AtomRef.exclusion causes bus error when the MDArena is not yet built. Fixed.

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@116 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/MolLib/Ruby_bind/ruby_bind.c b/MolLib/Ruby_bind/ruby_bind.c
index 71ef066..038ed1e 100644 (file)
--- a/MolLib/Ruby_bind/ruby_bind.c
+++ b/MolLib/Ruby_bind/ruby_bind.c
@@ -2074,8 +2074,9 @@ s_ParameterRef_ToString(VALUE self)
  *  is NULL, then the global parameters are looked for.  */
 
 /*  Rebuild the MD parameter record if necessary: may throw an exception  */
+/*  The second parameter is passed to md_arena.prepare; if true, then check only  */
 static void
-s_RebuildMDParameterIfNecessary(VALUE val)
+s_RebuildMDParameterIfNecessary(VALUE val, VALUE cval)
 {
        Molecule *mol;
        Data_Get_Struct(val, Molecule, mol);
@@ -2085,7 +2086,7 @@ s_RebuildMDParameterIfNecessary(VALUE val)
                /*  Do self.md_arena.prepare  */
                VALUE val2 = rb_funcall(val, rb_intern("md_arena"), 0);
                if (val2 != Qnil)
-                       val2 = rb_funcall(val2, rb_intern("prepare"), 1, Qtrue);
+                       val2 = rb_funcall(val2, rb_intern("prepare"), 1, cval);
        }
 }
 
@@ -2095,7 +2096,7 @@ s_NewParameterValueFromValue(VALUE val)
        Molecule *mol;
        if (rb_obj_is_kind_of(val, rb_cMolecule)) {
                Data_Get_Struct(val, Molecule, mol);
-               s_RebuildMDParameterIfNecessary(val);
+               s_RebuildMDParameterIfNecessary(val, Qtrue);
                MoleculeRetain(mol);
                return Data_Wrap_Struct(rb_cParameter, 0, (void (*)(void *))MoleculeRelease, mol);
        } else {
@@ -3373,8 +3374,10 @@ static VALUE s_AtomRef_GetExclusion(VALUE self) {
        idx = s_AtomIndexFromValue(self, &ap, &mol);
        if (mol->par == NULL || mol->arena == NULL || mol->arena->is_initialized == 0 || mol->needsMDRebuild) {
                VALUE mval = ValueFromMolecule(mol);
-               s_RebuildMDParameterIfNecessary(mval);
+               s_RebuildMDParameterIfNecessary(mval, Qnil);
        }
+       if (mol->arena->exinfo == NULL)
+               return Qnil;
        exinfo = mol->arena->exinfo + idx;
        exlist = mol->arena->exlist;
        retval = rb_ary_new();
@@ -4798,7 +4801,7 @@ s_Molecule_BondPar(VALUE self, VALUE val)
                rb_raise(rb_eMolbyError, "bond index (%d) out of range", ival);
        if (ival < 0)
                ival += mol->nbonds;
-       s_RebuildMDParameterIfNecessary(self);
+       s_RebuildMDParameterIfNecessary(self, Qtrue);
        t1 = ATOM_AT_INDEX(mol->atoms, mol->bonds[ival * 2])->type;
        t2 = ATOM_AT_INDEX(mol->atoms, mol->bonds[ival * 2 + 1])->type;
        bp = ParameterLookupBondPar(mol->par, t1, t2, 0);
@@ -4826,7 +4829,7 @@ s_Molecule_AnglePar(VALUE self, VALUE val)
                rb_raise(rb_eMolbyError, "angle index (%d) out of range", ival);
        if (ival < 0)
                ival += mol->nangles;
-       s_RebuildMDParameterIfNecessary(self);
+       s_RebuildMDParameterIfNecessary(self, Qtrue);
        t1 = ATOM_AT_INDEX(mol->atoms, mol->angles[ival * 3])->type;
        t2 = ATOM_AT_INDEX(mol->atoms, mol->angles[ival * 3 + 1])->type;
        t3 = ATOM_AT_INDEX(mol->atoms, mol->angles[ival * 3 + 2])->type;
@@ -4855,7 +4858,7 @@ s_Molecule_DihedralPar(VALUE self, VALUE val)
                rb_raise(rb_eMolbyError, "dihedral index (%d) out of range", ival);
        if (ival < 0)
                ival += mol->ndihedrals;
-       s_RebuildMDParameterIfNecessary(self);
+       s_RebuildMDParameterIfNecessary(self, Qtrue);
        t1 = ATOM_AT_INDEX(mol->atoms, mol->dihedrals[ival * 4])->type;
        t2 = ATOM_AT_INDEX(mol->atoms, mol->dihedrals[ival * 4 + 1])->type;
        t3 = ATOM_AT_INDEX(mol->atoms, mol->dihedrals[ival * 4 + 2])->type;
@@ -4885,7 +4888,7 @@ s_Molecule_ImproperPar(VALUE self, VALUE val)
                rb_raise(rb_eMolbyError, "improper index (%d) out of range", ival);
        if (ival < 0)
                ival += mol->nimpropers;
-       s_RebuildMDParameterIfNecessary(self);
+       s_RebuildMDParameterIfNecessary(self, Qtrue);
        t1 = ATOM_AT_INDEX(mol->atoms, mol->impropers[ival * 4])->type;
        t2 = ATOM_AT_INDEX(mol->atoms, mol->impropers[ival * 4 + 1])->type;
        t3 = ATOM_AT_INDEX(mol->atoms, mol->impropers[ival * 4 + 2])->type;
@@ -4915,7 +4918,7 @@ s_Molecule_VdwPar(VALUE self, VALUE val)
                rb_raise(rb_eMolbyError, "atom index (%d) out of range", ival);
        if (ival < 0)
                ival += mol->natoms;
-       s_RebuildMDParameterIfNecessary(self);
+       s_RebuildMDParameterIfNecessary(self, Qtrue);
        t1 = ATOM_AT_INDEX(mol->atoms, ival)->type;
        vp = ParameterLookupVdwPar(mol->par, t1, 0);
        if (vp == NULL)