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Marco Biasini authoredMarco Biasini authored
query_state.cc 13.75 KiB
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2010 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
/*
Author: Marco Biasini
*/
#include <ost/mol/query_state.hh>
#include <ost/mol/mol.hh>
#include <ost/mol/impl/entity_impl.hh>
#include <ost/mol/impl/chain_impl.hh>
#include <ost/mol/impl/residue_impl.hh>
#include <ost/mol/impl/atom_impl.hh>
#include <ost/mol/impl/query_impl.hh>
namespace ost { namespace mol {
struct LazilyBoundRef {
LazilyBoundRef& operator=(const LazilyBoundRef& rhs);
//EntityView for now, will be generalized to a point cloud later on.
EntityView view;
};
struct LazilyBoundData {
std::vector<LazilyBoundRef> refs;
};
using namespace impl;
bool cmp_string(CompOP op,const String& lhs, const String& rhs) {
switch (op) {
case COP_EQ:
return lhs == rhs;
case COP_NEQ:
return lhs != rhs;
default:
assert(0 && "should be checked during ast generation");
return false;
}
}
bool QueryState::do_within(const geom::Vec3& pos, const impl::WithinParam& p,
CompOP op)
{
if (!p.HasValidRef()) {
geom::Vec3 d=pos-p.GetCenter();
if (op==COP_LE)
return geom::Dot(d, d) <= p.GetRadiusSquare();
else
return geom::Dot(d, d) > p.GetRadiusSquare();
} else {
const LazilyBoundRef& r=this->GetBoundObject(p.GetRef());
for (AtomViewIter i=r.view.AtomsBegin(), e=r.view.AtomsEnd(); i!=e; ++i) {
geom::Vec3 d=pos-(*i).GetPos(); if (op==COP_LE) {
if (geom::Dot(d, d) <= p.GetRadiusSquare()) {
return true;
}
} else if (geom::Dot(d, d) > p.GetRadiusSquare()) {
return false;
}
}
return op!=COP_LE;
}
}
template <typename T>
bool cmp_num(CompOP op, T lhs, T rhs)
{
switch (op) {
case COP_EQ:
return lhs == rhs;
case COP_NEQ:
return lhs != rhs;
case COP_GE:
return lhs >= rhs;
case COP_LE:
return lhs <= rhs;
case COP_LT:
return lhs < rhs;
case COP_GT:
return lhs > rhs;
}
return true;
}
QueryState::~QueryState()
{
}
QueryState::QueryState(const QueryImpl& query, const EntityHandle& ref)
: q_(query) {
s_.resize(query.sel_values_.size(),boost::logic::indeterminate);
if (query.bracketed_expr_.size()>0) {
r_.reset(new LazilyBoundData);
r_->refs.resize(query.bracketed_expr_.size());
for (size_t i=0;i<query.bracketed_expr_.size(); ++i) {
r_->refs[i].view=ref.Select(Query(query.bracketed_expr_[i]));
}
}
}
LazilyBoundRef& LazilyBoundRef::operator=(const LazilyBoundRef& rhs) {
view=rhs.view;
return *this;
}
QueryState::QueryState(const QueryImpl& query, const EntityView& ref)
: q_(query) {
s_.resize(query.sel_values_.size(),boost::logic::indeterminate);
if (query.bracketed_expr_.size()>0) {
r_.reset(new LazilyBoundData);
r_->refs.resize(query.bracketed_expr_.size());
for (size_t i=0;i<query.bracketed_expr_.size(); ++i) {
r_->refs[i].view=ref.Select(Query(query.bracketed_expr_[i]));
}
}
}
const LazilyBoundRef& QueryState::GetBoundObject(int i) const {
return r_->refs[i];
}
boost::logic::tribool QueryState::EvalChain(const impl::ChainImplPtr& c) {
if (q_.empty_optimize_)
return true;
const std::set<size_t>& indices = q_.indices_[(int)Prop::CHAIN];
std::set<size_t>::const_iterator i = indices.begin();
for (; i != indices.end(); ++i) {
const SelStmt& ss = q_.sel_values_[*i];
String value;
float float_value;
switch (ss.sel_id) {
case Prop::CNAME:
value = c->GetName();
s_[*i] = cmp_string(ss.comp_op,
boost::get<String>(ss.param),value);
continue;
default:
if (ss.sel_id>=Prop::CUSTOM) {
int index=ss.sel_id-Prop::CUSTOM;
GenProp gen_prop=q_.gen_prop_list_[index];
if (gen_prop.has_default) {
float_value=gen_prop.mapper.Get(c, gen_prop.default_val);
} else {
float_value=gen_prop.mapper.Get(c);
}
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
} else {
assert(0 && "not implemented" );
}
}
}
return this->EvalStack(Prop::CHAIN);
}
boost::logic::tribool QueryState::EvalResidue(const impl::ResidueImplPtr& r) {
if (q_.empty_optimize_)
return true;
const std::set<size_t>& indices = q_.indices_[(int)Prop::RESIDUE];
std::set<size_t>::const_iterator i = indices.begin();
String str_value;
int int_value;
String p;
for (; i != indices.end(); ++i) {
const SelStmt& ss = q_.sel_values_[*i];
Real float_value;
switch (ss.sel_id) {
case Prop::RNAME:
str_value = r->GetKey();
s_[*i] = cmp_string(ss.comp_op,str_value,
boost::get<String>(ss.param));
continue;
case Prop::RNUM:
int_value=r->GetNumber().GetNum();
s_[*i]=cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
break;
case Prop::PEPTIDE:
int_value=r->GetChemClass().IsPeptideLinking();
s_[*i] = cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
break;
case Prop::RBFAC:
// This is ugly! Outcome is the same for a prefiltered view as it is for
// as for the full entity, even though the residue view might not have
// all the atoms included.
float_value=r->GetAverageBFactor();
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::LIGAND:
int_value=r->IsLigand();
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) {
bool b=false;
if (p=="helix") {
b=r->GetSecStructure().IsHelical();
} else if (p=="ext" || p=="strand") {
b=r->GetSecStructure().IsExtended();
} else if (p=="coil") {
b=r->GetSecStructure().IsCoil();
} else if (p=="*") {
b=true;
}
s_[*i]=ss.comp_op==COP_EQ ? b : !b;
} else {
str_value= String(1, (char)r->GetSecStructure());
s_[*i]=cmp_string(ss.comp_op,str_value,
boost::get<String>(ss.param));
}
break;
case Prop::RINDEX:
int_value=r->GetIndex();
s_[*i]=cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
break;
default:
if (ss.sel_id>=Prop::CUSTOM) {
int index=ss.sel_id-Prop::CUSTOM;
GenProp gen_prop=q_.gen_prop_list_[index];
if (gen_prop.has_default) {
float_value=gen_prop.mapper.Get(r, gen_prop.default_val);
} else {
float_value=gen_prop.mapper.Get(r);
}
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
} else {
assert(0 && "not implemented" );
}
}
}
return this->EvalStack(Prop::RESIDUE);
}
boost::logic::tribool QueryState::EvalStack(Prop::Level level) {
const SelStack& stack = q_.sel_stacks_[(int)level];
SelStack::const_reverse_iterator i = stack.rbegin();
std::vector<boost::logic::tribool> value_stack;
while (i!=stack.rend()) {
const SelItem& si = *i;
if (si.type==VALUE) {
value_stack.push_back(s_[si.value]);
++i;
continue;
} else {
boost::logic::tribool lhs = value_stack.back();
value_stack.pop_back(); boost::logic::tribool rhs = value_stack.back();
value_stack.pop_back();
LogicOP lop = (LogicOP)si.value;
boost::logic::tribool result;
switch(lop) {
case LOP_AND:
result = lhs && rhs;
break;
case LOP_OR:
result = lhs || rhs;
break;
}
value_stack.push_back(result);
++i;
}
}
assert(value_stack.size()==1);
return value_stack.back();
}
namespace {
// silences a warning for VS90
QueryImpl dummy_query_impl;
}
QueryState::QueryState()
: s_(), q_(dummy_query_impl) {
}
