diff --git a/modules/conop/src/heuristic_connect.cc b/modules/conop/src/heuristic_connect.cc
deleted file mode 100644
index c6de76d80d2a1801f11c8e1ad18904d170c55753..0000000000000000000000000000000000000000
--- a/modules/conop/src/heuristic_connect.cc
+++ /dev/null
@@ -1,417 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 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
-//------------------------------------------------------------------------------
-#include <map>
-#include <set>
-
-#include <ost/entity.hh>
-#include <ost/log.hh>
-
-#include "heuristic_connect.hh"
-#include "heuristic_connect_table.hh"
-
-namespace ost { namespace conop {
-
-namespace {
-
-class ConnResEntry {
-public:
- typedef std::pair<String,String> NamePair;
- typedef std::multiset<NamePair> PairSet;
- struct TorsionEntry {
- String a[4];
- String name;
- };
- typedef std::vector<TorsionEntry> TorsionEntryList;
-
-public:
- ConnResEntry(const String& rname=""):
- rkey_(rname),
- pset_(),
- prev_(""),
- next_(""),
- torsion_entry_list_()
- {}
-
- /*
- checks for connection between two atoms. if returned flag is zero,
- then the two bools that were passed in indicate wether the names
- actually exist in this entry or not. The return value is one for
- the correct order and 2 of the order is reversed
- */
- int Check(const String& name1, const String& name2, bool& ex1, bool& ex2) const
- {
- NamePair np1(name1,name2);
- NamePair np2(name2,name1);
- // does this pair exist?
- if(pset_.find(np1)!=pset_.end()) {
- ex1=true;
- ex2=true;
- return 1;
- } else if(pset_.find(np2)!=pset_.end()) {
- ex1=true;
- ex2=true;
- return 2;
- }
-
- // check for occurence of either names in the name pairs
- ex1=false;
- ex2=false;
- for(PairSet::const_iterator it=pset_.begin();it!=pset_.end();++it) {
- if(it->first==name1 || it->second==name1) ex1=true;
- if(it->first==name2 || it->second==name2) ex2=true;
- if(ex1 && ex2) break;
- }
-
- return false;
- }
-
- // add a connection entry
- void AddConn(const String& n1, const String& n2)
- {
- pset_.insert(std::make_pair(n1,n2));
- }
-
- void AddTors(const String& a1, const String& a2, const String& a3, const String& a4, const String& name)
- {
- TorsionEntry te={{a1,a2,a3,a4},name};
- torsion_entry_list_.push_back(te);
- }
-
- // atom that connects to previous residue in chain
- void SetPrev(const String& n)
- {
- prev_=n;
- }
-
- const String& GetPrev() const
- {
- return prev_;
- }
-
- // atom that connects to next residue in chain
- void SetNext(const String& n)
- {
- next_=n;
- }
-
- const String& GetNext() const
- {
- return next_;
- }
-
- TorsionEntryList GetTorsionList() const {return torsion_entry_list_;}
-
-private:
- ResidueKey rkey_;
- PairSet pset_;
- String prev_;
- String next_;
- TorsionEntryList torsion_entry_list_;
-};
-
-typedef std::map<ResidueKey,ConnResEntry> ConnResEntryMap;
-void fill_map(ConnResEntryMap& em)
-{
- int def_entry_count = sizeof(heuristic_connect::def_entry_table)/sizeof(heuristic_connect::CONN_DEF_ENTRY);
-
- for(int ec=0;ec<def_entry_count;++ec) {
- heuristic_connect::CONN_DEF_ENTRY& def_entry = heuristic_connect::def_entry_table[ec];
- ConnResEntry entry(def_entry.abbrev);
- LOG_DEBUG("creating default entry for " << def_entry.abbrev << std::endl);
- // first the connectivity entries
- for(int cc=0;cc<def_entry.conn_count;++cc) {
- int conn_id[] = {def_entry.conn_list[cc][0],def_entry.conn_list[cc][1]};
- String conn_nam[] = {"",""};
- bool special=false;
- for(int cid=0;cid<2;++cid) {
- if(conn_id[cid]>0) {
- conn_nam[cid]=def_entry.name_list[conn_id[cid]-1];
- } else if (conn_id[cid]==-2) {
- // PREV key
- conn_nam[cid]="-";
- special=true;
- } else if (conn_id[cid]==-3) {
- // NEXT key
- conn_nam[cid]="+";
- special=true;
- } else {
- // ignore
- continue;
- }
- }
- if(special) {
- if(conn_nam[0]==String("-")) { entry.SetPrev(conn_nam[1]);}
- else if(conn_nam[1]==String("-")) { entry.SetPrev(conn_nam[0]);}
- else if(conn_nam[0]==String("+")) { entry.SetNext(conn_nam[1]);}
- else if(conn_nam[1]==String("+")) { entry.SetNext(conn_nam[0]);}
- LOG_DEBUG(" " << conn_nam[0] << " " << conn_nam[1] << std::endl);
- } else {
- LOG_DEBUG(" " << conn_nam[0] << " " << conn_nam[1] << std::endl);
- entry.AddConn(conn_nam[0],conn_nam[1]);
- }
- }
- // then the torsion entries
- for(int cc=0;cc<def_entry.tor_count;++cc) {
- int tor_id[] = {def_entry.tor_list[cc].n1,
- def_entry.tor_list[cc].n2,
- def_entry.tor_list[cc].n3,
- def_entry.tor_list[cc].n4};
- String tor_nam[] = {"","","",""};
- String tor_nam2(def_entry.tor_list[cc].name);
- for(int cid=0;cid<4;++cid) {
- if(tor_id[cid]>0) {
- tor_nam[cid]=def_entry.name_list[tor_id[cid]-1];
- } else if (tor_id[cid]==-2) {
- tor_nam[cid]="-";
- } else if (tor_id[cid]==-3) {
- tor_nam[cid]="+";
- }
- }
- entry.AddTors(tor_nam[0],tor_nam[1],tor_nam[2],tor_nam[3],tor_nam2);
- }
-
- em[def_entry.abbrev]=entry;
-
- }
-}
-
-std::pair<ConnResEntry,bool> LookupResEntry(const ResidueKey& key)
-{
- static ConnResEntry dummy;
- static ConnResEntryMap emap;
- static bool initialized=false;
-
- if(!initialized) {
- LOG_DEBUG("initializing Connectivity Map" << std::endl);
- fill_map(emap);
- initialized=true;
- }
-
- LOG_DEBUG("Looking for reskey '" << key << "' in connectivity map... ");
-
- ConnResEntryMap::iterator pos = emap.find(key);
- if(pos!=emap.end()) {
- LOG_DEBUG("found" << std::endl);
- return std::make_pair(pos->second,true);
- } else {
- LOG_DEBUG("not found" << std::endl);
- }
- return std::make_pair(dummy,false);
-}
-
-class Connector: public EntityVisitor
-{
-public:
- Connector() {Reset();}
-
- // visitor interface
- virtual bool VisitChain(const ChainHandle& chain) {
- LOG_DEBUG("connect: setting current chain to " << chain.GetName() << std::endl);
- curr_chain_=chain;
- curr_residue_=ResidueHandle();
- prev_residue_=ResidueHandle();
- prev_atom_=AtomHandle();
- next_atom_=AtomHandle();
- return true;
- }
-
- virtual bool VisitResidue(const ResidueHandle& res) {
- LOG_DEBUG("connect: setting current residue to " << res.GetKey() << " " << res.GetNumber() << std::endl);
- // residue has changed
- curr_residue_=res;
- AtomHandleList atomlist = res.GetAtomList();
- LOG_DEBUG( "using atom list:" << std::endl);
- for(AtomHandleList::iterator it=atomlist.begin();it!=atomlist.end();++it) {
- LOG_DEBUG( " " << it->GetName() << " @" << it->GetPos() << std::endl);
- }
-
- std::pair<ConnResEntry,bool> ret = LookupResEntry(res.GetKey());
-
- if(ret.second) {
- // residue entry found
- ConnResEntry& centry=ret.first;
- for(AtomHandleList::iterator it1=atomlist.begin();it1!=atomlist.end();++it1) {
- AtomHandleList::iterator it2=it1;
- ++it2;
- for(;it2!=atomlist.end();++it2) {
- bool ex1,ex2;
- LOG_DEBUG( "checking for atom pair (" << it1->GetName() << "," << it2->GetName() << ") in connectivity table of " << res.GetKey() << "... ");
- int conn=centry.Check(it1->GetName(),it2->GetName(),ex1,ex2);
- if (conn==1) {
- LOG_DEBUG( "found" << std::endl);
- res.GetEntity().Connect(*it1,*it2);
- } else if(conn==2) {
- LOG_DEBUG( "found (reversed)" << std::endl);
- res.GetEntity().Connect(*it2,*it1);
- } else {
- LOG_DEBUG( "not found" << std::endl);
- // check ex1 and/or ex2
- }
- }
-
- // check this atom for interresidue connectivity
- /*
- make interresidue bond if
- - previous residue had a "next" entry
- - previous residue number is consecutive to this one
- */
- if(centry.GetPrev()==it1->GetName()) { // 'PREV' entry
- LOG_DEBUG( "found 'prev' atom entry: " << it1->GetName() << std::endl);
- if(prev_residue_) { // previous residue exists
- if(!next_atom_name_.empty()) { // previous residue 'NEXT' atom set
- if(InSequence(prev_residue_,res)) {
- AtomHandleList prev_atomlist = prev_residue_.GetAtomList();
- for(AtomHandleList::iterator pit=prev_atomlist.begin();
- pit!=prev_atomlist.end();++pit) {
- if(pit->GetName()==next_atom_name_) {
- LOG_DEBUG( "connecting previous atom " << pit->GetName() << " to " << it1->GetName() << std::endl);
- res.GetEntity().Connect(*pit,*it1);
- }
- }
- }
- }
- }
- }
-
- if(centry.GetNext()==it1->GetName()) {
- LOG_DEBUG( "found 'next' atom entry: " << it1->GetName() << std::endl);
- // remember this atom for the next residue
- next_atom_name_=it1->GetName();
- }
-
- } // connectivity
- } else {
- /*
- here a distance based lookup over all atoms of this residue compared
- to all other atoms should be implemented
- */
-
- }
-
- prev_residue_=res; // remember for next round
-
- return true;
- }
-
- virtual bool VisitAtom(const AtomHandle& a) {
- return true;
- }
-
- void Reset() {
- curr_chain_=ChainHandle();
- curr_residue_=ResidueHandle();
- prev_atom_=AtomHandle();
- next_atom_=AtomHandle();
- }
-
-private:
- ChainHandle curr_chain_;
- ResidueHandle curr_residue_;
- ResidueHandle prev_residue_;
- String next_atom_name_;
- AtomHandle prev_atom_;
- AtomHandle next_atom_;
-};
-
-class TorsionMaker: public EntityVisitor
-{
-public:
- TorsionMaker() {}
-
- // visitor interface
- virtual bool VisitChain(const ChainHandle& chain) {
- std::vector<ResidueHandle> rlist = chain.GetResidueList();
-
- for(unsigned int ri=0;ri<rlist.size();++ri) {
- ResidueHandle res=rlist[ri];
- std::pair<ConnResEntry,bool> centry2 = LookupResEntry(res.GetKey());
-
- if(centry2.second) {
- // residue entry found
- ConnResEntry& centry=centry2.first;
- AtomHandleList atom_list = res.GetAtomList();
- ConnResEntry::TorsionEntryList tel=centry.GetTorsionList();
- // for each entry in torsion list
- for(unsigned int ti=0;ti<tel.size();++ti) {
- // assign the four atom handles
- AtomHandle ah[4];
- for(unsigned int ahi=0;ahi<4;++ahi) {
- ResidueHandle cur_res=res;
- String cur_name=tel[ti].a[ahi];
- bool flag=false;
- if(cur_name=="+") {
- // NEXT
- if(ri+1<rlist.size()) {
- centry2=LookupResEntry(rlist[ri+1].GetKey());
- if(centry2.second) {
- cur_name=centry2.first.GetPrev();
- cur_res=rlist[ri+1];
- flag=true;
- }
- }
- } else if (tel[ti].a[ahi]=="-") {
- // PREV
- if(ri>0) {
- centry2=LookupResEntry(rlist[ri-1].GetKey());
- if(centry2.second) {
- cur_name=centry2.first.GetNext();
- cur_res=rlist[ri-1];
- flag=true;
- }
- }
- } else {
- flag=true;
- }
- if(flag) {
- // lookup atom based on cur_residue and cur_name
- ah[ahi]=cur_res.FindAtom(cur_name);
- }
- } // ahi
- if(ah[0] && ah[1] && ah[2] && ah[3]) {
- TorsionHandle th = chain.GetEntity().AddTorsion(tel[ti].name,ah[0],ah[1],ah[2],ah[3]);
- if(th) {
- LOG_DEBUG("added torsion entry for " << tel[ti].a[0] << " " << tel[ti].a[1] << " " << tel[ti].a[2] << " " << tel[ti].a[3] << std::endl);
- } else {
- LOG_DEBUG("no torsion entry for " << tel[ti].a[0] << " " << tel[ti].a[1] << " " << tel[ti].a[2] << " " << tel[ti].a[3] << std::endl);
- }
- }
- } // ti
- }
- }
-
- return false;
- }
-private:
-};
-
-} // ns
-
-/*
-
-*/
-void HeuristicConnect(EntityHandle& eh)
-{
- static Connector conn;
- static TorsionMaker tor;
- conn.Reset();
- eh.Apply(conn);
- eh.Apply(tor);
-}
-
-}} // ns
diff --git a/modules/conop/src/heuristic_connect.hh b/modules/conop/src/heuristic_connect.hh
deleted file mode 100644
index 9ed74e554dd1a89544044de9868f5c3e78980400..0000000000000000000000000000000000000000
--- a/modules/conop/src/heuristic_connect.hh
+++ /dev/null
@@ -1,28 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 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
-//------------------------------------------------------------------------------
-#ifndef OST_CONOP_HEURISTIC_CONNECT_H
-#define OST_CONOP_HEURISTIC_CONNECT_H
-
-namespace ost { namespace conop {
-
-void HeuristicConnect(EntityHandle& eh);
-
-}} // ns
-
-#endif