Include selection keyword details in user guide

- Make 'gmx help -export rst' write out the detailed selection keyword
  help as subsections of the keywords topic.
- Separate the titles from the help texts to make it possible to format
  the title separately.
- Make synopsis formatting the same for each keyword details help topic.
- Make HelpWriterContext not write leading empty lines to console output
  when the help text starts with a literal block.
- Remove unnecessary stars from the keyword lists in the
  reStructuredText output.

Some minor cleanup of the formatting could be done, but otherwise this
closes #679.

Change-Id: Id91ce3c01e9dd5f1c068498217dbc536a712c231

diff --git a/src/gromacs/onlinehelp/helpwritercontext.cpp b/src/gromacs/onlinehelp/helpwritercontext.cpp
index 4c928e02ab955075938ce4d2c63326176eefbba6..8d5a44903be1664c72c3b4578c3a5f5107dab949 100644 (file)
--- a/src/gromacs/onlinehelp/helpwritercontext.cpp
+++ b/src/gromacs/onlinehelp/helpwritercontext.cpp
@@ -630,6 +630,10 @@ void HelpWriterContext::Impl::processMarkup(const std::string &text,
                     bLiteral = true;
                     if (paragraph.length() == 2)
                     {
                     bLiteral = true;
                     if (paragraph.length() == 2)
                     {

+                        if (breakSize == 0)
+                        {
+                            nextBreakSize = 0;
+                        }

                         continue;
                     }
                     if (paragraph[paragraph.length() - 3] == ' ')
                         continue;
                     }
                     if (paragraph[paragraph.length() - 3] == ' ')

diff --git a/src/gromacs/onlinehelp/tests/helpwritercontext.cpp b/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
index ed08fb84b070f015025f0627a8d3f2c8e1c91b2e..4216fccf0ba70f3746af6348d04bdf8a8b3f4d97 100644 (file)
--- a/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
+++ b/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
@@ -155,6 +155,19 @@ TEST_F(HelpWriterContextTest, FormatsLiteralText)
     testFormatting(text);
 }
 
     testFormatting(text);
 }
 

+TEST_F(HelpWriterContextTest, FormatsLiteralTextAtBeginning)
+{
+    const char *const text[] = {
+        "::",
+        "",
+        "    literal block",
+        "    another line",
+        "",
+        "Normal paragraph"
+    };
+    testFormatting(text);
+}
+

 TEST_F(HelpWriterContextTest, FormatsBulletList)
 {
     const char *const text[] = {
 TEST_F(HelpWriterContextTest, FormatsBulletList)
 {
     const char *const text[] = {

diff --git a/src/gromacs/onlinehelp/tests/refdata/HelpWriterContextTest_FormatsLiteralTextAtBeginning.xml b/src/gromacs/onlinehelp/tests/refdata/HelpWriterContextTest_FormatsLiteralTextAtBeginning.xml
new file mode 100644 (file)
index 0000000..375cc6b
--- /dev/null
+++ b/src/gromacs/onlinehelp/tests/refdata/HelpWriterContextTest_FormatsLiteralTextAtBeginning.xml
@@ -0,0 +1,16 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <String Name="Console"><![CDATA[
+    literal block
+    another line
+
+Normal paragraph]]></String>
+  <String Name="reStructuredText"><![CDATA[
+::
+
+    literal block
+    another line
+
+Normal paragraph]]></String>
+</ReferenceData>

diff --git a/src/gromacs/selection/selhelp.cpp b/src/gromacs/selection/selhelp.cpp
index f51c0b5ff8ee27b05502798f12e21a970f1a127d..e521f1bc3084639ee831afbbf75c7dbc86d43eea 100644 (file)
--- a/src/gromacs/selection/selhelp.cpp
+++ b/src/gromacs/selection/selhelp.cpp
@@ -43,6 +43,7 @@
 
 #include "selhelp.h"
 
 
 #include "selhelp.h"
 

+#include <set>

 #include <string>
 #include <utility>
 #include <vector>
 #include <string>
 #include <utility>
 #include <vector>


@@ -53,6 +54,7 @@
 #include "gromacs/onlinehelp/helpwritercontext.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.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 "selmethod.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "selmethod.h"


@@ -495,7 +497,7 @@ class KeywordDetailsHelpTopic : public AbstractSimpleHelpTopic
         }
         virtual const char *title() const
         {
         }
         virtual const char *title() const
         {

