share/top/residues.dtd

   1 <!--                                                              -->
   2 <!-- GROMACS Data type description (DTD).
   3
   4                 This source code is part of
   5
   6                  G   R   O   M   A   C   S
   7
   8           GROningen MAchine for Chemical Simulations
   9
  10                         VERSION 3.1
  11
  12  Copyright (c) 1991-2002
  13  BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  University of Groningen, The Netherlands
  15
  16  This program is free software; you can redistribute it and/or
  17  modify it under the terms of the GNU General Public License
  18  as published by the Free Software Foundation; either version 2
  19  of the License, or (at your option) any later version.
  20
  21  If you want to redistribute modifications, please consider that
  22  scientific software is very special. Version control is crucial -
  23  bugs must be traceable. We will be happy to consider code for
  24  inclusion in the official distribution, but derived work must not
  25  be called official GROMACS. Details are found in the README & COPYING
  26  files - if they are missing, get the official version at www.gromacs.org.
  27
  28  To help us fund GROMACS development, we humbly ask that you cite
  29  the papers on the package - you can find them in the top README file.
  30
  31  Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
  32
  33  And Hey:
  34  GROningen Mixture of Alchemy and Childrens' Stories
  35
  36
  37  David van der Spoel 07/2001, 03/2002
  38  The authorative version of this document can be found at
  39  http://www.gromacs.org/gromacs3.1.dtd
  40  and also in the library directory of your local GROMACS
  41  installation.
  42
  43  Please use the following formal public identifier to identify it:
  44      "-//RESIDUES//DTD Residues XML V1.0//EN"
  45
  46  <!DOCTYPE residues PUBLIC "-//RESIDUES//DTD Gromacs XML V3.1.0//EN"
  47                     "http://www.gromacs.org/residues.dtd"
  48                    [...]>
  49 -->
  50
  51 <!-- This file defines the structure of the information necessary make
  52      a molecule from simple building blocks (called residues). The
  53      algorithm processing a sequence (or pdb file) should follow these
  54      steps:
  55      1. Do all the modification (moddef)
  56      2. Add all the links between residues
  57      3. Generate hydrogens
  58      4. Generate angle and torsion descriptions
  59 -->
  60
  61 <!ELEMENT macromolecules (residues,macromolecule*)>
  62
  63 <!ELEMENT residues (residue*,linkdef*,moddef*)>
  64
  65 <!ELEMENT residue (ratom+,rbond*,rangle*,rimproper*,rdihedral*,raddh*)>
  66 <!ATTLIST residue
  67           restype  ID    #REQUIRED
  68           longname CDATA #REQUIRED>
  69 <!-- We can not use ID here for atom names since there is no -->
  70 <!-- hope to make them unique, e.g. all amino acids have the -->
  71 <!-- same name for backbone atoms.                           -->
  72 <!ELEMENT ratom EMPTY>
  73 <!ATTLIST ratom
  74           name  CDATA #REQUIRED>
  75 <!ELEMENT rbond EMPTY>
  76 <!ATTLIST rbond
  77           a1 CDATA #REQUIRED
  78           a2 CDATA #REQUIRED>
  79 <!ELEMENT rangle EMPTY>
  80 <!ATTLIST rangle
  81           a1 CDATA #REQUIRED
  82           a2 CDATA #REQUIRED
  83           a3 CDATA #REQUIRED>
  84 <!ELEMENT rimproper EMPTY>
  85 <!ATTLIST rimproper
  86           a1 CDATA #REQUIRED
