Allow 'atomname' and 'atomtype' in selections.

'atomname' is now synonymous to 'name', and similarly for 'atomtype' and
'type'.  This reduces confusion, as the code uses atomname and atomtype
internally.  Also use the aliases in tests.

Change-Id: Ifa96840c1fc9c519be53b1bb5aae4f4910cdb0ff

diff --git a/src/gromacs/selection/selmethod.cpp b/src/gromacs/selection/selmethod.cpp
index 517baa550e512aa79cd422bf98bf20b92b00a85e..8f351e1df523481321a4b8be4a25cca639b73049 100644 (file)
--- a/src/gromacs/selection/selmethod.cpp
+++ b/src/gromacs/selection/selmethod.cpp
@@ -138,7 +138,9 @@ static const t_register_method smtable_def[] = {
     {"mol",        &sm_molindex},
     {"molecule",   &sm_molindex},
     {NULL,         &sm_atomname},
+    {"name",       &sm_atomname},
     {NULL,         &sm_atomtype},
+    {"type",       &sm_atomtype},
     {NULL,         &sm_resname},
     {NULL,         &sm_insertcode},
     {NULL,         &sm_chain},

diff --git a/src/gromacs/selection/sm_simple.cpp b/src/gromacs/selection/sm_simple.cpp
index a7ff1d43500f95c29ffc53ac55cdc958953838d7..1c52cb030eee09975cb1bebb26685bbb872c18f1 100644 (file)
--- a/src/gromacs/selection/sm_simple.cpp
+++ b/src/gromacs/selection/sm_simple.cpp
@@ -70,14 +70,14 @@ check_molecules(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data
 static void
 evaluate_molindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
-/** Evaluates the \p name selection keyword. */
+/** Evaluates the \p atomname selection keyword. */
 static void
 evaluate_atomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
 /** Checks whether atom types are present in the topology. */
 static void
 check_atomtype(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
-/** Evaluates the \p type selection keyword. */
+/** Evaluates the \p atomtype selection keyword. */
 static void
 evaluate_atomtype(t_topology *top, t_trxframe *fr, t_pbc *pbc,
                   gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
@@ -214,9 +214,9 @@ gmx_ana_selmethod_t sm_molindex = {
     NULL,
 };
 
-/** \internal Selection method data for \p name selection keyword. */
+/** \internal Selection method data for \p atomname selection keyword. */
 gmx_ana_selmethod_t sm_atomname = {
-    "name", STR_VALUE, SMETH_REQTOP,
+    "atomname", STR_VALUE, SMETH_REQTOP,
     0, NULL,
     NULL,
     NULL,
@@ -228,9 +228,9 @@ gmx_ana_selmethod_t sm_atomname = {
     NULL,
 };
 
-/** \internal Selection method data for \p type selection keyword. */
+/** \internal Selection method data for \p atomtype selection keyword. */
 gmx_ana_selmethod_t sm_atomtype = {
-    "type", STR_VALUE, SMETH_REQTOP,
+    "atomtype", STR_VALUE, SMETH_REQTOP,
     0, NULL,
     NULL,
     NULL,

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomname.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomname.xml
index c66b2312f725d12442f8cf05444ec96b5a3e2bc9..85a8d625c0d60e0c26814f27909a76b146f134a7 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomname.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesAtomname.xml
@@ -9,9 +9,9 @@
       <Bool Name="Dynamic">false</Bool>
     </ParsedSelection>
     <ParsedSelection Name="Selection2">
-      <String Name="Input">name S1 S2</String>
-      <String Name="Name">name S1 S2</String>
-      <String Name="Text">name S1 S2</String>
+      <String Name="Input">atomname S1 S2</String>
+      <String Name="Name">atomname S1 S2</String>
+      <String Name="Text">atomname S1 S2</String>
       <Bool Name="Dynamic">false</Bool>
     </ParsedSelection>
   </ParsedSelections>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResIndex.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResIndex.xml
index f602e13ff9088e950614d5bf336dab02c9a5e9e4..5351607e59174b243f8bbb5ab2c333574af81db4 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResIndex.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResIndex.xml
@@ -8,6 +8,12 @@
       <String Name="Text">resindex 1 4</String>
       <Bool Name="Dynamic">false</Bool>
     </ParsedSelection>
+    <ParsedSelection Name="Selection2">
+      <String Name="Input">residue 1 3</String>
+      <String Name="Name">residue 1 3</String>
+      <String Name="Text">residue 1 3</String>
+      <Bool Name="Dynamic">false</Bool>
+    </ParsedSelection>
   </ParsedSelections>
   <CompiledSelections Name="Compiled">
     <Selection Name="Selection1">
@@ -21,5 +27,16 @@
         <Int>11</Int>
       </Sequence>
     </Selection>
+    <Selection Name="Selection2">
+      <Sequence Name="Atoms">
+        <Int Name="Length">6</Int>
+        <Int>0</Int>
+        <Int>1</Int>
+        <Int>2</Int>
+        <Int>6</Int>
+        <Int>7</Int>
+        <Int>8</Int>
+      </Sequence>
+    </Selection>
   </CompiledSelections>
 </ReferenceData>

diff --git a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResnr.xml b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResnr.xml
index 23ef8aea3cd5406df457799d892e012c7445a8ab..d44e6b351275787543846da87548229e87250f0c 100644 (file)
--- a/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResnr.xml
+++ b/src/gromacs/selection/tests/refdata/SelectionCollectionDataTest_HandlesResnr.xml
@@ -9,9 +9,9 @@
       <Bool Name="Dynamic">false</Bool>
     </ParsedSelection>
     <ParsedSelection Name="Selection2">
-      <String Name="Input">resnr 4 to 3</String>
-      <String Name="Name">resnr 4 to 3</String>
-      <String Name="Text">resnr 4 to 3</String>
+      <String Name="Input">resid 4 to 3</String>
+      <String Name="Name">resid 4 to 3</String>
+      <String Name="Text">resid 4 to 3</String>
       <Bool Name="Dynamic">false</Bool>
     </ParsedSelection>
   </ParsedSelections>

diff --git a/src/gromacs/selection/tests/selectioncollection.cpp b/src/gromacs/selection/tests/selectioncollection.cpp
index 804dd51b8e5869082a8b8f1bd3eb61269095b651..6452971dae6d4672f718ba6b218138eabfcb9b7d 100644 (file)
--- a/src/gromacs/selection/tests/selectioncollection.cpp
+++ b/src/gromacs/selection/tests/selectioncollection.cpp
@@ -495,7 +495,7 @@ TEST_F(SelectionCollectionDataTest, HandlesResnr)
 {
     static const char * const selections[] = {
         "resnr 1 2 5",
-        "resnr 4 to 3",
+        "resid 4 to 3",
         NULL
     };
     runTest("simple.gro", selections);
@@ -505,6 +505,7 @@ TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 {
     static const char * const selections[] = {
         "resindex 1 4",
+        "residue 1 3",
         NULL
     };
     runTest("simple.pdb", selections);
@@ -516,7 +517,7 @@ TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 {
     static const char * const selections[] = {
         "name CB",
-        "name S1 S2",
+        "atomname S1 S2",
         NULL
     };
     runTest("simple.gro", selections);