AMBER atomtype feedback

author: Eric Messick <ericm@nanorex.com> 2008-09-15 17:52:11 +0000
committer: Eric Messick <ericm@nanorex.com> 2008-09-15 17:52:11 +0000
commit: a18c13f5263522b913ce2e072a9bf42872700539 (patch)
tree: 30fef287435ee47a5e45901c21b9a45f2d1c1e9a /sim
parent: 67f22548f66b9ad69e87058d3ae7c359984ccc4b (diff)
download: nanoengineer-a18c13f5263522b913ce2e072a9bf42872700539.tar.gz
nanoengineer-a18c13f5263522b913ce2e072a9bf42872700539.zip
10 files changed, 583 insertions, 78 deletions
diff --git a/sim/src/Makefile b/sim/src/Makefile
index a9d210573..789a9f265 100755
--- a/sim/src/Makefile
+++ b/sim/src/Makefile
@@ -67,6 +67,7 @@ endif
 
 COMMONOBJS=\
 	allocate.o \
+	amber_patterns.o \
 	dynamics.o \
 	globals.o \
 	hashtable.o \
@@ -88,7 +89,7 @@ COMMONOBJS=\
 	rigid-ode.o \
 	structcompare.o \
 	writemovie.o
-	
+
 ifeq ($(OS),Windows_NT)
 	COMMONOBJS+= strtok_r.o
 endif
@@ -244,129 +245,143 @@ depends: depend
 # DO NOT DELETE
 
 allocate.o: allocate.h
+amber_patterns.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h
+amber_patterns.o: minimize.h structcompare.h part.h newtables.h interpolate.h
+amber_patterns.o: readmmp.h readxyz.h printers.h dynamics.h jigs.h
+amber_patterns.o: amber_patterns.h pam5_patterns.h pattern.h potential.h
+amber_patterns.o: minstructure.h writemovie.h rigid.h printGromacsTopology.h
+amber_patterns.o: globals.h
 dynamics.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 dynamics.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-dynamics.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-dynamics.o: potential.h minstructure.h writemovie.h rigid.h
-dynamics.o: printGromacsTopology.h globals.h
+dynamics.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+dynamics.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+dynamics.o: rigid.h printGromacsTopology.h globals.h
 globals.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 globals.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-globals.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-globals.o: potential.h minstructure.h writemovie.h rigid.h
-globals.o: printGromacsTopology.h globals.h
+globals.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+globals.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+globals.o: rigid.h printGromacsTopology.h globals.h
 glviewer.o: allocate.h
 hashtable.o: allocate.h hashtable.h
 interpolate.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h
 interpolate.o: minimize.h structcompare.h part.h newtables.h interpolate.h
 interpolate.o: readmmp.h readxyz.h printers.h dynamics.h jigs.h
-interpolate.o: pam5_patterns.h pattern.h potential.h minstructure.h
-interpolate.o: writemovie.h rigid.h printGromacsTopology.h globals.h
+interpolate.o: amber_patterns.h pam5_patterns.h pattern.h potential.h
+interpolate.o: minstructure.h writemovie.h rigid.h printGromacsTopology.h
+interpolate.o: globals.h
 jigs.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 jigs.o: structcompare.h part.h newtables.h interpolate.h readmmp.h readxyz.h
-jigs.o: printers.h dynamics.h jigs.h pam5_patterns.h pattern.h potential.h
-jigs.o: minstructure.h writemovie.h rigid.h printGromacsTopology.h globals.h
+jigs.o: printers.h dynamics.h jigs.h amber_patterns.h pam5_patterns.h
+jigs.o: pattern.h potential.h minstructure.h writemovie.h rigid.h
+jigs.o: printGromacsTopology.h globals.h
 lin-alg.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 lin-alg.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-lin-alg.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-lin-alg.o: potential.h minstructure.h writemovie.h rigid.h
-lin-alg.o: printGromacsTopology.h globals.h
+lin-alg.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+lin-alg.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+lin-alg.o: rigid.h printGromacsTopology.h globals.h
 minimize.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 minimize.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-minimize.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-minimize.o: potential.h minstructure.h writemovie.h rigid.h
-minimize.o: printGromacsTopology.h globals.h
+minimize.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+minimize.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+minimize.o: rigid.h printGromacsTopology.h globals.h
 minstructure.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h
 minstructure.o: minimize.h structcompare.h part.h newtables.h interpolate.h
 minstructure.o: readmmp.h readxyz.h printers.h dynamics.h jigs.h
-minstructure.o: pam5_patterns.h pattern.h potential.h minstructure.h
-minstructure.o: writemovie.h rigid.h printGromacsTopology.h globals.h
+minstructure.o: amber_patterns.h pam5_patterns.h pattern.h potential.h
+minstructure.o: minstructure.h writemovie.h rigid.h printGromacsTopology.h
+minstructure.o: globals.h
 newtables.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 newtables.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-newtables.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-newtables.o: potential.h minstructure.h writemovie.h rigid.h
-newtables.o: printGromacsTopology.h globals.h bonds.gen bends.gen
+newtables.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+newtables.o: pam5_patterns.h pattern.h potential.h minstructure.h
+newtables.o: writemovie.h rigid.h printGromacsTopology.h globals.h bonds.gen
+newtables.o: bends.gen
 pam5_patterns.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h
 pam5_patterns.o: minimize.h structcompare.h part.h newtables.h interpolate.h
 pam5_patterns.o: readmmp.h readxyz.h printers.h dynamics.h jigs.h
-pam5_patterns.o: pam5_patterns.h pattern.h potential.h minstructure.h
-pam5_patterns.o: writemovie.h rigid.h printGromacsTopology.h globals.h
+pam5_patterns.o: amber_patterns.h pam5_patterns.h pattern.h potential.h
+pam5_patterns.o: minstructure.h writemovie.h rigid.h printGromacsTopology.h
+pam5_patterns.o: globals.h
 part.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 part.o: structcompare.h part.h newtables.h interpolate.h readmmp.h readxyz.h
-part.o: printers.h dynamics.h jigs.h pam5_patterns.h pattern.h potential.h
-part.o: minstructure.h writemovie.h rigid.h printGromacsTopology.h globals.h
+part.o: printers.h dynamics.h jigs.h amber_patterns.h pam5_patterns.h
+part.o: pattern.h potential.h minstructure.h writemovie.h rigid.h
+part.o: printGromacsTopology.h globals.h
 pattern.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 pattern.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-pattern.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-pattern.o: potential.h minstructure.h writemovie.h rigid.h
-pattern.o: printGromacsTopology.h globals.h
+pattern.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+pattern.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+pattern.o: rigid.h printGromacsTopology.h globals.h
 potential.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 potential.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-potential.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-potential.o: potential.h minstructure.h writemovie.h rigid.h
-potential.o: printGromacsTopology.h globals.h
+potential.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+potential.o: pam5_patterns.h pattern.h potential.h minstructure.h
+potential.o: writemovie.h rigid.h printGromacsTopology.h globals.h
