Format for Documenting Syntax

Font Conventions for Keywords

Several type style conventions are used to distinguish different kinds of keywords. For example:

command ?keyword = value? ...

Words (or letters) in bold indicate the names of commands and must be typed exactly as shown. Note that all commands and parameter names are case-sensitive and must be typed as shown.

Words in italics indicate options that must be replaced with appropriate text. These may be items that must be replaced by specific text (for example, path, keyword, filetype, operation), items to be replaced by values of the appropriate type (for example, value, arg), or user-supplied variable names (for example, varName).

Italics are also used to indicate the names of internal Discover databases and their named parts.

Assignment and Types of Values

The syntax keyword = value is used for many command options, where = value is used to change the default value of an option.

The lists of keywords in the Syntax sections explain the character sequences that may be used as keywords and their values for each command, including occasional synonymous keywords that may be used interchangeably. The keywords are case-sensitive and must be typed exactly as written.

Some of the listed keywords contain an asterisk (*) within the word. This indicates that the letters to the left of the asterisk must be typed exactly as written and that the word can be truncated at any point to the right of the asterisk. However, any characters that are typed must be exactly as written in the table. (Note that the asterisk itself is used only for documentation and must not be typed as part of the keyword.)

The values appropriate to each keyword are also specified in the table. Their type is indicated if it is real, integer, string, or Boolean; for enumerated constants, the allowed values are specified.

Real numbers can be represented in floating-point or exponential form. Both real and integer numbers are actually input as strings. The Discover program converts the string to the appropriate numerical form, depending on the context. Numbers are used for molecule numbers, force constants, etc.
Strings need to be enclosed in quotation marks or braces only if they contain spaces. These are case-sensitive. Character strings are typically used for file names, residue names, atom names, etc. Residue names must have the same case (or mixture of cases) as they have in the residue library or Cartesian coordinate file.
Boolean values are used to select items that can be present or absent; they can act as toggles to activate and deactivate some options; and they are used for setting some variables to true or false. Boolean values are case-insensitive (e.g., ON, on, and On are equivalent). Note that the Discover 95.0 program handles Booleans different than does the Discover 3.1 program.
Enumerated parameters (enums) take specific string constants (listed in the keyword tables) and are used for selecting mutually exclusive options. For example, in the minimize command, the method can be steepest, conjugate, newton, or cascade, and nothing else. Enum values are case-insensitive.

Where a value is expected, an appropriate variable or expression may also be used.

Punctuation Conventions

Optional items in the syntax line are enclosed between question marks (? ?). Ellipses (...) indicate that the preceding item can be repeated. A vertical line ( | ) separates alternative keywords. These symbols themselves are used for syntax-documentation only and should not be included in the real command.

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