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authorManoj Rajagopalan <manoj@nanorex.com>2008-02-25 18:48:04 +0000
committerManoj Rajagopalan <manoj@nanorex.com>2008-02-25 18:48:04 +0000
commitab49ca882be6d3dcfcb077304d200f9bb7fdceab (patch)
tree03057529c9cf98b13afc65bde9c44da3099a2a8d /cad/plugins/NanoVision-1/src/Plugins
parent33c5d07435d7129dd95184f5ca6f8e522e395ab9 (diff)
downloadnanoengineer-ab49ca882be6d3dcfcb077304d200f9bb7fdceab.tar.gz
nanoengineer-ab49ca882be6d3dcfcb077304d200f9bb7fdceab.zip
Results tree now shows molecule-set subtree for MMP files
Diffstat (limited to 'cad/plugins/NanoVision-1/src/Plugins')
-rw-r--r--cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.cpp116
-rw-r--r--cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.rl3
2 files changed, 61 insertions, 58 deletions
diff --git a/cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.cpp b/cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.cpp
index 7535c6999..e5a76d7e1 100644
--- a/cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.cpp
+++ b/cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.cpp
@@ -6,6 +6,7 @@
// Copyright 2008 Nanorex, Inc. See LICENSE file for details.
#include "NanorexMMPImportExport.h"
+#include <QFileInfo>
#define VERBOSE
@@ -27,12 +28,12 @@ inline void DEBUG_MSG(string const& filename, int line, string const& s)
-#line 270 "NanorexMMPImportExport.rl"
+#line 271 "NanorexMMPImportExport.rl"
-#line 274 "NanorexMMPImportExport.rl"
+#line 275 "NanorexMMPImportExport.rl"
-#line 36 "NanorexMMPImportExport.cpp"
+#line 37 "NanorexMMPImportExport.cpp"
static const char _mmp_parser_actions[] = {
0, 1, 0, 1, 1, 1, 3, 1,
4, 1, 5, 1, 6, 1, 7, 1,
@@ -429,7 +430,7 @@ static const int mmp_parser_en_group_record = 129;
static const int mmp_parser_en_egroup_record = 135;
static const int mmp_parser_en_main = 136;
-#line 275 "NanorexMMPImportExport.rl"
+#line 276 "NanorexMMPImportExport.rl"
// static data
@@ -475,12 +476,12 @@ void NanorexMMPImportExport::reset(void)
// initialize the ragel engine
-#line 479 "NanorexMMPImportExport.cpp"
+#line 480 "NanorexMMPImportExport.cpp"
{
cs = mmp_parser_start;
top = 0;
}
-#line 320 "NanorexMMPImportExport.rl"
+#line 321 "NanorexMMPImportExport.rl"
}
@@ -535,7 +536,7 @@ bool NanorexMMPImportExport::readMMP(istream& instream,
// Ragel parser implementation
bool success = true;
-#line 539 "NanorexMMPImportExport.cpp"
+#line 540 "NanorexMMPImportExport.cpp"
{
int _klen;
unsigned int _trans;
@@ -610,67 +611,67 @@ _match:
switch ( *_acts++ )
{
case 1:
-#line 39 "NanorexMMPImportExport.rl"
+#line 40 "NanorexMMPImportExport.rl"
{intval = intval*10 + ((*p)-'0');}
break;
case 2:
-#line 42 "NanorexMMPImportExport.rl"
+#line 43 "NanorexMMPImportExport.rl"
{intval=-intval;}
break;
case 4:
-#line 51 "NanorexMMPImportExport.rl"
+#line 52 "NanorexMMPImportExport.rl"
{stringval = stringval + (*p); }
break;
case 6:
-#line 56 "NanorexMMPImportExport.rl"
+#line 57 "NanorexMMPImportExport.rl"
{stringval2 = stringval2 + (*p); }
break;
case 7:
-#line 61 "NanorexMMPImportExport.rl"
+#line 62 "NanorexMMPImportExport.rl"
{atomID = intval;}
break;
case 8:
-#line 62 "NanorexMMPImportExport.rl"
+#line 63 "NanorexMMPImportExport.rl"
{atomicNum = intval;}
break;
case 9:
-#line 65 "NanorexMMPImportExport.rl"
+#line 66 "NanorexMMPImportExport.rl"
{ x=intval;}
break;
case 10:
-#line 66 "NanorexMMPImportExport.rl"
+#line 67 "NanorexMMPImportExport.rl"
{ y=intval;}
break;
case 11:
-#line 67 "NanorexMMPImportExport.rl"
