#include "selhelp.h"
+#include <set>
#include <string>
#include <utility>
#include <vector>
#include "gromacs/onlinehelp/helptopic.h"
#include "gromacs/onlinehelp/helpwritercontext.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/file.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textwriter.h"
#include "selmethod.h"
#include "symrec.h"
"if they are complex or for scripting.[PAR]",
"Each tool has different command-line arguments for specifying selections",
- "(listed by [TT][PROGRAM] help <tool>[tt]).",
+ "(see the help for the individual tools).",
"You can either pass a single string containing all selections (separated",
"by semicolons), or multiple strings, each containing one selection.",
"Note that you need to quote the selections to protect them from the",
"To use groups from a traditional index file, use argument [TT]-n[tt]",
"to provide a file. See the \"syntax\" subtopic for how to use them.",
"If this option is not provided, default groups are generated.",
- "The default groups are generated by reading selections from a file",
- "[TT]defselection.dat[tt]. If such a file is found in the current",
- "directory, it is used instead of the one provided by default.[PAR]",
-
+ "The default groups are generated with the same logic as for",
+ "non-selection tools.",
+ "",
"Depending on the tool, two additional command-line arguments may be",
"available to control the behavior:",
"",
const char ExamplesHelpText::title[] =
"Selection examples";
const char *const ExamplesHelpText::text[] = {
- // TODO: Once there are more tools available, use examples that invoke
- // tools and explain what the selections do in those tools.
- "Below, examples of increasingly complex selections are given.[PAR]",
-
- "Selection of all water oxygens::",
+ "Below, examples of different types of selections are given.",
"",
- " resname SOL and name OW",
+ "* Selection of all water oxygens::",
"",
-
- "Centers of mass of residues 1 to 5 and 10::",
+ " resname SOL and name OW",
"",
- " res_com of resnr 1 to 5 10",
+ "* Centers of mass of residues 1 to 5 and 10::",
"",
-
- "All atoms farther than 1 nm of a fixed position::",
+ " res_com of resnr 1 to 5 10",
"",
- " not within 1 of [1.2, 3.1, 2.4]",
+ "* All atoms farther than 1 nm of a fixed position::",
"",
-
- "All atoms of a residue LIG within 0.5 nm of a protein (with a custom name)::",
+ " not within 1 of [1.2, 3.1, 2.4]",
"",
- " \"Close to protein\" resname LIG and within 0.5 of group \"Protein\"",
+ "* All atoms of a residue LIG within 0.5 nm of a protein (with a custom name)::",
"",
-
- "All protein residues that have at least one atom within 0.5 nm of a residue LIG::",
+ " \"Close to protein\" resname LIG and within 0.5 of group \"Protein\"",
"",
- " group \"Protein\" and same residue as within 0.5 of resname LIG",
+ "* All protein residues that have at least one atom within 0.5 nm of a residue LIG::",
"",
-
- "All RES residues whose COM is between 2 and 4 nm from the COM of all of them::",
+ " group \"Protein\" and same residue as within 0.5 of resname LIG",
"",
- " rdist = res_com distance from com of resname RES",
- " resname RES and rdist >= 2 and rdist <= 4",
+ "* All RES residues whose COM is between 2 and 4 nm from the COM of all of them::",
"",
-
- "Selection like C1 C2 C2 C3 C3 C4 ... C8 C9 (e.g., for g_bond)::",
+ " rdist = res_com distance from com of resname RES",
+ " resname RES and rdist >= 2 and rdist <= 4",
+ "",
+ // TODO: Make it possible to use links below.