 printers.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 printers.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-printers.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-printers.o: potential.h minstructure.h writemovie.h rigid.h
-printers.o: printGromacsTopology.h globals.h
+printers.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+printers.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+printers.o: rigid.h printGromacsTopology.h globals.h
 printGromacsTopology.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h
 printGromacsTopology.o: minimize.h structcompare.h part.h newtables.h
 printGromacsTopology.o: interpolate.h readmmp.h readxyz.h printers.h
-printGromacsTopology.o: dynamics.h jigs.h pam5_patterns.h pattern.h
-printGromacsTopology.o: potential.h minstructure.h writemovie.h rigid.h
-printGromacsTopology.o: printGromacsTopology.h globals.h
+printGromacsTopology.o: dynamics.h jigs.h amber_patterns.h pam5_patterns.h
+printGromacsTopology.o: pattern.h potential.h minstructure.h writemovie.h
+printGromacsTopology.o: rigid.h printGromacsTopology.h globals.h
 readers.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 readers.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-readers.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-readers.o: potential.h minstructure.h writemovie.h rigid.h
-readers.o: printGromacsTopology.h globals.h
+readers.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+readers.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+readers.o: rigid.h printGromacsTopology.h globals.h
 readmmp.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 readmmp.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-readmmp.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-readmmp.o: potential.h minstructure.h writemovie.h rigid.h
-readmmp.o: printGromacsTopology.h globals.h
+readmmp.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+readmmp.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+readmmp.o: rigid.h printGromacsTopology.h globals.h
 readxyz.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 readxyz.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-readxyz.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-readxyz.o: potential.h minstructure.h writemovie.h rigid.h
-readxyz.o: printGromacsTopology.h globals.h
+readxyz.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+readxyz.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+readxyz.o: rigid.h printGromacsTopology.h globals.h
 rigid.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 rigid.o: structcompare.h part.h newtables.h interpolate.h readmmp.h readxyz.h
-rigid.o: printers.h dynamics.h jigs.h pam5_patterns.h pattern.h potential.h
-rigid.o: minstructure.h writemovie.h rigid.h printGromacsTopology.h globals.h
-rigid.o: rigid-ode.h
+rigid.o: printers.h dynamics.h jigs.h amber_patterns.h pam5_patterns.h
+rigid.o: pattern.h potential.h minstructure.h writemovie.h rigid.h
+rigid.o: printGromacsTopology.h globals.h rigid-ode.h
 rigid-ode.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 rigid-ode.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-rigid-ode.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-rigid-ode.o: potential.h minstructure.h writemovie.h rigid.h
-rigid-ode.o: printGromacsTopology.h globals.h rigid-ode.h
+rigid-ode.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+rigid-ode.o: pam5_patterns.h pattern.h potential.h minstructure.h
+rigid-ode.o: writemovie.h rigid.h printGromacsTopology.h globals.h
+rigid-ode.o: rigid-ode.h
 sim.o: simhelp.c simulator.h debug.h lin-alg.h allocate.h hashtable.h
 sim.o: minimize.h structcompare.h part.h newtables.h interpolate.h readmmp.h
-sim.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-sim.o: potential.h minstructure.h writemovie.h rigid.h printGromacsTopology.h
-sim.o: globals.h version.h
+sim.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+sim.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+sim.o: rigid.h printGromacsTopology.h globals.h version.h
 simhelp.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 simhelp.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-simhelp.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-simhelp.o: potential.h minstructure.h writemovie.h rigid.h
-simhelp.o: printGromacsTopology.h globals.h version.h
+simhelp.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+simhelp.o: pam5_patterns.h pattern.h potential.h minstructure.h writemovie.h
+simhelp.o: rigid.h printGromacsTopology.h globals.h version.h
 simulator.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 simulator.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-simulator.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-simulator.o: potential.h minstructure.h writemovie.h rigid.h
-simulator.o: printGromacsTopology.h globals.h version.h
+simulator.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+simulator.o: pam5_patterns.h pattern.h potential.h minstructure.h
+simulator.o: writemovie.h rigid.h printGromacsTopology.h globals.h version.h
 simulator.o: debug.h lin-alg.h allocate.h hashtable.h minimize.h
 simulator.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-simulator.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h pattern.h
-simulator.o: potential.h minstructure.h writemovie.h rigid.h
-simulator.o: printGromacsTopology.h globals.h
+simulator.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+simulator.o: pam5_patterns.h pattern.h potential.h minstructure.h
+simulator.o: writemovie.h rigid.h printGromacsTopology.h globals.h
 structcompare.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h
 structcompare.o: minimize.h structcompare.h part.h newtables.h interpolate.h
 structcompare.o: readmmp.h readxyz.h printers.h dynamics.h jigs.h
-structcompare.o: pam5_patterns.h pattern.h potential.h minstructure.h
-structcompare.o: writemovie.h rigid.h printGromacsTopology.h globals.h
+structcompare.o: amber_patterns.h pam5_patterns.h pattern.h potential.h
+structcompare.o: minstructure.h writemovie.h rigid.h printGromacsTopology.h
+structcompare.o: globals.h
 writemovie.o: simulator.h debug.h lin-alg.h allocate.h hashtable.h minimize.h
 writemovie.o: structcompare.h part.h newtables.h interpolate.h readmmp.h
-writemovie.o: readxyz.h printers.h dynamics.h jigs.h pam5_patterns.h
-writemovie.o: pattern.h potential.h minstructure.h writemovie.h rigid.h
-writemovie.o: printGromacsTopology.h globals.h
+writemovie.o: readxyz.h printers.h dynamics.h jigs.h amber_patterns.h
+writemovie.o: pam5_patterns.h pattern.h potential.h minstructure.h
+writemovie.o: writemovie.h rigid.h printGromacsTopology.h globals.h
diff --git a/sim/src/amber_patterns.c b/sim/src/amber_patterns.c
new file mode 100644
index 000000000..440cfdd1b
--- /dev/null
+++ b/sim/src/amber_patterns.c
@@ -0,0 +1,415 @@
+// Copyright 2008 Nanorex, Inc.  See LICENSE file for details. 
+
+#include "simulator.h"
+
+static char const rcsid[] = "$Id$";
+
+static void
+trace_set_amber_type(struct atom *a, char *type, struct patternMatch *match)
+{
+  char buf[1024];
+
+  sprintf(buf, "# Pattern setType: [%d] %d %s\n", match->sequenceNumber, a->atomID, type);
+  write_traceline(buf);
+}
+
+static void
+set_AMBER_type(struct atom *a, char *type, struct patternMatch *match)
+{
+  if (TypeFeedback) {
+    trace_set_amber_type(a, type, match);
+  }
+}
+
+static void
+amber_match_CT_CA_CZ(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a = p->atoms[match->atomIndices[0]];
+
+  if (a->hybridization == sp3) {
+    set_AMBER_type(a, "CT", match);
+  } else if (a->hybridization == sp2) {
+    set_AMBER_type(a, "CA", match);
+  } else if (a->hybridization == sp) {
+    set_AMBER_type(a, "CZ", match);
+  }
+}
+
+static void
+amber_match_C_star_(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a;
+  int i;
+
+  for (i=0; i<5; i++) {
+    a = p->atoms[match->atomIndices[i]];
+    if (a->hybridization != sp2) {
+      return;
+    }
+  }
+  a = p->atoms[match->atomIndices[5]];
+  if (strcmp(a->type->symbol, "H")) {
+    a = p->atoms[match->atomIndices[2]];
+    set_AMBER_type(a, "C*", match);
+  }
+}
+
+static void
+amber_match_CB(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a;
+  int i;
+
+  for (i=0; i<9; i++) {
+    a = p->atoms[match->atomIndices[i]];
+    if (a->hybridization != sp2) {
+      return;
+    }
+  }
+  a = p->atoms[match->atomIndices[0]];
+  set_AMBER_type(a, "CB", match);
+  a = p->atoms[match->atomIndices[4]];
+  if (!strcmp(a->type->symbol, "C")) {
+    set_AMBER_type(a, "CB", match);
+  }
+}
+
+static void
+amber_match_CC_CR_CV(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a;
+  int i;
+
+  for (i=0; i<5; i++) {
+    a = p->atoms[match->atomIndices[i]];
+    if (a->hybridization != sp2) {
+      return;
+    }
+  }
+  a = p->atoms[match->atomIndices[6]];
+  if (strcmp(a->type->symbol, "H")) {
+    a = p->atoms[match->atomIndices[0]];
+    set_AMBER_type(a, "CC", match);
+    a = p->atoms[match->atomIndices[2]];
+    set_AMBER_type(a, "CR", match);
+    a = p->atoms[match->atomIndices[3]];
+    if (a->num_bonds == 2) {
+      a = p->atoms[match->atomIndices[4]];
+      set_AMBER_type(a, "CV", match);
+    }
+  }
+}
+
+static void
+amber_match_C(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a = p->atoms[match->atomIndices[0]];
+
+  if (a->hybridization == sp2) {
+    set_AMBER_type(a, "C", match);
+  }
+}
+
+static void
+amber_match_CD(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a1 = p->atoms[match->atomIndices[1]];
+  struct atom *a2 = p->atoms[match->atomIndices[2]];
+
+  set_AMBER_type(a1, "CD", match);
+  set_AMBER_type(a2, "CD", match);
+}
+
+static void
+amber_match_CK(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a;
+  int i;
+
+  for (i=0; i<9; i++) {
+    a = p->atoms[match->atomIndices[i]];
+    if (a->hybridization != sp2) {
+      return;
+    }
+  }
+  a = p->atoms[match->atomIndices[2]];
+  set_AMBER_type(a, "CK", match);
+}
+
+static void
+amber_match_CM(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a;
+  int i;
+
+  for (i=0; i<7; i++) {
+    a = p->atoms[match->atomIndices[i]];
+    if (a->hybridization != sp2) {
+      return;
+    }
+  }
+  a = p->atoms[match->atomIndices[7]];
+  if (!strcmp(a->type->symbol, "N") || !strcmp(a->type->symbol, "O")) {
+    a = p->atoms[match->atomIndices[0]];
+    set_AMBER_type(a, "CM", match);
+    a = p->atoms[match->atomIndices[1]];
+    set_AMBER_type(a, "CM", match);
+  }
+
+}
+
+static void
+amber_match_CN(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a;
+  int i;
+
+  for (i=0; i<9; i++) {
+    a = p->atoms[match->atomIndices[i]];
+    if (a->hybridization != sp2) {
+      return;
+    }
+  }
+  a = p->atoms[match->atomIndices[1]];
+  set_AMBER_type(a, "CN", match);
+}
+
+static void
+amber_match_CQ(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a;
+  int i;
+
+  for (i=0; i<9; i++) {
+    a = p->atoms[match->atomIndices[i]];
+    if (a->hybridization != sp2) {
+      return;
+    }
+  }
+  a = p->atoms[match->atomIndices[6]];
+  set_AMBER_type(a, "CQ", match);
+}
+
+static void
+amber_match_CW(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a;
+  int i;
+
+  for (i=0; i<5; i++) {
+    a = p->atoms[match->atomIndices[i]];
+    if (a->hybridization != sp2) {
+      return;
+    }
+  }
+  a = p->atoms[match->atomIndices[6]];
+  if (strcmp(a->type->symbol, "H")) {
+    a = p->atoms[match->atomIndices[1]];
+    if (!strcmp(a->type->symbol, "N") || !strcmp(a->type->symbol, "C")) {
+      a = p->atoms[match->atomIndices[4]];
+      set_AMBER_type(a, "CW", match);
+    }
+  }
+}
+
+static void
+amber_match_CY(struct patternMatch *match)
+{
+  struct part *p = match->p;
+  struct atom *a = p->atoms[match->atomIndices[0]];
+
+  set_AMBER_type(a, "CY", match);
+}
+
+void
+createAMBERPatterns(void)
+{
+  struct compiledPatternTraversal *t[15];
+  struct compiledPatternAtom *a[15];
+
+  a[0] = makePatternAtom(0, "C");
+  t[0] = makeTraversal(a[0], a[0], '1');
+  makePattern("AMBER-CT-CA-CZ", amber_match_CT_CA_CZ, 1, 1, t);
+
+  a[0] = makePatternAtom(0, "N");
+  a[1] = makePatternAtom(1, "C");
+  a[2] = makePatternAtom(2, "C");
+  a[3] = makePatternAtom(3, "C");
+  a[4] = makePatternAtom(4, "C");
+  a[5] = makePatternAtom(5, "Elt"); // not H
+  t[0] = makeTraversal2(a[0], a[1], "1ag2");
+  t[1] = makeTraversal2(a[1], a[2], "1ag2");
+  t[2] = makeTraversal2(a[2], a[3], "1ag2");
+  t[3] = makeTraversal2(a[3], a[4], "1ag2");
+  t[4] = makeTraversal2(a[4], a[0], "1ag2");
+  t[5] = makeTraversal(a[2], a[5], '1');
+  makePattern("AMBER-C*", amber_match_C_star_, 6, 6, t);
+
+  a[0] = makePatternAtom(0, "C");
+  a[1] = makePatternAtom(1, "Elt");
+  a[2] = makePatternAtom(2, "Elt");
+  a[3] = makePatternAtom(3, "Elt");
+  a[4] = makePatternAtom(4, "Elt");
+  a[5] = makePatternAtom(5, "Elt");
+  a[6] = makePatternAtom(6, "Elt");
+  a[7] = makePatternAtom(7, "Elt");
+  a[8] = makePatternAtom(8, "Elt");
+  t[0] = makeTraversal2(a[0], a[1], "1ag2");
+  t[1] = makeTraversal2(a[1], a[2], "1ag2");
+  t[2] = makeTraversal2(a[2], a[3], "1ag2");
+  t[3] = makeTraversal2(a[3], a[4], "1ag2");
+  t[4] = makeTraversal2(a[4], a[0], "1ag2");
+  t[5] = makeTraversal2(a[0], a[5], "1ag2");
+  t[6] = makeTraversal2(a[5], a[6], "1ag2");
+  t[7] = makeTraversal2(a[6], a[7], "1ag2");
+  t[8] = makeTraversal2(a[7], a[8], "1ag2");
+  t[9] = makeTraversal2(a[8], a[4], "1ag2");
+  makePattern("AMBER-CB", amber_match_CB, 9, 10, t);
+
+  a[0] = makePatternAtom(0, "C");
+  a[1] = makePatternAtom(1, "N");
+  a[2] = makePatternAtom(2, "C");
+  a[3] = makePatternAtom(3, "N");
+  a[4] = makePatternAtom(4, "C");
+  a[5] = makePatternAtom(5, "H");
+  a[6] = makePatternAtom(6, "Elt");
+  t[0] = makeTraversal2(a[0], a[1], "1ag2");
+  t[1] = makeTraversal2(a[1], a[2], "1ag2");
+  t[2] = makeTraversal2(a[2], a[3], "1ag2");
+  t[3] = makeTraversal2(a[3], a[4], "1ag2");
+  t[4] = makeTraversal2(a[4], a[0], "1ag2");
+  t[5] = makeTraversal(a[4], a[5], '1');
+  t[6] = makeTraversal(a[0], a[6], '1');
+  makePattern("AMBER-CC-CR-CV", amber_match_CC_CR_CV, 7, 7, t);
+
+  a[0] = makePatternAtom(0, "C");
+  a[1] = makePatternAtom(1, "O");
+  a[2] = makePatternAtom(2, "Elt");
+  t[0] = makeTraversal2(a[0], a[1], "ag2");
+  t[1] = makeTraversal2(a[0], a[2], "1ag");
+  makePattern("AMBER-C", amber_match_C, 3, 2, t);
+
+  a[0] = makePatternAtom(0, "C");
+  a[1] = makePatternAtom(1, "C");
+  a[2] = makePatternAtom(2, "C");
+  a[3] = makePatternAtom(3, "C");
+  t[0] = makeTraversal(a[0], a[1], '2');
+  t[1] = makeTraversal(a[1], a[2], '1');
+  t[2] = makeTraversal(a[2], a[3], '2');
+  makePattern("AMBER-CD", amber_match_CD, 4, 3, t);
+
+  a[0] = makePatternAtom(0, "C");
+  a[1] = makePatternAtom(1, "N");
+  a[2] = makePatternAtom(2, "C");
+  a[3] = makePatternAtom(3, "N");
+  a[4] = makePatternAtom(4, "C");
+  a[5] = makePatternAtom(5, "N");
+  a[6] = makePatternAtom(6, "C");
+  a[7] = makePatternAtom(7, "N");
+  a[8] = makePatternAtom(8, "C");
+  t[0] = makeTraversal2(a[0], a[1], "1ag2");
+  t[1] = makeTraversal2(a[1], a[2], "1ag2");
+  t[2] = makeTraversal2(a[2], a[3], "1ag2");
+  t[3] = makeTraversal2(a[3], a[4], "1ag2");
+  t[4] = makeTraversal2(a[4], a[0], "1ag2");
+  t[5] = makeTraversal2(a[0], a[5], "1ag2");
+  t[6] = makeTraversal2(a[5], a[6], "1ag2");
+  t[7] = makeTraversal2(a[6], a[7], "1ag2");
+  t[8] = makeTraversal2(a[7], a[8], "1ag2");
+  t[9] = makeTraversal2(a[8], a[4], "1ag2");
+  makePattern("AMBER-CK", amber_match_CK, 9, 10, t);
+
+  a[0] = makePatternAtom(0, "C");
+  a[1] = makePatternAtom(1, "C");
+  a[2] = makePatternAtom(2, "N");
+  a[3] = makePatternAtom(3, "C");
+  a[4] = makePatternAtom(4, "N");
+  a[5] = makePatternAtom(5, "C");
+  a[6] = makePatternAtom(6, "O");
+  a[7] = makePatternAtom(7, "Elt");
+  t[0] = makeTraversal2(a[0], a[1], "1ag2");
+  t[1] = makeTraversal2(a[1], a[2], "1ag2");
+  t[2] = makeTraversal2(a[2], a[3], "1ag2");
+  t[3] = makeTraversal2(a[3], a[4], "1ag2");
+  t[4] = makeTraversal2(a[4], a[5], "1ag2");
+  t[5] = makeTraversal2(a[5], a[0], "1ag2");
+  t[6] = makeTraversal2(a[3], a[6], "ag2");
+  t[7] = makeTraversal2(a[5], a[7], "1ag2");
+  makePattern("AMBER-CM", amber_match_CM, 8, 8, t);
+
+  a[0] = makePatternAtom(0, "N");
+  a[1] = makePatternAtom(1, "C");
+  a[2] = makePatternAtom(2, "C");
+  a[3] = makePatternAtom(3, "C");
+  a[4] = makePatternAtom(4, "C");
+  a[5] = makePatternAtom(5, "C");
+  a[6] = makePatternAtom(6, "C");
+  a[7] = makePatternAtom(7, "C");
+  a[8] = makePatternAtom(8, "C");
+  t[0] = makeTraversal2(a[0], a[1], "1ag2");
+  t[1] = makeTraversal2(a[1], a[2], "1ag2");
+  t[2] = makeTraversal2(a[2], a[3], "1ag2");
+  t[3] = makeTraversal2(a[3], a[4], "1ag2");
+  t[4] = makeTraversal2(a[4], a[0], "1ag2");
+  t[5] = makeTraversal2(a[1], a[5], "1ag2");
+  t[6] = makeTraversal2(a[5], a[6], "1ag2");
+  t[7] = makeTraversal2(a[6], a[7], "1ag2");
+  t[8] = makeTraversal2(a[7], a[8], "1ag2");
+  t[9] = makeTraversal2(a[8], a[2], "1ag2");
+  makePattern("AMBER-CN", amber_match_CN, 9, 10, t);
+
+  a[0] = makePatternAtom(0, "N");
+  a[1] = makePatternAtom(1, "C");
+  a[2] = makePatternAtom(2, "C");
+  a[3] = makePatternAtom(3, "N");
+  a[4] = makePatternAtom(4, "C");
+  a[5] = makePatternAtom(5, "N");
+  a[6] = makePatternAtom(6, "C");
+  a[7] = makePatternAtom(7, "N");
+  a[8] = makePatternAtom(8, "C");
+  t[0] = makeTraversal2(a[0], a[1], "1ag2");
+  t[1] = makeTraversal2(a[1], a[2], "1ag2");
+  t[2] = makeTraversal2(a[2], a[3], "1ag2");
+  t[3] = makeTraversal2(a[3], a[4], "1ag2");
+  t[4] = makeTraversal2(a[4], a[0], "1ag2");
+  t[5] = makeTraversal2(a[1], a[5], "1ag2");
+  t[6] = makeTraversal2(a[5], a[6], "1ag2");
+  t[7] = makeTraversal2(a[6], a[7], "1ag2");
+  t[8] = makeTraversal2(a[7], a[8], "1ag2");
+  t[9] = makeTraversal2(a[8], a[2], "1ag2");
+  makePattern("AMBER-CQ", amber_match_CQ, 9, 10, t);
+
+  a[0] = makePatternAtom(0, "C");
+  a[1] = makePatternAtom(1, "Elt"); // N or C
+  a[2] = makePatternAtom(2, "C");
+  a[3] = makePatternAtom(3, "N");
+  a[4] = makePatternAtom(4, "C");
+  a[5] = makePatternAtom(5, "H");
+  a[6] = makePatternAtom(6, "Elt"); // not H
+  a[7] = makePatternAtom(7, "H");
+  t[0] = makeTraversal2(a[0], a[1], "1ag2");
+  t[1] = makeTraversal2(a[1], a[2], "1ag2");
+  t[2] = makeTraversal2(a[2], a[3], "1ag2");
+  t[3] = makeTraversal2(a[3], a[4], "1ag2");
+  t[4] = makeTraversal2(a[4], a[0], "1ag2");
+  t[5] = makeTraversal(a[4], a[5], '1');
+  t[6] = makeTraversal(a[0], a[6], '1');
+  t[7] = makeTraversal(a[3], a[7], '1');
+  makePattern("AMBER-CW", amber_match_CW, 8, 8, t);
+
+  a[0] = makePatternAtom(0, "C");
+  a[1] = makePatternAtom(1, "N");
+  t[0] = makeTraversal(a[0], a[1], '3');
+  makePattern("AMBER-CY", amber_match_CY, 2, 1, t);
+}
diff --git a/sim/src/amber_patterns.h b/sim/src/amber_patterns.h
new file mode 100644
index 000000000..858e9c6d0
--- /dev/null
+++ b/sim/src/amber_patterns.h
@@ -0,0 +1,10 @@
+// Copyright 2008 Nanorex, Inc.  See LICENSE file for details. 
+#ifndef AMBER_PATTERNS_H_INCLUDED
+#define AMBER_PATTERNS_H_INCLUDED
+
+#define RCSID_AMBER_PATTERNS_H  "$Id$"
+
+extern void createAMBERPatterns(void);
+
+#endif
+
diff --git a/sim/src/globals.c b/sim/src/globals.c
index 15d91272f..f8ab772ef 100755
--- a/sim/src/globals.c
+++ b/sim/src/globals.c
@@ -57,6 +57,8 @@ double MinimizeThresholdEndMax;
 int TimeReversal;
 double ThermostatGamma;
 double ThermostatG1;
+int UseAMBER;
+int TypeFeedback;
 