+#line 68 "NanorexMMPImportExport.rl"
{ z=intval;}
break;
case 12:
-#line 70 "NanorexMMPImportExport.rl"
+#line 71 "NanorexMMPImportExport.rl"
{atomStyleID = NXAtomData::DEF;}
break;
case 13:
-#line 71 "NanorexMMPImportExport.rl"
+#line 72 "NanorexMMPImportExport.rl"
{atomStyleID = NXAtomData::INV;}
break;
case 14:
-#line 72 "NanorexMMPImportExport.rl"
+#line 73 "NanorexMMPImportExport.rl"
{atomStyleID = NXAtomData::VDW;}
break;
case 15:
-#line 73 "NanorexMMPImportExport.rl"
+#line 74 "NanorexMMPImportExport.rl"
{atomStyleID = NXAtomData::LIN;}
break;
case 16:
-#line 74 "NanorexMMPImportExport.rl"
+#line 75 "NanorexMMPImportExport.rl"
{atomStyleID = NXAtomData::CPK;}
break;
case 17:
-#line 75 "NanorexMMPImportExport.rl"
+#line 76 "NanorexMMPImportExport.rl"
{atomStyleID = NXAtomData::TUB;}
break;
case 18:
-#line 87 "NanorexMMPImportExport.rl"
+#line 88 "NanorexMMPImportExport.rl"
{
++line;
if(molPtr != NULL) {
@@ -699,31 +700,31 @@ _match:
}
break;
case 19:
-#line 118 "NanorexMMPImportExport.rl"
+#line 119 "NanorexMMPImportExport.rl"
{bond_order=1;}
break;
case 20:
-#line 119 "NanorexMMPImportExport.rl"
+#line 120 "NanorexMMPImportExport.rl"
{bond_order=2;}
break;
case 21:
-#line 120 "NanorexMMPImportExport.rl"
+#line 121 "NanorexMMPImportExport.rl"
{bond_order=3;}
break;
case 22:
-#line 121 "NanorexMMPImportExport.rl"
+#line 122 "NanorexMMPImportExport.rl"
{bond_order=4;}
break;
case 23:
-#line 122 "NanorexMMPImportExport.rl"
+#line 123 "NanorexMMPImportExport.rl"
{bond_order=5;}
break;
case 24:
-#line 123 "NanorexMMPImportExport.rl"
+#line 124 "NanorexMMPImportExport.rl"
{bond_order=6;}
break;
case 25:
-#line 126 "NanorexMMPImportExport.rl"
+#line 127 "NanorexMMPImportExport.rl"
{
int const& targetAtomIdx = intval;
map<int,OBAtom*>::iterator targetAtomExistsQuery =
@@ -757,11 +758,11 @@ _match:
}
break;
case 26:
-#line 161 "NanorexMMPImportExport.rl"
+#line 162 "NanorexMMPImportExport.rl"
{ CDEBUG("clearing targetAtomList"); targetAtomList.clear(); }
break;
case 27:
-#line 165 "NanorexMMPImportExport.rl"
+#line 166 "NanorexMMPImportExport.rl"
{
++line;
{
@@ -789,7 +790,7 @@ _match:
}
break;
case 28:
-#line 201 "NanorexMMPImportExport.rl"
+#line 202 "NanorexMMPImportExport.rl"
{
++line;
createNewMolecule();
@@ -803,7 +804,7 @@ _match:
}
break;
case 29:
-#line 217 "NanorexMMPImportExport.rl"
+#line 218 "NanorexMMPImportExport.rl"
{ {
ostringstream msg;
msg << "atom-property: " << stringval
@@ -814,14 +815,14 @@ _match:
}
break;
case 30:
-#line 227 "NanorexMMPImportExport.rl"
+#line 228 "NanorexMMPImportExport.rl"
{
++line;
{cs = stack[--top]; goto _again;}
}
break;
case 31:
-#line 234 "NanorexMMPImportExport.rl"
+#line 235 "NanorexMMPImportExport.rl"
{
++line;
createNewMoleculeSet();
@@ -834,7 +835,7 @@ _match:
}
break;
case 32:
-#line 248 "NanorexMMPImportExport.rl"
+#line 249 "NanorexMMPImportExport.rl"
{
++line;
closeMoleculeSet();
@@ -842,42 +843,42 @@ _match:
}
break;
case 33:
-#line 257 "NanorexMMPImportExport.rl"
+#line 258 "NanorexMMPImportExport.rl"
{{stack[top++] = cs; cs = 129; goto _again;}}
break;
case 34:
-#line 258 "NanorexMMPImportExport.rl"
+#line 259 "NanorexMMPImportExport.rl"
{{stack[top++] = cs; cs = 135; goto _again;}}
break;
case 35:
-#line 259 "NanorexMMPImportExport.rl"
+#line 260 "NanorexMMPImportExport.rl"
{{stack[top++] = cs; cs = 98; goto _again;}}
break;
case 36:
-#line 260 "NanorexMMPImportExport.rl"
+#line 261 "NanorexMMPImportExport.rl"
{{stack[top++] = cs; cs = 40; goto _again;}}
break;
