onedep-webfe_ccmodule/help.html at master · wwPDB/onedep-webfe_ccmodule · GitHub

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  <title>Chemical Components Development Site</title>
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<h1>On-line Help for Chemical Components Toolbox</h1>
<hr />
<a id="viewer" ></a>
<h2>Viewer Tool</h2>
<p>
The chemical component viewer provides summary profiles for components
in the current component dictionary.  The input to this tool is
one or a collection of chemical component 3-letter-code identifiers (multiple identifiers may be separated by commas or just spaces).
Multiple chemical components can be displayed for comparative viewing.
</p>
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<h2>Edit Tool</h2>
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<p>
The chemical diagram editor provides the functionality to build new molecules or load and modify existing ones.
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<h2>Search Tool</h2>
<a id="searchTool" ></a>
<a id="searchNameFormula" ></a>
<h3>Name and Formula Search</h3>
<p>
This form below provides access to searches for molecular name and molecular formula.  A number of
search types are supported.
</p>
Molecular formula search options:
<p>
<ul>
<li>Exact all atom formula matches</li>
<li>Exact heavy atom formula matches</li>
<li>Exact formula will match any dictionary component containing the partial query formula. For instance,
    a query for <i>C6 N2</i> will match any formula containing exactly six carbons and two nitrogens.</li>
<li>A formula subset query will find molecules with formula containing a minimum of the query formula composition.
    For instance, <i>C6 H7 Hg N2 O2 S</i> will match  <i>C8 H10 Hg N2 O4 S</i>.
</ul>
</p>
<p>
Note: formulas must be entered with spaces like: <i>C6 H11 N2 O7 P</i>.
</p>

<p>
Molecular name search options:
<ul>
<li>Exact name matches.</li>
<li>Exact substring name matches. These search will find cases where a query name is contained
   with the dictionary name.  For instance, pyridine will match 2-aminopyridine</li>

<li>The similar name option will math names which are lexigraphically similar but not exact matches.
In other words the names may differ in a small number of characters.  For instance, a search for
pyridine will match uridine and pyrimidine.
</ul>
</p>

<a id="searchSubstructure"></a>
<h3>Substructure Search</h3>
<p>
The substructure search will try to match the 2D chemical structure in uploaded chemical component
definition file with components in the current chemical dictionary.    The following matching options
are supported:
</p>
<p>
<ul>
<li>Strict (all atom) queries will match cases in which atom types, bond types, stereochemistry, and aromaticity
    are the same. </li>
<li>Strict (heavy atom) queries will match cases in which atom types, bond types, stereochemistry, and aromaticity
    are the same among heavy atoms. </li>
<li>Relaxed (all atom) queries will match atom types and connectivity (with any bond type) among all atoms.
<li>Relaxed (heavy atom) queries will match atom types and connectivity (with any bond type) among only heavy atoms.
<li>Close matching is similar to relaxed heavy atom matching except that a wider range of candidate molecules
    are compared.  This is a useful option if it is possible that the query molecule may be missing a few atoms.
</ul>
</p>
<p>
Note:  Strict and relaxed matches are only performed on molecules with corresponding all/heavy formulas.  Close matches
are performed on molecules that have similar but larger formulas (up to +3 in any element).
</p>

<a id="searchInstance"></a>
<h3>Instance Search</h3>
<p>
The input to an instance search is a 3-letter-code component identifier.   This search will produce a
table containing the PDB entries containing the component.   The table is divided into sections for
released and unreleased entries.
</p>
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