  87           a2 CDATA #REQUIRED
  88           a3 CDATA #REQUIRED
  89           a4 CDATA #REQUIRED>
  90 <!ELEMENT rdihedral EMPTY>
  91 <!ATTLIST rdihedral
  92           a1 CDATA #REQUIRED
  93           a2 CDATA #REQUIRED
  94           a3 CDATA #REQUIRED
  95           a4 CDATA #REQUIRED>
  96 <!-- Definition of how to add (hydrogen) atoms to molecules  -->
  97 <!-- using a certain geometry (see GROMACS manual)           -->
  98 <!ELEMENT raddh EMPTY>
  99 <!ATTLIST raddh
 100           hclass   ( polar | aromatic | aliphatic )
 101           addgeom  CDATA #REQUIRED
 102           addnum   CDATA #REQUIRED
 103           addto    CDATA #REQUIRED>
 104
 105 <!-- Define a covalent link between two residues, given in restyp -->
 106 <!-- and the atoms are given as well (atomprev and atomnext)      -->
 107 <!-- A reference distance between the atoms does also have to be  -->
 108 <!-- given in nm (but that does not have to be used).             -->
 109 <!ELEMENT linkdef EMPTY>
 110 <!ATTLIST linkdef
 111           linktype ID     #REQUIRED
 112           restype  IDREFS #REQUIRED
 113           atomprev CDATA  #REQUIRED
 114           atomnext CDATA  #REQUIRED
 115           refdist  CDATA  #REQUIRED>
 116
 117 <!-- Description of termini, etc. or maybe other modifications too -->
 118 <!-- It is important that the implementation deletes first, and    -->
 119 <!-- adds atoms afterwards                                         -->
 120 <!ELEMENT moddef (moddelete*,modadd*,modrepl*)>
 121 <!ATTLIST moddef
 122           modtype ID    #REQUIRED>
 123 <!ELEMENT moddelete EMPTY>
 124 <!ATTLIST moddelete
 125           delname CDATA #REQUIRED>
 126 <!ELEMENT modreplace EMPTY>
 127 <!ATTLIST modreplace
 128           oldname CDATA #REQUIRED
 129           newname CDATA #REQUIRED>
 130 <!ELEMENT modadd EMPTY>
 131 <!ATTLIST modadd
 132           addname CDATA #REQUIRED
 133           addbond CDATA #REQUIRED>
 134
 135 <!-- Generic stuff to define proteins etc. as built up from blocks -->
 136 <!-- such as amino acids and HEME etc.                             -->
 137 <!ELEMENT macromolecule (mblock+,mlink*,mmod*)>
 138 <!ATTLIST macromolecule
 139           mname ID #REQUIRED>
 140 <!ELEMENT mblock EMPTY>
 141 <!ATTLIST mblock
 142           resname   ID    #REQUIRED
 143           restype   IDREF #REQUIRED
 144           protonated ( no | polar | all ) "polar">
 145 <!ELEMENT mlink EMPTY>
 146 <!ATTLIST mlink
 147           mlinktype  ( peptide | disulphide | special ) "peptide"
 148           resname   IDREFS #REQUIRED>
 149 <!ELEMENT mmod EMPTY>
 150 <!ATTLIST mmod
 151           resname IDREF #REQUIRED
 152           modtype IDREF #REQUIRED>
 153
 154 <!-- Generic stuff to define proteins etc. as built up from blocks -->
 155 <!-- such as amino acids and HEME etc.                             -->
 156 <!ELEMENT macromolecule (mblock+,mlink*,mmod*)>
 157 <!ATTLIST macromolecule
 158           mname ID #REQUIRED>
 159 <!ELEMENT mblock EMPTY>
 160 <!ATTLIST mblock
 161           resname   ID    #REQUIRED
 162           restype   IDREF #REQUIRED
 163           protonated ( no | polar | all ) "polar">
 164 <!ELEMENT mlink EMPTY>
 165 <!ATTLIST mlink
 166           mlinktype  ( peptide | disulphide | special ) "peptide"
 167           resname   IDREFS #REQUIRED>
 168 <!ELEMENT mmod EMPTY>
 169 <!ATTLIST mmod
 170           resname IDREF #REQUIRED
 171           modtype IDREF #REQUIRED>
 172