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Line length
Open

| RMF::decorator::Alternatives    | any            |  You can use RMF::decorator::Alternatives::add_alternative() to add an alternative representation and RMF::decorator::Alternatives::get_alternatives() or RMF::decorator::Alternatives::get_alternative() to get them. |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

The attributes and decorators are divided into several categories, each associated with a different RMF::Category. Each decorator has three associated types eg RMF::decorator::Particle, RMF::decorator::ParticleConst and RMF::decorator::ParticleFactory. The non-const decorator inherits from the const one. The factory is used to test whether a given node has the needed attributes and to create decorators decorating a given node. Note, that if passed an RMF::NodeConstHandle, the node already having the required attributes is a precondition for the factory `get()` method.
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| `path`           | string    |  Relative path to the external file              |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| `sequence`       | string    |  Primary sequence of a chain                     |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| Name                            |  Node Type              | Attributes                         |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| `copy index`     | int       |  The index of this particular copy of a protein (when there are multiple copies of the same protein) |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| `structure residue offset` | int     |  Model residue # = Structure residue # + offset |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| RMF::decorator::Score           | RMF::FEATURE            |  score                             |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| `sampling replicas`   | int          |  Number of sampling replicas used         |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| RMF::decorator::SampleProvenance    |  RMF::PROVENANCE    | sampling method, sampling frames, sampling iterations, sampling replicas |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| `coordinates list` | RMF::Vector3s  |  A list of coordinates.                          |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

|RMF::FloatsTraits | RMF::FloatsTraits | a traits classes to tell HDF5 how to read and write one or more lists of floating point values |
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Line length
Open

| RMF::decorator::Ellipsoid       | RMF::GEOMETRY           |  coordinates, axis lengths, orientation |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Multiple top level headers in the same document
Open

# The RMF Hierarchy # {#hierarchy}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Multiple top level headers in the same document
Open

# Adding custom data to an RMF # {#adding}
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD025 - Multiple top level headers in the same document

Tags: headers

Aliases: single-h1

Parameters: level (number; default 1)

This rule is triggered when a top level header is in use (the first line of the file is a h1 header), and more than one h1 header is in use in the document:

# Top level header

# Another top level header

To fix, structure your document so that there is a single h1 header that is the title for the document, and all later headers are h2 or lower level headers:

# Title

## Header

## Another header

Rationale: A top level header is a h1 on the first line of the file, and serves as the title for the document. If this convention is in use, then there can not be more than one title for the document, and the entire document should be contained within this header.

Note: The level parameter can be used to change the top level (ex: to h2) in cases where an h1 is added externally.

Line length
Open

| `types`          | RMF::Ints |  The RMF::decorator::RepresentationType entries for the alternative representations. |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Lists should be surrounded by blank lines
Open

- feature information about parts of the structures, such as how well it
Severity: Info
Found in doc/FileFormat.md by markdownlint

MD032 - Lists should be surrounded by blank lines

Tags: bullet, ul, ol, blank_lines

Aliases: blanks-around-lists

This rule is triggered when lists (of any kind) are either not preceded or not followed by a blank line:

Some text
* Some
* List

1. Some
2. List
Some text

To fix this, ensure that all lists have a blank line both before and after (except where the block is at the beginning or end of the document):

Some text

* Some
* List

1. Some
2. List

Some text

Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will not parse lists that don't have blank lines before and after them.

Note: List items without hanging indents are a violation of this rule; list items with hanging indents are okay:

* This is
not okay

* This is
  okay

Header style
Open

Severity: Info
Found in doc/VMDPlugin.md by markdownlint

MD003 - Header style

Tags: headers

Aliases: header-style

Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")

This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:

# ATX style H1

## Closed ATX style H2 ##

Setext style H1
===============

Be consistent with the style of header used in a document:

# ATX style H1

## ATX style H2

The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:

Setext style H1
===============

Setext style H2
---------------

### ATX style H3

Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.

Line length
Open

| `software version`    | string       |  Version of the software used to make the model |
Severity: Info
Found in doc/DecoratorsAndAttributes.md by markdownlint

MD013 - Line length

Tags: line_length

Aliases: line-length Parameters: linelength, codeblocks, tables (number; default 80, boolean; default true)

This rule is triggered when there are lines that are longer than the configured line length (default: 80 characters). To fix this, split the line up into multiple lines.

This rule has an exception where there is no whitespace beyond the configured line length. This allows you to still include items such as long URLs without being forced to break them in the middle.

You also have the option to exclude this rule for code blocks and tables. To do this, set the code_blocks and/or tables parameters to false.

Code blocks are included in this rule by default since it is often a requirement for document readability, and tentatively compatible with code rules. Still, some languages do not lend themselves to short lines.

Header style
Open

Severity: Info
Found in doc/VMDPlugin.md by markdownlint

MD003 - Header style

Tags: headers

Aliases: header-style

Parameters: style ("consistent", "atx", "atxclosed", "setext", "setextwith_atx"; default "consistent")

This rule is triggered when different header styles (atx, setext, and 'closed' atx) are used in the same document:

# ATX style H1

## Closed ATX style H2 ##

Setext style H1
===============

Be consistent with the style of header used in a document:

# ATX style H1

## ATX style H2

The setextwithatx doc style allows atx-style headers of level 3 or more in documents with setext style headers:

Setext style H1
===============

Setext style H2
---------------

### ATX style H3

Note: the configured header style can be a specific style to use (atx, atxclosed, setext, setextwith_atx), or simply require that the usage be consistent within the document.

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