From 9f0fc39fa963609d070535bf5887d5a86d2731f6 Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Tue, 21 Sep 2010 12:34:42 +0000
Subject: [PATCH] introduce protein/water property at the residue level
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2713 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/conop/src/chemdict_tool.cc | 16 +++++++++++-----
modules/conop/src/heuristic_builder.cc | 11 +++++++++--
modules/conop/src/rule_based_builder.cc | 2 ++
modules/mol/base/src/chem_class.hh | 3 +++
modules/mol/base/src/impl/residue_impl.hh | 7 ++++++-
modules/mol/base/src/property_id.cc | 8 +++++++-
modules/mol/base/src/property_id.hh | 3 ++-
modules/mol/base/src/query_state.cc | 10 +++++++++-
modules/mol/base/src/residue_base.cc | 12 ++++++++++++
modules/mol/base/src/residue_base.hh | 6 +++++-
modules/mol/base/src/residue_handle.hh | 2 +-
11 files changed, 67 insertions(+), 13 deletions(-)
diff --git a/modules/conop/src/chemdict_tool.cc b/modules/conop/src/chemdict_tool.cc
index 156b7f2d1..8671b4fa4 100644
--- a/modules/conop/src/chemdict_tool.cc
+++ b/modules/conop/src/chemdict_tool.cc
@@ -122,13 +122,19 @@ public:
for (String::iterator i=type.begin(), e=type.end(); i!=e; ++i) {
*i=toupper(*i);
}
- std::map<String, mol::ChemClass>::iterator i=tm_.find(type);
- if (i!=tm_.end()) {
- compound_->SetChemClass(i->second);
+ // The type of water is set to "?". let's change it to water...
+ if (compound_->GetID()=="HOH") {
+ compound_->SetChemClass(mol::ChemClass(mol::ChemClass::Water));
} else {
- std::cout << "unknown type '" << type << "' for compound "
- << compound_->GetID() << std::endl;
+ std::map<String, mol::ChemClass>::iterator i=tm_.find(type);
+ if (i!=tm_.end()) {
+ compound_->SetChemClass(i->second);
+ } else {
+ std::cout << "unknown type '" << type << "' for compound "
+ << compound_->GetID() << std::endl;
+ }
}
+
} else if (item.GetName()==StringRef("formula", 7)) {
compound_->SetFormula(item.GetValue().str());
} else if (item.GetName()==StringRef("one_letter_code", 15)) {
diff --git a/modules/conop/src/heuristic_builder.cc b/modules/conop/src/heuristic_builder.cc
index 5429a5697..bb4a63a22 100644
--- a/modules/conop/src/heuristic_builder.cc
+++ b/modules/conop/src/heuristic_builder.cc
@@ -309,11 +309,18 @@ void ConnectPrevNext(HeuristicBuilder* builder,mol::ResidueHandle res0,
if(res0_atom && res1_atom) {
LOG_DEBUG(fname << ": found atoms, connecting");
if(flag) {
- if (builder->DoesPeptideBondExist(res0_atom, res1_atom))
+ if (builder->DoesPeptideBondExist(res0_atom, res1_atom)) {
editor.Connect(res0_atom,res1_atom);
+ res0.SetIsProtein(true);
+ res1.SetIsProtein(true);
+ }
} else {
- if (builder->DoesPeptideBondExist(res1_atom, res0_atom))
+ if (builder->DoesPeptideBondExist(res1_atom, res0_atom)) {
editor.Connect(res1_atom, res0_atom);
+ res0.SetIsProtein(true);
+ res1.SetIsProtein(true);
+ }
+
}
}
} else {
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index 755d03dd5..3353dfb46 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -202,6 +202,8 @@ void RuleBasedBuilder::ConnectResidueToNext(mol::ResidueHandle rh,
// the peptide bond.
if (c.IsValid() && n.IsValid() && this->DoesPeptideBondExist(c, n)) {
e.Connect(c, n, 1);
+ rh.SetIsProtein(true);
+ next.SetIsProtein(true);
}
}
diff --git a/modules/mol/base/src/chem_class.hh b/modules/mol/base/src/chem_class.hh
index b7740a942..f9c0f8279 100644
--- a/modules/mol/base/src/chem_class.hh
+++ b/modules/mol/base/src/chem_class.hh
@@ -37,6 +37,7 @@ struct ChemClass {
const static char LSaccharide ='X';
const static char DSaccharide ='Y';
const static char Saccharide ='Z';
+ const static char Water ='W';
const static char Unknown ='U';
explicit ChemClass(char chem_class)
: chem_class_(chem_class) {
@@ -62,6 +63,8 @@ struct ChemClass {
return (chem_class_==ChemClass::DNALinking ||
chem_class_==ChemClass::RNALinking);
}
+
+ bool IsWater() const { return chem_class_==ChemClass::Water; }
operator char() const {
return chem_class_;
}
diff --git a/modules/mol/base/src/impl/residue_impl.hh b/modules/mol/base/src/impl/residue_impl.hh
index 0e0393767..183a9ccef 100644
--- a/modules/mol/base/src/impl/residue_impl.hh
+++ b/modules/mol/base/src/impl/residue_impl.hh
@@ -199,6 +199,9 @@ public:
int GetIntProperty(Prop::ID prop_id) const;
+ void SetProtein(bool protein) { protein_=protein; }
+
+ bool IsProtein() const { return protein_; }
private:
void AddAltAtom(const String& group, const AtomImplPtr& atom,
const geom::Vec3& position);
@@ -207,13 +210,15 @@ private:
AtomEntryGroups alt_groups_;
EntityImplW ent_;
ChainImplW chain_;
- ResNum num_;
+ ResNum num_;
ResidueKey key_;
AtomImplList atom_list_;
TorsionImplList torsion_list_;
SecStructure sec_structure_;
ChemClass chem_class_;
char olc_;
+ // whether the residue is part of the protein.
+ bool protein_;
};
}}} // ns
diff --git a/modules/mol/base/src/property_id.cc b/modules/mol/base/src/property_id.cc
index ed19a4f3e..a6408b83e 100644
--- a/modules/mol/base/src/property_id.cc
+++ b/modules/mol/base/src/property_id.cc
@@ -49,7 +49,9 @@ struct Properties : public boost::spirit::symbols<Prop> {
("abfac", Prop(Prop::ABFAC, Prop::FLOAT, Prop::ATOM))
("rbfac", Prop(Prop::RBFAC, Prop::FLOAT, Prop::RESIDUE))
("peptide", Prop(Prop::PEPTIDE, Prop::INT, Prop::RESIDUE))
- ("rindex", Prop(Prop::RINDEX, Prop::INT, Prop::RESIDUE))
+ ("rindex", Prop(Prop::RINDEX, Prop::INT, Prop::RESIDUE))
+ ("protein", Prop(Prop::PROTEIN, Prop::INT, Prop::RESIDUE))
+ ("water", Prop(Prop::WATER, Prop::INT, Prop::RESIDUE))
("acharge", Prop(Prop::ACHARGE, Prop::FLOAT, Prop::ATOM));
}
} properties;
@@ -112,6 +114,10 @@ String Prop::GetName() const
return "acharge";
case RINDEX:
return "rindex";
+ case PROTEIN:
+ return "protein";
+ case WATER:
+ return "water";
default:
return "";
}
diff --git a/modules/mol/base/src/property_id.hh b/modules/mol/base/src/property_id.hh
index dfc984bc2..4ea4be13f 100644
--- a/modules/mol/base/src/property_id.hh
+++ b/modules/mol/base/src/property_id.hh
@@ -40,7 +40,8 @@ public:
/// respectively.
typedef enum {
RNAME, ANAME, CNAME, ELE, RNUM, ANUM, AX, AY, AZ, OCC, RTYPE, ISHETATM,
- RBFAC, ABFAC, PEPTIDE, ACHARGE, RINDEX, WITHIN, UNDEF, CUSTOM
+ RBFAC, ABFAC, PEPTIDE, ACHARGE, RINDEX, PROTEIN, WATER, WITHIN,
+ UNDEF, CUSTOM
} ID;
typedef enum {
diff --git a/modules/mol/base/src/query_state.cc b/modules/mol/base/src/query_state.cc
index c84670d78..95dc07e16 100644
--- a/modules/mol/base/src/query_state.cc
+++ b/modules/mol/base/src/query_state.cc
@@ -198,7 +198,7 @@ boost::logic::tribool QueryState::EvalResidue(const impl::ResidueImplPtr& r) {
s_[*i]=cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
break;
case Prop::PEPTIDE:
- int_value=r->GetChemClass().IsPeptideLinking() ? 1 : 0;
+ int_value=r->GetChemClass().IsPeptideLinking();
s_[*i] = cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
break;
case Prop::RBFAC:
@@ -209,6 +209,14 @@ boost::logic::tribool QueryState::EvalResidue(const impl::ResidueImplPtr& r) {
s_[*i] = cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
+ case Prop::PROTEIN:
+ int_value=r->IsProtein();
+ s_[*i]=cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
+ break;
+ case Prop::WATER:
+ int_value=r->GetChemClass().IsWater();
+ s_[*i]=cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
+ break;
case Prop::RTYPE:
p=boost::get<String>(ss.param);
if (p.length()>1) {
diff --git a/modules/mol/base/src/residue_base.cc b/modules/mol/base/src/residue_base.cc
index f4ce54ee5..9ae05d783 100644
--- a/modules/mol/base/src/residue_base.cc
+++ b/modules/mol/base/src/residue_base.cc
@@ -181,5 +181,17 @@ int ResidueBase::GetIntProperty(Prop::ID prop_id) const
return Impl()->GetIntProperty(prop_id);
}
+bool ResidueBase::IsProtein() const
+{
+ this->CheckValidity();
+ return Impl()->IsProtein();
+}
+
+void ResidueBase::SetIsProtein(bool protein)
+{
+ this->CheckValidity();
+ Impl()->SetProtein(protein);
+}
+
}}
diff --git a/modules/mol/base/src/residue_base.hh b/modules/mol/base/src/residue_base.hh
index 69749ed49..1ad743879 100644
--- a/modules/mol/base/src/residue_base.hh
+++ b/modules/mol/base/src/residue_base.hh
@@ -139,7 +139,11 @@ public:
/// \brief Get int property by id
int GetIntProperty(Prop::ID prop_id) const;
-
+
+ /// \brief whether the residue is part of the protein.
+ bool IsProtein() const;
+
+ void SetIsProtein(bool protein);
public:
impl::ResidueImplPtr& Impl();
diff --git a/modules/mol/base/src/residue_handle.hh b/modules/mol/base/src/residue_handle.hh
index 57b7c5619..f1eb07850 100644
--- a/modules/mol/base/src/residue_handle.hh
+++ b/modules/mol/base/src/residue_handle.hh
@@ -197,7 +197,7 @@ public:
/// \brief return view based on query String.
/// \sa Query
EntityView Select(const String& query_string, QueryFlags flags=0) const;
-
+
bool operator==(const ResidueHandle& ref) const;
bool operator!=(const ResidueHandle& ref) const;
--
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