 // absolute distance in nm beyond which gromacs will consider vdW
 // forces to be exactly zero.  If less than zero, user defined tables
@@ -157,6 +159,8 @@ reinit_globals(void)
     SimpleMovieForceScale = 1.0;
     TimeReversal = 0;
     ThermostatGamma = 0.01;
+    UseAMBER = 0;
+    TypeFeedback = 0;
     
     MinimizeThresholdCutoverRMS = 50.0; // pN
     MinimizeThresholdCutoverMax = 0.0; // set by constrainGlobals, below
@@ -237,6 +241,7 @@ printGlobals()
     write_traceline("# EnableElectrostatic: %d\n", EnableElectrostatic);
     write_traceline("# NeighborSearching: %d\n", NeighborSearching);
     write_traceline("# ThermostatGamma: %f\n", ThermostatGamma);
+    write_traceline("# UseAMBER: %d\n", UseAMBER);
     if (SystemParametersFileName != NULL && LoadedSystemParameters) {
         write_traceline("# SystemParametersFileName: %s\n", SystemParametersFileName);
     }
diff --git a/sim/src/globals.h b/sim/src/globals.h
index bd8f02ff5..144cbb5fc 100755
--- a/sim/src/globals.h
+++ b/sim/src/globals.h
@@ -50,6 +50,8 @@ extern int NeighborSearching;
 extern int TimeReversal;
 extern double ThermostatGamma;
 extern double ThermostatG1;
+extern int UseAMBER;
+extern int TypeFeedback;
 