-            return NULL;
+            return method_.help.helpTitle;

         }
 
     protected:
         }
 
     protected:


@@ -560,6 +562,11 @@ class KeywordsHelpTopic : public CompositeHelpTopic<KeywordsHelpText>
         void printKeywordList(const HelpWriterContext &context,
                               e_selvalue_t type, bool bModifiers) const;
 
         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_;
 };
 
         MethodList              methods_;
 };
 


@@ -618,6 +625,8 @@ void KeywordsHelpTopic::writeHelp(const HelpWriterContext &context) const
     printKeywordList(context, POS_VALUE, true);
     printKeywordList(context, NO_VALUE, true);
     writeKeywordListEnd(context, NULL);
     printKeywordList(context, POS_VALUE, true);
     printKeywordList(context, NO_VALUE, true);
     writeKeywordListEnd(context, NULL);

+
+    writeKeywordSubTopics(context);

 }
 
 void KeywordsHelpTopic::writeKeywordListStart(const HelpWriterContext &context,
 }
 
 void KeywordsHelpTopic::writeKeywordListStart(const HelpWriterContext &context,


@@ -655,11 +664,14 @@ void KeywordsHelpTopic::printKeywordList(const HelpWriterContext &context,
     for (iter = methods_.begin(); iter != methods_.end(); ++iter)
     {
         const gmx_ana_selmethod_t &method = *iter->second;
     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)
         {
         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 bPrintStar
+                = bHasHelp && context.outputFormat() == eHelpOutputFormat_Console;
+            file.writeString(formatString(" %c ", bPrintStar ? '*' : ' '));

             if (method.help.syntax != NULL)
             {
                 file.writeLine(method.help.syntax);
             if (method.help.syntax != NULL)
             {
                 file.writeLine(method.help.syntax);


@@ -677,6 +689,51 @@ void KeywordsHelpTopic::printKeywordList(const HelpWriterContext &context,
     }
 }
 
     }
 }
 

+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 HelpTopicInterface *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 */
 }   // namespace
 
 //! \cond libapi */

diff --git a/src/gromacs/selection/selmethod.h b/src/gromacs/selection/selmethod.h
index 8df079d3f142572a99b1afaf514bb7c6c39cfda4..d5142d6aae2f6747820c33b71fe3103ec4ccc4e7 100644 (file)
--- a/src/gromacs/selection/selmethod.h
+++ b/src/gromacs/selection/selmethod.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
 /*
  * This file is part of the GROMACS molecular simulation package.
  *

- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.


@@ -60,7 +60,7 @@
        &init_frame_example,
        &evaluate_example,
         NULL,
        &init_frame_example,
        &evaluate_example,
         NULL,

-       {"example from POS_EXPR [cutoff REAL]", 0, NULL},
+       {"example from POS_EXPR [cutoff REAL]", NULL, 0, NULL},

    };
  * \endcode
  *
    };
  * \endcode
  *


@@ -615,6 +615,13 @@ struct gmx_ana_selmethod_help_t
      * If NULL, the name of the method is used.
      */
     const char         *syntax;
      * If NULL, the name of the method is used.
      */
     const char         *syntax;

+    /*! \brief
+     * Title for the help text in \p help.
+     *
+     * If NULL, the name of the method is used.
+     * Only used if `nlhelp > 0`.
+     */
+    const char         *helpTitle;

     /*! \brief
      * Number of strings in \p help.
      *
     /*! \brief
      * Number of strings in \p help.
      *


@@ -627,7 +634,7 @@ struct gmx_ana_selmethod_help_t
      * If there is no help available in addition to \p syntax, this can be set
      * to NULL.
      */
      * If there is no help available in addition to \p syntax, this can be set
      * to NULL.
      */

-    const char        **help;
+    const char *const  *help;

 };
 
 /*! \internal
 };
 
 /*! \internal

diff --git a/src/gromacs/selection/sm_compare.cpp b/src/gromacs/selection/sm_compare.cpp
index be899fd7e7f37ed4514c8dad1d5ac11d649b4b24..13c8483766a440f6cfbb718223876c828713e55d 100644 (file)
--- a/src/gromacs/selection/sm_compare.cpp
+++ b/src/gromacs/selection/sm_compare.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
 /*
  * This file is part of the GROMACS molecular simulation package.
  *

- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.


@@ -158,7 +158,7 @@ gmx_ana_selmethod_t sm_compare = {
     NULL,
     &evaluate_compare,
     NULL,
     NULL,
     &evaluate_compare,
     NULL,

-    {NULL, 0, NULL},
+    {NULL, NULL, 0, NULL},

 };
 
 /*! \brief
 };
 
 /*! \brief

diff --git a/src/gromacs/selection/sm_distance.cpp b/src/gromacs/selection/sm_distance.cpp
index 14b055c7fbfe6ff23c7f156a1205c39d8c19544f..dda1b15567e84c0ef51c2006708854f0efea5e7e 100644 (file)
--- a/src/gromacs/selection/sm_distance.cpp
+++ b/src/gromacs/selection/sm_distance.cpp
@@ -153,10 +153,10 @@ static gmx_ana_selparam_t smparams_within[] = {
     {"of", {POS_VALUE,  -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
 };
 
     {"of", {POS_VALUE,  -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
 };
 

-/** Help text for the distance selection methods. */
-static const char *help_distance[] = {
-    "DISTANCE-BASED SELECTION KEYWORDS",
-    "",
+//! Help title for distance selection methods.
+static const char        helptitle_distance[] = "Selecting based on distance";
+//! Help text for distance selection methods.
+static const char *const help_distance[] = {

     "::",
     "",
     "  distance from POS [cutoff REAL]",
     "::",
     "",
     "  distance from POS [cutoff REAL]",


@@ -188,7 +188,8 @@ gmx_ana_selmethod_t sm_distance = {
     &init_frame_common,
     NULL,
     &evaluate_distance,
     &init_frame_common,
     NULL,
     &evaluate_distance,

-    {"distance from POS [cutoff REAL]", asize(help_distance), help_distance},
+    {"distance from POS [cutoff REAL]",
+     helptitle_distance, asize(help_distance), help_distance},

 };
 
 /** Selection method data for the \p distance method. */
 };
 
 /** Selection method data for the \p distance method. */


@@ -203,7 +204,8 @@ gmx_ana_selmethod_t sm_mindistance = {
     &init_frame_common,
     NULL,
     &evaluate_distance,
     &init_frame_common,
     NULL,
     &evaluate_distance,

-    {"mindistance from POS_EXPR [cutoff REAL]", asize(help_distance), help_distance},
+    {"mindistance from POS_EXPR [cutoff REAL]",
+     helptitle_distance, asize(help_distance), help_distance},

 };
 
 /** Selection method data for the \p within method. */
 };
 
 /** Selection method data for the \p within method. */


@@ -218,7 +220,8 @@ gmx_ana_selmethod_t sm_within = {
     &init_frame_common,
     NULL,
     &evaluate_within,
     &init_frame_common,
     NULL,
     &evaluate_within,

-    {"within REAL of POS_EXPR", asize(help_distance), help_distance},
+    {"within REAL of POS_EXPR",
+     helptitle_distance, asize(help_distance), help_distance},

 };
 
 static void *
 };
 
 static void *

diff --git a/src/gromacs/selection/sm_insolidangle.cpp b/src/gromacs/selection/sm_insolidangle.cpp
index 9c163e097f2db673c3f30e10791c1e66af9a0ae1..a9fd783704ee499f20bfdd98aad9eb6f9c190e8a 100644 (file)
--- a/src/gromacs/selection/sm_insolidangle.cpp
+++ b/src/gromacs/selection/sm_insolidangle.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
 /*
  * This file is part of the GROMACS molecular simulation package.
  *

- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.


@@ -334,11 +334,11 @@ static gmx_ana_selparam_t smparams_insolidangle[] = {
 };
 
 /** Help text for the \p insolidangle selection method. */
 };
 
 /** Help text for the \p insolidangle selection method. */

-static const char *help_insolidangle[] = {
-    "SELECTING ATOMS IN A SOLID ANGLE[PAR]",
-
-    "[TT]insolidangle center POS span POS_EXPR [cutoff REAL][tt][PAR]",
-
+static const char *const help_insolidangle[] = {
+    "::",
+    "",
+    "  insolidangle center POS span POS_EXPR [cutoff REAL]",
+    "",

     "This keyword selects atoms that are within [TT]REAL[tt] degrees",
     "(default=5) of any position in [TT]POS_EXPR[tt] as seen from [TT]POS[tt]",
     "a position expression that evaluates to a single position), i.e., atoms",
     "This keyword selects atoms that are within [TT]REAL[tt] degrees",
     "(default=5) of any position in [TT]POS_EXPR[tt] as seen from [TT]POS[tt]",
     "a position expression that evaluates to a single position), i.e., atoms",


