From b68a90d85d06517f23e47afe712a6451908b1227 Mon Sep 17 00:00:00 2001 From: lunamorrow Date: Fri, 14 Feb 2025 15:33:07 +1000 Subject: [PATCH] Replace 'paper_worked_examples.ipynb' with a set of scripts to remove reliability on Jupyter Notebooks. As part of this, renamed 'data_paper_examples' to 'polytop_examples', placed the new scripts in this folder, placed all data and output files into a new subfolder 'data' and removed data files no longer required/used --- data_paper_examples/ethanol.itp | 124 --- data_paper_examples/ethylene_glycol.itp | 131 --- data_paper_examples/polyester.itp | 817 ------------------ data_paper_examples/polyester.png | Bin 12883 -> 0 bytes data_paper_examples/propanol.itp | 146 ---- .../six_arm_star_monomer_build.itp | 774 ----------------- .../six_arm_star_monomer_build.json | 1 - .../six_arm_star_monomer_build.png | Bin 17408 -> 0 bytes data_paper_examples/terephthalic_acid.itp | 193 ----- paper_worked_examples.ipynb | 409 --------- .../data}/dendrimer_bifurcating.itp | 0 .../data}/dendrimer_core.itp | 0 .../data}/dendrimer_terminal.itp | 0 .../data}/ethylamine_dendrimer.itp | 0 .../data}/ethylamine_dendrimer.json | 0 .../data}/ethylamine_dendrimer.png | Bin .../data}/extended_ethanol.itp | 0 .../data}/extended_methane.itp | 0 .../data}/extended_neopentane.itp | 0 .../four_arm_star_overlapped_monomers.itp | 0 .../four_arm_star_overlapped_monomers.json | 0 .../four_arm_star_overlapped_monomers.png | Bin .../data}/pei.itp | 0 .../data}/pei_linear_polymer.itp | 0 .../data}/pei_linear_polymer.json | 0 .../data}/pei_linear_polymer.png | Bin polytop_examples/dendrimer_ethylamine.py | 87 ++ polytop_examples/linear_PEI.py | 33 + polytop_examples/star_PEG.py | 73 ++ 29 files changed, 193 insertions(+), 2595 deletions(-) delete mode 100644 data_paper_examples/ethanol.itp delete mode 100644 data_paper_examples/ethylene_glycol.itp delete mode 100644 data_paper_examples/polyester.itp delete mode 100644 data_paper_examples/polyester.png delete mode 100644 data_paper_examples/propanol.itp delete mode 100644 data_paper_examples/six_arm_star_monomer_build.itp delete mode 100644 data_paper_examples/six_arm_star_monomer_build.json delete mode 100644 data_paper_examples/six_arm_star_monomer_build.png delete mode 100644 data_paper_examples/terephthalic_acid.itp delete mode 100644 paper_worked_examples.ipynb rename {data_paper_examples => polytop_examples/data}/dendrimer_bifurcating.itp (100%) rename {data_paper_examples => polytop_examples/data}/dendrimer_core.itp (100%) rename {data_paper_examples => polytop_examples/data}/dendrimer_terminal.itp (100%) rename {data_paper_examples => polytop_examples/data}/ethylamine_dendrimer.itp (100%) rename {data_paper_examples => polytop_examples/data}/ethylamine_dendrimer.json (100%) rename {data_paper_examples => polytop_examples/data}/ethylamine_dendrimer.png (100%) rename {data_paper_examples => polytop_examples/data}/extended_ethanol.itp (100%) rename {data_paper_examples => polytop_examples/data}/extended_methane.itp (100%) rename {data_paper_examples => polytop_examples/data}/extended_neopentane.itp (100%) rename {data_paper_examples => polytop_examples/data}/four_arm_star_overlapped_monomers.itp (100%) rename {data_paper_examples => polytop_examples/data}/four_arm_star_overlapped_monomers.json (100%) rename {data_paper_examples => polytop_examples/data}/four_arm_star_overlapped_monomers.png (100%) rename {data_paper_examples => polytop_examples/data}/pei.itp (100%) rename {data_paper_examples => polytop_examples/data}/pei_linear_polymer.itp (100%) rename {data_paper_examples => polytop_examples/data}/pei_linear_polymer.json (100%) rename {data_paper_examples => polytop_examples/data}/pei_linear_polymer.png (100%) create mode 100644 polytop_examples/dendrimer_ethylamine.py create mode 100644 polytop_examples/linear_PEI.py create mode 100644 polytop_examples/star_PEG.py diff --git a/data_paper_examples/ethanol.itp b/data_paper_examples/ethanol.itp deleted file mode 100644 index 2c96bda..0000000 --- a/data_paper_examples/ethanol.itp +++ /dev/null @@ -1,124 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; Ethanol -; -; This file was generated at 18:19 on 2023-07-31 by -; -; Automatic Topology Builder -; -; REVISION 2023-06-14 20:38:16 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 : BWD8 -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 360413 -; ATB Topology Hash: 940bb -;--------------------------------------------------------------------------------------------------------------------------- -; 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 nrexcl -BWD8 3 -[ atoms ] -; nr type resnr resid atom cgnr charge mass - 1 HS14 1 BWD8 H6 1 0.413 1.0080 - 2 OAlc 1 BWD8 O1 2 -0.679 15.9994 - 3 CPos 1 BWD8 C1 3 0.372 12.0110 - 4 HC 1 BWD8 H1 4 -0.029 1.0080 - 5 HC 1 BWD8 H2 5 -0.029 1.0080 - 6 C 1 BWD8 C2 6 -0.285 12.0110 - 7 HC 1 BWD8 H3 7 0.079 1.0080 - 8 HC 1 BWD8 H4 8 0.079 1.0080 - 9 HC 1 BWD8 H5 9 0.079 1.0080 -; total charge of the molecule: -0.000 -[ bonds ] -; ai aj funct c0 c1 - 1 2 2 0.0972 1.9581e+07 - 2 3 2 0.1430 8.1800e+06 - 3 4 2 0.1100 1.2100e+07 - 3 5 2 0.1100 1.2100e+07 - 3 6 2 0.1520 5.4300e+06 - 6 7 2 0.1090 1.2300e+07 - 6 8 2 0.1090 1.2300e+07 - 6 9 2 0.1090 1.2300e+07 -[ pairs ] -; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp - 1 4 1 - 1 5 1 - 1 6 1 - 2 7 1 - 2 8 1 - 2 9 1 - 4 7 1 - 4 8 1 - 4 9 1 - 5 7 1 - 5 8 1 - 5 9 1 -[ angles ] -; ai aj ak funct angle fc - 1 2 3 2 109.50 450.00 - 2 3 4 2 111.00 530.00 - 2 3 5 2 111.00 530.00 - 2 3 6 2 109.50 520.00 - 4 3 5 2 107.57 484.00 - 4 3 6 2 110.30 524.00 - 5 3 6 2 110.30 524.00 - 3 6 7 2 110.30 524.00 - 3 6 8 2 110.30 524.00 - 3 6 9 2 110.30 524.00 - 7 6 8 2 108.53 443.00 - 7 6 9 2 108.53 443.00 - 8 6 9 2 108.53 443.00 -[ dihedrals ] -; GROMOS improper dihedrals -; ai aj ak al funct angle fc -[ dihedrals ] -; ai aj ak al funct ph0 cp mult - 1 2 3 6 1 0.00 1.26 3 - 2 3 6 7 1 0.00 5.92 3 -[ exclusions ] -; ai aj funct ; GROMOS 1-4 exclusions \ No newline at end of file diff --git a/data_paper_examples/ethylene_glycol.itp b/data_paper_examples/ethylene_glycol.itp deleted file mode 100644 index f67eb37..0000000 --- a/data_paper_examples/ethylene_glycol.itp +++ /dev/null @@ -1,131 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; Ethyleneglycol -; -; This file was generated at 07:17 on 2023-10-20 by -; -; Automatic Topology Builder -; -; REVISION 2023-06-14 20:38:16 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 : E6SD -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 30424 -; ATB Topology Hash: 022f3 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 nrexcl -E6SD 3 -[ atoms ] -; nr type resnr resid atom cgnr charge mass - 1 H 1 E6SD H6 1 0.414 1.0080 - 2 OAlc 1 E6SD O2 2 -0.633 15.9994 - 3 CPos 1 E6SD C2 3 0.139 12.0110 - 4 HC 1 E6SD H3 4 0.040 1.0080 - 5 HC 1 E6SD H4 5 0.040 1.0080 - 6 CPos 1 E6SD C1 6 0.139 12.0110 - 7 HC 1 E6SD H1 7 0.040 1.0080 - 8 HC 1 E6SD H2 8 0.040 1.0080 - 9 OAlc 1 E6SD O1 9 -0.633 15.9994 - 10 H 1 E6SD H5 10 0.414 1.0080 -; total charge of the molecule: 0.000 -[ bonds ] -; ai aj funct c0 c1 - 1 2 2 0.0972 1.9581e+07 - 2 3 2 0.1430 8.1800e+06 - 3 4 2 0.1090 1.2300e+07 - 3 5 2 0.1090 1.2300e+07 - 3 6 2 0.1520 5.4300e+06 - 6 7 2 0.1090 1.2300e+07 - 6 8 2 0.1090 1.2300e+07 - 6 9 2 0.1430 8.1800e+06 - 9 10 2 0.0972 1.9581e+07 -[ pairs ] -; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp - 1 4 1 - 1 5 1 - 1 6 1 - 2 7 1 - 2 8 1 - 2 9 1 - 3 10 1 - 4 7 1 - 4 8 1 - 4 9 1 - 5 7 1 - 5 8 1 - 5 9 1 - 7 10 1 - 8 10 1 -[ angles ] -; ai aj ak funct angle fc - 1 2 3 2 109.50 450.00 - 2 3 4 2 107.57 484.00 - 2 3 5 2 107.57 484.00 - 2 3 6 2 109.50 520.00 - 4 3 5 2 108.53 443.00 - 4 3 6 2 109.60 450.00 - 5 3 6 2 109.60 450.00 - 3 6 7 2 109.60 450.00 - 3 6 8 2 109.60 450.00 - 3 6 9 2 109.50 520.00 - 7 6 8 2 108.53 