 extern int LoadedSystemParameters;
 extern char *UserParametersFileName;
diff --git a/sim/src/pattern.c b/sim/src/pattern.c
index 02f4032e9..9c64bbaf1 100644
--- a/sim/src/pattern.c
+++ b/sim/src/pattern.c
@@ -310,6 +310,25 @@ checkForDuplicateMatch(struct patternMatch *match)
   return !dup;
 }
 
+static int
+matchBondOrder(char order, struct compiledPatternTraversal *traversal)
+{
+  int i;
+  char matchBondOrder;
+  
+  for (i=0; i<4; i++) {
+    matchBondOrder = traversal->bondOrder[i];
+    if (matchBondOrder) {
+      if (matchBondOrder == order) {
+        return 1;
+      }
+    } else {
+      return 0;
+    }
+  }
+  return 0;
+}
+
 // Matches one traversal in a compiled pattern.  See
 // http://www.nanoengineer-1.net/mediawiki/index.php?title=User:Emessick/Molecular_pattern_matching
 // for a description of the algorithm.  Basically, each traversal
@@ -365,7 +384,7 @@ matchOneTraversal(struct patternMatch *match,
       continue;
     }
     // build list of atoms bonded to a
-    if (traversal->bondOrder == '0') {
+    if (traversal->bondOrder[0] == '0') {
       // a must not be bonded to b
       while ((atomB = matchOneAtom(match,
                                    pattern,
@@ -390,7 +409,7 @@ matchOneTraversal(struct patternMatch *match,
     }
     for (bondNumber=atomA->num_bonds-1; bondNumber>=0; bondNumber--) {
       bond = atomA->bonds[bondNumber];
-      if (bond->order == traversal->bondOrder) {
+      if (matchBondOrder(bond->order, traversal)) {
         if (atomA == bond->a1) {
           atomB = bond->a2;
         } else {
@@ -473,9 +492,9 @@ makePatternAtom(int id, char *type)
 }
 
 struct compiledPatternTraversal *
-makeTraversal(struct compiledPatternAtom *a,
-              struct compiledPatternAtom *b,
-              char bondOrder)
+makeTraversal2(struct compiledPatternAtom *a,
+               struct compiledPatternAtom *b,
+               char *bondOrders)
 {
   struct compiledPatternTraversal *t;
 
@@ -483,10 +502,25 @@ makeTraversal(struct compiledPatternAtom *a,
     allocate(sizeof(struct compiledPatternTraversal));
   t->a = a;
   t->b = b;
-  t->bondOrder = bondOrder;
+  t->bondOrder[0] = bondOrders[0];
+  t->bondOrder[1] = bondOrders[1];
+  t->bondOrder[2] = bondOrders[2];
+  t->bondOrder[3] = bondOrders[3];
   return t;
 }
 
+struct compiledPatternTraversal *
+makeTraversal(struct compiledPatternAtom *a,
+              struct compiledPatternAtom *b,
+              char bondOrder)
+{
+  char buf[4];
+
+  buf[0] = bondOrder;
+  buf[1] = '\0';
+  return makeTraversal2(a, b, buf);
+}
+
 static int numPatterns;
 static struct compiledPattern **allPatterns;
 
@@ -535,5 +569,9 @@ createPatterns(void)
 {
   numPatterns = 0;
   makeUnmatchableType();
-  createPam5Patterns();
+  if (UseAMBER) {
+    createAMBERPatterns();
+  } else {
+    createPam5Patterns();
+  }
 }
diff --git a/sim/src/pattern.h b/sim/src/pattern.h
index af2cb4943..e6adb8d7f 100644
--- a/sim/src/pattern.h
+++ b/sim/src/pattern.h
@@ -14,7 +14,7 @@ struct compiledPatternTraversal
 {
   struct compiledPatternAtom *a;
   struct compiledPatternAtom *b;
-  char bondOrder;
+  char bondOrder[4];
 };
 
 struct patternMatch 
@@ -44,6 +44,8 @@ extern int atomIsType(struct atom *a, struct atomType *type);
 
 extern struct compiledPatternAtom *makePatternAtom(int id, char *type);
 
+extern struct compiledPatternTraversal *makeTraversal2(struct compiledPatternAtom *a, struct compiledPatternAtom *b, char *bondOrders);
+
 extern struct compiledPatternTraversal *makeTraversal(struct compiledPatternAtom *a, struct compiledPatternAtom *b, char bondOrder);
 
 extern void makePattern(char *name, void (*matchFunction)(struct patternMatch *match), int numAtoms, int numTraversals, struct compiledPatternTraversal **traversals);
diff --git a/sim/src/sim.pyx b/sim/src/sim.pyx
index 47bb456b5..3b339f719 100755
--- a/sim/src/sim.pyx
+++ b/sim/src/sim.pyx
@@ -48,6 +48,8 @@ cdef extern from "simhelp.c":
     int EnableElectrostatic
     int NeighborSearching
     double ThermostatGamma
+    int UseAMBER
+    int TypeFeedback
     char *IDKey
     char *BaseFileName
     char *InputFileName
@@ -153,6 +155,10 @@ cdef class _Simulator:
             return EnableElectrostatic
         elif strcmp(key, "NeighborSearching") == 0:
             return NeighborSearching
+        elif strcmp(key, "UseAMBER") == 0:
+            return UseAMBER
+        elif strcmp(key, "TypeFeedback") == 0:
+            return TypeFeedback
         elif strcmp(key, "ThermostatGamma") == 0:
             return ThermostatGamma
         elif strcmp(key, "IDKey") == 0:
@@ -269,6 +275,12 @@ cdef class _Simulator:
         elif strcmp(key, "NeighborSearching") == 0:
             global NeighborSearching
             NeighborSearching = value
+        elif strcmp(key, "UseAMBER") == 0:
+            global UseAMBER
+            UseAMBER = value
+        elif strcmp(key, "TypeFeedback") == 0:
+            global TypeFeedback
+            TypeFeedback = value
         elif strcmp(key, "ThermostatGamma") == 0:
             global ThermostatGamma
             ThermostatGamma = value
diff --git a/sim/src/simhelp.c b/sim/src/simhelp.c
index 8a8b322ea..a3503b7bd 100755
--- a/sim/src/simhelp.c
+++ b/sim/src/simhelp.c
@@ -370,6 +370,10 @@ everythingElse(void) // WARNING: this duplicates some code from simulator.c
     matchPartToAllPatterns(part);
     PYBAIL();
 
+    if (TypeFeedback) {
+        return finish_python_call(Py_None);
+    }
+
     // ##e should print options set before run, but it's too early to do that in this code
 
     if (IterPerFrame <= 0) IterPerFrame = 1;
diff --git a/sim/src/simulator.h b/sim/src/simulator.h
index bd061e25a..0e4810673 100755
--- a/sim/src/simulator.h
+++ b/sim/src/simulator.h
@@ -18,6 +18,7 @@
     RCSID_INTERPOLATE_H \
     RCSID_READMMP_H \
     RCSID_READXYZ_H \
+    RCSID_AMBER_PATTERNS_H \
     RCSID_PAM5_PATTERNS_H \
     RCSID_PATTERN_H \
     RCSID_PRINTERS_H \
@@ -148,6 +149,7 @@
 #include "printers.h"
 #include "dynamics.h"
 #include "jigs.h"
+#include "amber_patterns.h"
 #include "pam5_patterns.h"
 #include "pattern.h"
 #include "potential.h"
author	Eric Messick <ericm@nanorex.com>	2008-09-15 17:52:11 +0000
committer	Eric Messick <ericm@nanorex.com>	2008-09-15 17:52:11 +0000
commit	a18c13f5263522b913ce2e072a9bf42872700539 (patch)
tree	30fef287435ee47a5e45901c21b9a45f2d1c1e9a /sim
parent	67f22548f66b9ad69e87058d3ae7c359984ccc4b (diff)
download	nanoengineer-a18c13f5263522b913ce2e072a9bf42872700539.tar.gz nanoengineer-a18c13f5263522b913ce2e072a9bf42872700539.zip