Format documentation

.readthedocs.yaml

@@ -15,4 +15,9 @@ conda:
 python:
   install:
     - method: pip
-      path: .
+      path: .
+
+python:
+  install:
+    - method: pip
+      path: docs/source/polyconstruct-sphinx-theme

data_paper_examples/pei.itp

@@ -0,0 +1,117 @@
+;----------------------------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 ]
+; Name   nrexcl
+LHCU     3
+[ atoms ]
+;  nr  type  resnr  resid  atom  cgnr  charge    mass
+    1   CH3    1    LHCU    C62    1    0.001  15.0350
+    2   CH2    1    LHCU    C51    2    0.201  14.0270
+    3  NOpt    1    LHCU    N71    3   -0.698  14.0067
+    4  HS14    1    LHCU    H72    4    0.292   1.0080
+    5   CH2    1    LHCU    C61    5    0.198  14.0270
+    6   CH2    1    LHCU     C5    6    0.213  14.0270
+    7  NOpt    1    LHCU     N7    7   -0.711  14.0067
+    8  HS14    1    LHCU    H21    8    0.306   1.0080
+    9   CH3    1    LHCU     C6    9    0.198  15.0350
+; total charge of the molecule:   0.000
+[ bonds ]
+;  ai   aj  funct   c0         c1
+    1    2    2   0.1530   7.1500e+06
+    2    3    2   0.1470   8.7100e+06
+    3    4    2   0.1020   1.7782e+07
+    3    5    2   0.1470   8.7100e+06
+    5    6    2   0.1530   7.1500e+06
+    6    7    2   0.1470   8.7100e+06
+    7    8    2   0.1020   1.7782e+07
+    7    9    2   0.1470   8.7100e+06
+[ pairs ]
+;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
+    1    4    1
+    1    5    1
+    2    6    1
+    3    7    1
+    4    6    1
+    5    8    1
+    5    9    1
+[ angles ]
+;  ai   aj   ak  funct   angle     fc
+    1    2    3    2    111.00   530.00
+    2    3    4    2    109.50   425.00
+    2    3    5    2    116.00   620.00
+    4    3    5    2    109.50   425.00
+    3    5    6    2    111.00   530.00
+    5    6    7    2    111.00   530.00
+    6    7    8    2    109.50   425.00
+    6    7    9    2    116.00   620.00
+    8    7    9    2    109.50   425.00
+[ dihedrals ]
+; GROMOS improper dihedrals
+;  ai   aj   ak   al  funct   angle     fc
+[ dihedrals ]
+;  ai   aj   ak   al  funct    ph0      cp     mult
+    1    2    3    5    1    180.00     1.00    6
+    2    3    5    6    1    180.00     1.00    6
+    3    5    6    7    1      0.00     5.92    3
+    5    6    7    9    1    180.00     1.00    6
+[ exclusions ]
+;  ai   aj  funct  ;  GROMOS 1-4 exclusions