443.00 - 7 6 9 2 107.57 484.00 - 8 6 9 2 107.57 484.00 - 6 9 10 2 109.50 450.00 -[ dihedrals ] -; GROMOS improper dihedrals -; ai aj ak al funct angle fc -[ dihedrals ] -; ai aj ak al funct ph0 cp mult - 1 2 3 6 1 0.00 1.26 3 - 2 3 6 9 1 0.00 5.92 3 - 3 6 9 10 1 0.00 1.26 3 -[ exclusions ] -; ai aj funct ; GROMOS 1-4 exclusions \ No newline at end of file diff --git a/data_paper_examples/polyester.itp b/data_paper_examples/polyester.itp deleted file mode 100644 index 288c74d..0000000 --- a/data_paper_examples/polyester.itp +++ /dev/null @@ -1,817 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; Ethyleneglycol -; -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; Ethyleneglycol -; -; This file was generated at 07:17 on 2023-10-20 by -; -; Automatic Topology Builder -; -; REVISION 2023-06-14 20:38:16 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 : E6SD -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 30424 -; ATB Topology Hash: 022f3 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 ] -E6SD 3 -[ atoms ] - 1 H 1 E6SD H6 1 0.425720 1.0080 - 2 OAlc 1 E6SD O2 2 -0.621280 15.9994 - 3 CPos 1 E6SD C2 3 0.150720 12.0110 - 4 HC 1 E6SD H3 4 0.051720 1.0080 - 5 HC 1 E6SD H4 5 0.051720 1.0080 - 6 CPos 1 E6SD C1 6 0.150720 12.0110 - 7 HC 1 E6SD H1 7 0.051720 1.0080 - 8 HC 1 E6SD H2 8 0.051720 1.0080 - 9 OAlc 1 E6SD O1 9 -0.621280 15.9994 - 10 CPos 2 _MJ4 C7 10 0.664478 12.0110 - 11 OEOpt 2 _MJ4 O1 11 -0.524522 15.9994 - 12 CAro 2 _MJ4 C6 12 0.019478 12.0110 - 13 CAro 2 _MJ4 C1 13 -0.099522 12.0110 - 14 HC 2 _MJ4 H1 14 0.169478 1.0080 - 15 CAro 2 _MJ4 C2 15 -0.099522 12.0110 - 16 HC 2 _MJ4 H2 16 0.169478 1.0080 - 17 CAro 2 _MJ4 C3 17 0.019478 12.0110 - 18 CAro 2 _MJ4 C4 18 -0.099522 12.0110 - 19 HC 2 _MJ4 H3 19 0.169478 1.0080 - 20 CAro 2 _MJ4 C5 20 -0.099522 12.0110 - 21 HC 2 _MJ4 H4 21 0.169478 1.0080 - 22 CPos 2 _MJ4 C8 22 0.664478 12.0110 - 23 OEOpt 2 _MJ4 O2 23 -0.524522 15.9994 - 24 OAlc 3 E6SD O2 24 -0.606460 15.9994 - 25 CPos 3 E6SD C2 25 0.165540 12.0110 - 26 HC 3 E6SD H3 26 0.066540 1.0080 - 27 HC 3 E6SD H4 27 0.066540 1.0080 - 28 CPos 3 E6SD C1 28 0.165540 12.0110 - 29 HC 3 E6SD H1 29 0.066540 1.0080 - 30 HC 3 E6SD H2 30 0.066540 1.0080 - 31 OAlc 3 E6SD O1 31 -0.606460 15.9994 - 32 CPos 4 _MJ4 C7 32 0.665632 12.0110 - 33 OEOpt 4 _MJ4 O1 33 -0.523368 15.9994 - 34 CAro 4 _MJ4 C6 34 0.020632 12.0110 - 35 CAro 4 _MJ4 C1 35 -0.098368 12.0110 - 36 HC 4 _MJ4 H1 36 0.170632 1.0080 - 37 CAro 4 _MJ4 C2 37 -0.098368 12.0110 - 38 HC 4 _MJ4 H2 38 0.170632 1.0080 - 39 CAro 4 _MJ4 C3 39 0.020632 12.0110 - 40 CAro 4 _MJ4 C4 40 -0.098368 12.0110 - 41 HC 4 _MJ4 H3 41 0.170632 1.0080 - 42 CAro 4 _MJ4 C5 42 -0.098368 12.0110 - 43 HC 4 _MJ4 H4 43 0.170632 1.0080 - 44 CPos 4 _MJ4 C8 44 0.665632 12.0110 - 45 OEOpt 4 _MJ4 O2 45 -0.523368 15.9994 - 46 OAlc 5 E6SD O2 46 -0.606364 15.9994 - 47 CPos 5 E6SD C2 47 0.165636 12.0110 - 48 HC 5 E6SD H3 48 0.066636 1.0080 - 49 HC 5 E6SD H4 49 0.066636 1.0080 - 50 CPos 5 E6SD C1 50 0.165636 12.0110 - 51 HC 5 E6SD H1 51 0.066636 1.0080 - 52 HC 5 E6SD H2 52 0.066636 1.0080 - 53 OAlc 5 E6SD O1 53 -0.606364 15.9994 - 54 CPos 6 _MJ4 C7 54 0.665636 12.0110 - 55 OEOpt 6 _MJ4 O1 55 -0.523364 15.9994 - 56 CAro 6 _MJ4 C6 56 0.020636 12.0110 - 57 CAro 6 _MJ4 C1 57 -0.098364 12.0110 - 58 HC 6 _MJ4 H1 58 0.170636 1.0080 - 59 CAro 6 _MJ4 C2 59 -0.098364 12.0110 - 60 HC 6 _MJ4 H2 60 0.170636 1.0080 - 61 CAro 6 _MJ4 C3 61 0.020636 12.0110 - 62 CAro 6 _MJ4 C4 62 -0.098364 12.0110 - 63 HC 6 _MJ4 H3 63 0.170636 1.0080 - 64 CAro 6 _MJ4 C5 64 -0.098364 12.0110 - 65 HC 6 _MJ4 H4 65 0.170636 1.0080 - 66 CPos 6 _MJ4 C8 66 0.665636 12.0110 - 67 OEOpt 6 _MJ4 O2 67 -0.523364 15.9994 - 68 OAlc 7 E6SD O2 68 -0.606364 15.9994 - 69 CPos 7 E6SD C2 69 0.165636 12.0110 - 70 HC 7 E6SD H3 70 0.066636 1.0080 - 71 HC 7 E6SD H4 71 0.066636 1.0080 - 72 CPos 7 E6SD C1 72 0.165636 12.0110 - 73 HC 7 E6SD H1 73 0.066636 1.0080 - 74 HC 7 E6SD H2 74 0.066636 1.0080 - 75 OAlc 7 E6SD O1 75 -0.606364 15.9994 - 76 CPos 8 _MJ4 C7 76 0.665636 12.0110 - 77 OEOpt 8 _MJ4 O1 77 -0.523364 15.9994 - 78 CAro 8 _MJ4 C6 78 0.020636 12.0110 - 79 CAro 8 _MJ4 C1 79 -0.098364 12.0110 - 80 HC 8 _MJ4 H1 80 0.170636 1.0080 - 81 CAro 8 _MJ4 C2 81 -0.098364 12.0110 - 82 HC 8 _MJ4 H2 82 0.170636 1.0080 - 83 CAro 8 _MJ4 C3 83 0.020636 12.0110 - 84 CAro 8 _MJ4 C4 84 -0.098364 12.0110 - 85 HC 8 _MJ4 H3 85 0.170636 1.0080 - 86 CAro 8 _MJ4 C5 86 -0.098364 12.0110 - 87 HC 8 _MJ4 H4 87 0.170636 1.0080 - 88 CPos 8 _MJ4 C8 88 0.665636 12.0110 - 89 OEOpt 8 _MJ4 O2 89 -0.523364 15.9994 - 90 OAlc 9 E6SD O2 90 -0.606364 15.9994 - 91 CPos 9 E6SD C2 91 0.165636 12.0110 - 92 HC 9 E6SD H3 92 0.066636 1.0080 - 93 HC 9 E6SD H4 93 0.066636 1.0080 - 94 CPos 9 E6SD C1 94 0.165636 12.0110 - 95 HC 9 E6SD H1 95 0.066636 1.0080 - 96 HC 9 E6SD H2 96 0.066636 1.0080 - 97 OAlc 9 E6SD O1 97 -0.606364 15.9994 - 98 CPos 10 _MJ4 C7 98 0.665636 12.0110 - 99 OEOpt 10 _MJ4 O1 99 -0.523364 15.9994 - 100 CAro 10 _MJ4 C6 100 0.020636 12.0110 - 101 CAro 10 _MJ4 C1 101 -0.098364 12.0110 - 102 HC 10 _MJ4 H1 102 0.170636 1.0080 - 103 CAro 10 _MJ4 C2 103 -0.098364 12.0110 - 104 HC 10 _MJ4 H2 104 0.170636 1.0080 - 105 CAro 10 _MJ4 C3 105 0.020636 12.0110 - 106 CAro 10 _MJ4 C4 106 -0.098364 12.0110 - 107 HC 10 _MJ4 H3 107 0.170636 1.0080 - 108 CAro 10 _MJ4 C5 108 -0.098364 12.0110 - 109 HC 10 _MJ4 H4 109 0.170636 1.0080 - 110 CPos 10 _MJ4 C8 110 0.665636 12.0110 - 111 OEOpt 10 _MJ4 O2 111 -0.523364 15.9994 - 112 OAlc 11 E6SD O2 112 -0.619149 15.9994 - 113 CPos 11 E6SD C2 113 0.152851 12.0110 - 114 HC 11 E6SD H3 114 0.053851 1.0080 - 115 HC 11 E6SD H4 115 0.053851 1.0080 - 116 CPos 11 E6SD C1 116 0.152851 12.0110 - 117 HC 11 E6SD H1 117 0.053851 1.0080 - 118 HC 11 E6SD H2 118 0.053851 1.0080 - 119 OAlc 11 E6SD O1 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zMTnI_XT{*B=sBw6Y)r0U*!m$-i*}Fso)rN@;V`TLeuWYLVA?ZAC8LRigzWUMqbf*? zO9?CdH(*n!*cU>;^!zrOz;-GcuaDb;-+fQg>O}DB^1D-s%8a>)zO-y5+7rdAGw$Ne z)w8Rm6K1fq~^Sw*_xjl~09FB0Xvz8k4lv4cQ zHot~8-}U6kh*MHvW{h)#iJtASSkgbhOZL<8NZ0YkfGb$d8`%4fjqo^2kDLs(6cN{(zSuwP~!*WY5VJ zKS}shCoLzY{E|YNeIf__zK=q6(rkkf)fLi_7WBvcxpn!6VgZiZcLa?DjcDi&^vyMI z)2u@6T==z^z8<{$9r%1uI;uc3OeG*Ug#Q!TT0qc8J)KciW$$CWsA=6gG>N*e?RAwe zHR=zS+u}XYh|W&~TPWnn776%@7mN8W+?ysYv}KDQjvj^@_?jN>QBG|Im`ihWHo*T9 OK@u015h@bU_4+@nzPpbA diff --git a/data_paper_examples/propanol.itp b/data_paper_examples/propanol.itp deleted file mode 100644 index 77b452a..0000000 --- a/data_paper_examples/propanol.itp +++ /dev/null @@ -1,146 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; 1-Propanol -; -; This file was generated at 03:55 on 2023-10-20 by -; -; Automatic Topology Builder -; -; REVISION 2023-06-14 20:38:16 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 : 6ZJN -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 26332 -; ATB Topology Hash: 95165 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 nrexcl -6ZJN 3 -[ atoms ] -; nr type resnr resid atom cgnr charge mass - 1 HS14 1 6ZJN HAH 1 0.419 1.0080 - 2 OAlc 1 6ZJN OAB 2 -0.690 15.9994 - 3 CPos 1 6ZJN CAD 3 0.240 12.0110 - 4 HC 1 6ZJN HAF 4 0.014 1.0080 - 5 HC 1 6ZJN HAG 5 0.014 1.0080 - 6 C 1 6ZJN CAC 6 0.075 12.0110 - 7 HC 1 6ZJN HAD 7 0.000 1.0080 - 8 HC 1 6ZJN HAE 8 0.000 1.0080 - 9 C 1 6ZJN CAA 9 -0.282 12.0110 - 10 HC 1 6ZJN HAA 10 0.070 1.0080 - 11 HC 1 6ZJN HAB 11 0.070 1.0080 - 12 HC 1 6ZJN HAC 12 0.070 1.0080 -; total charge of the molecule: 0.000 -[ bonds ] -; ai aj funct c0 c1 - 1 2 2 0.0971 7.9547e+06 - 2 3 2 0.1430 8.1800e+06 - 3 4 2 0.1090 1.2300e+07 - 3 5 2 0.1090 1.2300e+07 - 3 6 2 0.1530 7.1500e+06 - 6 7 2 0.1090 1.2300e+07 - 6 8 2 0.1090 1.2300e+07 - 6 9 2 0.1530 7.1500e+06 - 9 10 2 0.1090 1.2300e+07 - 9 11 2 0.1090 1.2300e+07 - 9 12 2 0.1090 1.2300e+07 -[ pairs ] -; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp - 1 4 1 - 1 5 1 - 1 6 1 - 2 7 1 - 2 8 1 - 2 9 1 - 3 10 1 - 3 11 