@@ -365,6 +365,7 @@ gmx_ana_selmethod_t sm_insolidangle = {
     NULL,
     &evaluate_insolidangle,
     {"insolidangle center POS span POS_EXPR [cutoff REAL]",
     NULL,
     &evaluate_insolidangle,
     {"insolidangle center POS span POS_EXPR [cutoff REAL]",

+     "Selecting atoms in a solid angle",

      asize(help_insolidangle), help_insolidangle},
 };
 
      asize(help_insolidangle), help_insolidangle},
 };
 

diff --git a/src/gromacs/selection/sm_keywords.cpp b/src/gromacs/selection/sm_keywords.cpp
index ef063d7463681891e9892dbfc61a107c60b9e68e..be69f1196d562f9659d2b217dc5c6f2885f9d570 100644 (file)
--- a/src/gromacs/selection/sm_keywords.cpp
+++ b/src/gromacs/selection/sm_keywords.cpp
@@ -303,7 +303,7 @@ gmx_ana_selmethod_t sm_keyword_int = {
     NULL,
     &evaluate_keyword_int,
     NULL,
     NULL,
     &evaluate_keyword_int,
     NULL,

-    {NULL, 0, NULL},
+    {NULL, NULL, 0, NULL},

 };
 
 /** Selection method data for real keyword evaluation. */
 };
 
 /** Selection method data for real keyword evaluation. */


@@ -318,7 +318,7 @@ gmx_ana_selmethod_t sm_keyword_real = {
     NULL,
     &evaluate_keyword_real,
     NULL,
     NULL,
     &evaluate_keyword_real,
     NULL,

-    {NULL, 0, NULL},
+    {NULL, NULL, 0, NULL},

 };
 
 /** Selection method data for string keyword evaluation. */
 };
 
 /** Selection method data for string keyword evaluation. */


@@ -333,7 +333,7 @@ gmx_ana_selmethod_t sm_keyword_str = {
     NULL,
     &evaluate_keyword_str,
     NULL,
     NULL,
     &evaluate_keyword_str,
     NULL,

-    {NULL, 0, NULL},
+    {NULL, NULL, 0, NULL},

 };
 
 /*! \brief
 };
 
 /*! \brief

diff --git a/src/gromacs/selection/sm_merge.cpp b/src/gromacs/selection/sm_merge.cpp
index 4b9a50c5555e09eccc00b5cf9a08d412704b7b49..4e3e6d1a9f6505a5202006f03f9dd3495c059286 100644 (file)
--- a/src/gromacs/selection/sm_merge.cpp
+++ b/src/gromacs/selection/sm_merge.cpp
@@ -120,10 +120,10 @@ static gmx_ana_selparam_t smparams_merge[] = {
     {"stride",   {INT_VALUE,  1, {NULL}}, NULL, SPAR_OPTIONAL},
 };
 
     {"stride",   {INT_VALUE,  1, {NULL}}, NULL, SPAR_OPTIONAL},
 };
 

-/** Help text for the merging selection modifiers. */
-static const char *help_merge[] = {
-    "MERGING SELECTIONS[PAR]",
-    "",
+//! Help title for the merging selection modifiers.
+static const char        helptitle_merge[] = "Merging selections";
+//! Help text for the merging selection modifiers.
+static const char *const help_merge[] = {

     "::",
     "",
     "  POSEXPR merge POSEXPR [stride INT]",
     "::",
     "",
     "  POSEXPR merge POSEXPR [stride INT]",


@@ -160,7 +160,7 @@ gmx_ana_selmethod_t sm_merge = {
     NULL,
     NULL,
     &evaluate_merge,
     NULL,
     NULL,
     &evaluate_merge,

-    {"merge POSEXPR", asize(help_merge), help_merge},
+    {"merge POSEXPR", helptitle_merge, asize(help_merge), help_merge},

 };
 
 /** Selection method data for the \p plus modifier. */
 };
 
 /** Selection method data for the \p plus modifier. */


@@ -175,7 +175,7 @@ gmx_ana_selmethod_t sm_plus = {
     NULL,
     NULL,
     &evaluate_plus,
     NULL,
     NULL,
     &evaluate_plus,

-    {"plus POSEXPR", asize(help_merge), help_merge},
+    {"plus POSEXPR", helptitle_merge, asize(help_merge), help_merge},