+ "* Selection like with duplicate atoms like C1 C2 C2 C3 C3 C4 ... C8 C9::",
+ "",
+ " name \"C[1-8]\" merge name \"C[2-9]\"",
+ "",
+ " This can be used with [TT]gmx distance[tt] to compute C1-C2, C2-C3 etc.",
+ " distances.",
+ "",
+ "* Selection with atoms in order C2 C1::",
+ "",
+ " name C1 C2 permute 2 1",
+ "",
+ " This can be used with [TT]gmx gangle[tt] to get C2->C1 vectors instead of",
+ " C1->C2.",
+ "",
+ "* Selection with COMs of two index groups::",
+ "",
+ " com of group 1 plus com of group 2",
+ "",
+ " This can be used with [TT]gmx distance[tt] to compute the distance between",
+ " these two COMs.",
+ "",
+ "* Fixed vector along x (can be used as a reference with [TT]gmx gangle[tt])::",
"",
- " name \"C[1-8]\" merge name \"C[2-9]\"",
+ " [0, 0, 0] plus [1, 0, 0]",
+ "",
+ "* The following examples explain the difference between the various",
+ " position types. This selection selects a position for each residue",
+ " where any of the three atoms C[123] has [TT]x < 2[tt]. The positions",
+ " are computed as the COM of all three atoms.",
+ " This is the default behavior if you just write [TT]res_com of[tt]. ::",
+ "",
+ " part_res_com of name C1 C2 C3 and x < 2",
+ "",
+ " This selection does the same, but the positions are computed as COM",
+ " positions of whole residues::",
+ "",
+ " whole_res_com of name C1 C2 C3 and x < 2",
+ "",
+ " Finally, this selection selects the same residues, but the positions",
+ " are computed as COM of exactly those atoms atoms that match the",
+ " [TT]x < 2[tt] criterion::",
+ "",
+ " dyn_res_com of name C1 C2 C3 and x < 2",
+ "",
+ "* Without the [TT]of[tt] keyword, the default behavior is different from",
+ " above, but otherwise the rules are the same::",
+ "",
+ " name C1 C2 C3 and res_com x < 2",
+ "",
+ " works as if [TT]whole_res_com[tt] was specified, and selects the three",
+ " atoms from residues whose COM satisfiex [TT]x < 2[tt].",
+ " Using ::",
+ "",
+ " name C1 C2 C3 and part_res_com x < 2",
+ "",
+ " instead selects residues based on the COM computed from the C[123] atoms.",
};
struct KeywordsHelpText
"Selection keywords";
const char *const KeywordsHelpText::text[] = {
"The following selection keywords are currently available.",
- "For keywords marked with a star, additional help is available through",
+ "For keywords marked with a plus, additional help is available through",
"a subtopic KEYWORD, where KEYWORD is the name of the keyword.",
};
const char PositionsHelpText::title[] =
"Specifying positions in selections";
const char *const PositionsHelpText::text[] = {
- "Possible ways of specifying positions in selections are:[PAR]",
-
+ "Possible ways of specifying positions in selections are:",
+ "",
"1. A constant position can be defined as [TT][XX, YY, ZZ][tt], where",
- "[TT]XX[tt], [TT]YY[tt] and [TT]ZZ[tt] are real numbers.[PAR]",
-
+ " [TT]XX[tt], [TT]YY[tt] and [TT]ZZ[tt] are real numbers.[PAR]",
+ "",
"2. [TT]com of ATOM_EXPR [pbc][tt] or [TT]cog of ATOM_EXPR [pbc][tt]",
- "calculate the center of mass/geometry of [TT]ATOM_EXPR[tt]. If",
- "[TT]pbc[tt] is specified, the center is calculated iteratively to try",
- "to deal with cases where [TT]ATOM_EXPR[tt] wraps around periodic",
- "boundary conditions.[PAR]",
-
+ " calculate the center of mass/geometry of [TT]ATOM_EXPR[tt]. If",
+ " [TT]pbc[tt] is specified, the center is calculated iteratively to try",
+ " to deal with cases where [TT]ATOM_EXPR[tt] wraps around periodic",
+ " boundary conditions.",
+ "",
"3. [TT]POSTYPE of ATOM_EXPR[tt] calculates the specified positions for",
- "the atoms in [TT]ATOM_EXPR[tt].",
- "[TT]POSTYPE[tt] can be [TT]atom[tt], [TT]res_com[tt], [TT]res_cog[tt],",
- "[TT]mol_com[tt] or [TT]mol_cog[tt], with an optional prefix [TT]whole_[tt]",
- "[TT]part_[tt] or [TT]dyn_[tt].",
- "[TT]whole_[tt] calculates the centers for the whole residue/molecule,",
- "even if only part of it is selected.",
- "[TT]part_[tt] prefix calculates the centers for the selected atoms, but",
- "uses always the same atoms for the same residue/molecule. The used atoms",
- "are determined from the the largest group allowed by the selection.",
- "[TT]dyn_[tt] calculates the centers strictly only for the selected atoms.",
- "If no prefix is specified, whole selections default to [TT]part_[tt] and",
- "other places default to [TT]whole_[tt].",
- "The latter is often desirable to select the same molecules in different",
- "tools, while the first is a compromise between speed ([TT]dyn_[tt]",
- "positions can be slower to evaluate than [TT]part_[tt]) and intuitive",
- "behavior.[PAR]",
-
+ " the atoms in [TT]ATOM_EXPR[tt].",
+ " [TT]POSTYPE[tt] can be [TT]atom[tt], [TT]res_com[tt], [TT]res_cog[tt],",
+ " [TT]mol_com[tt] or [TT]mol_cog[tt], with an optional prefix [TT]whole_[tt]",
+ " [TT]part_[tt] or [TT]dyn_[tt].",
+ " [TT]whole_[tt] calculates the centers for the whole residue/molecule,",
+ " even if only part of it is selected.",
+ " [TT]part_[tt] prefix calculates the centers for the selected atoms, but",
+ " uses always the same atoms for the same residue/molecule. The used atoms",
+ " are determined from the the largest group allowed by the selection.",
+ " [TT]dyn_[tt] calculates the centers strictly only for the selected atoms.",
+ " If no prefix is specified, whole selections default to [TT]part_[tt] and",
+ " other places default to [TT]whole_[tt].",
+ " The latter is often desirable to select the same molecules in different",
+ " tools, while the first is a compromise between speed ([TT]dyn_[tt]",
+ " positions can be slower to evaluate than [TT]part_[tt]) and intuitive",
+ " behavior.",
+ "",
"4. [TT]ATOM_EXPR[tt], when given for whole selections, is handled as 3.",
- "above, using the position type from the command-line argument",
- "[TT]-seltype[tt].[PAR]",
-
+ " above, using the position type from the command-line argument",
+ " [TT]-seltype[tt].",
+ "",
"Selection keywords that select atoms based on their positions, such as",
"[TT]dist from[tt], use by default the positions defined by the",
"[TT]-selrpos[tt] command-line option.",
}
virtual const char *title() const
{
- return NULL;
+ return method_.help.helpTitle;
}
protected:
void printKeywordList(const HelpWriterContext &context,
e_selvalue_t type, bool bModifiers) const;
+ /*! \brief
+ * Prints the detailed help for keywords for rst export.