1 - 3 12 1 - 4 7 1 - 4 8 1 - 4 9 1 - 5 7 1 - 5 8 1 - 5 9 1 - 7 10 1 - 7 11 1 - 7 12 1 - 8 10 1 - 8 11 1 - 8 12 1 -[ angles ] -; ai aj ak funct angle fc - 1 2 3 2 109.50 450.00 - 2 3 4 2 111.00 530.00 - 2 3 5 2 111.00 530.00 - 2 3 6 2 111.00 530.00 - 4 3 5 2 107.57 484.00 - 4 3 6 2 110.30 524.00 - 5 3 6 2 110.30 524.00 - 3 6 7 2 108.53 443.00 - 3 6 8 2 108.53 443.00 - 3 6 9 2 111.00 530.00 - 7 6 8 2 106.75 503.00 - 7 6 9 2 110.30 524.00 - 8 6 9 2 110.30 524.00 - 6 9 10 2 111.30 632.00 - 6 9 11 2 111.30 632.00 - 6 9 12 2 111.30 632.00 - 10 9 11 2 107.60 507.00 - 10 9 12 2 107.60 507.00 - 11 9 12 2 107.60 507.00 -[ dihedrals ] -; GROMOS improper dihedrals -; ai aj ak al funct angle fc -[ dihedrals ] -; ai aj ak al funct ph0 cp mult - 1 2 3 6 1 0.00 1.26 3 - 2 3 6 9 1 0.00 5.92 3 - 3 6 9 10 1 0.00 5.92 3 -[ exclusions ] -; ai aj funct ; GROMOS 1-4 exclusions \ No newline at end of file diff --git a/data_paper_examples/six_arm_star_monomer_build.itp b/data_paper_examples/six_arm_star_monomer_build.itp deleted file mode 100644 index f5d3261..0000000 --- a/data_paper_examples/six_arm_star_monomer_build.itp +++ /dev/null @@ -1,774 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; six arm star polymer - from monomers -; -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; Ethanol -; -; This file was generated at 18:19 on 2023-07-31 by -; -; Automatic Topology Builder -; -; REVISION 2023-06-14 20:38:16 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 : BWD8 -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 360413 -; ATB Topology Hash: 940bb -;--------------------------------------------------------------------------------------------------------------------------- -; 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 ] -BWD8 3 -[ atoms ] - 1 OAlc 1 BWD8 O1 1 -0.648250 15.9994 - 2 CPos 1 BWD8 C1 2 0.402750 12.0110 - 3 HC 1 BWD8 H1 3 0.001750 1.0080 - 4 HC 1 BWD8 H2 4 0.001750 1.0080 - 5 C 1 BWD8 C2 5 -0.254250 12.0110 - 6 HC 1 BWD8 H5 6 0.109750 1.0080 - 7 OAlc 2 BWD8 O1 7 -0.613400 15.9994 - 8 CPos 2 BWD8 C1 8 0.437600 12.0110 - 9 HC 2 BWD8 H1 9 0.036600 1.0080 - 10 HC 2 BWD8 H2 10 0.036600 1.0080 - 11 C 2 BWD8 C2 11 -0.219400 12.0110 - 12 HC 2 BWD8 H5 12 0.144600 1.0080 - 13 OAlc 3 BWD8 O1 13 -0.631161 15.9994 - 14 CPos 3 BWD8 C1 14 0.419839 12.0110 - 15 HC 3 BWD8 H1 15 0.018839 1.0080 - 16 HC 3 BWD8 H2 16 0.018839 1.0080 - 17 C 3 BWD8 C2 17 -0.237161 12.0110 - 18 HC 3 BWD8 H5 18 0.126839 1.0080 - 19 CPos 4 BWD8 C1 19 0.406948 12.0110 - 20 HC 4 BWD8 H2 20 0.005948 1.0080 - 21 C 4 BWD8 C2 21 -0.250052 12.0110 - 22 HC 4 BWD8 H4 22 0.113948 1.0080 - 23 HC 4 BWD8 H5 23 0.113948 1.0080 - 24 OAlc 5 BWD8 O1 24 -0.615466 15.9994 - 25 CPos 5 BWD8 C1 25 0.435534 12.0110 - 26 HC 5 BWD8 H1 26 0.034534 1.0080 - 27 HC 5 BWD8 H2 27 0.034534 1.0080 - 28 HC 5 BWD8 H4 28 0.142534 1.0080 - 29 HC 5 BWD8 H5 29 0.142534 1.0080 - 30 C 5 BWD8 C2 30 -0.221466 12.0110 - 31 OAlc 5 6ZJN OAB 31 -0.626466 15.9994 - 32 CPos 5 6ZJN CAD 32 0.303534 12.0110 - 33 HC 5 6ZJN HAF 33 0.077534 1.0080 - 34 HC 5 6ZJN HAG 34 0.077534 1.0080 - 35 C 5 6ZJN CAC 35 0.138534 12.0110 - 36 HC 5 6ZJN HAD 36 0.063534 1.0080 - 37 HC 5 6ZJN HAE 37 0.063534 1.0080 - 38 C 5 6ZJN CAA 38 -0.218466 12.0110 - 39 HC 5 6ZJN HAA 39 0.133534 1.0080 - 40 HC 5 6ZJN HAB 40 0.133534 1.0080 - 41 HC 5 6ZJN HAC 41 0.133534 1.0080 - 42 OAlc 6 BWD8 O1 42 -0.621700 15.9994 - 43 CPos 6 BWD8 C1 43 0.429300 12.0110 - 44 HC 6 BWD8 H1 44 0.028300 1.0080 - 45 HC 6 BWD8 H2 45 0.028300 1.0080 - 46 HC 6 BWD8 H4 46 0.136300 1.0080 - 47 HC 6 BWD8 H5 47 0.136300 1.0080 - 48 C 6 BWD8 C2 48 -0.227700 12.0110 - 49 OAlc 6 6ZJN OAB 49 -0.632700 15.9994 - 50 CPos 6 6ZJN CAD 50 0.297300 12.0110 - 51 HC 6 6ZJN HAF 51 0.071300 1.0080 - 52 HC 6 6ZJN HAG 52 0.071300 1.0080 - 53 C 6 6ZJN CAC 53 0.132300 12.0110 - 54 HC 6 6ZJN HAD 54 0.057300 1.0080 - 55 HC 6 6ZJN HAE 55 0.057300 1.0080 - 56 C 6 6ZJN CAA 56 -0.224700 12.0110 - 57 HC 6 6ZJN HAA 57 0.127300 1.0080 - 58 HC 6 6ZJN HAB 58 0.127300 1.0080 - 59 HC 6 6ZJN HAC 59 0.127300 1.0080 - 60 OAlc 7 BWD8 O1 60 -0.620849 15.9994 - 61 CPos 7 BWD8 C1 61 0.430151 12.0110 - 62 HC 7 BWD8 H1 62 0.029151 1.0080 - 63 HC 7 BWD8 H2 63 0.029151 1.0080 - 64 HC 7 BWD8 H4 64 0.137151 1.0080 - 65 HC 7 BWD8 H5 65 0.137151 1.0080 - 66 C 7 BWD8 C2 66 -0.226849 12.0110 - 67 OAlc 7 6ZJN OAB 67 -0.631849 15.9994 - 68 CPos 7 6ZJN CAD 68 0.298151 12.0110 - 69 HC 7 6ZJN HAF 69 0.072151 1.0080 - 70 HC 7 6ZJN HAG 70 0.072151 1.0080 - 71 C 7 6ZJN CAC 71 0.133151 12.0110 - 72 HC 7 6ZJN HAD 72 0.058151 1.0080 - 73 HC 7 6ZJN HAE 73 0.058151 1.0080 - 74 C 7 6ZJN CAA 74 -0.223849 12.0110 - 75 HC 7 6ZJN HAA 75 0.128151 1.0080 - 76 HC 7 6ZJN HAB 76 0.128151 1.0080 - 77 HC 7 6ZJN HAC 77 0.128151 1.0080 - 78 OAlc 8 BWD8 O1 78 -0.621324 15.9994 - 79 CPos 8 BWD8 C1 79 0.429676 12.0110 - 80 HC 8 BWD8 H1 80 0.028676 1.0080 - 81 HC 8 BWD8 H2 81 0.028676 1.0080 - 82 HC 8 BWD8 H4 82 0.136676 1.0080 - 83 HC 8 BWD8 H5 83 0.136676 1.0080 - 84 C 8 BWD8 C2 84 -0.227324 12.0110 - 85 OAlc 8 6ZJN OAB 85 -0.632324 15.9994 - 86 CPos 8 6ZJN CAD 86 0.297676 12.0110 - 87 HC 8 6ZJN HAF 87 0.071676 1.0080 - 88 HC 8 6ZJN HAG 88 0.071676 1.0080 - 89 C 8 6ZJN CAC 89 0.132676 12.0110 - 90 HC 8 6ZJN HAD 90 0.057676 1.0080 - 91 HC 8 6ZJN HAE 91 0.057676 1.0080 - 92 C 8 6ZJN CAA 92 -0.224324 12.0110 - 93 HC 8 6ZJN HAA 93 0.127676 1.0080 - 94 HC 8 6ZJN HAB 94 0.127676 1.0080 - 95 HC 8 6ZJN HAC 95 0.127676 1.0080 - 96 OAlc 9 BWD8 O1 96 -0.625175 15.9994 - 97 CPos 9 BWD8 C1 97 0.425825 12.0110 - 98 HC 9 BWD8 H1 98 0.024825 1.0080 - 99 HC 9 BWD8 H2 99 0.024825 1.0080 - 100 HC 9 BWD8 H4 100 0.132825 1.0080 - 101 HC 9 BWD8 H5 101 0.132825 1.0080 - 102 C 9 BWD8 C2 102 -0.231175 12.0110 - 103 OAlc 9 6ZJN OAB 103 -0.636175 15.9994 - 104 CPos 9 6ZJN CAD 104 0.293825 12.0110 - 105 HC 9 6ZJN HAF 105 0.067825 1.0080 - 106 HC 9 6ZJN HAG 106 0.067825 1.0080 - 107 C 9 6ZJN CAC 107 0.128825 12.0110 - 108 HC 9 6ZJN HAD 108 0.053825 1.0080 - 109 HC 9 6ZJN HAE 109 0.053825 1.0080 - 110 C 9 6ZJN CAA 110 -0.228175 12.0110 - 111 HC 9 6ZJN HAA 111 0.123825 1.0080 - 112 HC 9 6ZJN HAB 112 0.123825 1.0080 - 113 HC 9 6ZJN HAC 113 0.123825 1.0080 - 114 OAlc 10 BWD8 O1 114 -0.640424 15.9994 - 115 CPos 10 BWD8 C1 115 0.410576 12.0110 - 116 HC 10 BWD8 H1 116 0.009576 1.0080 - 117 HC 10 BWD8 H2 117 0.009576 1.0080 - 118 HC 10 BWD8 H4 118 0.117576 1.0080 - 119 HC 10 BWD8 H5 119 0.117576 1.0080 - 120 C 10 BWD8 C2 120 -0.246424 12.0110 - 121 OAlc 10 6ZJN OAB 121 -0.651424 15.9994 - 122 CPos 10 6ZJN CAD 122 0.278576 12.0110 - 123 HC 10 6ZJN HAF 123 0.052576 1.0080 - 124 HC 10 6ZJN HAG 124 0.052576 1.0080 - 125 C 10 6ZJN CAC 125 0.113576 12.0110 - 126 HC 10 6ZJN HAD 126 0.038576 1.0080 - 127 HC 10 6ZJN HAE 127 0.038576 1.0080 - 128 C 10 6ZJN CAA 128 -0.243424 12.0110 - 129 HC 10 6ZJN HAA 129 0.108576 1.0080 - 130 HC 10 6ZJN HAB 130 0.108576 1.0080 - 131 HC 10 6ZJN HAC 131 0.108576 1.0080 - -[ bonds ] - 1 2 2 0.1430 8.1800e+06 - 1 11 2 0.1031 1.9581e+07 - 2 3 2 0.1100 1.2100e+07 - 2 5 2 0.1520 5.4300e+06 - 2 4 2 0.1100 1.2100e+07 - 5 6 2 0.1090 1.2300e+07 - 5 96 2 0.1031 1.2300e+07 - 5 24 2 0.1031 1.2300e+07 - 7 8 2 0.1430 8.1800e+06 - 7 17 2 0.1031 1.9581e+07 - 8 9 2 0.1100 1.2100e+07 - 8 11 2 0.1520 5.4300e+06 - 8 10 2 0.1100 1.2100e+07 - 11 78 2 0.1031 1.2300e+07 - 11 12 2 0.1090 1.2300e+07 - 13 19 2 0.1201 1.9581e+07 - 13 14 2 0.1430 8.1800e+06 - 14 17 2 0.1520 5.4300e+06 - 14 16 2 0.1100 1.2100e+07 - 14 15 2 0.1100 1.2100e+07 - 17 60 2 0.1031 1.2300e+07 - 17 18 2 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[";----------------------------TITLE -----------------------------------------------------------------------------------------", "; Ethanol", ";", "; This file was generated at 18:19 on 2023-07-31 by", ";", "; Automatic Topology Builder", ";", "; REVISION 2023-06-14 20:38:16", ";---------------------------------------------------------------------------------------------------------------------------", "; 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 : BWD8", "; Output : ALL ATOM topology", ";\tUse in conjunction with the corresponding all atom PDB file.", ";---------------------------------------------------------------------------------------------------------------------------", "; Citing this topology file", "; ATB molid: 360413", "; ATB Topology Hash: 940bb", ";---------------------------------------------------------------------------------------------------------------------------", "; 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": "BWD8", "nrexcl": 3}}, "junctions": []} \ No newline at end of file diff --git a/data_paper_examples/six_arm_star_monomer_build.png b/data_paper_examples/six_arm_star_monomer_build.png deleted file mode 100644 index e3fc6db6c214be17c3997407b8e7ef39a4a42cb8..