Vdw and Vdw-pair parameters can now have atom indices instead of atom types. (This...

git-svn-id: svn+ssh://svn.sourceforge.jp/svnroot/molby/trunk@389 a2be9bc6-48de-4e38-9406-05402d4bc13c

diff --git a/MolLib/MD/MDCore.c b/MolLib/MD/MDCore.c
index d06921b..daf2731 100644 (file)
--- a/MolLib/MD/MDCore.c
+++ b/MolLib/MD/MDCore.c
@@ -569,22 +569,19 @@ s_find_vdw_parameters(MDArena *arena)
            (3) variant->aware in global par, (4) global par ignoring variants  */
        for (i = 0, ap = mol->atoms; i < mol->natoms; i++, ap = ATOM_NEXT(ap)) {
                if (mol->par != NULL) {
-                       vp = ParameterLookupVdwPar(mol->par, ap->type, 0);
-               /*      vp = ParameterLookupVdwPar(mol->par, i, kParameterLookupLocal | kParameterLookupNoWildcard);
-                       if (vp == NULL)
-                               vp = ParameterLookupVdwPar(mol->par, ap->type, kParameterLookupLocal | kParameterLookupGlobal); */
+                       vp = ParameterLookupVdwPar(mol->par, ap->type, i, 0);
                        if (vp != NULL) {
                                arena->vdw_par_i[i] = (vp - mol->par->vdwPars) + ATOMS_MAX_NUMBER * 2;
                                continue;
                        }
                }
-               vp = ParameterLookupVdwPar(gBuiltinParameters, ap->type, 0);
+               vp = ParameterLookupVdwPar(gBuiltinParameters, ap->type, -1, 0);
                if (vp != NULL) {
                        arena->vdw_par_i[i] = (vp - gBuiltinParameters->vdwPars) + ATOMS_MAX_NUMBER;
                        continue;
                }
                /*  Record as missing  */
-               vp = ParameterLookupVdwPar(par, ap->type, kParameterLookupMissing | kParameterLookupNoBaseAtomType);
+               vp = ParameterLookupVdwPar(par, ap->type, i, kParameterLookupMissing | kParameterLookupNoBaseAtomType);
                if (vp == NULL) {
                        vp = AssignArray(&par->vdwPars, &par->nvdwPars, sizeof(VdwPar), par->nvdwPars, NULL);
                        vp->src = -1;
@@ -684,10 +681,10 @@ s_find_vdw_parameters(MDArena *arena)
                        type2 = par->vdwPars[j].type1;  /*  Not type2  */
                        /*  Look up the pair-specific van der Waals parameters  */
                        if (mol->par != NULL) {
-                               vpp = ParameterLookupVdwPairPar(mol->par, type1, type2, 0);
+                               vpp = ParameterLookupVdwPairPar(mol->par, type1, type2, type1, type2, 0);
                        }
                        if (vpp == NULL)
-                               vpp = ParameterLookupVdwPairPar(gBuiltinParameters, type1, type2, 0);
+                               vpp = ParameterLookupVdwPairPar(gBuiltinParameters, type1, type2, type1, type2, 0);
                        if (vpp != NULL) {
                                newpar = *vpp;
                        } else {

diff --git a/MolLib/Parameter.c b/MolLib/Parameter.c
index a480c0a..a0e5529 100755 (executable)
--- a/MolLib/Parameter.c
+++ b/MolLib/Parameter.c
@@ -1651,7 +1651,7 @@ ParameterLookupImproperPar(Parameter *par, UInt t1, UInt t2, UInt t3, UInt t4, I
 }
 
 VdwPar *
-ParameterLookupVdwPar(Parameter *par, UInt t1, Int options)
+ParameterLookupVdwPar(Parameter *par, UInt t1, Int idx1, Int options)
 {
        int i;
        VdwPar *vp;
@@ -1665,16 +1665,16 @@ ParameterLookupVdwPar(Parameter *par, UInt t1, Int options)
                        || (vp->src == 0 && !(options & kParameterLookupLocal))
                        || (vp->src < 0 && !(options & kParameterLookupMissing)))
                        continue;
-               if (s_ParMatch(vp->type1, t1, -1, nowildcard))
+               if (s_ParMatch(vp->type1, t1, idx1, nowildcard))
                        return vp;
        }
        if (options & kParameterLookupNoBaseAtomType)
                return NULL;
-       return ParameterLookupVdwPar(par, t1 % kAtomTypeVariantBase, options | kParameterLookupNoBaseAtomType);
+       return ParameterLookupVdwPar(par, t1 % kAtomTypeVariantBase, idx1, options | kParameterLookupNoBaseAtomType);
 }
 
 VdwPairPar *
-ParameterLookupVdwPairPar(Parameter *par, UInt t1, UInt t2, Int options)
+ParameterLookupVdwPairPar(Parameter *par, UInt t1, UInt t2, Int idx1, Int idx2, Int options)
 {
        int i;
        VdwPairPar *vp;
@@ -1688,13 +1688,13 @@ ParameterLookupVdwPairPar(Parameter *par, UInt t1, UInt t2, Int options)
                        || (vp->src == 0 && !(options & kParameterLookupLocal))
                        || (vp->src < 0 && !(options & kParameterLookupMissing)))
                        continue;
-               if ((s_ParMatch(vp->type1, t1, -1, nowildcard) && s_ParMatch(vp->type2, t2, -1, nowildcard))
-                       || (s_ParMatch(vp->type1, t2, -1, nowildcard) && s_ParMatch(vp->type2, t1, -1, nowildcard)))
+               if ((s_ParMatch(vp->type1, t1, idx1, nowildcard) && s_ParMatch(vp->type2, t2, idx2, nowildcard))
+                       || (s_ParMatch(vp->type1, t2, idx2, nowildcard) && s_ParMatch(vp->type2, t1, idx1, nowildcard)))
                        return vp;
        }
        if (options & kParameterLookupNoBaseAtomType)
                return NULL;
-       return ParameterLookupVdwPairPar(par, t1 % kAtomTypeVariantBase, t2 % kAtomTypeVariantBase, options | kParameterLookupNoBaseAtomType);
+       return ParameterLookupVdwPairPar(par, t1 % kAtomTypeVariantBase, t2 % kAtomTypeVariantBase, idx1, idx2, options | kParameterLookupNoBaseAtomType);
 }
 