 };
 
 /*!
 };
 
 /*!

diff --git a/src/gromacs/selection/sm_permute.cpp b/src/gromacs/selection/sm_permute.cpp
index eb7467149f342cc362c350aaa7f4dbb50ba39e23..a2c41176866528c2e9ddabe9391dcdcd49fcd2a9 100644 (file)
--- a/src/gromacs/selection/sm_permute.cpp
+++ b/src/gromacs/selection/sm_permute.cpp
@@ -125,11 +125,11 @@ static gmx_ana_selparam_t smparams_permute[] = {
 };
 
 /** Help text for the \p permute selection modifier. */
 };
 
 /** Help text for the \p permute selection modifier. */

-static const char *help_permute[] = {
-    "PERMUTING SELECTIONS[PAR]",
-
-    "[TT]permute P1 ... PN[tt][PAR]",
-
+static const char *const help_permute[] = {
+    "::",
+    "",
+    "  permute P1 ... PN",
+    "",

     "By default, all selections are evaluated such that the atom indices are",
     "returned in ascending order. This can be changed by appending",
     "[TT]permute P1 P2 ... PN[tt] to an expression.",
     "By default, all selections are evaluated such that the atom indices are",
     "returned in ascending order. This can be changed by appending",
     "[TT]permute P1 P2 ... PN[tt] to an expression.",


@@ -155,7 +155,8 @@ gmx_ana_selmethod_t sm_permute = {
     NULL,
     NULL,
     &evaluate_permute,
     NULL,
     NULL,
     &evaluate_permute,

-    {"permute P1 ... PN", asize(help_permute), help_permute},
+    {"POSEXPR permute P1 ... PN",
+     "Permuting selections", asize(help_permute), help_permute},

 };
 
 static void *
 };
 
 static void *

diff --git a/src/gromacs/selection/sm_position.cpp b/src/gromacs/selection/sm_position.cpp
index 3a92f82d69edb8972e5f757fc4a59920de4de58b..fe85404536f1c6e8bf3355c3cbd7f7da6c270ec4 100644 (file)
--- a/src/gromacs/selection/sm_position.cpp
+++ b/src/gromacs/selection/sm_position.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
 /*
  * This file is part of the GROMACS molecular simulation package.
  *

- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.


@@ -153,7 +153,7 @@ gmx_ana_selmethod_t sm_keyword_pos = {
     NULL,
     &evaluate_pos,
     NULL,
     NULL,
     &evaluate_pos,
     NULL,

-    {NULL, 0, NULL},
+    {NULL, NULL, 0, NULL},

 };
 
 /** Selection method data for the \p cog method. */
 };
 
 /** Selection method data for the \p cog method. */


@@ -168,7 +168,7 @@ gmx_ana_selmethod_t sm_cog = {
     NULL,
     &evaluate_pos,
     NULL,
     NULL,
     &evaluate_pos,
     NULL,

-    {"cog of ATOM_EXPR [pbc]", 0, NULL},
+    {"cog of ATOM_EXPR [pbc]", NULL, 0, NULL},

 };
 
 /** Selection method data for the \p com method. */
 };
 
 /** Selection method data for the \p com method. */


@@ -183,7 +183,7 @@ gmx_ana_selmethod_t sm_com = {
     NULL,
     &evaluate_pos,
     NULL,
     NULL,
     &evaluate_pos,
     NULL,

-    {"com of ATOM_EXPR [pbc]", 0, NULL},
+    {"com of ATOM_EXPR [pbc]", NULL, 0, NULL},

 };
 
 /*!
 };
 
 /*!

diff --git a/src/gromacs/selection/sm_same.cpp b/src/gromacs/selection/sm_same.cpp
index 01450da98f516905f7ecd4ebc0743bcb63d5b1f6..67e0629fc3a42ee74b8ae011163f3db12df80894 100644 (file)
--- a/src/gromacs/selection/sm_same.cpp
+++ b/src/gromacs/selection/sm_same.cpp
@@ -170,10 +170,11 @@ static gmx_ana_selparam_t smparams_same_str[] = {
 };
 
 /** Help text for the \p same selection method. */
 };
 
 /** Help text for the \p same selection method. */

-static const char *help_same[] = {
-    "EXTENDING SELECTIONS[PAR]",
-
-    "[TT]same KEYWORD as ATOM_EXPR[tt][PAR]",
+static const char *const help_same[] = {
+    "::",
+    "",
+    "  same KEYWORD as ATOM_EXPR",
+    "",

 
     "The keyword [TT]same[tt] can be used to select all atoms for which",
     "the given [TT]KEYWORD[tt] matches any of the atoms in [TT]ATOM_EXPR[tt].",
 
     "The keyword [TT]same[tt] can be used to select all atoms for which",
     "the given [TT]KEYWORD[tt] matches any of the atoms in [TT]ATOM_EXPR[tt].",


@@ -192,7 +193,8 @@ gmx_ana_selmethod_t sm_same = {
     &init_frame_same_int,
     &evaluate_same_int,
     NULL,
     &init_frame_same_int,
     &evaluate_same_int,
     NULL,

-    {"same KEYWORD as ATOM_EXPR", asize(help_same), help_same},
+    {"same KEYWORD as ATOM_EXPR",
+     "Extending selections", asize(help_same), help_same},

 };
 
 /*! \brief
 };
 
 /*! \brief


@@ -213,7 +215,7 @@ static gmx_ana_selmethod_t sm_same_str = {
     &init_frame_same_str,
     &evaluate_same_str,
     NULL,
     &init_frame_same_str,
     &evaluate_same_str,
     NULL,

-    {"same KEYWORD as ATOM_EXPR", asize(help_same), help_same},
+    {NULL, NULL, 0, NULL},

 };
 
 static void *
 };
 
 static void *

diff --git a/src/gromacs/selection/sm_simple.cpp b/src/gromacs/selection/sm_simple.cpp
index b257effe742642093f1848f136bcbfaca37fbbf3..b5ee784d5d6712755b44c5d6bdc2ac07a2a470f3 100644 (file)
--- a/src/gromacs/selection/sm_simple.cpp
+++ b/src/gromacs/selection/sm_simple.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
 /*
  * This file is part of the GROMACS molecular simulation package.
  *

- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by

  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.


@@ -171,14 +171,19 @@ static void
 evaluate_z(t_topology *top, t_trxframe *fr, t_pbc *pbc,
            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 
 evaluate_z(t_topology *top, t_trxframe *fr, t_pbc *pbc,
            gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
 

-/** Help text for atom name selection keywords. */
-static const char *help_atomname[] = {
-    "ATOM NAME SELECTION KEYWORDS[PAR]",
-
-    "[TT]name[tt] [TT]pdbname[tt] [TT]atomname[tt] [TT]pdbatomname[tt][PAR]",
-
+//! Help title for atom name selection keywords.
+static const char        helptitle_atomname[] = "Selecting atoms by name";
+//! Help text for atom name selection keywords.
+static const char *const help_atomname[] = {
+    "::",
+    "",
+    "  name",
+    "  pdbname",
+    "  atomname",
+    "  pdbatomname",
+    "",

     "These keywords select atoms by name. [TT]name[tt] selects atoms using",
     "These keywords select atoms by name. [TT]name[tt] selects atoms using",

-    "the Gromacs atom naming convention.",
+    "the GROMACS atom naming convention.",

     "For input formats other than PDB, the atom names are matched exactly",
     "as they appear in the input file. For PDB files, 4 character atom names",
     "that start with a digit are matched after moving the digit to the end",
     "For input formats other than PDB, the atom names are matched exactly",
     "as they appear in the input file. For PDB files, 4 character atom names",
     "that start with a digit are matched after moving the digit to the end",


@@ -287,7 +292,7 @@ gmx_ana_selmethod_t sm_atomname = {
     NULL,
     &evaluate_atomname,
     NULL,
     NULL,
     &evaluate_atomname,
     NULL,

-    {NULL, asize(help_atomname), help_atomname}
+    {NULL, helptitle_atomname, asize(help_atomname), help_atomname}

 };
 
 /** Selection method data for \p pdbatomname selection keyword. */
 };
 
 /** Selection method data for \p pdbatomname selection keyword. */


@@ -302,7 +307,7 @@ gmx_ana_selmethod_t sm_pdbatomname = {
     NULL,
     &evaluate_pdbatomname,
     NULL,
     NULL,
     &evaluate_pdbatomname,
     NULL,

-    {NULL, asize(help_atomname), help_atomname}
+    {NULL, helptitle_atomname, asize(help_atomname), help_atomname}

 };
 
 /** Selection method data for \p atomtype selection keyword. */
 };
 
 /** Selection method data for \p atomtype selection keyword. */