110 - 97 HC 14 PHGY H3 97 0.024960 1.0080 - 98 HC 14 PHGY H4 98 0.024960 1.0080 - 99 C 14 PHGY C1 99 -0.037040 12.0110 - 100 HC 14 PHGY H1 100 0.064960 1.0080 - 101 HC 14 PHGY H2 101 0.064960 1.0080 - 102 HS14 15 PHGY H12 102 0.377742 1.0080 - 103 NPri 15 PHGY N2 103 -1.036258 14.0067 - 104 HS14 15 PHGY H11 104 0.377742 1.0080 - 105 CPos 15 PHGY C2 105 0.354742 12.0110 - 106 HC 15 PHGY H3 106 0.025742 1.0080 - 107 HC 15 PHGY H4 107 0.025742 1.0080 - 108 C 15 PHGY C1 108 -0.036258 12.0110 - 109 HC 15 PHGY H1 109 0.065742 1.0080 - 110 HC 15 PHGY H2 110 0.065742 1.0080 - 111 HS14 16 PHGY H12 111 0.377761 1.0080 - 112 NPri 16 PHGY N2 112 -1.036239 14.0067 - 113 HS14 16 PHGY H11 113 0.377761 1.0080 - 114 CPos 16 PHGY C2 114 0.354761 12.0110 - 115 HC 16 PHGY H3 115 0.025761 1.0080 - 116 HC 16 PHGY H4 116 0.025761 1.0080 - 117 C 16 PHGY C1 117 -0.036239 12.0110 - 118 HC 16 PHGY H1 118 0.065761 1.0080 - 119 HC 16 PHGY H2 119 0.065761 1.0080 - 120 HS14 17 PHGY H12 120 0.377712 1.0080 - 121 NPri 17 PHGY N2 121 -1.036288 14.0067 - 122 HS14 17 PHGY H11 122 0.377712 1.0080 - 123 CPos 17 PHGY C2 123 0.354712 12.0110 - 124 HC 17 PHGY H3 124 0.025712 1.0080 - 125 HC 17 PHGY H4 125 0.025712 1.0080 - 126 C 17 PHGY C1 126 -0.036288 12.0110 - 127 HC 17 PHGY H1 127 0.065712 1.0080 - 128 HC 17 PHGY H2 128 0.065712 1.0080 - 129 HS14 18 PHGY H12 129 0.377663 1.0080 - 130 NPri 18 PHGY N2 130 -1.036337 14.0067 - 131 HS14 18 PHGY H11 131 0.377663 1.0080 - 132 CPos 18 PHGY C2 132 0.354663 12.0110 - 133 HC 18 PHGY H3 133 0.025663 1.0080 - 134 HC 18 PHGY H4 134 0.025663 1.0080 - 135 C 18 PHGY C1 135 -0.036337 12.0110 - 136 HC 18 PHGY H1 136 0.065663 1.0080 - 137 HC 18 PHGY H2 137 0.065663 1.0080 - 138 HS14 19 PHGY H12 138 0.377490 1.0080 - 139 NPri 19 PHGY N2 139 -1.036510 14.0067 - 140 HS14 19 PHGY H11 140 0.377490 1.0080 - 141 CPos 19 PHGY C2 141 0.354490 12.0110 - 142 HC 19 PHGY H3 142 0.025490 1.0080 - 143 HC 19 PHGY H4 143 0.025490 1.0080 - 144 C 19 PHGY C1 144 -0.036510 12.0110 - 145 HC 19 PHGY H1 145 0.065490 1.0080 - 146 HC 19 PHGY H2 146 0.065490 1.0080 - 147 HS14 20 PHGY H12 147 0.377490 1.0080 - 148 NPri 20 PHGY N2 148 -1.036510 14.0067 - 149 HS14 20 PHGY H11 149 0.377490 1.0080 - 150 CPos 20 PHGY C2 150 0.354490 12.0110 - 151 HC 20 PHGY H3 151 0.025490 1.0080 - 152 HC 20 PHGY H4 152 0.025490 1.0080 - 153 C 20 PHGY C1 153 -0.036510 12.0110 - 154 HC 20 PHGY H1 154 0.065490 1.0080 - 155 HC 20 PHGY H2 155 0.065490 1.0080 - 156 HS14 21 PHGY H12 156 0.377693 1.0080 - 157 NPri 21 PHGY N2 157 -1.036307 14.0067 - 158 HS14 21 PHGY H11 158 0.377693 1.0080 - 159 CPos 21 PHGY C2 159 0.354693 12.0110 - 160 HC 21 PHGY H3 160 0.025693 1.0080 - 161 HC 21 PHGY H4 161 0.025693 1.0080 - 162 C 21 PHGY C1 162 -0.036307 12.0110 - 163 HC 21 PHGY H1 163 0.065693 1.0080 - 164 HC 21 PHGY H2 164 0.065693 1.0080 - 165 HS14 22 PHGY H12 165 0.377722 1.0080 - 166 NPri 22 PHGY N2 166 -1.036278 14.0067 - 167 HS14 22 PHGY H11 167 0.377722 1.0080 - 168 CPos 22 PHGY C2 168 0.354722 12.0110 - 169 HC 22 PHGY H3 169 0.025722 1.0080 - 170 HC 22 PHGY H4 170 0.025722 1.0080 - 171 C 22 PHGY C1 171 -0.036278 12.0110 - 172 HC 22 PHGY H1 172 0.065722 1.0080 - 173 HC 22 PHGY H2 173 0.065722 1.0080 - 174 HS14 23 PHGY H12 174 0.377742 1.0080 - 175 NPri 23 PHGY N2 175 -1.036258 14.0067 - 176 HS14 23 PHGY H11 176 0.377742 1.0080 - 177 CPos 23 PHGY C2 177 0.354742 12.0110 - 178 HC 23 PHGY H3 178 0.025742 1.0080 - 179 HC 23 PHGY H4 179 0.025742 1.0080 - 180 C 23 PHGY C1 180 -0.036258 12.0110 - 181 HC 23 PHGY H1 181 0.065742 1.0080 - 182 HC 23 PHGY H2 182 0.065742 1.0080 - 183 HS14 24 PHGY H12 183 0.377732 1.0080 - 184 NPri 24 PHGY N2 184 -1.036268 14.0067 - 185 HS14 24 PHGY H11 185 0.377732 1.0080 - 186 CPos 24 PHGY C2 186 0.354732 12.0110 - 187 HC 24 PHGY H3 187 0.025732 1.0080 - 188 HC 24 PHGY H4 188 0.025732 1.0080 - 189 C 24 PHGY C1 189 -0.036268 12.0110 - 190 HC 24 PHGY H1 190 0.065732 1.0080 - 191 HC 24 PHGY H2 191 0.065732 1.0080 - 192 HS14 25 PHGY H12 192 0.377712 1.0080 - 193 NPri 25 PHGY N2 193 -1.036288 14.0067 - 194 HS14 25 PHGY H11 194 0.377712 1.0080 - 195 CPos 25 PHGY C2 195 0.354712 12.0110 - 196 HC 25 PHGY H3 196 0.025712 1.0080 - 197 HC 25 PHGY H4 197 0.025712 1.0080 - 198 C 25 PHGY C1 198 -0.036288 12.0110 - 199 HC 25 PHGY H1 199 0.065712 1.0080 - 200 HC 25 PHGY H2 200 0.065712 1.0080 - 201 HS14 26 PHGY H12 201 0.377742 1.0080 - 202 NPri 26 PHGY N2 202 -1.036258 14.0067 - 203 HS14 26 PHGY H11 203 0.377742 1.0080 - 204 CPos 26 PHGY C2 204 0.354742 12.0110 - 205 HC 26 PHGY H3 205 0.025742 1.0080 - 206 HC 26 PHGY H4 206 0.025742 1.0080 - 207 C 26 PHGY C1 207 -0.036258 12.0110 - 208 HC 26 PHGY H1 208 0.065742 1.0080 - 209 HC 26 PHGY H2 209 0.065742 1.0080 - 210 HS14 27 PHGY H12 210 0.377732 1.0080 - 211 NPri 27 PHGY N2 211 -1.036268 14.0067 - 212 HS14 27 PHGY H11 212 0.377732 1.0080 - 213 CPos 27 PHGY C2 213 0.354732 12.0110 - 214 HC 27 PHGY H3 214 0.025732 1.0080 - 215 HC 27 PHGY H4 215 0.025732 1.0080 - 216 C 27 PHGY C1 216 -0.036268 12.0110 - 217 HC 27 PHGY H1 217 0.065732 1.0080 - 218 HC 27 PHGY H2 218 0.065732 1.0080 - 219 HS14 28 PHGY H12 219 0.377510 1.0080 - 220 NPri 28 PHGY N2 220 -1.036490 14.0067 - 221 HS14 28 PHGY H11 221 0.377510 1.0080 - 222 CPos 28 PHGY C2 222 0.354510 12.0110 - 223 HC 28 PHGY H3 223 0.025510 1.0080 - 224 HC 28 PHGY H4 224 0.025510 1.0080 - 225 C 28 PHGY C1 225 -0.036490 12.0110 - 226 HC 28 PHGY H1 226 0.065510 1.0080 - 227 HC 28 PHGY H2 227 0.065510 1.0080 - 228 HS14 29 PHGY H12 228 0.375659 1.0080 - 229 NPri 29 PHGY N2 229 -1.038342 14.0067 - 230 HS14 29 PHGY H11 230 0.375659 1.0080 - 231 CPos 29 PHGY C2 231 0.352658 12.0110 - 232 HC 29 PHGY H3 232 0.023658 1.0080 - 233 HC 29 PHGY H4 233 0.023658 1.0080 - 234 C 29 PHGY C1 234 -0.038342 12.0110 - 235 HC 29 PHGY H1 235 0.063658 1.0080 - 236 HC 29 PHGY H2 236 0.063658 1.0080 - -[ bonds ] - 1 16 2 0.1470 8.7100e+06 - 1 9 2 0.1470 8.7100e+06 - 1 2 2 0.1470 8.7100e+06 - 2 5 2 0.1540 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0.0000 5.9200e+00 3 - 1 9 12 15 1 0.0000 5.9200e+00 3 - 1 2 5 8 1 0.0000 5.9200e+00 3 - 2 5 8 23 1 180.0000 1.0000e+00 6 - 8 30 33 36 1 0.0000 5.9200e+00 3 - 8 23 26 29 1 0.0000 5.9200e+00 3 - 9 12 15 51 1 0.0000 3.7700e+00 6 - 15 72 75 78 1 0.0000 5.9200e+00 3 - 15 51 54 57 1 0.0000 5.9200e+00 3 - 16 19 22 37 1 0.0000 3.7700e+00 6 - 22 86 89 92 1 0.0000 5.9200e+00 3 - 22 37 40 43 1 0.0000 5.9200e+00 3 - 23 26 29 79 1 0.0000 3.7700e+00 6 - 29 58 61 64 1 0.0000 5.9200e+00 3 - 29 79 82 85 1 0.0000 5.9200e+00 3 - 30 33 36 65 1 0.0000 3.7700e+00 6 - 36 65 68 71 1 0.0000 5.9200e+00 3 - 36 44 47 50 1 0.0000 5.9200e+00 3 - 37 40 43 117 1 0.0000 3.7700e+00 6 - 112 114 117 43 1 0.0000 5.9200e+00 3 - 211 213 216 43 1 0.0000 5.9200e+00 3 - 44 47 50 171 1 0.0000 3.7700e+00 6 - 166 168 171 50 1 0.0000 5.9200e+00 3 - 175 177 180 50 1 0.0000 5.9200e+00 3 - 51 54 57 99 1 0.0000 3.7700e+00 6 - 94 96 99 57 1 0.0000 5.9200e+00 3 - 139 141 144 57 1 0.0000 5.9200e+00 3 - 58 61 64 189 1 0.0000 3.7700e+00 6 - 121 123 126 64 1 0.0000 5.9200e+00 3 - 184 186 189 64 1 0.0000 5.9200e+00 3 - 65 68 71 207 1 0.0000 3.7700e+00 6 - 103 105 108 71 1 0.0000 5.9200e+00 3 - 202 204 207 71 1 0.0000 5.9200e+00 3 - 72 75 78 135 1 0.0000 3.7700e+00 6 - 130 132 135 78 1 0.0000 5.9200e+00 3 - 157 159 162 78 1 0.0000 5.9200e+00 3 - 79 82 85 225 1 0.0000 3.7700e+00 6 - 220 222 225 85 1 0.0000 5.9200e+00 3 - 193 195 198 85 1 0.0000 5.9200e+00 3 - 86 89 92 153 1 0.0000 3.7700e+00 6 - 148 150 153 92 1 0.0000 5.9200e+00 3 - 229 231 234 92 1 0.0000 5.9200e+00 3 - 95 94 96 99 1 180.0000 1.0000e+00 6 - 104 103 105 108 1 180.0000 1.0000e+00 6 - 113 112 114 117 1 180.0000 1.0000e+00 6 - 122 121 123 126 1 180.0000 1.0000e+00 6 - 131 130 132 135 1 180.0000 1.0000e+00 6 - 140 139 141 144 1 180.0000 1.0000e+00 6 - 149 148 150 153 1 180.0000 1.0000e+00 6 - 158 157 159 162 1 180.0000 1.0000e+00 6 - 167 166 168 171 1 180.0000 1.0000e+00 6 - 176 175 177 180 1 180.0000 1.0000e+00 6 - 185 184 186 189 1 180.0000 1.0000e+00 6 - 194 193 195 198 1 180.0000 1.0000e+00 6 - 203 202 204 207 1 180.0000 1.0000e+00 6 - 212 211 213 216 1 180.0000 1.0000e+00 6 - 221 220 222 225 1 180.0000 1.0000e+00 6 - 230 229 231 234 1 180.0000 1.0000e+00 6 - -[ exclusions ] From 396909e275fe27f5223fd901b31fa8593e04110e Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:40:16 +1100 Subject: [PATCH 12/14] Delete polytop_examples/data/ethylamine_dendrimer.json --- polytop_examples/data/ethylamine_dendrimer.json | 1 - 1 file changed, 1 deletion(-) delete mode 100644 polytop_examples/data/ethylamine_dendrimer.json diff --git a/polytop_examples/data/ethylamine_dendrimer.json b/polytop_examples/data/ethylamine_dendrimer.json deleted file mode 100644 index ba4a9ec..0000000 --- a/polytop_examples/data/ethylamine_dendrimer.json +++ /dev/null @@ -1 +0,0 @@ -{"topology": {"atoms": [{"atom_id": 1, "atom_type": "CPos", "residue_id": 1, "residue_name": "6HTJ", "atom_name": "C6", 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"pair_type": 1}], "exclusions": [], "preamble": [";----------------------------TITLE -----------------------------------------------------------------------------------------", "; None", ";", "; This file was generated at 14:09 on 2024-12-06 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2024-11-20 12:06:25", ";---------------------------------------------------------------------------------------------------------------------------", "; Authors : Martin Stroet, Bertrand Caron, Alpeshkumar K. Malde, Thomas Lee, Alan E. Mark", ";", "; Institute : Molecular Dynamics group,", "; School of Chemistry and Molecular Biosciences (SCMB),", "; The University of Queensland, QLD 4072, Australia", "; URL : https://atb.uq.edu.au", "; Citations : 1. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.", "; An Automated force field Topology Builder (ATB) and repository: version 1.0.", "; Journal of Chemical Theory and Computation, 2011, 7, 4026-4037.", "; 2. Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.", "; Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.", "; DOI:10.1021/acs.jctc.8b00768", ";", "; Disclaimer :", "; While every effort has been made to ensure the accuracy and validity of parameters provided below", "; the assignment of parameters is being based on an automated procedure combining data provided by a", "; given user as well as calculations performed using third party software. They are provided as a guide.", "; The authors of the ATB cannot guarantee that the parameters are complete or that the parameters provided", "; are appropriate for use in any specific application. Users are advised to treat these parameters with discretion", "; and to perform additional validation tests for their specific application if required. Neither the authors", "; of the ATB or The University of Queensland except any responsibly for how the parameters may be used.", ";", "; Release notes and warnings:", "; (1) The topology is based on a set of atomic coordinates and other data provided by the user after", "; after quantum mechanical optimization of the structure using different levels of theory depending on", "; the nature of the molecule.", "; (2) In some cases the automatic bond, bond angle and dihedral type assignment is ambiguous.", "; In these cases alternative type codes are provided at the end of the line.", "; (3) While bonded parameters are taken where possible from the nominated force field non-standard bond, angle and dihedral", "; type code may be incorporated in cases where an exact match could not be found. These are marked as \"non-standard\"", "; or \"uncertain\" in comments.", "; (4) In some cases it is not possible to assign an appropriate parameter automatically. \"%%\" is used as a place holder", "; for those fields that could not be determined automatically. The parameters in these fields must be assigned manually", "; before the file can be used.", ";---------------------------------------------------------------------------------------------------------------------------", "; Input Structure : 6HTJ", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 1746623", "; ATB Topology Hash: f4741", ";---------------------------------------------------------------------------------------------------------------------------", "; Final Topology Generation was performed using:", "; A B3LYP/6-31G* optimized geometry.", "; Bonded and van der Waals parameters were taken from the GROMOS 54A7 parameter set.", "; Initial charges were estimated using the ESP method of Merz-Kollman.", "; Final charges and charge groups were generated by method described in the ATB paper.", "; If required, additional bonded parameters were generated from a Hessian matrix calculated at the B3LYP/6-31G* level of theory.", ";---------------------------------------------------------------------------------------------------------------------------", ";", ";"], "moleculetype": {"name": "6HTJ", "nrexcl": 3}}, "junctions": []} \ No newline at end of file From 5b17ca531c979cfa8da9de5464a63211918ac6d7 Mon Sep 17 00:00:00 2001 From: Ada <85986321+recombinatrix@users.noreply.github.com> Date: Mon, 24 Feb 2025 11:40:25 +1100 Subject: [PATCH 13/14] Delete polytop_examples/data/ethylamine_dendrimer.png --- polytop_examples/data/ethylamine_dendrimer.png | Bin 22654 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 polytop_examples/data/ethylamine_dendrimer.png diff --git a/polytop_examples/data/ethylamine_dendrimer.png b/polytop_examples/data/ethylamine_dendrimer.png deleted file mode 100644 index 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insertions(+), 0 deletions(-) delete mode 100644 polybuild/.DS_Store diff --git a/polybuild/.DS_Store b/polybuild/.DS_Store deleted file mode 100644 index c44b6ff3259fe4663e91547f915496a2272c3fb6..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHKyG{c!5S)b+k