 VdwCutoffPar *

diff --git a/MolLib/Parameter.h b/MolLib/Parameter.h
index 57242b0..9811a03 100755 (executable)
--- a/MolLib/Parameter.h
+++ b/MolLib/Parameter.h
@@ -230,8 +230,8 @@ BondPar *ParameterLookupBondPar(Parameter *par, UInt t1, UInt t2, Int idx1, Int
 AnglePar *ParameterLookupAnglePar(Parameter *par, UInt t1, UInt t2, UInt t3, Int idx1, Int idx2, Int idx3, Int options);
 TorsionPar *ParameterLookupDihedralPar(Parameter *par, UInt t1, UInt t2, UInt t3, UInt t4, Int idx1, Int idx2, Int idx3, Int idx4, Int options);
 TorsionPar *ParameterLookupImproperPar(Parameter *par, UInt t1, UInt t2, UInt t3, UInt t4, Int idx1, Int idx2, Int idx3, Int idx4, Int options);
-VdwPar *ParameterLookupVdwPar(Parameter *par, UInt t1, Int options);
-VdwPairPar *ParameterLookupVdwPairPar(Parameter *par, UInt t1, UInt t2, Int options);
+VdwPar *ParameterLookupVdwPar(Parameter *par, UInt t1, Int idx1, Int options);
+VdwPairPar *ParameterLookupVdwPairPar(Parameter *par, UInt t1, UInt t2, Int idx1, Int idx2, Int options);
 VdwCutoffPar *ParameterLookupVdwCutoffPar(Parameter *par, UInt t1, UInt t2, Int options);
 
 int ElementParameterInitialize(const char *fname, char **outWarningMessage);

diff --git a/MolLib/Ruby_bind/ruby_bind.c b/MolLib/Ruby_bind/ruby_bind.c
index 88bfbeb..244bd3b 100644 (file)
--- a/MolLib/Ruby_bind/ruby_bind.c
+++ b/MolLib/Ruby_bind/ruby_bind.c
@@ -2870,13 +2870,13 @@ s_Parameter_Lookup_sub(int argc, VALUE *argv, int parType, Molecule *mol)
                case kVdwParType: {
                        VdwPar *vp;
                        if (mol != NULL) {
-                               vp = ParameterLookupVdwPar(mol->par, t[0], flags);
+                               vp = ParameterLookupVdwPar(mol->par, t[0], ii[0], flags);
                                if (vp != NULL) {
                                        idx = vp - mol->par->vdwPars;
                                        break;
                                }
                        }
-                       vp = ParameterLookupVdwPar(gBuiltinParameters, t[0], flags);
+                       vp = ParameterLookupVdwPar(gBuiltinParameters, t[0], -1, flags);
                        if (vp != NULL) {
                                idx = vp - gBuiltinParameters->vdwPars;
                                is_global = 1;
@@ -2886,13 +2886,13 @@ s_Parameter_Lookup_sub(int argc, VALUE *argv, int parType, Molecule *mol)
                case kVdwPairParType: {
                        VdwPairPar *vp;
                        if (mol != NULL) {
-                               vp = ParameterLookupVdwPairPar(mol->par, t[0], t[1], flags);
+                               vp = ParameterLookupVdwPairPar(mol->par, t[0], t[1], ii[0], ii[1], flags);
                                if (vp != NULL) {
                                        idx = vp - mol->par->vdwpPars;
                                        break;
                                }
                        }
-                       vp = ParameterLookupVdwPairPar(gBuiltinParameters, t[0], t[1], flags);
+                       vp = ParameterLookupVdwPairPar(gBuiltinParameters, t[0], t[1], -1, -1, flags);
                        if (vp != NULL) {
                                idx = vp - gBuiltinParameters->vdwpPars;
                                is_global = 1;
@@ -5496,34 +5496,6 @@ s_Molecule_ImproperPar(VALUE self, VALUE val)
        return ValueFromMoleculeWithParameterTypeAndIndex(mol, kImproperParType, tp - mol->par->improperPars);
 }
 */
-/*
- *  call-seq:
- *     vdw_par(idx)    -> ParameterRef
- *
- *  Returns the vdw parameter for the idx-th atom.
- */
-/*
-static VALUE
-s_Molecule_VdwPar(VALUE self, VALUE val)
-{
-    Molecule *mol;
-       Int ival;
-       VdwPar *vp;
-       UInt t1;
-    Data_Get_Struct(self, Molecule, mol);
-       ival = NUM2INT(rb_Integer(val));
-       if (ival < -mol->natoms || ival >= mol->natoms)
-               rb_raise(rb_eMolbyError, "atom index (%d) out of range", ival);
-       if (ival < 0)
-               ival += mol->natoms;
-       s_RebuildMDParameterIfNecessary(self, Qtrue);
-       t1 = ATOM_AT_INDEX(mol->atoms, ival)->type;
-       vp = ParameterLookupVdwPar(mol->par, t1, 0);
-       if (vp == NULL)
-               return Qnil;
-       return ValueFromMoleculeWithParameterTypeAndIndex(mol, kVdwParType, vp - mol->par->vdwPars);
-}
-*/
 
 /*
  *  call-seq: