diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst
index 73d45b8adb81a4d786b981bf9c0e8ab2b230e3cb..4d272dd561c285de3e69f1ff296da8660d2bd7af 100644
--- a/modules/mol/base/doc/editors.rst
+++ b/modules/mol/base/doc/editors.rst
@@ -235,13 +235,13 @@ The basic functionality of editors is implemented in the EditorBase class.
:type atom: :class:`EntityHandle`
- .. method:: DeleteAtoms(residue)
+ .. method:: DeleteAtoms(atoms)
Deletes a set specified atoms. All associated torsions and bonds will be
removed as well
- :type residue: :class:`AtomHandleList`
- :param residue: A valid set of atoms
+ :type atoms: :class:`AtomHandleList`
+ :param atoms: A valid set of atoms
.. method:: DeleteResidue(residue)
diff --git a/modules/mol/mm/pymod/export_block_modifiers.cc b/modules/mol/mm/pymod/export_block_modifiers.cc
index a6570e3aa5e342ae3724c54f827ec6b822e0d0c6..08287f08f7b7ae33080e6e9d9948ec4b060b90e3 100644
--- a/modules/mol/mm/pymod/export_block_modifiers.cc
+++ b/modules/mol/mm/pymod/export_block_modifiers.cc
@@ -26,6 +26,18 @@ using namespace boost::python;
namespace{
+template <typename Iterator>
+void AppendToList(Iterator first, Iterator last, boost::python::list& l) {
+ for (Iterator i = first; i != last; ++i) {
+ l.append(*i);
+ }
+}
+
+template <typename Vec>
+void AppendVectorToList(const Vec& v, boost::python::list& l) {
+ AppendToList(v.begin(), v.end(), l);
+}
+
template<typename T>
std::vector<T> ListToVec(const boost::python::list& l){
std::vector<T> vec;
@@ -47,7 +59,8 @@ void WrapAddAddRule(ost::mol::mm::GromacsBlockModifierPtr p,
}
-void WrapAddHydrogenRule(ost::mol::mm::GromacsHydrogenConstructorPtr p, int number, int method,
+void WrapAddHydrogenRule(ost::mol::mm::GromacsHydrogenConstructorPtr p,
+ int number, int method,
const boost::python::list& hydrogen_names,
const boost::python::list& anchors){
std::vector<String> v_hydrogen_names = ListToVec<String>(hydrogen_names);
@@ -55,6 +68,91 @@ void WrapAddHydrogenRule(ost::mol::mm::GromacsHydrogenConstructorPtr p, int numb
p->AddHydrogenRule(number,method,v_hydrogen_names,v_anchors);
}
+boost::python::list
+WrapGetHydrogenRules(ost::mol::mm::GromacsHydrogenConstructorPtr p) {
+ // for data extraction: get all rules as list of tuples
+ // -> data: (number, method, names, anchors)
+ boost::python::list result;
+ for (uint i = 0; i < p->GetNumHydrogenRules(); ++i) {
+ int number = p->GetHydrogenRuleNumber(i);
+ int method = p->GetHydrogenRuleMethod(i);
+ boost::python::list names;
+ AppendVectorToList(p->GetHydrogenRuleNames(i), names);
+ boost::python::list anchors;
+ AppendVectorToList(p->GetHydrogenRuleAnchors(i), anchors);
+ result.append(boost::python::make_tuple(number, method, names, anchors));
+ }
+ return result;
+}
+
+boost::python::list WrapGetBonds(ost::mol::mm::GromacsBlockModifierPtr p) {
+ boost::python::list result;
+ AppendVectorToList(p->GetBonds(), result);
+ return result;
+}
+
+boost::python::list WrapGetAngles(ost::mol::mm::GromacsBlockModifierPtr p) {
+ boost::python::list result;
+ AppendVectorToList(p->GetAngles(), result);
+ return result;
+}
+
+boost::python::list WrapGetDihedrals(ost::mol::mm::GromacsBlockModifierPtr p) {
+ boost::python::list result;
+ AppendVectorToList(p->GetDihedrals(), result);
+ return result;
+}
+
+boost::python::list WrapGetImpropers(ost::mol::mm::GromacsBlockModifierPtr p) {
+ boost::python::list result;
+ AppendVectorToList(p->GetImpropers(), result);
+ return result;
+}
+
+boost::python::list WrapGetCmaps(ost::mol::mm::GromacsBlockModifierPtr p) {
+ boost::python::list result;
+ AppendVectorToList(p->GetCmaps(), result);
+ return result;
+}
+
+boost::python::list WrapGetDeleteAtoms(ost::mol::mm::GromacsBlockModifierPtr p) {
+ boost::python::list result;
+ AppendVectorToList(p->GetDeleteAtoms(), result);
+ return result;
+}
+
+boost::python::list
+WrapGetReplaceRules(ost::mol::mm::GromacsBlockModifierPtr p) {
+ // for data extraction: get all rules as list of tuples
+ // -> data: (name, new_name, new_type, new_charge)
+ boost::python::list result;
+ for (uint i = 0; i < p->GetNumReplaceRules(); ++i) {
+ result.append(boost::python::make_tuple(p->GetReplaceRuleName(i),
+ p->GetReplaceRuleNewName(i),
+ p->GetReplaceRuleNewType(i),
+ p->GetReplaceRuleNewCharge(i)));
+ }
+ return result;
+}
+
+boost::python::list
+WrapGetAddRules(ost::mol::mm::GromacsBlockModifierPtr p) {
+ // for data extraction: get all rules as list of tuples
+ // -> data: (number, method, names, anchors, type, charge)
+ boost::python::list result;
+ for (uint i = 0; i < p->GetNumAddRules(); ++i) {
+ boost::python::list names;
+ AppendVectorToList(p->GetAddRuleNames(i), names);
+ boost::python::list anchors;
+ AppendVectorToList(p->GetAddRuleAnchors(i), anchors);
+ result.append(boost::python::make_tuple(p->GetAddRuleNumber(i),
+ p->GetAddRuleMethod(i),
+ names, anchors,
+ p->GetAddRuleType(i),
+ p->GetAddRuleCharge(i)));
+ }
+ return result;
+}
}
@@ -72,6 +170,7 @@ void export_BlockModifiers()
.def("ApplyOnBuildingBlock",&ost::mol::mm::GromacsHydrogenConstructor::ApplyOnBuildingBlock,(arg("block")))
.def("ApplyOnResidue",&ost::mol::mm::GromacsHydrogenConstructor::ApplyOnResidue,(arg("residue"),arg("editor")))
.def("AddHydrogenRule",&WrapAddHydrogenRule,(arg("number"),arg("method"),arg("hydrogen_names"),arg("anchors")))
+ .def("GetHydrogenRules",&WrapGetHydrogenRules)
;
class_<ost::mol::mm::GromacsBlockModifier, bases<ost::mol::mm::BlockModifier> >("GromacsBlockModifier", init<>())
@@ -85,6 +184,14 @@ void export_BlockModifiers()
.def("AddImproper",&ost::mol::mm::GromacsBlockModifier::AddImproper,(arg("improper")))
.def("AddCMap",&ost::mol::mm::GromacsBlockModifier::AddCMap,(arg("cmap")))
.def("AddDeleteAtom",&ost::mol::mm::GromacsBlockModifier::AddDeleteAtom,(arg("name")))
+ .def("GetBonds", &WrapGetBonds)
+ .def("GetAngles", &WrapGetAngles)
+ .def("GetDihedrals", &WrapGetDihedrals)
+ .def("GetImpropers", &WrapGetImpropers)
+ .def("GetCmaps", &WrapGetCmaps)
+ .def("GetDeleteAtoms", &WrapGetDeleteAtoms)
+ .def("GetReplaceRules", &WrapGetReplaceRules)
+ .def("GetAddRules", &WrapGetAddRules)
;
class_<ost::mol::mm::HeuristicHydrogenConstructor, bases<ost::mol::mm::HydrogenConstructor> >("HeuristicHydrogenConstructor", init<ost::mol::mm::BuildingBlockPtr>())
diff --git a/modules/mol/mm/pymod/export_forcefield.cc b/modules/mol/mm/pymod/export_forcefield.cc
index 096b6eef433b075dd3e47ab0d08791103f44a879..4a36a728e1e0f2dcf567f69953b82f2574443e70 100644
--- a/modules/mol/mm/pymod/export_forcefield.cc
+++ b/modules/mol/mm/pymod/export_forcefield.cc
@@ -23,16 +23,29 @@
using namespace boost::python;
-namespace{
+namespace {
+ost::mol::mm::InteractionPtr GetLJOneType(ost::mol::mm::ForcefieldPtr p,
+ String type) {
+ return p->GetLJ(type);
+}
- ost::mol::mm::InteractionPtr GetLJOneType(ost::mol::mm::ForcefieldPtr p, String type){
- return p->GetLJ(type);
- }
+ost::mol::mm::InteractionPtr GetLJTwoTypes(ost::mol::mm::ForcefieldPtr p,
+ String type1, String type2,
+ bool pair) {
+ return p->GetLJ(type1, type2, pair);
+}
- ost::mol::mm::InteractionPtr GetLJTwoTypes(ost::mol::mm::ForcefieldPtr p, String type1, String type2, bool pair){
- return p->GetLJ(type1,type2,pair);
+boost::python::list WrapGetAtomRenamingRules(ost::mol::mm::ForcefieldPtr p,
+ const String& res_name) {
+ boost::python::list result;
+ typedef ost::mol::mm::Forcefield::AtomRenamingType AtomRenamingType;
+ const AtomRenamingType& rules = p->GetAtomRenamingRules(res_name);
+ for (uint i = 0; i < rules.size(); ++i) {
+ result.append(boost::python::make_tuple(rules[i].first, rules[i].second));
}
+ return result;
+}
}
@@ -86,6 +99,9 @@ void export_Forcefield()
.def("GetResidueRenamingTwoTer",&ost::mol::mm::Forcefield::GetResidueRenamingTwoTer,(arg("res_name")))
.def("GetAtomRenaming",&ost::mol::mm::Forcefield::GetAtomRenaming,(arg("res_name"),arg("atom_name")))
.def("AssignFFSpecificNames",&ost::mol::mm::Forcefield::AssignFFSpecificNames,(arg("ent"),arg("reverse")=false))
+ .def("HasAtomRenamingRules", &ost::mol::mm::Forcefield::HasAtomRenamingRules,
+ (arg("res_name")))
+ .def("GetAtomRenamingRules", &WrapGetAtomRenamingRules, (arg("res_name")))
;
boost::python::register_ptr_to_python<ost::mol::mm::ForcefieldPtr>();
diff --git a/modules/mol/mm/src/forcefield.cc b/modules/mol/mm/src/forcefield.cc
index 5e1b1ac7102f9fbb32841016a6a4d179078a146a..af349dbbb5df877657d7c1c72214cc460748fe6c 100644
--- a/modules/mol/mm/src/forcefield.cc
+++ b/modules/mol/mm/src/forcefield.cc
@@ -836,8 +836,10 @@ String Forcefield::GetResidueRenamingTwoTer(const String& name) const{
return i->second->twoter;
}
-String Forcefield::GetAtomRenaming(const String& res_name, const String& atom_name) const{
- boost::unordered_map<String,std::vector<std::pair<String,String> > >::const_iterator i = atom_renaming_ff_specific_.find(res_name);
+String Forcefield::GetAtomRenaming(const String& res_name,
+ const String& atom_name) const {
+ boost::unordered_map<String,AtomRenamingType>::const_iterator i;
+ i = atom_renaming_ff_specific_.find(res_name);
if(i == atom_renaming_ff_specific_.end()) return atom_name;
for(std::vector<std::pair<String,String> >::const_iterator j = i->second.begin(), e = i->second.end();
j != e; ++j){
@@ -846,6 +848,16 @@ String Forcefield::GetAtomRenaming(const String& res_name, const String& atom_na
return atom_name;
}
+const Forcefield::AtomRenamingType&
+Forcefield::GetAtomRenamingRules(const String& res_name) const {
+ boost::unordered_map<String,AtomRenamingType>::const_iterator i;
+ i = atom_renaming_ff_specific_.find(res_name);
+ if (i == atom_renaming_ff_specific_.end()) {
+ throw ost::Error(String("No atom renaming rules for ") + res_name);
+ }
+ return i->second;
+}
+
void Forcefield::AssignFFSpecificNames(ost::mol::EntityHandle& handle, bool reverse) const{
//the whole FF specific renaming procedure assumes a standard naming,
diff --git a/modules/mol/mm/src/forcefield.hh b/modules/mol/mm/src/forcefield.hh
index 3c65e37fea4673f5f7f4dba2dae582e3871ad269..2c19506204284d13e9d1ddca1718e1148dec02f1 100644
--- a/modules/mol/mm/src/forcefield.hh
+++ b/modules/mol/mm/src/forcefield.hh
@@ -195,6 +195,14 @@ public:
//Renaming to the forcefield specific names (residues/atoms)
void AssignFFSpecificNames(ost::mol::EntityHandle& handle, bool reverse=false) const;
+ // get renaming rules (for data extraction)
+ bool HasAtomRenamingRules(const String& res_name) const {
+ return (atom_renaming_ff_specific_.find(res_name)
+ != atom_renaming_ff_specific_.end());
+ }
+ typedef std::vector<std::pair<String,String> > AtomRenamingType;
+ const AtomRenamingType& GetAtomRenamingRules(const String& res_name) const;
+
private:
String AtomTypesToKeyword(std::vector<String>& types, bool allow_reordering = true) const;
@@ -220,7 +228,7 @@ private:
boost::unordered_map<String,std::vector<InteractionPtr> > dihedrals_;
boost::unordered_map<String,std::vector<InteractionPtr> > improper_dihedrals_;
- boost::unordered_map<String, std::vector<std::pair<String,String> > > atom_renaming_ff_specific_;
+ boost::unordered_map<String, AtomRenamingType> atom_renaming_ff_specific_;
boost::unordered_map<String, ResidueNamesPtr> res_renaming_ff_specific_;
boost::unordered_map<String, HydrogenConstructorPtr> hydrogen_constructors_;
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.cc b/modules/mol/mm/src/gromacs_block_modifiers.cc
index b74b567ea03ff4c8f6737fb42e5ae79400927e32..b7c6d38eabe9dd41e435bbd8cfd174473da5ee91 100644
--- a/modules/mol/mm/src/gromacs_block_modifiers.cc
+++ b/modules/mol/mm/src/gromacs_block_modifiers.cc
@@ -21,9 +21,9 @@
namespace ost{ namespace mol{ namespace mm{
-std::vector<geom::Vec3> GromacsPositionRuleEvaluator::EvaluatePosRule(int rule,
- int number,
- const std::vector<geom::Vec3>& anchors){
+std::vector<geom::Vec3> GromacsPositionRuleEvaluator::EvaluatePosRule(
+ int rule, int number,
+ const std::vector<geom::Vec3>& anchors) {
std::vector<geom::Vec3> positions;
@@ -194,11 +194,12 @@ std::vector<geom::Vec3> GromacsPositionRuleEvaluator::EvaluatePosRule(int rule,
}
-void GromacsHydrogenConstructor::ApplyOnBuildingBlock(BuildingBlockPtr p){
+void GromacsHydrogenConstructor::ApplyOnBuildingBlock(BuildingBlockPtr p) {
//we assume, that the hydrogens are already correct in the building block...
}
-void GromacsHydrogenConstructor::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed){
+void GromacsHydrogenConstructor::ApplyOnResidue(ost::mol::ResidueHandle& res,
+ ost::mol::XCSEditor& ed) {
if(!res.IsValid()) return;
@@ -230,7 +231,8 @@ void GromacsHydrogenConstructor::ApplyOnResidue(ost::mol::ResidueHandle& res, os
ost::mol::AtomHandle atom;
bool found_anchors = true;
- for(std::vector<String>::iterator it = anchor_names.begin();it!=anchor_names.end();++it){
+ for (std::vector<String>::iterator it = anchor_names.begin();
+ it!=anchor_names.end(); ++it) {
temp_res = res;
atom_name = *it;
@@ -272,23 +274,28 @@ void GromacsHydrogenConstructor::ApplyOnResidue(ost::mol::ResidueHandle& res, os
continue;
}
- hydrogen_positions = GromacsPositionRuleEvaluator::EvaluatePosRule(method,
- number,
- anchor_positions);
+ hydrogen_positions
+ = GromacsPositionRuleEvaluator::EvaluatePosRule(method, number,
+ anchor_positions);
for(int b=0;b<number;++b){
//only add hydrogen if not already present!
atom = res.FindAtom(hydrogen_names[b]);
- if(!atom.IsValid()) atom = ed.InsertAtom(res,hydrogen_names[b],hydrogen_positions[b],"H");
- else ed.SetAtomPos(atom,hydrogen_positions[b]);
+ if (!atom.IsValid()) {
+ atom = ed.InsertAtom(res, hydrogen_names[b], hydrogen_positions[b], "H");
+ }
+ else {
+ ed.SetAtomPos(atom, hydrogen_positions[b]);
+ }
}
}
}
-void GromacsHydrogenConstructor::AddHydrogenRule(uint number, int method,
- const std::vector<String>& hydrogen_names,
- const std::vector<String>& anchors){
+void GromacsHydrogenConstructor::AddHydrogenRule(
+ uint number, int method,
+ const std::vector<String>& hydrogen_names,
+ const std::vector<String>& anchors) {
if(number != hydrogen_names.size()){
std::stringstream ss;
@@ -390,7 +397,8 @@ void GromacsBlockModifier::ApplyOnBuildingBlock(BuildingBlockPtr p){
}
}
-void GromacsBlockModifier::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol::XCSEditor& ed){
+void GromacsBlockModifier::ApplyOnResidue(ost::mol::ResidueHandle& res,
+ ost::mol::XCSEditor& ed) {
//let's resolve the replace statement
for(uint i = 0; i < replace_old_atom_name_.size(); ++i){
@@ -423,9 +431,9 @@ void GromacsBlockModifier::ApplyOnResidue(ost::mol::ResidueHandle& res, ost::mol
anchor_positions.push_back(at.GetPos());
anchor_atoms.push_back(at);
}
- std::vector<geom::Vec3> positions = GromacsPositionRuleEvaluator::EvaluatePosRule(method,
- number,
- anchor_positions);
+ std::vector<geom::Vec3> positions
+ = GromacsPositionRuleEvaluator::EvaluatePosRule(method, number,
+ anchor_positions);
String ele = "H";
if(method == 8 || method == 9){
diff --git a/modules/mol/mm/src/gromacs_block_modifiers.hh b/modules/mol/mm/src/gromacs_block_modifiers.hh
index af8fbbdc2ade9a8d9fcaf65d286fe68e3589c068..8ee115a3bfbc929cac62fbfc7a00942efbac0ec6 100644
--- a/modules/mol/mm/src/gromacs_block_modifiers.hh
+++ b/modules/mol/mm/src/gromacs_block_modifiers.hh
@@ -65,6 +65,16 @@ public:
const std::vector<String>& hydrogen_names,
const std::vector<String>& anchors);
+ // GET STUFF (for data extraction)
+ uint GetNumHydrogenRules() const { return add_number_.size(); }
+ // all getters for idx < GetNumHydrogenRules()
+ int GetHydrogenRuleNumber(uint idx) const { return add_number_[idx]; }
+ int GetHydrogenRuleMethod(uint idx) const { return methods_[idx]; }
+ const std::vector<String>&
+ GetHydrogenRuleNames(uint idx) const { return hydrogen_names_[idx]; }
+ const std::vector<String>&
+ GetHydrogenRuleAnchors(uint idx) const { return anchor_atom_names_[idx]; }
+
virtual void OnSave(ost::io::BinaryDataSink& ds) { ds << *this; }
virtual BlockModifierType GetBlockModifierType() { return GromacsBlockModifiers; }
@@ -145,6 +155,38 @@ public:
void AddDeleteAtom(const String& atom_name) { delete_atom_names_.push_back(atom_name); }
+ // GET STUFF (for data extraction)
+ const std::vector<InteractionPtr>& GetBonds() const { return bonds_; }
+ const std::vector<InteractionPtr>& GetAngles() const { return angles_; }
+ const std::vector<InteractionPtr>& GetDihedrals() const { return dihedrals_; }
+ const std::vector<InteractionPtr>& GetImpropers() const { return impropers_; }
+ const std::vector<InteractionPtr>& GetCmaps() const { return cmaps_; }
+ const std::vector<String>& GetDeleteAtoms() const { return delete_atom_names_; }
+ // all idx for replace rules < GetNumReplaceRules()
+ uint GetNumReplaceRules() const { return replace_old_atom_name_.size(); }
+ const String& GetReplaceRuleName(uint idx) const {
+ return replace_old_atom_name_[idx];
+ }
+ const String& GetReplaceRuleNewName(uint idx) const {
+ return replace_new_atom_name_[idx];
+ }
+ const String& GetReplaceRuleNewType(uint idx) const {
+ return replace_new_atom_type_[idx];
+ }
+ Real GetReplaceRuleNewCharge(uint idx) const {
+ return replace_new_charge_[idx];
+ }
+ // all idx for add rules < GetNumAddRules()
+ uint GetNumAddRules() const { return add_add_number_.size(); }
+ int GetAddRuleNumber(uint idx) const { return add_add_number_[idx]; }
+ int GetAddRuleMethod(uint idx) const { return add_methods_[idx]; }
+ const std::vector<String>&
+ GetAddRuleNames(uint idx) const { return add_atom_names_[idx]; }
+ const std::vector<String>&
+ GetAddRuleAnchors(uint idx) const { return add_anchor_atom_names_[idx]; }
+ const String& GetAddRuleType(uint idx) const { return add_atom_types_[idx]; }
+ Real GetAddRuleCharge(uint idx) const { return add_charges_[idx]; }
+
virtual void OnSave(ost::io::BinaryDataSink& ds) { ds << *this; }
virtual BlockModifierType GetBlockModifierType() { return GromacsBlockModifiers; }