case 37:
-#line 261 "NanorexMMPImportExport.rl"
+#line 262 "NanorexMMPImportExport.rl"
{{stack[top++] = cs; cs = 88; goto _again;}}
break;
case 38:
-#line 262 "NanorexMMPImportExport.rl"
+#line 263 "NanorexMMPImportExport.rl"
{++line;{stack[top++] = cs; cs = 118; goto _again;}}
break;
case 39:
-#line 263 "NanorexMMPImportExport.rl"
+#line 264 "NanorexMMPImportExport.rl"
{++line; CDEBUG("comment"); }
break;
case 40:
-#line 264 "NanorexMMPImportExport.rl"
+#line 265 "NanorexMMPImportExport.rl"
{++line; CDEBUG("ignored"); }
break;
case 41:
-#line 267 "NanorexMMPImportExport.rl"
+#line 268 "NanorexMMPImportExport.rl"
{success = false;}
break;
-#line 881 "NanorexMMPImportExport.cpp"
+#line 882 "NanorexMMPImportExport.cpp"
}
}
@@ -887,18 +888,18 @@ _again:
while ( _nacts-- > 0 ) {
switch ( *_acts++ ) {
case 0:
-#line 38 "NanorexMMPImportExport.rl"
+#line 39 "NanorexMMPImportExport.rl"
{intval=0;}
break;
case 3:
-#line 50 "NanorexMMPImportExport.rl"
+#line 51 "NanorexMMPImportExport.rl"
{stringval.clear(); stringval = stringval + (*p);}
break;
case 5:
-#line 55 "NanorexMMPImportExport.rl"
+#line 56 "NanorexMMPImportExport.rl"
{stringval2.clear(); stringval2 = stringval2 + (*p);}
break;
-#line 902 "NanorexMMPImportExport.cpp"
+#line 903 "NanorexMMPImportExport.cpp"
}
}
@@ -914,25 +915,25 @@ _again:
while ( __nacts-- > 0 ) {
switch ( *__acts++ ) {
case 39:
-#line 263 "NanorexMMPImportExport.rl"
+#line 264 "NanorexMMPImportExport.rl"
{++line; CDEBUG("comment"); }
break;
case 40:
-#line 264 "NanorexMMPImportExport.rl"
+#line 265 "NanorexMMPImportExport.rl"
{++line; CDEBUG("ignored"); }
break;
case 41:
-#line 267 "NanorexMMPImportExport.rl"
+#line 268 "NanorexMMPImportExport.rl"
{success = false;}
break;
-#line 929 "NanorexMMPImportExport.cpp"
+#line 930 "NanorexMMPImportExport.cpp"
}
}
}
_out: {}
}
-#line 374 "NanorexMMPImportExport.rl"
+#line 375 "NanorexMMPImportExport.rl"
// End-of-parsing sanity checks
if(molSetPtrStack.size() != 1) {
@@ -948,6 +949,7 @@ void NanorexMMPImportExport::createNewMoleculeSet(void)
{
if(molSetPtr != NULL) {
NXMoleculeSet *newMolSetPtr = new NXMoleculeSet;
+ newMolSetPtr->setTitle(stringval);
molSetPtr->addChild(newMolSetPtr);
molSetPtrStack.push(newMolSetPtr);
molSetPtr = newMolSetPtr;
@@ -1066,7 +1068,7 @@ void NanorexMMPImportExport::PrintMolecule(ostream& o,
if(atomPtr->GetHyb() != 0) {
o << "info atom atomtype = "
- << _s_hybridizationName[atomPtr->GetHyb()] << endl;
+ << _s_hybridizationName[atomPtr->GetHyb()];
}
// ... write the 'bond' lines for this atom ...
diff --git a/cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.rl b/cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.rl
index 3b9e3fbbb..7d3fabd37 100644
--- a/cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.rl
+++ b/cad/plugins/NanoVision-1/src/Plugins/NanorexMMPImportExport/NanorexMMPImportExport.rl
@@ -387,6 +387,7 @@ void NanorexMMPImportExport::createNewMoleculeSet(void)
{
if(molSetPtr != NULL) {
NXMoleculeSet *newMolSetPtr = new NXMoleculeSet;
+ newMolSetPtr->setTitle(stringval);
molSetPtr->addChild(newMolSetPtr);
molSetPtrStack.push(newMolSetPtr);
molSetPtr = newMolSetPtr;
@@ -505,7 +506,7 @@ void NanorexMMPImportExport::PrintMolecule(ostream& o,
if(atomPtr->GetHyb() != 0) {
o << "info atom atomtype = "
- << _s_hybridizationName[atomPtr->GetHyb()] << endl;
+ << _s_hybridizationName[atomPtr->GetHyb()];
}
// ... write the 'bond' lines for this atom ...
generated by cgit v1.2.3 (git 2.39.1) at 2025-07-29 06:48:11 +0000