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feat: parse coarse-grained polymer ffs (#435)
 fix: render parameters for builtin reactions --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
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‎_reference/topology.atomic.qmd

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@@ -22,6 +22,7 @@ See [gromacs manual](https://manual.gromacs.org/current/reference-manual/topolog
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| [Exclusion](#kimmdy.topology.atomic.Exclusion) | Information about one exclusion |
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| [MultipleDihedralTypes](#kimmdy.topology.atomic.MultipleDihedralTypes) | Multiple ``DihedralTypes``s with the same ai, aj, ak, al |
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| [MultipleDihedrals](#kimmdy.topology.atomic.MultipleDihedrals) | Multiple ``Dihedral``s with the same ai, aj, ak, al |
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| [NonbondParamType](#kimmdy.topology.atomic.NonbondParamType) | Information about one nonbonded parameterize |
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| [Pair](#kimmdy.topology.atomic.Pair) | Information about one pair |
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| [PositionRestraint](#kimmdy.topology.atomic.PositionRestraint) | Information about one position restraint. |
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| [ResidueAtomSpec](#kimmdy.topology.atomic.ResidueAtomSpec) | Information about one atom in a residue |
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### AtomType { #kimmdy.topology.atomic.AtomType }
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`topology.atomic.AtomType(self, type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)`
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`topology.atomic.AtomType(self, type, id, id_sym, mass, charge, ptype, sigma, epsilon, at_num=None)`
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Information about one atom type
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funct should always be "9" when the length of dihedrals is > 1.
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The key of the dihedrals dict is the periodicity (c2).
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### NonbondParamType { #kimmdy.topology.atomic.NonbondParamType }
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`topology.atomic.NonbondParamType(self, i, j, id, id_sym, funct, c0=None, c1=None, c2=None)`
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Information about one nonbonded parameterize
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typical in coarse grained models.
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A class containing nonbonded information as in the nonbond_params section of the forcefield.
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From gromacs:
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; Lennard jones between beads
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; i j funda sigma(nm) epsilon (kmol/mol)
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Where i and j are atomtypes
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### Pair { #kimmdy.topology.atomic.Pair }
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`topology.atomic.Pair(self, ai, aj, funct, c0=None, c1=None, c2=None, c3=None)`

‎docs/_reference/topology.atomic.html

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<li><a href="#kimmdy.topology.atomic.Exclusion" id="toc-kimmdy.topology.atomic.Exclusion" class="nav-link" data-scroll-target="#kimmdy.topology.atomic.Exclusion">Exclusion</a></li>
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<li><a href="#kimmdy.topology.atomic.MultipleDihedralTypes" id="toc-kimmdy.topology.atomic.MultipleDihedralTypes" class="nav-link" data-scroll-target="#kimmdy.topology.atomic.MultipleDihedralTypes">MultipleDihedralTypes</a></li>
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<li><a href="#kimmdy.topology.atomic.MultipleDihedrals" id="toc-kimmdy.topology.atomic.MultipleDihedrals" class="nav-link" data-scroll-target="#kimmdy.topology.atomic.MultipleDihedrals">MultipleDihedrals</a></li>
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<li><a href="#kimmdy.topology.atomic.NonbondParamType" id="toc-kimmdy.topology.atomic.NonbondParamType" class="nav-link" data-scroll-target="#kimmdy.topology.atomic.NonbondParamType">NonbondParamType</a></li>
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<li><a href="#kimmdy.topology.atomic.Pair" id="toc-kimmdy.topology.atomic.Pair" class="nav-link" data-scroll-target="#kimmdy.topology.atomic.Pair">Pair</a></li>
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<li><a href="#kimmdy.topology.atomic.PositionRestraint" id="toc-kimmdy.topology.atomic.PositionRestraint" class="nav-link" data-scroll-target="#kimmdy.topology.atomic.PositionRestraint">PositionRestraint</a></li>
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<li><a href="#kimmdy.topology.atomic.ResidueAtomSpec" id="toc-kimmdy.topology.atomic.ResidueAtomSpec" class="nav-link" data-scroll-target="#kimmdy.topology.atomic.ResidueAtomSpec">ResidueAtomSpec</a></li>
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<td>Multiple <code>Dihedral</code>s with the same ai, aj, ak, al</td>
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</tr>
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<tr class="odd">
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<td><a href="#kimmdy.topology.atomic.NonbondParamType">NonbondParamType</a></td>
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<td>Information about one nonbonded parameterize</td>
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</tr>
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<tr class="even">
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<td><a href="#kimmdy.topology.atomic.Pair">Pair</a></td>
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<td>Information about one pair</td>
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<tr class="even">
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<tr class="odd">
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<td><a href="#kimmdy.topology.atomic.PositionRestraint">PositionRestraint</a></td>
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<td>Information about one position restraint.</td>
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<tr class="odd">
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<tr class="even">
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<td><a href="#kimmdy.topology.atomic.ResidueAtomSpec">ResidueAtomSpec</a></td>
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<td>Information about one atom in a residue</td>
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<tr class="odd">
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<td><a href="#kimmdy.topology.atomic.ResidueBondSpec">ResidueBondSpec</a></td>
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<td>Information about one bond in a residue</td>
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<tr class="odd">
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<tr class="even">
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<td><a href="#kimmdy.topology.atomic.ResidueImproperSpec">ResidueImproperSpec</a></td>
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<td>Information about one improper dihedral in a residue</td>
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<td><a href="#kimmdy.topology.atomic.ResidueProperSpec">ResidueProperSpec</a></td>
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<td>Information about one proper dihedral in a residue</td>
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<td><a href="#kimmdy.topology.atomic.ResidueType">ResidueType</a></td>
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<td>Information about one residuetype from aminoacids.rtp</td>
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<tr class="odd">
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<td><a href="#kimmdy.topology.atomic.Settle">Settle</a></td>
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<td>Information about one settles</td>
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</section>
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<section id="kimmdy.topology.atomic.AtomType" class="level3">
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<h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.AtomType">AtomType</h3>
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<p><code>topology.atomic.AtomType(self, type, id_sym, at_num, mass, charge, ptype, sigma, epsilon, id)</code></p>
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<p><code>topology.atomic.AtomType(self, type, id, id_sym, mass, charge, ptype, sigma, epsilon, at_num=None)</code></p>
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<p>Information about one atom type</p>
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<p>A class containing atom type information as in the atomtypes section of the forcefield.</p>
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<p>From gromacs version of the amber* ff: ; name at.num mass charge ptype sigma epsilon</p>
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<p><code>topology.atomic.MultipleDihedrals(self, ai, aj, ak, al, funct, dihedrals)</code></p>
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<p>Multiple <code>Dihedral</code>s with the same ai, aj, ak, al but different periodicities. funct should always be “9” when the length of dihedrals is &gt; 1. The key of the dihedrals dict is the periodicity (c2).</p>
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<section id="kimmdy.topology.atomic.NonbondParamType" class="level3">
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<h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.NonbondParamType">NonbondParamType</h3>
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<p><code>topology.atomic.NonbondParamType(self, i, j, id, id_sym, funct, c0=None, c1=None, c2=None)</code></p>
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<p>Information about one nonbonded parameterize</p>
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<p>typical in coarse grained models. A class containing nonbonded information as in the nonbond_params section of the forcefield.</p>
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<p>From gromacs: ; Lennard jones between beads ; i j funda sigma(nm) epsilon (kmol/mol) Where i and j are atomtypes</p>
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</section>
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<section id="kimmdy.topology.atomic.Pair" class="level3">
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<h3 class="anchored" data-anchor-id="kimmdy.topology.atomic.Pair">Pair</h3>
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<p><code>topology.atomic.Pair(self, ai, aj, funct, c0=None, c1=None, c2=None, c3=None)</code></p>

‎docs/guide/explanation/index.html

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<a href="../../guide/explanation/components.html" class="title listing-title">Components of KIMMDY</a>
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<span class="listing-author">Kai Riedmiller</span>
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<tr data-index="1" data-listing-file-modified-sort="1716213165985" data-listing-reading-time-sort="1" data-listing-title-sort="Visualize Topologies" data-listing-filename-sort="topology.qmd">
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<a href="../../guide/explanation/topology.html" class="title listing-title">Visualize Topologies</a>
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‎docs/guide/how-to/index.html

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<tr data-index="0" data-listing-file-modified-sort="1718099362172" data-listing-reading-time-sort="2" data-listing-title-sort="Analyze a KIMMDY run" data-listing-filename-sort="analyze.qmd">
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<span class="listing-author">Kai Riedmiller</span>
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<tr data-index="1" data-listing-file-modified-sort="1718099362172" data-listing-reading-time-sort="2" data-listing-title-sort="Contribute" data-listing-filename-sort="contribute.qmd">
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<a href="../../guide/how-to/examples.html" class="title listing-title">Examples</a>
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<span class="listing-author">&nbsp;</span>
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<a href="../../guide/how-to/hcp.html" class="title listing-title">High Performance Computing</a>
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<span class="listing-author">&nbsp;</span>
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<tr data-index="4" data-listing-file-modified-sort="1718099362176" data-listing-reading-time-sort="1" data-listing-title-sort="Install Machine Learning Plugins" data-listing-filename-sort="install-ml-plugins.qmd">
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<a href="../../guide/how-to/install-ml-plugins.html" class="title listing-title">Install Machine Learning Plugins</a>
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<span class="listing-author">&nbsp;</span>
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<tr data-index="5" data-listing-file-modified-sort="1718099362176" data-listing-reading-time-sort="1" data-listing-title-sort="Reaction only" data-listing-filename-sort="reaction_only.qmd">
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‎docs/guide/tutorials/getting-started.html

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<p>Our starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin <code>hat_reaction</code> to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.</p>
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<div id="app-./getting-started-files/vis-ala.molj" class="molstar-app"></div>
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‎docs/guide/tutorials/index.html

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<p><a href="../../guide/tutorials/getting-started.html"> <img src="../../guide/tutorials/img/getting-started-vmd-radicals.png" class="thumbnail-image"> </a></p>
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‎docs/guide/tutorials/modify-topology.html

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<h3 class="anchored" data-anchor-id="minimized-structure-of-native-peptide">Minimized structure of native peptide</h3>
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