diff --git a/modules/conop/pymod/export_processor.cc b/modules/conop/pymod/export_processor.cc
index 180da8f48363571c1c8465bb4f8f2b01271f900f..c9298c25de569fd882a28fbf1bf949739581be03 100644
--- a/modules/conop/pymod/export_processor.cc
+++ b/modules/conop/pymod/export_processor.cc
@@ -75,5 +75,6 @@ void export_processor() {
.def("Copy", &WrappedProcessor::CopyDefault)
.def("DoProcess", &WrappedProcessor::DoProcessDefault)
;
+ def("IsBondFeasible", &IsBondFeasible);
}
diff --git a/modules/conop/src/processor.cc b/modules/conop/src/processor.cc
index e1a3e6b6607dd68491cdfbb99a5350190ce8156f..1e996b77ab0aeb8a7437eb55e91c2ea069106ce9 100644
--- a/modules/conop/src/processor.cc
+++ b/modules/conop/src/processor.cc
@@ -98,4 +98,88 @@ void AssignBackboneTorsions(mol::ResidueHandle prev,
}
}
+void Processor::ProcessUnkResidue(DiagnosticsPtr diags,
+ mol::ResidueHandle res) const
+{
+ // Don't do anything if treatment is set to SILENT
+ if (this->GetUnkResidueTreatment() == CONOP_SILENT) {
+ return;
+ }
+ switch (this->GetUnkResidueTreatment()) {
+ case CONOP_WARN:
+ diags->AddDiag(DIAG_UNK_RESIDUE, "unknown residue %0")
+ .AddResidue(res);
+ break;
+ case CONOP_FATAL:
+ // FIXME: Implement a ConopError based on Diag...
+ break;
+ case CONOP_REMOVE_RESIDUE:
+ case CONOP_REMOVE:
+ diags->AddDiag(DIAG_UNK_RESIDUE, "removed unknown residue %0")
+ .AddResidue(res);
+ res.GetEntity().EditXCS().DeleteResidue(res);
+ return;
+ default:
+ assert(0 && "unhandled switch");
+ }
+}
+
+void Processor::ProcessUnkAtoms(DiagnosticsPtr diags,
+ mol::AtomHandleList unks) const
+{
+ // Don't do anything if treatment is set to SILENT
+ if (this->GetUnkAtomTreatment() == CONOP_SILENT) {
+ return;
+ }
+
+ assert(!unks.empty() && "empty unk list");
+ mol::XCSEditor edi = unks.front().GetEntity().EditXCS();
+ for (mol::AtomHandleList::iterator
+ i = unks.begin(), e = unks.end(); i != e; ++i) {
+ switch (this->GetUnkAtomTreatment()) {
+ case CONOP_REMOVE_ATOM:
+ case CONOP_REMOVE:
+ edi.DeleteAtom(*i);
+ diags->AddDiag(DIAG_UNK_ATOM, "removed unknown atom %0 from residue %1")
+ .AddString(i->GetName()).AddResidue(i->GetResidue());
+ break;
+ case CONOP_WARN:
+ diags->AddDiag(DIAG_UNK_ATOM, "residue %0 contains unknown atom %1")
+ .AddResidue(i->GetResidue()).AddString(i->GetName());
+ break;
+ case CONOP_FATAL:
+ // FIXME: Implement a ConopError based on Diag...
+ break;
+ case CONOP_REMOVE_RESIDUE:
+ diags->AddDiag(DIAG_UNK_ATOM, "removed residue %0 with unknown atom %1")
+ .AddString(i->GetResidue().GetQualifiedName())
+ .AddString(i->GetName());
+ edi.DeleteResidue(i->GetResidue());
+ return;
+ default:
+ assert(0 && "unhandled switch");
+ }
+ }
+}
+
+bool IsBondFeasible(const mol::AtomHandle& atom_a,
+ const mol::AtomHandle& atom_b)
+{
+ Real radii=0.0;
+ if (atom_a.GetRadius()>0.0) {
+ radii=atom_a.GetRadius();
+ } else {
+ return false;
+ }
+ if (atom_b.GetRadius()>0.0) {
+ radii+=atom_b.GetRadius();
+ } else {
+ return false;
+ }
+ Real len=geom::Length2(atom_a.GetPos()-atom_b.GetPos());
+ Real lower_bound=radii*radii*0.0625;
+ Real upper_bound=lower_bound*6.0;
+ return (len<=upper_bound && len>=lower_bound);
+}
+
}}
diff --git a/modules/conop/src/processor.hh b/modules/conop/src/processor.hh
index 0fdaee40dba0ce591e445f6882ee10004e7b7005..79406e72e6803109855b90eb3c90b4189ae8cce1 100644
--- a/modules/conop/src/processor.hh
+++ b/modules/conop/src/processor.hh
@@ -53,6 +53,10 @@ protected:
mol::EntityHandle ent) const { return true; }
virtual bool EndProcessing(DiagnosticsPtr diags,
mol::EntityHandle ent) const { return true; }
+ void ProcessUnkResidue(DiagnosticsPtr diags,
+ mol::ResidueHandle res) const;
+ void ProcessUnkAtoms(DiagnosticsPtr diags,
+ mol::AtomHandleList unks) const;
public:
Processor(): strict_hydrogens_(false), check_bond_feasibility_(false),
assign_torsions_(false), connect_(true), unk_atom_treatment_(CONOP_WARN),
@@ -132,6 +136,8 @@ void DLLEXPORT_OST_CONOP AssignBackboneTorsions(mol::ResidueHandle prev,
mol::ResidueHandle res,
mol::ResidueHandle next);
+bool DLLEXPORT_OST_CONOP IsBondFeasible(const mol::AtomHandle&,
+ const mol::AtomHandle&);
}}
#endif
diff --git a/modules/conop/src/rule_based.cc b/modules/conop/src/rule_based.cc
index 224b11024058375c5c33fab1b229b5cff954913a..98018f29f3a2cf1c3a0d56c7fb967078e09c4c3c 100644
--- a/modules/conop/src/rule_based.cc
+++ b/modules/conop/src/rule_based.cc
@@ -35,69 +35,6 @@ struct OrdinalAtomComp {
}
};
-void RuleBasedProcessor::ProcessUnkResidue(DiagnosticsPtr diags,
- mol::ResidueHandle res) const
-{
- // Don't do anything if treatment is set to SILENT
- if (this->GetUnkResidueTreatment() == CONOP_SILENT) {
- return;
- }
- switch (this->GetUnkResidueTreatment()) {
- case CONOP_WARN:
- diags->AddDiag(DIAG_UNK_RESIDUE, "unknown residue %0")
- .AddResidue(res);
- break;
- case CONOP_FATAL:
- // FIXME: Implement a ConopError based on Diag...
- break;
- case CONOP_REMOVE_RESIDUE:
- case CONOP_REMOVE:
- diags->AddDiag(DIAG_UNK_RESIDUE, "removed unknown residue %0")
- .AddResidue(res);
- res.GetEntity().EditXCS().DeleteResidue(res);
- return;
- default:
- assert(0 && "unhandled switch");
- }
-}
-
-void RuleBasedProcessor::ProcessUnkAtoms(DiagnosticsPtr diags,
- mol::AtomHandleList unks) const
-{
- // Don't do anything if treatment is set to SILENT
- if (this->GetUnkAtomTreatment() == CONOP_SILENT) {
- return;
- }
-
- assert(!unks.empty() && "empty unk list");
- mol::XCSEditor edi = unks.front().GetEntity().EditXCS();
- for (mol::AtomHandleList::iterator
- i = unks.begin(), e = unks.end(); i != e; ++i) {
- switch (this->GetUnkAtomTreatment()) {
- case CONOP_REMOVE_ATOM:
- case CONOP_REMOVE:
- edi.DeleteAtom(*i);
- diags->AddDiag(DIAG_UNK_ATOM, "removed unknown atom %0 from residue %1")
- .AddString(i->GetName()).AddResidue(i->GetResidue());
- break;
- case CONOP_WARN:
- diags->AddDiag(DIAG_UNK_ATOM, "residue %0 contains unknown atom %1")
- .AddResidue(i->GetResidue()).AddString(i->GetName());
- break;
- case CONOP_FATAL:
- // FIXME: Implement a ConopError based on Diag...
- break;
- case CONOP_REMOVE_RESIDUE:
- diags->AddDiag(DIAG_UNK_ATOM, "removed residue %0 with unknown atom %1")
- .AddString(i->GetResidue().GetQualifiedName())
- .AddString(i->GetName());
- edi.DeleteResidue(i->GetResidue());
- return;
- default:
- assert(0 && "unhandled switch");
- }
- }
-}
void RuleBasedProcessor::DoProcess(DiagnosticsPtr diags,
mol::EntityHandle ent) const
@@ -163,7 +100,7 @@ void RuleBasedProcessor::ConnectResidues(mol::ResidueHandle rh,
mol::AtomHandle n=next.FindAtom("N");
// Give subclasses a chance to give us their opinions on the feasibility of
// the peptide bond.
- if (c.IsValid() && n.IsValid() && this->IsBondFeasible(c, n)) {
+ if (c.IsValid() && n.IsValid() && IsBondFeasible(c, n)) {
e.Connect(c, n, 1);
rh.SetIsProtein(true);
next.SetIsProtein(true);
@@ -171,7 +108,7 @@ void RuleBasedProcessor::ConnectResidues(mol::ResidueHandle rh,
} else if (rh.IsNucleotideLinking() && next.IsNucleotideLinking()) {
mol::AtomHandle c=rh.FindAtom("O3'");
mol::AtomHandle n=next.FindAtom("P");
- if (c.IsValid() && n.IsValid() && this->IsBondFeasible(c, n)) {
+ if (c.IsValid() && n.IsValid() && IsBondFeasible(c, n)) {
e.Connect(c, n, 1);
}
}
@@ -231,7 +168,7 @@ void RuleBasedProcessor::ConnectAtomsOfResidue(mol::ResidueHandle rh,
}
e.Connect(a1, a2, bond.order);
} else {
- if (this->IsBondFeasible(a1, a2)) {
+ if (IsBondFeasible(a1, a2)) {
if (this->GetStrictHydrogens() && (a1.GetElement()=="H" ||
a2.GetElement()=="D")) {
continue;
@@ -243,25 +180,6 @@ void RuleBasedProcessor::ConnectAtomsOfResidue(mol::ResidueHandle rh,
}
}
-bool RuleBasedProcessor::IsBondFeasible(const mol::AtomHandle& atom_a,
- const mol::AtomHandle& atom_b) const
-{
- Real radii=0.0;
- if (atom_a.GetRadius()>0.0) {
- radii=atom_a.GetRadius();
- } else {
- return false;
- }
- if (atom_b.GetRadius()>0.0) {
- radii+=atom_b.GetRadius();
- } else {
- return false;
- }
- Real len=geom::Length2(atom_a.GetPos()-atom_b.GetPos());
- Real lower_bound=radii*radii*0.0625;
- Real upper_bound=lower_bound*6.0;
- return (len<=upper_bound && len>=lower_bound);
-}
void RuleBasedProcessor::ReorderAtoms(mol::ResidueHandle residue,
CompoundPtr compound) const
diff --git a/modules/conop/src/rule_based.hh b/modules/conop/src/rule_based.hh
index f014fe9d5fd6b9d4b9e02a050d3405bc688b9ec0..2b857398e3caa3d57ceda1397816b2c010b1148d 100644
--- a/modules/conop/src/rule_based.hh
+++ b/modules/conop/src/rule_based.hh
@@ -54,16 +54,11 @@ protected:
virtual void DoProcess(DiagnosticsPtr diags,
mol::EntityHandle ent) const;
private:
- void ProcessUnkResidue(DiagnosticsPtr diags,
- mol::ResidueHandle res) const;
- void ProcessUnkAtoms(DiagnosticsPtr diags,
- mol::AtomHandleList unks) const;
bool HasUnknownAtoms(mol::ResidueHandle residue, CompoundPtr compound) const;
void ReorderAtoms(mol::ResidueHandle residue, CompoundPtr compound) const;
void FillResidueProps(mol::ResidueHandle residue, CompoundPtr compound) const;
void ConnectAtomsOfResidue(mol::ResidueHandle residue, CompoundPtr compound) const;
void ConnectResidues(mol::ResidueHandle residue, mol::ResidueHandle next) const;
- bool IsBondFeasible(const mol::AtomHandle&, const mol::AtomHandle&) const;
mol::AtomHandle LocateAtom(const mol::AtomHandleList&, int ordinal) const;
CompoundLibPtr lib_;
bool fix_element_;