+ */
+ void writeKeywordSubTopics(const HelpWriterContext &context) const;
+
MethodList methods_;
};
printKeywordList(context, POS_VALUE, true);
printKeywordList(context, NO_VALUE, true);
writeKeywordListEnd(context, NULL);
+
+ writeKeywordSubTopics(context);
}
void KeywordsHelpTopic::writeKeywordListStart(const HelpWriterContext &context,
const char *heading) const
{
- context.writeTextBlock(heading);
+ std::string fullHeading("* ");
+ fullHeading.append(heading);
+ context.writeTextBlock(fullHeading);
if (context.outputFormat() == eHelpOutputFormat_Rst)
{
context.writeTextBlock("");
- context.writeTextBlock("::");
+ context.writeTextBlock(" ::");
context.writeTextBlock("");
}
}
}
if (!isNullOrEmpty(extraInfo))
{
- context.writeTextBlock(extraInfo);
+ std::string fullInfo(" ");
+ fullInfo.append(extraInfo);
+ context.writeTextBlock(fullInfo);
}
context.writeTextBlock("");
}
e_selvalue_t type,
bool bModifiers) const
{
- File &file = context.outputFile();
+ TextWriter &file = context.outputFile();
MethodList::const_iterator iter;
for (iter = methods_.begin(); iter != methods_.end(); ++iter)
{
const gmx_ana_selmethod_t &method = *iter->second;
- bool bIsModifier = (method.flags & SMETH_MODIFIER) != 0;
+ const bool bIsModifier
+ = (method.flags & SMETH_MODIFIER) != 0;
if (method.type == type && bModifiers == bIsModifier)
{
- bool bHasHelp = (method.help.nlhelp > 0 && method.help.help != NULL);
- file.writeString(formatString(" %c ", bHasHelp ? '*' : ' '));
+ const bool bHasHelp = (method.help.nlhelp > 0 && method.help.help != NULL);
+ const bool bPrintHelpMark
+ = bHasHelp && context.outputFormat() == eHelpOutputFormat_Console;
+ file.writeString(formatString(" %c ", bPrintHelpMark ? '+' : ' '));
if (method.help.syntax != NULL)
{
file.writeLine(method.help.syntax);
}
}
+void KeywordsHelpTopic::writeKeywordSubTopics(const HelpWriterContext &context) const
+{
+ if (context.outputFormat() != eHelpOutputFormat_Rst)
+ {
+ return;
+ }
+ std::set<std::string> usedSymbols;
+ MethodList::const_iterator iter;
+ for (iter = methods_.begin(); iter != methods_.end(); ++iter)
+ {
+ const gmx_ana_selmethod_t &method = *iter->second;
+ const bool bHasHelp
+ = (method.help.nlhelp > 0 && method.help.help != NULL);
+ if (!bHasHelp || usedSymbols.count(iter->first) > 0)
+ {
+ continue;
+ }
+
+ std::string title;
+ if (method.help.helpTitle != NULL)
+ {
+ title = method.help.helpTitle;
+ title.append(" - ");
+ }
+ title.append(iter->first);
+ MethodList::const_iterator mergeIter = iter;
+ for (++mergeIter; mergeIter != methods_.end(); ++mergeIter)
+ {
+ if (mergeIter->second->help.help == method.help.help)
+ {
+ title.append(", ");
+ title.append(mergeIter->first);
+ usedSymbols.insert(mergeIter->first);
+ }
+ }
+
+ const IHelpTopic *subTopic = findSubTopic(iter->first.c_str());
+ GMX_RELEASE_ASSERT(subTopic != NULL, "Keyword subtopic no longer exists");
+ HelpWriterContext subContext(context);
+ subContext.enterSubSection(title);
+ subTopic->writeHelp(subContext);
+ context.writeTextBlock("");
+ }
+}
+
} // namespace
//! \cond libapi */
HelpTopicPointer createSelectionHelpTopic()
{
CompositeHelpTopicPointer root(new CompositeHelpTopic<CommonHelpText>);
- root->registerSubTopic<SimpleHelpTopic<ArithmeticHelpText> >();
root->registerSubTopic<SimpleHelpTopic<CmdLineHelpText> >();
- root->registerSubTopic<SimpleHelpTopic<EvaluationHelpText> >();
- root->registerSubTopic<SimpleHelpTopic<ExamplesHelpText> >();
+ root->registerSubTopic<SimpleHelpTopic<SyntaxHelpText> >();
+ root->registerSubTopic<SimpleHelpTopic<PositionsHelpText> >();
+ root->registerSubTopic<SimpleHelpTopic<ArithmeticHelpText> >();
root->registerSubTopic<KeywordsHelpTopic>();
+ root->registerSubTopic<SimpleHelpTopic<EvaluationHelpText> >();
root->registerSubTopic<SimpleHelpTopic<LimitationsHelpText> >();
- root->registerSubTopic<SimpleHelpTopic<PositionsHelpText> >();
- root->registerSubTopic<SimpleHelpTopic<SyntaxHelpText> >();
+ root->registerSubTopic<SimpleHelpTopic<ExamplesHelpText> >();
return move(root);
}
//! \endcond
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff