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37 * Implements functions in selhelp.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
50 #include <boost/scoped_ptr.hpp>
52 #include "gromacs/onlinehelp/helptopic.h"
53 #include "gromacs/onlinehelp/helpwritercontext.h"
54 #include "gromacs/utility/exceptions.h"
55 #include "gromacs/utility/file.h"
56 #include "gromacs/utility/stringutil.h"
58 #include "selmethod.h"
66 static const char name[];
67 static const char title[];
68 static const char *const text[];
71 const char CommonHelpText::name[] = "selections";
72 const char CommonHelpText::title[] =
73 "Selection syntax and usage";
74 const char *const CommonHelpText::text[] = {
75 "Selections are used to select atoms/molecules/residues for analysis.",
76 "In contrast to traditional index files, selections can be dynamic, i.e.,",
77 "select different atoms for different trajectory frames. The GROMACS",
78 "manual contains a short introductory section to selections in the",
79 "Analysis chapter, including suggestions on how to get familiar with",
80 "selections if you are new to the concept. The subtopics listed below",
81 "provide more details on the technical and syntactic aspects of",
84 "Each analysis tool requires a different number of selections and the",
85 "selections are interpreted differently. The general idea is still the",
86 "same: each selection evaluates to a set of positions, where a position",
87 "can be an atom position or center-of-mass or center-of-geometry of",
88 "a set of atoms. The tool then uses these positions for its analysis to",
89 "allow very flexible processing. Some analysis tools may have limitations",
90 "on the types of selections allowed."
93 struct ArithmeticHelpText
95 static const char name[];
96 static const char title[];
97 static const char *const text[];
100 const char ArithmeticHelpText::name[] = "arithmetic";
101 const char ArithmeticHelpText::title[] =
102 "Arithmetic expressions in selections";
103 const char *const ArithmeticHelpText::text[] = {
104 "Basic arithmetic evaluation is supported for numeric expressions.",
105 "Supported operations are addition, subtraction, negation, multiplication,",
106 "division, and exponentiation (using ^).",
107 "Result of a division by zero or other illegal operations is undefined.",
110 struct CmdLineHelpText
112 static const char name[];
113 static const char title[];
114 static const char *const text[];
117 const char CmdLineHelpText::name[] = "cmdline";
118 const char CmdLineHelpText::title[] =
119 "Specifying selections from command line";
120 const char *const CmdLineHelpText::text[] = {
121 "If no selections are provided on the command line, you are prompted to",
122 "type the selections interactively (a pipe can also be used to provide",
123 "the selections in this case for most tools). While this works well for",
124 "testing, it is easier to provide the selections from the command line",
125 "if they are complex or for scripting.[PAR]",
127 "Each tool has different command-line arguments for specifying selections",
128 "(listed by [TT][PROGRAM] help <tool>[tt]).",
129 "You can either pass a single string containing all selections (separated",
130 "by semicolons), or multiple strings, each containing one selection.",
131 "Note that you need to quote the selections to protect them from the",
134 "If you set a selection command-line argument, but do not provide any",
135 "selections, you are prompted to type the selections for that argument",
136 "interactively. This is useful if that selection argument is optional,",
137 "in which case it is not normally prompted for.[PAR]",
139 "To provide selections from a file, use [TT]-sf file.dat[tt] in the place",
140 "of the selection for a selection argument (e.g.,",
141 "[TT]-select -sf file.dat[tt]). In general, the [TT]-sf[tt] argument reads",
142 "selections from the provided file and assigns them to selection arguments",
143 "that have been specified up to that point, but for which no selections",
144 "have been provided.",
145 "As a special case, [TT]-sf[tt] provided on its own, without preceding",
146 "selection arguments, assigns the selections to all (yet unset) required",
147 "selections (i.e., those that would be promted interactively if no",
148 "selections are provided on the command line).[PAR]",
150 "To use groups from a traditional index file, use argument [TT]-n[tt]",
151 "to provide a file. See the \"syntax\" subtopic for how to use them.",
152 "If this option is not provided, default groups are generated.",
153 "The default groups are generated by reading selections from a file",
154 "[TT]defselection.dat[tt]. If such a file is found in the current",
155 "directory, it is used instead of the one provided by default.[PAR]",
157 "Depending on the tool, two additional command-line arguments may be",
158 "available to control the behavior:",
160 "* [TT]-seltype[tt] can be used to specify the default type of",
161 " positions to calculate for each selection.",
162 "* [TT]-selrpos[tt] can be used to specify the default type of",
163 " positions used in selecting atoms by coordinates.",
165 "See the \"positions\" subtopic for more information on these options.",
168 struct EvaluationHelpText
170 static const char name[];
171 static const char title[];
172 static const char *const text[];
175 const char EvaluationHelpText::name[] = "evaluation";
176 const char EvaluationHelpText::title[] =
177 "Selection evaluation and optimization";
178 const char *const EvaluationHelpText::text[] = {
179 "Boolean evaluation proceeds from left to right and is short-circuiting",
180 "i.e., as soon as it is known whether an atom will be selected, the",
181 "remaining expressions are not evaluated at all.",
182 "This can be used to optimize the selections: you should write the",
183 "most restrictive and/or the most inexpensive expressions first in",
184 "boolean expressions.",
185 "The relative ordering between dynamic and static expressions does not",
186 "matter: all static expressions are evaluated only once, before the first",
187 "frame, and the result becomes the leftmost expression.[PAR]",
189 "Another point for optimization is in common subexpressions: they are not",
190 "automatically recognized, but can be manually optimized by the use of",
191 "variables. This can have a big impact on the performance of complex",
192 "selections, in particular if you define several index groups like this::",
194 " rdist = distance from com of resnr 1 to 5;",
195 " resname RES and rdist < 2;",
196 " resname RES and rdist < 4;",
197 " resname RES and rdist < 6;",
199 "Without the variable assignment, the distances would be evaluated three",
200 "times, although they are exactly the same within each selection.",
201 "Anything assigned into a variable becomes a common subexpression that",
202 "is evaluated only once during a frame.",
203 "Currently, in some cases the use of variables can actually lead to a small",
204 "performance loss because of the checks necessary to determine for which",
205 "atoms the expression has already been evaluated, but this should not be",
209 struct ExamplesHelpText
211 static const char name[];
212 static const char title[];
213 static const char *const text[];
216 const char ExamplesHelpText::name[] = "examples";
217 const char ExamplesHelpText::title[] =
218 "Selection examples";
219 const char *const ExamplesHelpText::text[] = {
220 // TODO: Once there are more tools available, use examples that invoke
221 // tools and explain what the selections do in those tools.
222 "Below, examples of increasingly complex selections are given.[PAR]",
224 "Selection of all water oxygens::",
226 " resname SOL and name OW",
229 "Centers of mass of residues 1 to 5 and 10::",
231 " res_com of resnr 1 to 5 10",
234 "All atoms farther than 1 nm of a fixed position::",
236 " not within 1 of [1.2, 3.1, 2.4]",
239 "All atoms of a residue LIG within 0.5 nm of a protein (with a custom name)::",
241 " \"Close to protein\" resname LIG and within 0.5 of group \"Protein\"",
244 "All protein residues that have at least one atom within 0.5 nm of a residue LIG::",
246 " group \"Protein\" and same residue as within 0.5 of resname LIG",
249 "All RES residues whose COM is between 2 and 4 nm from the COM of all of them::",
251 " rdist = res_com distance from com of resname RES",
252 " resname RES and rdist >= 2 and rdist <= 4",
255 "Selection like C1 C2 C2 C3 C3 C4 ... C8 C9 (e.g., for g_bond)::",
257 " name \"C[1-8]\" merge name \"C[2-9]\"",
260 struct KeywordsHelpText
262 static const char name[];
263 static const char title[];
264 static const char *const text[];
267 const char KeywordsHelpText::name[] = "keywords";
268 const char KeywordsHelpText::title[] =
269 "Selection keywords";
270 const char *const KeywordsHelpText::text[] = {
271 "The following selection keywords are currently available.",
272 "For keywords marked with a star, additional help is available through",
273 "a subtopic KEYWORD, where KEYWORD is the name of the keyword.",
276 struct LimitationsHelpText
278 static const char name[];
279 static const char title[];
280 static const char *const text[];
283 const char LimitationsHelpText::name[] = "limitations";
284 const char LimitationsHelpText::title[] =
285 "Selection limitations";
286 const char *const LimitationsHelpText::text[] = {
287 "* Some analysis programs may require a special structure for the input",
288 " selections (e.g., some options of [TT]gmx gangle[tt] require the index",
289 " group to be made of groups of three or four atoms).",
290 " For such programs, it is up to the user to provide a proper selection",
291 " expression that always returns such positions.",
293 "* All selection keywords select atoms in increasing order, i.e., you can",
294 " consider them as set operations that in the end return the atoms in",
295 " sorted numerical order. For example, the following selections select",
296 " the same atoms in the same order::",
303 " atomnr 10 11 12 13",
304 " atomnr 12 13 10 11",
308 " If you need atoms/positions in a different order, you can:",
310 " * use external index groups (for some static selections),",
311 " * use the [TT]permute[tt] keyword to change the final order, or",
312 " * use the [TT]merge[tt] or [TT]plus[tt] keywords to compose the",
313 " final selection from multiple distinct selections.",
315 "* Due to technical reasons, having a negative value as the first value in",
316 " expressions like ::",
318 " charge -1 to -0.7",
320 " result in a syntax error. A workaround is to write ::",
322 " charge {-1 to -0.7}",
326 "* When [TT]name[tt] selection keyword is used together with PDB input",
327 " files, the behavior may be unintuitive. When GROMACS reads in a PDB",
328 " file, 4 character atom names that start with a digit are transformed",
329 " such that, e.g., 1HG2 becomes HG21, and the latter is what is matched",
330 " by the [TT]name[tt] keyword. Use [TT]pdbname[tt] to match the atom name",
331 " as it appears in the input PDB file.",
334 struct PositionsHelpText
336 static const char name[];
337 static const char title[];
338 static const char *const text[];
341 const char PositionsHelpText::name[] = "positions";
342 const char PositionsHelpText::title[] =
343 "Specifying positions in selections";
344 const char *const PositionsHelpText::text[] = {
345 "Possible ways of specifying positions in selections are:[PAR]",
347 "1. A constant position can be defined as [TT][XX, YY, ZZ][tt], where",
348 "[TT]XX[tt], [TT]YY[tt] and [TT]ZZ[tt] are real numbers.[PAR]",
350 "2. [TT]com of ATOM_EXPR [pbc][tt] or [TT]cog of ATOM_EXPR [pbc][tt]",
351 "calculate the center of mass/geometry of [TT]ATOM_EXPR[tt]. If",
352 "[TT]pbc[tt] is specified, the center is calculated iteratively to try",
353 "to deal with cases where [TT]ATOM_EXPR[tt] wraps around periodic",
354 "boundary conditions.[PAR]",
356 "3. [TT]POSTYPE of ATOM_EXPR[tt] calculates the specified positions for",
357 "the atoms in [TT]ATOM_EXPR[tt].",
358 "[TT]POSTYPE[tt] can be [TT]atom[tt], [TT]res_com[tt], [TT]res_cog[tt],",
359 "[TT]mol_com[tt] or [TT]mol_cog[tt], with an optional prefix [TT]whole_[tt]",
360 "[TT]part_[tt] or [TT]dyn_[tt].",
361 "[TT]whole_[tt] calculates the centers for the whole residue/molecule,",
362 "even if only part of it is selected.",
363 "[TT]part_[tt] prefix calculates the centers for the selected atoms, but",
364 "uses always the same atoms for the same residue/molecule. The used atoms",
365 "are determined from the the largest group allowed by the selection.",
366 "[TT]dyn_[tt] calculates the centers strictly only for the selected atoms.",
367 "If no prefix is specified, whole selections default to [TT]part_[tt] and",
368 "other places default to [TT]whole_[tt].",
369 "The latter is often desirable to select the same molecules in different",
370 "tools, while the first is a compromise between speed ([TT]dyn_[tt]",
371 "positions can be slower to evaluate than [TT]part_[tt]) and intuitive",
374 "4. [TT]ATOM_EXPR[tt], when given for whole selections, is handled as 3.",
375 "above, using the position type from the command-line argument",
376 "[TT]-seltype[tt].[PAR]",
378 "Selection keywords that select atoms based on their positions, such as",
379 "[TT]dist from[tt], use by default the positions defined by the",
380 "[TT]-selrpos[tt] command-line option.",
381 "This can be overridden by prepending a [TT]POSTYPE[tt] specifier to the",
382 "keyword. For example, [TT]res_com dist from POS[tt] evaluates the",
383 "residue center of mass distances. In the example, all atoms of a residue",
384 "are either selected or not, based on the single distance calculated.",
387 struct SyntaxHelpText
389 static const char name[];
390 static const char title[];
391 static const char *const text[];
394 const char SyntaxHelpText::name[] = "syntax";
395 const char SyntaxHelpText::title[] =
397 const char *const SyntaxHelpText::text[] = {
398 "A set of selections consists of one or more selections, separated by",
399 "semicolons. Each selection defines a set of positions for the analysis.",
400 "Each selection can also be preceded by a string that gives a name for",
401 "the selection for use in, e.g., graph legends.",
402 "If no name is provided, the string used for the selection is used",
403 "automatically as the name.[PAR]",
405 "For interactive input, the syntax is slightly altered: line breaks can",
406 "also be used to separate selections. \\ followed by a line break can",
407 "be used to continue a line if necessary.",
408 "Notice that the above only applies to real interactive input,",
409 "not if you provide the selections, e.g., from a pipe.[PAR]",
411 "It is possible to use variables to store selection expressions.",
412 "A variable is defined with the following syntax::",
416 "where [TT]EXPR[tt] is any valid selection expression.",
417 "After this, [TT]VARNAME[tt] can be used anywhere where [TT]EXPR[tt]",
418 "would be valid.[PAR]",
420 "Selections are composed of three main types of expressions, those that",
421 "define atoms ([TT]ATOM_EXPR[tt]), those that define positions",
422 "([TT]POS_EXPR[tt]), and those that evaluate to numeric values",
423 "([TT]NUM_EXPR[tt]). Each selection should be a [TT]POS_EXPR[tt]",
424 "or a [TT]ATOM_EXPR[tt] (the latter is automatically converted to",
425 "positions). The basic rules are as follows:",
427 "* An expression like [TT]NUM_EXPR1 < NUM_EXPR2[tt] evaluates to an",
428 " [TT]ATOM_EXPR[tt] that selects all the atoms for which the comparison",
430 "* Atom expressions can be combined with boolean operations such as",
431 " [TT]not ATOM_EXPR[tt], [TT]ATOM_EXPR and ATOM_EXPR[tt], or",
432 " [TT]ATOM_EXPR or ATOM_EXPR[tt]. Parentheses can be used to alter the",
433 " evaluation order.",
434 "* [TT]ATOM_EXPR[tt] expressions can be converted into [TT]POS_EXPR[tt]",
435 " expressions in various ways, see the \"positions\" subtopic for more",
437 "* [TT]POS_EXPR[tt] can be converted into [TT]NUM_EXPR[tt] using syntax",
438 " like \"[TT]x of POS_EXPR[tt]\". Currently, this is only supported for single",
439 " positions like in expression \"[TT]x of cog of ATOM_EXPR[tt]\".",
442 "Some keywords select atoms based on string values such as the atom name.",
443 "For these keywords, it is possible to use wildcards ([TT]name \"C*\"[tt])",
444 "or regular expressions (e.g., [TT]resname \"R[AB]\"[tt]).",
445 "The match type is automatically guessed from the string: if it contains",
446 "other characters than letters, numbers, '*', or '?', it is interpreted",
447 "as a regular expression.",
448 "To force the matching to use literal string matching, use",
449 "[TT]name = \"C*\"[tt] to match a literal C*.",
450 "To force other type of matching, use '?' or '~' in place of '=' to force",
451 "wildcard or regular expression matching, respectively.[PAR]",
453 "Strings that contain non-alphanumeric characters should be enclosed in",
454 "double quotes as in the examples. For other strings, the quotes are",
455 "optional, but if the value conflicts with a reserved keyword, a syntax",
456 "error will occur. If your strings contain uppercase letters, this should",
459 "Index groups provided with the [TT]-n[tt] command-line option or",
460 "generated by default can be accessed with [TT]group NR[tt] or",
461 "[TT]group NAME[tt], where [TT]NR[tt] is a zero-based index of the group",
462 "and [TT]NAME[tt] is part of the name of the desired group.",
463 "The keyword [TT]group[tt] is optional if the whole selection is",
464 "provided from an index group.",
465 "To see a list of available groups in the interactive mode, press enter",
466 "in the beginning of a line.",
478 * Help topic implementation for an individual selection method.
480 * \ingroup module_selection
482 class KeywordDetailsHelpTopic : public AbstractSimpleHelpTopic
485 //! Initialize help topic for the given selection method.
486 KeywordDetailsHelpTopic(const std::string &name,
487 const gmx_ana_selmethod_t &method)
488 : name_(name), method_(method)
492 virtual const char *name() const
494 return name_.c_str();
496 virtual const char *title() const
502 virtual std::string helpText() const
504 return joinStrings(method_.help.help,
505 method_.help.help + method_.help.nlhelp, "\n");
510 const gmx_ana_selmethod_t &method_;
512 GMX_DISALLOW_COPY_AND_ASSIGN(KeywordDetailsHelpTopic);
516 * Custom help topic for printing a list of selection keywords.
518 * \ingroup module_selection
520 class KeywordsHelpTopic : public CompositeHelpTopic<KeywordsHelpText>
525 virtual void writeHelp(const HelpWriterContext &context) const;
529 * Container for known selection methods.
531 * The first item in the pair is the name of the selection method, and
532 * the second points to the static data structure that describes the
534 * The name in the first item may differ from the name of the static
535 * data structure if an alias is defined for that method.
537 typedef std::vector<std::pair<std::string,
538 const gmx_ana_selmethod_t *> >
542 * Prints markup for starting a list of keywords.
544 void writeKeywordListStart(const HelpWriterContext &context,
545 const char *heading) const;
547 * Prints markup for ending a list of keywords.
549 void writeKeywordListEnd(const HelpWriterContext &context,
550 const char *extraInfo) const;
553 * Prints a brief list of keywords (selection methods) available.
555 * \param[in] context Context for printing the help.
556 * \param[in] type Only methods that return this type are printed.
557 * \param[in] bModifiers If false, \ref SMETH_MODIFIER methods are
558 * excluded, otherwise only them are printed.