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 17408 zcmd6PcQ}`S`0r!ynNemGNg^3pA(53mlfC!eTS&-CHd!HMZ<)zRwrsLjM#$dh_C446 z@Av1qu5)xHKG)~-JnwP8@B4MXUazN6MR`dATq;}yK?tO!#FY^QB^v&+VWYw;hQp3= z@DHY;tfV+{dG#lwAukp|ZX(j+PgLDgH-Ec{s%V^IZQo(oAm)8@^OOI45UTBcbJ{{5 ziSYRoHJj2`Hici*DvBmPV_1DDEY?!AsthA{qqRvZ&Z;R1`=OXyhWhXtFGJr}l 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a/data_paper_examples/terephthalic_acid.itp b/data_paper_examples/terephthalic_acid.itp deleted file mode 100644 index db8d443..0000000 --- a/data_paper_examples/terephthalic_acid.itp +++ /dev/null @@ -1,193 +0,0 @@ -;----------------------------TITLE ----------------------------------------------------------------------------------------- -; None -; -; This file was generated at 21:10 on 2023-10-20 by -; -; Automatic Topology Builder -; -; REVISION 2023-06-14 20:38:16 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 : _MJ4 -; Output : ALL ATOM topology -; Use in conjunction with the corresponding all atom PDB file. -;--------------------------------------------------------------------------------------------------------------------------- -; Citing this topology file -; ATB molid: 5872 -; ATB Topology Hash: 689d8 -;--------------------------------------------------------------------------------------------------------------------------- -; 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 nrexcl -_MJ4 3 -[ atoms ] -; nr type resnr resid atom cgnr charge mass - 1 HS14 1 _MJ4 H6 1 0.458 1.0080 - 2 OA 1 _MJ4 O4 2 -0.579 15.9994 - 3 CPos 1 _MJ4 C7 3 0.639 12.0110 - 4 OEOpt 1 _MJ4 O1 4 -0.550 15.9994 - 5 CAro 1 _MJ4 C6 5 -0.006 12.0110 - 6 CAro 1 _MJ4 C1 6 -0.125 12.0110 - 7 HC 1 _MJ4 H1 7 0.144 1.0080 - 8 CAro 1 _MJ4 C2 8 -0.125 12.0110 - 9 HC 1 _MJ4 H2 9 0.144 1.0080 - 10 CAro 1 _MJ4 C3 10 -0.006 12.0110 - 11 CAro 1 _MJ4 C4 11 -0.125 12.0110 - 12 HC 1 _MJ4 H3 12 0.144 1.0080 - 13 CAro 1 _MJ4 C5 13 -0.125 12.0110 - 14 HC 1 _MJ4 H4 14 0.144 1.0080 - 15 CPos 1 _MJ4 C8 15 0.639 12.0110 - 16 OEOpt 1 _MJ4 O2 16 -0.550 15.9994 - 17 OA 1 _MJ4 O3 17 -0.579 15.9994 - 18 HS14 1 _MJ4 H5 18 0.458 1.0080 -; total charge of the molecule: -0.000 -[ bonds ] -; ai aj funct c0 c1 - 1 2 2 0.0972 1.9581e+07 - 2 3 2 0.1350 1.0300e+07 - 3 4 2 0.1220 2.2843e+07 - 3 5 2 0.1500 8.3700e+06 - 5 6 2 0.1400 8.5400e+06 - 5 13 2 0.1400 8.5400e+06 - 6 7 2 0.1090 1.2300e+07 - 6 8 2 0.1390 8.6600e+06 - 8 9 2 0.1090 1.2300e+07 - 8 10 2 0.1400 8.5400e+06 - 10 11 2 0.1400 8.5400e+06 - 10 15 2 0.1500 8.3700e+06 - 11 12 2 0.1090 1.2300e+07 - 11 13 2 0.1390 8.6600e+06 - 13 14 2 0.1090 1.2300e+07 - 15 16 2 0.1220 2.2843e+07 - 15 17 2 0.1350 1.0300e+07 - 17 18 2 0.0972 1.9581e+07 -[ pairs ] -; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp - 1 4 1 - 1 5 1 - 2 6 1 - 2 13 1 - 3 7 1 - 3 8 1 - 3 11 1 - 3 14 1 - 4 6 1 - 4 13 1 - 5 9 1 - 5 12 1 - 6 14 1 - 6 15 1 - 7 9 1 - 7 10 1 - 7 13 1 - 8 12 1 - 8 16 1 - 8 17 1 - 9 11 1 - 9 15 1 - 10 14 1 - 10 18 1 - 11 16 1 - 11 17 1 - 12 14 1 - 12 15 1 - 13 15 1 - 16 18 1 -[ angles ] -; ai aj ak funct angle fc - 1 2 3 2 109.50 450.00 - 2 3 4 2 124.00 730.00 - 2 3 5 2 115.00 610.00 - 4 3 5 2 121.00 685.00 - 3 5 6 2 120.00 560.00 - 3 5 13 2 120.00 560.00 - 6 5 13 2 120.00 560.00 - 5 6 7 2 120.00 505.00 - 5 6 8 2 120.00 560.00 - 7 6 8 2 120.00 505.00 - 6 8 9 2 120.00 505.00 - 6 8 10 2 120.00 560.00 - 9 8 10 2 120.00 505.00 - 8 10 11 2 120.00 560.00 - 8 10 15 2 120.00 560.00 - 11 10 15 2 120.00 560.00 - 10 11 12 2 120.00 505.00 - 10 11 13 2 120.00 560.00 - 12 11 13 2 120.00 505.00 - 5 13 11 2 120.00 560.00 - 5 13 14 2 120.00 505.00 - 11 13 14 2 120.00 505.00 - 10 15 16 2 121.00 685.00 - 10 15 17 2 115.00 610.00 - 16 15 17 2 124.00 730.00 - 15 17 18 2 109.50 450.00 -[ dihedrals ] -; GROMOS improper dihedrals -; ai aj ak al funct angle fc - 6 5 7 8 2 0.00 167.36 - 8 6 9 10 2 0.00 167.36 - 10 8 11 15 2 0.00 167.36 - 11 10 12 13 2 0.00 167.36 - 13 5 11 14 2 0.00 167.36 - 5 3 6 13 2 0.00 167.36 - 3 2 4 5 2 0.00 167.36 - 15 10 16 17 2 0.00 167.36 -[ dihedrals ] -; ai aj ak al funct ph0 cp mult - 1 2 3 5 1 180.00 16.70 2 - 4 3 5 6 1 180.00 5.86 2 - 5 6 8 10 1 180.00 41.80 2 - 6 5 13 11 1 180.00 41.80 2 - 6 8 10 11 1 180.00 41.80 2 - 8 10 11 13 1 180.00 41.80 2 - 8 10 15 16 1 180.00 5.86 2 - 10 11 13 5 1 180.00 41.80 2 - 10 15 17 18 1 180.00 16.70 2 - 13 5 6 8 1 180.00 41.80 2 -[ exclusions ] -; ai aj funct ; GROMOS 1-4 exclusions - 5 10 - 6 11 - 8 13 \ No newline at end of file diff --git a/paper_worked_examples.ipynb b/paper_worked_examples.ipynb deleted file mode 100644 index 1ff27ef..0000000 --- a/paper_worked_examples.ipynb +++ /dev/null @@ -1,409 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "**Important Note!!**\n", - "\n", - "If you would like to repeat these examples in a script outside of the repository structure, please change the import paths as described below:\n", - "\n", - "Import paths used in the examples below:\n", - "```\n", - "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n", - "```\n", - "\n", - "Import path to use for your scripts existing *outside* of the PolyConstruct file structure:\n", - "```\n", - "from polytop.Junction import Junction\n", - "from polytop.Monomer import Monomer\n", - "from polytop.Visualize import Visualize\n", - "from polytop.Polymer import Polymer\n", - "from polytop.Topology import Topology\n", - "```" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Construction of a simple linear homopolymer of PEI" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "# Import required classes from PolyTop\n", - "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n", - "\n", - "# Load in monomer Topology from ITP file\n", - "top = Topology.from_ITP(\"data_paper_examples/pei.itp\")\n", - "\n", - "# Create a Junction to join 'to' and another to join 'from'.\n", - "# Provide the bonding atom and the leaving atom, in that order, for the\n", - "# Junction - they must have a bond between them.\n", - "to_j = Junction(top.get_atom(\"C51\"), top.get_atom(\"C62\"), name = \"to\")\n", - "from_j = Junction(top.get_atom(\"N7\"), top.get_atom(\"C6\"), name = \"from\")\n", - "\n", - "# Create a Monomer from the Topology and a list of the Junctions\n", - "monomer = Monomer(top, [to_j, from_j])\n", - "\n", - "# Start the Polymer with one Monomer\n", - "polymer = Polymer(monomer)\n", - "\n", - "# Extend the Polymer to the desired length (in this case 20)\n", - "for i in range(19):\n", - " polymer.extend(monomer, from_junction_name=\"from\", to_junction_name=\"to\")\n", - "\n", - "# Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check\n", - "polymer.topology.title = \"pei polymer\" # renames the ITP header and image\n", - "polymer.save_to_file('data_paper_examples/pei_linear_polymer.json') # text dump\n", - "polymer.topology.to_ITP('data_paper_examples/pei_linear_polymer.itp')\n", - "Visualize.polymer(polymer,infer_bond_order=False).draw2D('data_paper_examples/pei_linear_polymer.png',(400,300))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Construction of a 4-arm PEG star polymer from single monomeric units" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "netcharge = 7.91033905045424e-16\n" - ] - } - ], - "source": [ - "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n", - "\n", - "# load in monomer topologies from ITP files\n", - "ethanol = Topology.from_ITP(\"data_paper_examples/extended_ethanol.itp\") # main arm monomer\n", - "methane = Topology.from_ITP(\"data_paper_examples/extended_methane.itp\") # terminal monomer\n", - "neopentane = Topology.from_ITP(\"data_paper_examples/extended_neopentane.itp\") # central monomer\n", - "\n", - "# create junctions for each monomer with the bonding atom and then the leaving atom specified, in that order, with a unique name\n", - "oxy_j1 = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"C1\"), name = \"oxy1\")\n", - "carb_j1 = Junction(ethanol.get_atom(\"C3\"), ethanol.get_atom(\"O2\"), name = \"carb1\")\n", - "oxy_j2 = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"C1\"), name = \"oxy2\")\n", - "carb_j2 = Junction(ethanol.get_atom(\"C3\"), ethanol.get_atom(\"O2\"), name = \"carb2\")\n", - "oxy_j3 = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"C1\"), name = \"oxy3\")\n", - "carb_j3 = Junction(ethanol.get_atom(\"C3\"), ethanol.get_atom(\"O2\"), name = \"carb3\")\n", - "oxy_j4 = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"C1\"), name = \"oxy4\")\n", - "carb_j4 = Junction(ethanol.get_atom(\"C3\"), ethanol.get_atom(\"O2\"), name = \"carb4\")\n", - "\n", - "j1 = Junction(neopentane.get_atom(\"C1\"), neopentane.get_atom(\"O1\"), name = \"branch1\")\n", - "j2 = Junction(neopentane.get_atom(\"C3\"), neopentane.get_atom(\"O2\"), name = \"branch2\")\n", - "j3 = Junction(neopentane.get_atom(\"C4\"), neopentane.get_atom(\"O3\"), name = \"branch3\")\n", - "j4 = Junction(neopentane.get_atom(\"C5\"), neopentane.get_atom(\"O4\"), name = \"branch4\")\n", - "\n", - "term_j = Junction(methane.get_atom(\"C1\"), methane.get_atom(\"O1\"), name = \"term\")\n", - "\n", - "# create monomers from their topologies and any specified junctions\n", - "e1 = Monomer(ethanol, [oxy_j1, carb_j1])\n", - "e2 = Monomer(ethanol, [oxy_j2, carb_j2])\n", - "e3 = Monomer(ethanol, [oxy_j3, carb_j3])\n", - "e4 = Monomer(ethanol, [oxy_j4, carb_j4])\n", - "\n", - "central = Monomer(neopentane, [j1, j2, j3, j4])\n", - "\n", - "terminal = Monomer(methane, [term_j]) # only needs one junction to join to the ends of each arm\n", - "\n", - "# start the polymer with the central monomer\n", - "four_polymer = Polymer(central)\n", - "\n", - "# attach three ethanols to each of the four junctions (j1-j4) of the central monomer\n", - "four_polymer.extend(e1, from_junction_name=\"branch1\", to_junction_name=\"oxy1\")\n", - "four_polymer.extend(e2, from_junction_name=\"branch2\", to_junction_name=\"oxy2\")\n", - "four_polymer.extend(e3, from_junction_name=\"branch3\", to_junction_name=\"oxy3\")\n", - "four_polymer.extend(e4, from_junction_name=\"branch4\", to_junction_name=\"oxy4\")\n", - "\n", - "four_polymer.extend(e1, from_junction_name=\"carb1\", to_junction_name=\"oxy1\")\n", - "four_polymer.extend(e2, from_junction_name=\"carb2\", to_junction_name=\"oxy2\")\n", - "four_polymer.extend(e3, from_junction_name=\"carb3\", to_junction_name=\"oxy3\")\n", - "four_polymer.extend(e4, from_junction_name=\"carb4\", to_junction_name=\"oxy4\")\n", - "\n", - "four_polymer.extend(e1, from_junction_name=\"carb1\", to_junction_name=\"oxy1\")\n", - "four_polymer.extend(e2, from_junction_name=\"carb2\", to_junction_name=\"oxy2\")\n", - "four_polymer.extend(e3, from_junction_name=\"carb3\", to_junction_name=\"oxy3\")\n", - "four_polymer.extend(e4, from_junction_name=\"carb4\", to_junction_name=\"oxy4\")\n", - "\n", - "four_polymer.extend(terminal, from_junction_name=\"carb1\", to_junction_name=\"term\")\n", - "four_polymer.extend(terminal, from_junction_name=\"carb2\", to_junction_name=\"term\")\n", - "four_polymer.extend(terminal, from_junction_name=\"carb3\", to_junction_name=\"term\")\n", - "four_polymer.extend(terminal, from_junction_name=\"carb4\", to_junction_name=\"term\")\n", - "\n", - "# check polymer charge and give it a descriptive name\n", - "print(f\"netcharge = {four_polymer.topology.netcharge}\")\n", - "four_polymer.topology.title = \"four arm star polymer - overlapped monomers\" # rename your ITP header and image name\n", - "\n", - "# save the polymer to a file and visualise the structure with RDKit for an easy visual structure check\n", - "four_polymer.save_to_file('data_paper_examples/four_arm_star_overlapped_monomers.json') # text dump\n", - "four_polymer.topology.to_ITP('data_paper_examples/four_arm_star_overlapped_monomers.itp')\n", - "Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('data_paper_examples/four_arm_star_overlapped_monomers.png',(400,300))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Construction of an ethylamine dendrimer" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "-1.6653345369377348e-15\n" - ] - } - ], - "source": [ - "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n", - "\n", - "# load in monomer topologies from ITP files\n", - "core_mono = Topology.from_ITP(\"data_paper_examples/dendrimer_core.itp\")\n", - "bifurcating_mono = Topology.from_ITP(\"data_paper_examples/dendrimer_bifurcating.itp\")\n", - "terminal_mono = Topology.from_ITP(\"data_paper_examples/dendrimer_terminal.itp\")\n", - "\n", - "# create junctions for different 'levels' of monomers, depending on what level of branching they exist at in the dendrimer\n", - "# junctions are created with the bonding atom and then the leaving atom specified, in that order, and should be given a unique name\n", - "central1 = Junction(core_mono.get_atom(\"N2\"), core_mono.get_atom(\"C9\"), name=\"C1\")\n", - "central2 = Junction(core_mono.get_atom(\"N2\"), core_mono.get_atom(\"C7\"), name=\"C2\")\n", - "central3 = Junction(core_mono.get_atom(\"N1\"), core_mono.get_atom(\"C2\"), name=\"C3\")\n", - "central4 = Junction(core_mono.get_atom(\"N1\"), core_mono.get_atom(\"C3\"), name=\"C4\")\n", - "\n", - "b1 = Junction(bifurcating_mono.get_atom(\"C6\"), bifurcating_mono.get_atom(\"N2\"), name = \"to\")\n", - "b2a = Junction(bifurcating_mono.get_atom(\"N1\"), bifurcating_mono.get_atom(\"C2\"), name = \"from1\")\n", - "b2b = Junction(bifurcating_mono.get_atom(\"N1\"), bifurcating_mono.get_atom(\"C3\"), name = \"from2\")\n", - "\n", - "c1 = Junction(bifurcating_mono.get_atom(\"C6\"), bifurcating_mono.get_atom(\"N2\"), name = \"to2\")\n", - "c2a = Junction(bifurcating_mono.get_atom(\"N1\"), bifurcating_mono.get_atom(\"C2\"), name = \"from12\")\n", - "c2b = Junction(bifurcating_mono.get_atom(\"N1\"), bifurcating_mono.get_atom(\"C3\"), name = \"from22\")\n", - "\n", - "t = Junction(terminal_mono.get_atom(\"C1\"), terminal_mono.get_atom(\"N1\"), name = \"term\")\n", - "\n", - "# create monomers from their topologies and any specified junctions\n", - "# note that different 'levels' of monomers have different names for their junctions.\n", - "# This ensures that layers are added on sequentially. \n", - "# If all monomers have the same junction names the polymerisation will be random and often defaults to a linear shape!