boost::logic::tribool QueryState::EvalAtom(const impl::AtomImplPtr& a) {
if (q_.empty_optimize_)
return true;
const std::set<size_t>& indices = q_.indices_[(int)Prop::ATOM];
std::set<size_t>::const_iterator i = indices.begin();
for (; i != indices.end(); ++i) {
const SelStmt& ss = q_.sel_values_[*i];
String str_value;
Real float_value;
int int_value;
switch (ss.sel_id) {
case Prop::ANAME:
str_value = a->GetName();
s_[*i] = cmp_string(ss.comp_op,str_value,
boost::get<String>(ss.param));
break;
case Prop::AX:
float_value=(a->GetPos())[0];
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
case Prop::AY:
float_value=(a->GetPos())[1];
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
case Prop::AZ:
float_value=(a->GetPos())[2];
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
case Prop::OCC:
float_value=a->GetOccupancy();
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
case Prop::ELE:
str_value = a->GetElement();
s_[*i] = cmp_string(ss.comp_op,str_value,
boost::get<String>(ss.param));
break;
case Prop::ABFAC: float_value=a->GetBFactor();
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
case Prop::WITHIN:
s_[*i]= this->do_within(a->GetPos(),
boost::get<WithinParam>(ss.param),
ss.comp_op);
break;
case Prop::ISHETATM:
int_value = a->IsHetAtom();
s_[*i] = cmp_num<int>(ss.comp_op,int_value,boost::get<int>(ss.param));
break;
case Prop::ACHARGE:
float_value=a->GetCharge();
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
break;
default:
if (ss.sel_id>=Prop::CUSTOM) {
int index=ss.sel_id-Prop::CUSTOM;
GenProp gen_prop=q_.gen_prop_list_[index];
if (gen_prop.has_default) {
float_value=gen_prop.mapper.Get(a, gen_prop.default_val);
} else {
float_value=gen_prop.mapper.Get(a);
}
s_[*i]=cmp_num<Real>(ss.comp_op, float_value,
boost::get<float>(ss.param));
} else {
assert(0 && "not implemented" );
}
}
}
return this->EvalStack(Prop::ATOM);
}
void QueryState::Reset(Prop::Level level) {
if (q_.empty_optimize_)
return;
const std::set<size_t>& indices = q_.indices_[(int)level];
std::set<size_t>::const_iterator i = indices.begin();
for (; i != indices.end(); ++i) {
s_[*i] = boost::logic::indeterminate;
}
}
bool QueryState::IsAtomSelected(const AtomHandle& h)
{
boost::logic::tribool ret = this->EvalChain(h.GetResidue().GetChain().Impl());
if(ret==false) return false;
ret = this->EvalResidue(h.GetResidue().Impl());
if(ret==false) return false;
return this->EvalAtom(h.Impl());
}
bool QueryState::IsResidueSelected(const ResidueHandle& r)
{
boost::logic::tribool ret = this->EvalChain(r.GetChain().Impl());
if(ret==false) return false;
ret = this->EvalResidue(r.Impl());
if(ret==false) return false;
AtomHandleList atoms=r.GetAtomList();
for (AtomHandleList::iterator i=atoms.begin(), e=atoms.end(); i!=e; ++i) {
if (this->EvalAtom((*i).Impl())==true)
return true;
}
return false;
}
bool QueryState::IsChainSelected(const ChainHandle& chain)
{
boost::logic::tribool ret = this->EvalChain(chain.Impl());
if(ret==false) return false;
ResidueHandleList res=chain.GetResidueList();
for (ResidueHandleList::iterator j=res.begin(), k=res.end(); j!=k; ++j) {
ResidueHandle r=*j;
ret = this->EvalResidue(r.Impl());
if(ret==false)
continue;
AtomHandleList atoms=r.GetAtomList();
for (AtomHandleList::iterator i=atoms.begin(), e=atoms.end(); i!=e; ++i) {
if (this->EvalAtom((*i).Impl())==true)
return true;
}
}
return false;
}
}} // ns