560 void printKeywordList(const HelpWriterContext &context,
561 e_selvalue_t type, bool bModifiers) const;
566 KeywordsHelpTopic::KeywordsHelpTopic()
568 // TODO: This is not a very elegant way of getting the list of selection
569 // methods, but this needs to be rewritten in any case if/when #652 is
571 boost::scoped_ptr<SelectionParserSymbolTable> symtab(
572 new SelectionParserSymbolTable);
573 gmx_ana_selmethod_register_defaults(symtab.get());
575 SelectionParserSymbolIterator symbol
576 = symtab->beginIterator(SelectionParserSymbol::MethodSymbol);
577 while (symbol != symtab->endIterator())
579 const std::string &symname = symbol->name();
580 const gmx_ana_selmethod_t *method = symbol->methodValue();
581 methods_.push_back(std::make_pair(std::string(symname), method));
582 if (method->help.nlhelp > 0 && method->help.help != NULL)
584 addSubTopic(HelpTopicPointer(
585 new KeywordDetailsHelpTopic(symname, *method)));
591 void KeywordsHelpTopic::writeHelp(const HelpWriterContext &context) const
593 context.writeTextBlock(helpText());
594 context.writeTextBlock("");
596 // Print the list of keywords
597 writeKeywordListStart(context, "Keywords that select atoms by an integer property:");
598 printKeywordList(context, INT_VALUE, false);
599 writeKeywordListEnd(context, "(use in expressions or like \"atomnr 1 to 5 7 9\")");
601 writeKeywordListStart(context, "Keywords that select atoms by a numeric property:");
602 printKeywordList(context, REAL_VALUE, false);
603 writeKeywordListEnd(context, "(use in expressions or like \"occupancy 0.5 to 1\")");
605 writeKeywordListStart(context, "Keywords that select atoms by a string property:");
606 printKeywordList(context, STR_VALUE, false);
607 writeKeywordListEnd(context, "(use like \"name PATTERN [PATTERN] ...\")");
609 writeKeywordListStart(context, "Additional keywords that directly select atoms:");
610 printKeywordList(context, GROUP_VALUE, false);
611 writeKeywordListEnd(context, NULL);
613 writeKeywordListStart(context, "Keywords that directly evaluate to positions:");
614 printKeywordList(context, POS_VALUE, false);
615 writeKeywordListEnd(context, "(see also \"positions\" subtopic)");
617 writeKeywordListStart(context, "Additional keywords:");
618 printKeywordList(context, POS_VALUE, true);
619 printKeywordList(context, NO_VALUE, true);
620 writeKeywordListEnd(context, NULL);
623 void KeywordsHelpTopic::writeKeywordListStart(const HelpWriterContext &context,
624 const char *heading) const
626 context.writeTextBlock(heading);
627 if (context.outputFormat() == eHelpOutputFormat_Rst)
629 context.writeTextBlock("");
630 context.writeTextBlock("::");
631 context.writeTextBlock("");
635 void KeywordsHelpTopic::writeKeywordListEnd(const HelpWriterContext &context,
636 const char *extraInfo) const
638 if (context.outputFormat() == eHelpOutputFormat_Rst)
640 context.writeTextBlock("");
642 if (!isNullOrEmpty(extraInfo))
644 context.writeTextBlock(extraInfo);
646 context.writeTextBlock("");
649 void KeywordsHelpTopic::printKeywordList(const HelpWriterContext &context,
651 bool bModifiers) const
653 File &file = context.outputFile();
654 MethodList::const_iterator iter;
655 for (iter = methods_.begin(); iter != methods_.end(); ++iter)
657 const gmx_ana_selmethod_t &method = *iter->second;
658 bool bIsModifier = (method.flags & SMETH_MODIFIER) != 0;
659 if (method.type == type && bModifiers == bIsModifier)
661 bool bHasHelp = (method.help.nlhelp > 0 && method.help.help != NULL);
662 file.writeString(formatString(" %c ", bHasHelp ? '*' : ' '));
663 if (method.help.syntax != NULL)
665 file.writeLine(method.help.syntax);
669 std::string symname = iter->first;
670 if (symname != method.name)
672 symname.append(formatString(" (synonym for %s)", method.name));
674 file.writeLine(symname);
683 HelpTopicPointer createSelectionHelpTopic()
685 CompositeHelpTopicPointer root(new CompositeHelpTopic<CommonHelpText>);
686 root->registerSubTopic<SimpleHelpTopic<ArithmeticHelpText> >();
687 root->registerSubTopic<SimpleHelpTopic<CmdLineHelpText> >();
688 root->registerSubTopic<SimpleHelpTopic<EvaluationHelpText> >();
689 root->registerSubTopic<SimpleHelpTopic<ExamplesHelpText> >();
690 root->registerSubTopic<KeywordsHelpTopic>();
691 root->registerSubTopic<SimpleHelpTopic<LimitationsHelpText> >();
692 root->registerSubTopic<SimpleHelpTopic<PositionsHelpText> >();
693 root->registerSubTopic<SimpleHelpTopic<SyntaxHelpText> >();