\n", - "central = Monomer(core_mono, [central1, central2, central3, central4])\n", - "bifur1 = Monomer(bifurcating_mono, [b1, b2a, b2b])\n", - "bifur2 = Monomer(bifurcating_mono, [c1, c2a, c2b])\n", - "cap = Monomer(terminal_mono, [t])\n", - "\n", - "# start the polymer with the central monomer\n", - "polymer = Polymer(central)\n", - "\n", - "# extend first layer of dendrimer\n", - "polymer.extend(bifur1, from_junction_name=\"C1\", to_junction_name=\"to\")\n", - "polymer.extend(bifur1, from_junction_name=\"C2\", to_junction_name=\"to\")\n", - "polymer.extend(bifur1, from_junction_name=\"C3\", to_junction_name=\"to\")\n", - "polymer.extend(bifur1, from_junction_name=\"C4\", to_junction_name=\"to\")\n", - "\n", - "# extend second layer of dendrimer\n", - "# note how the first and second 'layers' have different monomers with different\n", - "# Junction names to ensure the correct structure is always formed. Junction and\n", - "# Monomer name ambiguity WILL cause formation of random, unreplicatable polymer topologies\n", - "polymer.extend(bifur2, from_junction_name=\"from1\", to_junction_name=\"to2\")\n", - "polymer.extend(bifur2, from_junction_name=\"from2\", to_junction_name=\"to2\")\n", - "polymer.extend(bifur2, from_junction_name=\"from1\", to_junction_name=\"to2\")\n", - "polymer.extend(bifur2, from_junction_name=\"from2\", to_junction_name=\"to2\")\n", - "polymer.extend(bifur2, from_junction_name=\"from1\", to_junction_name=\"to2\")\n", - "polymer.extend(bifur2, from_junction_name=\"from2\", to_junction_name=\"to2\")\n", - "polymer.extend(bifur2, from_junction_name=\"from1\", to_junction_name=\"to2\")\n", - "polymer.extend(bifur2, from_junction_name=\"from2\", to_junction_name=\"to2\")\n", - "\n", - "# finish polymer by extending on the capping monomer\n", - "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from12\", to_junction_name=\"term\")\n", - "polymer.extend(cap, from_junction_name=\"from22\", to_junction_name=\"term\")\n", - "\n", - "# check netcharge of the monomers is preserved (in this case, close to 0)\n", - "print(polymer.topology.netcharge)\n", - "\n", - "# save the dendrimer to a file and visualise the structure with RDKit for an easy visual structure check\n", - "polymer.save_to_file('data_paper_examples/ethylamine_dendrimer.json') # text dump\n", - "polymer.topology.to_ITP('data_paper_examples/ethylamine_dendrimer.itp')\n", - "Visualize.polymer(polymer,infer_bond_order=False).draw2D('data_paper_examples/ethylamine_dendrimer.png',(400,300))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "-----------------------------------------------------------------------------------------------------------------------------------------\n", - "\n", - "ALL EXAMPLES FROM HERE DOWN DO *NOT* USE EXTENDED TOPOLOGIES AND THUS PRODUCE INCORRECT PARAMETERS - THEY ARE FOR INTEREST AND AS EXAMPLES FOR WORKFLOWS USED TO BUILD OTHER COMPLEX POLYMER TOPOLOGIES ONLY!\n", - "\n", - "-----------------------------------------------------------------------------------------------------------------------------------------" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Construction of an alternating homopolymer of polyester" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [], - "source": [ - "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n", - "\n", - "# load in monomer topologies\n", - "ethylene_glycol = Topology.from_ITP(\"data_paper_examples/ethylene_glycol.itp\")\n", - "terephthalic_acid = Topology.from_ITP(\"data_paper_examples/terephthalic_acid.itp\")\n", - "\n", - "# define junctions for both monomers\n", - "ej1 = Junction(ethylene_glycol.get_atom(\"O2\"), ethylene_glycol.get_atom(\"H6\"), name=\"ej1\")\n", - "ej2 = Junction(ethylene_glycol.get_atom(\"O1\"), ethylene_glycol.get_atom(\"H5\"), name=\"ej2\")\n", - "\n", - "tj1 = Junction(terephthalic_acid.get_atom(\"C7\"), terephthalic_acid.get_atom(\"O4\"), name=\"tj1\")\n", - "tj2 = Junction(terephthalic_acid.get_atom(\"C8\"), terephthalic_acid.get_atom(\"O3\"), name=\"tj2\")\n", - "\n", - "# create monomers from their respctive topologies and lists of junctions\n", - "e_mono = Monomer(ethylene_glycol, [ej1, ej2])\n", - "t_mono = Monomer(terephthalic_acid, [tj1, tj2])\n", - "\n", - "# start polymer\n", - "polyester = Polymer(e_mono)\n", - "\n", - "# extend polymer in alternating fashion for a total length of 10\n", - "for i in range(10):\n", - " if (i%2):\n", - " polyester.extend(e_mono, from_junction_name=\"tj2\", to_junction_name=\"ej1\")\n", - " else:\n", - " polyester.extend(t_mono, from_junction_name=\"ej2\", to_junction_name=\"tj1\")\n", - "\n", - "# save polymer topology to file and visualise with RDKit\n", - "polyester.topology.to_ITP('data_paper_examples/polyester.itp')\n", - "Visualize.polymer(polyester,infer_bond_order=False).draw2D('data_paper_examples/polyester.png',(400,300))" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "Construction of a 6-arm PEG star polymer from single monomeric units" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "netcharge = -1.6653345369377348e-16\n" - ] - } - ], - "source": [ - "from polytop.polytop import Topology, Junction, Monomer, Polymer, Visualize\n", - "\n", - "# load in monomer topologies from ITP files\n", - "ethanol = Topology.from_ITP(\"data_paper_examples/ethanol.itp\") # main monomer\n", - "propanol = Topology.from_ITP(\"data_paper_examples/propanol.itp\") # terminal monomer\n", - "\n", - "# create junctions for each monomer with the bonding atom and then the leaving atom specified, in that order, with a unique name\n", - "oxy_j = Junction(ethanol.get_atom(\"O1\"), ethanol.get_atom(\"H6\"), name = \"oxy\")\n", - "carb_j = Junction(ethanol.get_atom(\"C2\"), ethanol.get_atom(\"H3\"), name = \"carb\")\n", - "extra_carb_j = Junction(ethanol.get_atom(\"C2\"), ethanol.get_atom(\"H4\"), name = \"carb2\")\n", - "carb1_j = Junction(ethanol.get_atom(\"C1\"), ethanol.get_atom(\"H1\"), name = \"carb1\")\n", - "bye_j = Junction(ethanol.get_atom(\"C1\"), ethanol.get_atom(\"O1\"), name = \"byeO\")\n", - "\n", - "term_j = Junction(propanol.get_atom(\"OAB\"), propanol.get_atom(\"HAH\"), name = \"term\")\n", - "\n", - "# create monomers from their topologies and any specified junctions\n", - "main = Monomer(ethanol, [oxy_j, carb_j, extra_carb_j])\n", - "extraC = Monomer(ethanol, [carb_j, bye_j, carb1_j])\n", - "branch = Monomer(ethanol, [oxy_j, carb_j])\n", - "terminal = Monomer(propanol, [term_j]) # only needs one junction to join to the backbone\n", - "\n", - "# build the arms\n", - "arm_polymer = Polymer(branch)\n", - "arm_polymer.extend(terminal, from_junction_name=\"carb\", to_junction_name=\"term\", keep_charge=True)\n", - "arm = Monomer(arm_polymer.topology, arm_polymer.junctions)\n", - "\n", - "# start the polymer by building the linear backbone\n", - "star_polymer = Polymer(main)\n", - "star_polymer.extend(main, from_junction_name=\"oxy\", to_junction_name=\"carb\", keep_charge=True)\n", - "star_polymer.extend(main, from_junction_name=\"oxy\", to_junction_name=\"carb\", keep_charge=True)\n", - "star_polymer.extend(extraC, from_junction_name=\"oxy\", to_junction_name=\"byeO\", keep_charge=True)\n", - "\n", - "# join all six arms to the backbone to make 6-arm star polymer\n", - "star_polymer.extend(arm, from_junction_name=\"carb\", to_junction_name=\"oxy\", keep_charge=True)\n", - "star_polymer.extend(arm, from_junction_name=\"carb\", to_junction_name=\"oxy\", keep_charge=True)\n", - "star_polymer.extend(arm, from_junction_name=\"carb2\", to_junction_name=\"oxy\", keep_charge=True)\n", - "star_polymer.extend(arm, from_junction_name=\"carb2\", to_junction_name=\"oxy\", keep_charge=True)\n", - "star_polymer.extend(arm, from_junction_name=\"carb2\", to_junction_name=\"oxy\", keep_charge=True)\n", - "star_polymer.extend(arm, from_junction_name=\"carb1\", to_junction_name=\"oxy\", keep_charge=True)\n", - "\n", - "# check polymer charge and give it a descriptive name\n", - "print(f\"netcharge = {star_polymer.topology.netcharge}\")\n", - "star_polymer.topology.title = \"six arm star polymer - from monomers\" # rename your ITP header and image name\n", - "\n", - "# save the polymer to a file and visualise the structure with RDKit for an easy visual structure check\n", - "star_polymer.save_to_file('data_paper_examples/six_arm_star_monomer_build.json') # text dump\n", - "star_polymer.topology.to_ITP('data_paper_examples/six_arm_star_monomer_build.itp')\n", - "Visualize.polymer(star_polymer,infer_bond_order=False).draw2D('data_paper_examples/six_arm_star_monomer_build.png',(400,300))" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "polyconstruct-env", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.15" - } - }, - "nbformat": 4, - "nbformat_minor": 2 -} diff --git a/data_paper_examples/dendrimer_bifurcating.itp b/polytop_examples/data/dendrimer_bifurcating.itp similarity index 100% rename from data_paper_examples/dendrimer_bifurcating.itp rename to polytop_examples/data/dendrimer_bifurcating.itp diff --git a/data_paper_examples/dendrimer_core.itp b/polytop_examples/data/dendrimer_core.itp similarity index 100% rename from data_paper_examples/dendrimer_core.itp rename to polytop_examples/data/dendrimer_core.itp diff --git a/data_paper_examples/dendrimer_terminal.itp b/polytop_examples/data/dendrimer_terminal.itp similarity index 100% rename from data_paper_examples/dendrimer_terminal.itp rename to polytop_examples/data/dendrimer_terminal.itp diff --git a/data_paper_examples/ethylamine_dendrimer.itp b/polytop_examples/data/ethylamine_dendrimer.itp similarity index 100% rename from data_paper_examples/ethylamine_dendrimer.itp rename to polytop_examples/data/ethylamine_dendrimer.itp diff --git a/data_paper_examples/ethylamine_dendrimer.json b/polytop_examples/data/ethylamine_dendrimer.json similarity index 100% rename from data_paper_examples/ethylamine_dendrimer.json rename to polytop_examples/data/ethylamine_dendrimer.json diff --git a/data_paper_examples/ethylamine_dendrimer.png b/polytop_examples/data/ethylamine_dendrimer.png similarity index 100% rename from data_paper_examples/ethylamine_dendrimer.png rename to polytop_examples/data/ethylamine_dendrimer.png diff --git a/data_paper_examples/extended_ethanol.itp b/polytop_examples/data/extended_ethanol.itp similarity index 100% rename from data_paper_examples/extended_ethanol.itp rename to polytop_examples/data/extended_ethanol.itp diff --git a/data_paper_examples/extended_methane.itp b/polytop_examples/data/extended_methane.itp similarity index 100% rename from data_paper_examples/extended_methane.itp rename to polytop_examples/data/extended_methane.itp diff --git a/data_paper_examples/extended_neopentane.itp b/polytop_examples/data/extended_neopentane.itp similarity index 100% rename from data_paper_examples/extended_neopentane.itp rename to polytop_examples/data/extended_neopentane.itp diff --git a/data_paper_examples/four_arm_star_overlapped_monomers.itp b/polytop_examples/data/four_arm_star_overlapped_monomers.itp similarity index 100% rename from data_paper_examples/four_arm_star_overlapped_monomers.itp rename to polytop_examples/data/four_arm_star_overlapped_monomers.itp diff --git a/data_paper_examples/four_arm_star_overlapped_monomers.json b/polytop_examples/data/four_arm_star_overlapped_monomers.json similarity index 100% rename from data_paper_examples/four_arm_star_overlapped_monomers.json rename to polytop_examples/data/four_arm_star_overlapped_monomers.json diff --git a/data_paper_examples/four_arm_star_overlapped_monomers.png b/polytop_examples/data/four_arm_star_overlapped_monomers.png similarity index 100% rename from data_paper_examples/four_arm_star_overlapped_monomers.png rename to polytop_examples/data/four_arm_star_overlapped_monomers.png diff --git a/data_paper_examples/pei.itp b/polytop_examples/data/pei.itp similarity index 100% rename from data_paper_examples/pei.itp rename to polytop_examples/data/pei.itp diff --git a/data_paper_examples/pei_linear_polymer.itp b/polytop_examples/data/pei_linear_polymer.itp similarity index 100% rename from data_paper_examples/pei_linear_polymer.itp rename to polytop_examples/data/pei_linear_polymer.itp diff --git a/data_paper_examples/pei_linear_polymer.json b/polytop_examples/data/pei_linear_polymer.json similarity index 100% rename from data_paper_examples/pei_linear_polymer.json rename to polytop_examples/data/pei_linear_polymer.json diff --git a/data_paper_examples/pei_linear_polymer.png b/polytop_examples/data/pei_linear_polymer.png similarity index 100% rename from data_paper_examples/pei_linear_polymer.png rename to polytop_examples/data/pei_linear_polymer.png diff --git a/polytop_examples/dendrimer_ethylamine.py b/polytop_examples/dendrimer_ethylamine.py new file mode 100644 index 0000000..247f465 --- /dev/null +++ b/polytop_examples/dendrimer_ethylamine.py @@ -0,0 +1,87 @@ +# Construction of an ethylamine dendrimer + +# import required classes from PolyTop +from polytop.Junction import Junction +from polytop.Monomer import Monomer +from polytop.Visualize import Visualize +from polytop.Polymer import Polymer +from polytop.Topology import Topology + +# load in monomer topologies from ITP files +core_mono = Topology.from_ITP("data/dendrimer_core.itp") +bifurcating_mono = Topology.from_ITP("data/dendrimer_bifurcating.itp") +terminal_mono = Topology.from_ITP("data/dendrimer_terminal.itp") + +# create junctions for different 'levels' of monomers, depending on what level of branching they exist at in the dendrimer +# junctions are created with the bonding atom and then the leaving atom specified, in that order, and should be given a unique name +central1 = Junction(core_mono.get_atom("N2"), core_mono.get_atom("C9"), name="C1") +central2 = Junction(core_mono.get_atom("N2"), core_mono.get_atom("C7"), name="C2") +central3 = Junction(core_mono.get_atom("N1"), core_mono.get_atom("C2"), name="C3") +central4 = Junction(core_mono.get_atom("N1"), core_mono.get_atom("C3"), name="C4") + +b1 = Junction(bifurcating_mono.get_atom("C6"), bifurcating_mono.get_atom("N2"), name = "to") +b2a = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C2"), name = "from1") +b2b = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C3"), name = "from2") + +c1 = Junction(bifurcating_mono.get_atom("C6"), bifurcating_mono.get_atom("N2"), name = "to2") +c2a = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C2"), name = "from12") +c2b = Junction(bifurcating_mono.get_atom("N1"), bifurcating_mono.get_atom("C3"), name = "from22") + +t = Junction(terminal_mono.get_atom("C1"), terminal_mono.get_atom("N1"), name = "term") + +# create monomers from their topologies and any specified junctions +# note that different 'levels' of monomers have different names for their junctions. +# This ensures that layers are added on sequentially. +# If all monomers have the same junction names the polymerisation will be random and often defaults to a linear shape! +central = Monomer(core_mono, [central1, central2, central3, central4]) +bifur1 = Monomer(bifurcating_mono, [b1, b2a, b2b]) +bifur2 = Monomer(bifurcating_mono, [c1, c2a, c2b]) +cap = Monomer(terminal_mono, [t]) + +# start the polymer with the central monomer +polymer = Polymer(central) + +# extend first layer of dendrimer +polymer.extend(bifur1, from_junction_name="C1", to_junction_name="to") +polymer.extend(bifur1, from_junction_name="C2", to_junction_name="to") +polymer.extend(bifur1, from_junction_name="C3", to_junction_name="to") +polymer.extend(bifur1, from_junction_name="C4", to_junction_name="to") + +# extend second layer of dendrimer +# note how the first and second 'layers' have different monomers with different +# Junction names to ensure the correct structure is always formed. Junction and +# Monomer name ambiguity WILL cause formation of random, unreplicatable polymer topologies +polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") +polymer.extend(bifur2, from_junction_name="from2", to_junction_name="to2") +polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") +polymer.extend(bifur2, from_junction_name="from2", to_junction_name="to2") +polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") +polymer.extend(bifur2, from_junction_name="from2", to_junction_name="to2") +polymer.extend(bifur2, from_junction_name="from1", to_junction_name="to2") +polymer.extend(bifur2, from_junction_name="from2", to_junction_name="to2") + +# finish polymer by extending on the capping monomer +polymer.extend(cap, from_junction_name="from12", to_junction_name="term") +polymer.extend(cap, from_junction_name="from22", to_junction_name="term") +polymer.extend(cap, from_junction_name="from12", to_junction_name="term") +polymer.extend(cap, from_junction_name="from22", to_junction_name="term") +polymer.extend(cap, from_junction_name="from12", to_junction_name="term") +polymer.extend(cap, from_junction_name="from22", to_junction_name="term") +polymer.extend(cap, from_junction_name="from12", to_junction_name="term") +polymer.extend(cap, from_junction_name="from22", to_junction_name="term") +polymer.extend(cap, from_junction_name="from12", to_junction_name="term") +polymer.extend(cap, from_junction_name="from22", to_junction_name="term") +polymer.extend(cap, from_junction_name="from12", to_junction_name="term") +polymer.extend(cap, from_junction_name="from22", to_junction_name="term") +polymer.extend(cap, from_junction_name="from12", to_junction_name="term") +polymer.extend(cap, from_junction_name="from22", to_junction_name="term") +polymer.extend(cap, from_junction_name="from12", to_junction_name="term") +polymer.extend(cap, from_junction_name="from22", to_junction_name="term") + +# check netcharge of the monomers is preserved (in this case, close to 0) +print(polymer.topology.netcharge) + +# save the dendrimer to a file and visualise the structure with RDKit for an easy visual structure check +polymer.save_to_file('data/ethylamine_dendrimer.json') # text dump +polymer.topology.to_ITP('data/ethylamine_dendrimer.itp') +Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/ethylamine_dendrimer.png',(400,300)) \ No newline at end of file diff --git a/polytop_examples/linear_PEI.py b/polytop_examples/linear_PEI.py new file mode 100644 index 0000000..1943729 --- /dev/null +++ b/polytop_examples/linear_PEI.py @@ -0,0 +1,33 @@ +# Construction of a simple linear homopolymer of PEI + +# Import required classes from PolyTop +from polytop.Junction import Junction +from polytop.Monomer import Monomer +from polytop.Visualize import Visualize +from polytop.Polymer import Polymer +from polytop.Topology import Topology + +# Load in monomer Topology from ITP file +top = Topology.from_ITP("data/pei.itp") + +# Create a Junction to join 'to' and another to join 'from'. +# Provide the bonding atom and the leaving atom, in that order, for the +# Junction - they must have a bond between them. +to_j = Junction(top.get_atom("C51"), top.get_atom("C62"), name = "to") +from_j = Junction(top.get_atom("N7"), top.get_atom("C6"), name = "from") + +# Create a Monomer from the Topology and a list of the Junctions +monomer = Monomer(top, [to_j, from_j]) + +# Start the Polymer with one Monomer +polymer = Polymer(monomer) + +# Extend the Polymer to the desired length (in this case 20) +for i in range(19): + polymer.extend(monomer, from_junction_name="from", to_junction_name="to") + +# Save the polymer to a file and visualise the structure with RDKit for an easy visual structure check +polymer.topology.title = "pei polymer" # renames the ITP header and image +polymer.save_to_file('data/pei_linear_polymer.json') # text dump +polymer.topology.to_ITP('data/pei_linear_polymer.itp') +Visualize.polymer(polymer,infer_bond_order=False).draw2D('data/pei_linear_polymer.png',(400,300)) \ No newline at end of file diff --git a/polytop_examples/star_PEG.py b/polytop_examples/star_PEG.py new file mode 100644 index 0000000..f93df60 --- /dev/null +++ b/polytop_examples/star_PEG.py @@ -0,0 +1,73 @@ +# Construction of a 4-arm PEG star polymer from single monomeric units + +# import required classes from PolyTop +from polytop.Junction import Junction +from polytop.Monomer import Monomer +from polytop.Visualize import Visualize +from polytop.Polymer import Polymer +from polytop.Topology import Topology + +# load in monomer topologies from ITP files +ethanol = Topology.from_ITP("data/extended_ethanol.itp") # main arm monomer +methane = Topology.from_ITP("data/extended_methane.itp") # terminal monomer +neopentane = Topology.from_ITP("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 +oxy_j1 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy1") +carb_j1 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb1") +oxy_j2 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy2") +carb_j2 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb2") +oxy_j3 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy3") +carb_j3 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb3") +oxy_j4 = Junction(ethanol.get_atom("O1"), ethanol.get_atom("C1"), name = "oxy4") +carb_j4 = Junction(ethanol.get_atom("C3"), ethanol.get_atom("O2"), name = "carb4") + +j1 = Junction(neopentane.get_atom("C1"), neopentane.get_atom("O1"), name = "branch1") +j2 = Junction(neopentane.get_atom("C3"), neopentane.get_atom("O2"), name = "branch2") +j3 = Junction(neopentane.get_atom("C4"), neopentane.get_atom("O3"), name = "branch3") +j4 = Junction(neopentane.get_atom("C5"), neopentane.get_atom("O4"), name = "branch4") + +term_j = Junction(methane.get_atom("C1"), methane.get_atom("O1"), name = "term") + +# create monomers from their topologies and any specified junctions +e1 = Monomer(ethanol, [oxy_j1, carb_j1]) +e2 = Monomer(ethanol, [oxy_j2, carb_j2]) +e3 = Monomer(ethanol, [oxy_j3, carb_j3]) +e4 = Monomer(ethanol, [oxy_j4, carb_j4]) + +central = Monomer(neopentane, [j1, j2, j3, j4]) + +terminal = Monomer(methane, [term_j]) # only needs one junction to join to the ends of each arm + +# start the polymer with the central monomer +four_polymer = Polymer(central) + +# attach three ethanols to each of the four junctions (j1-j4) of the central monomer +four_polymer.extend(e1, from_junction_name="branch1", to_junction_name="oxy1") +four_polymer.extend(e2, from_junction_name="branch2", to_junction_name="oxy2") +four_polymer.extend(e3, from_junction_name="branch3", to_junction_name="oxy3") +four_polymer.extend(e4, from_junction_name="branch4", to_junction_name="oxy4") + +four_polymer.extend(e1, from_junction_name="carb1", to_junction_name="oxy1") +four_polymer.extend(e2, from_junction_name="carb2", to_junction_name="oxy2") +four_polymer.extend(e3, from_junction_name="carb3", to_junction_name="oxy3") +four_polymer.extend(e4, from_junction_name="carb4", to_junction_name="oxy4") + +four_polymer.extend(e1, from_junction_name="carb1", to_junction_name="oxy1") +four_polymer.extend(e2, from_junction_name="carb2", to_junction_name="oxy2") +four_polymer.extend(e3, from_junction_name="carb3", to_junction_name="oxy3") +four_polymer.extend(e4, from_junction_name="carb4", to_junction_name="oxy4") + +four_polymer.extend(terminal, from_junction_name="carb1", to_junction_name="term") +four_polymer.extend(terminal, from_junction_name="carb2", to_junction_name="term") +four_polymer.extend(terminal, from_junction_name="carb3", to_junction_name="term") +four_polymer.extend(terminal, from_junction_name="carb4", to_junction_name="term") + +# check polymer charge and give it a descriptive name +print(f"netcharge = {four_polymer.topology.netcharge}") +four_polymer.topology.title = "four arm star polymer - overlapped monomers" # rename your ITP header and image name + +# save the polymer to a file and visualise the structure with RDKit for an easy visual structure check +four_polymer.save_to_file('data/four_arm_star_overlapped_monomers.json') # text dump +four_polymer.topology.to_ITP('data/four_arm_star_overlapped_monomers.itp') +Visualize.polymer(four_polymer,infer_bond_order=False).draw2D('data/four_arm_star_overlapped_monomers.png',(400,300)) \ No newline at end of file