"Another point for optimization is in common subexpressions: they are not",
"automatically recognized, but can be manually optimized by the use of",
"variables. This can have a big impact on the performance of complex",
- "selections, in particular if you define several index groups like this:",
- " [TT]rdist = distance from com of resnr 1 to 5;[tt][BR]",
- " [TT]resname RES and rdist < 2;[tt][BR]",
- " [TT]resname RES and rdist < 4;[tt][BR]",
- " [TT]resname RES and rdist < 6;[tt][BR]",
+ "selections, in particular if you define several index groups like this::",
+ "",
+ " rdist = distance from com of resnr 1 to 5;",
+ " resname RES and rdist < 2;",
+ " resname RES and rdist < 4;",
+ " resname RES and rdist < 6;",
+ "",
"Without the variable assignment, the distances would be evaluated three",
"times, although they are exactly the same within each selection.",
"Anything assigned into a variable becomes a common subexpression that",
// tools and explain what the selections do in those tools.
"Below, examples of increasingly complex selections are given.[PAR]",
- "Selection of all water oxygens:[BR]",
+ "Selection of all water oxygens::",
+ "",
" resname SOL and name OW",
- "[PAR]",
+ "",
- "Centers of mass of residues 1 to 5 and 10:[BR]",
+ "Centers of mass of residues 1 to 5 and 10::",
+ ""
" res_com of resnr 1 to 5 10",
- "[PAR]",
+ "",
- "All atoms farther than 1 nm of a fixed position:[BR]",
+ "All atoms farther than 1 nm of a fixed position::",
+ "",
" not within 1 of [1.2, 3.1, 2.4]",
- "[PAR]",
+ "",
- "All atoms of a residue LIG within 0.5 nm of a protein (with a custom name):[BR]",
+ "All atoms of a residue LIG within 0.5 nm of a protein (with a custom name)::",
+ "",
" \"Close to protein\" resname LIG and within 0.5 of group \"Protein\"",
- "[PAR]",
+ "",
- "All protein residues that have at least one atom within 0.5 nm of a residue LIG:[BR]",
+ "All protein residues that have at least one atom within 0.5 nm of a residue LIG::",
+ "",
" group \"Protein\" and same residue as within 0.5 of resname LIG",
- "[PAR]",
+ "",
- "All RES residues whose COM is between 2 and 4 nm from the COM of all of them:[BR]",
- " rdist = res_com distance from com of resname RES[BR]",
+ "All RES residues whose COM is between 2 and 4 nm from the COM of all of them::",
+ "",
+ " rdist = res_com distance from com of resname RES",
" resname RES and rdist >= 2 and rdist <= 4",
- "[PAR]",
+ "",
- "Selection like C1 C2 C2 C3 C3 C4 ... C8 C9 (e.g., for g_bond):[BR]",
+ "Selection like C1 C2 C2 C3 C3 C4 ... C8 C9 (e.g., for g_bond)::",
+ "",
" name \"C[1-8]\" merge name \"C[2-9]\"",
};
"[PAR]",
"Due to technical reasons, having a negative value as the first value in",
- "expressions like[BR]",
- "[TT]charge -1 to -0.7[tt][BR]",
- "result in a syntax error. A workaround is to write[BR]",
- "[TT]charge {-1 to -0.7}[tt][BR]",
+ "expressions like ::",
+ "",
+ " charge -1 to -0.7",
+ "",
+ "result in a syntax error. A workaround is to write ::",
+ "",
+ " charge {-1 to -0.7}",
+ "",
"instead.[PAR]",
"When [TT]name[tt] selection keyword is used together with PDB input",
"not if you provide the selections, e.g., from a pipe.[PAR]",
"It is possible to use variables to store selection expressions.",
- "A variable is defined with the following syntax:[BR]",
- "[TT]VARNAME = EXPR ;[tt][BR]",
+ "A variable is defined with the following syntax::",
+ "",
+ " VARNAME = EXPR ;",
+ "",
"where [TT]EXPR[tt] is any valid selection expression.",
"After this, [TT]VARNAME[tt] can be used anywhere where [TT]EXPR[tt]",
"would be valid.[PAR]",
protected:
virtual std::string helpText() const
{
- return concatenateStrings(method_.help.help, method_.help.nlhelp);
+ return joinStrings(method_.help.help,
+ method_.help.help + method_.help.nlhelp, "\n");
}
private:
// still prints raw text, but these are waiting for discussion of the
// markup format in #969.
writeBasicHelpTopic(context, *this, helpText());
- context.writeTextBlock("[BR]");
+ context.writeTextBlock("");
// Print the list of keywords
- context.writeTextBlock(
- "Keywords that select atoms by an integer property:[BR]"
- "(use in expressions or like \"atomnr 1 to 5 7 9\")[BR]");
+ context.writeTextBlock("Keywords that select atoms by an integer property:");
+ context.writeTextBlock("(use in expressions or like \"atomnr 1 to 5 7 9\")");
printKeywordList(context, INT_VALUE, false);
- context.writeTextBlock("[BR]");
+ context.writeTextBlock("");
- context.writeTextBlock(
- "Keywords that select atoms by a numeric property:[BR]"
- "(use in expressions or like \"occupancy 0.5 to 1\")[BR]");
+ context.writeTextBlock("Keywords that select atoms by a numeric property:");
+ context.writeTextBlock("(use in expressions or like \"occupancy 0.5 to 1\")");
printKeywordList(context, REAL_VALUE, false);
- context.writeTextBlock("[BR]");
+ context.writeTextBlock("");
- context.writeTextBlock(
- "Keywords that select atoms by a string property:[BR]"
- "(use like \"name PATTERN [PATTERN] ...\")[BR]");
+ context.writeTextBlock("Keywords that select atoms by a string property:");
+ context.writeTextBlock("(use like \"name PATTERN [PATTERN] ...\")");
printKeywordList(context, STR_VALUE, false);
- context.writeTextBlock("[BR]");
+ context.writeTextBlock("");
- context.writeTextBlock(
- "Additional keywords that directly select atoms:[BR]");
+ context.writeTextBlock("Additional keywords that directly select atoms:");
printKeywordList(context, GROUP_VALUE, false);
- context.writeTextBlock("[BR]");
+ context.writeTextBlock("");
- context.writeTextBlock(
- "Keywords that directly evaluate to positions:[BR]"
- "(see also \"positions\" subtopic)[BR]");
+ context.writeTextBlock("Keywords that directly evaluate to positions:");
+ context.writeTextBlock("(see also \"positions\" subtopic)");
printKeywordList(context, POS_VALUE, false);
- context.writeTextBlock("[BR]");
+ context.writeTextBlock("");
- context.writeTextBlock("Additional keywords:[BR]");
+ context.writeTextBlock("Additional keywords:");
printKeywordList(context, POS_VALUE, true);
printKeywordList(context, NO_VALUE, true);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff