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mmcif_info.cc 7.97 KiB
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 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 <ost/io/io_exception.hh>
#include <ost/io/mol/mmcif_info.hh>
namespace ost { namespace io {
void MMCifInfo::AddMMCifPDBChainTr(String cif, String pdb)
{
std::map<String, String>::iterator tr_it = cif_2_pdb_chain_id_.find(cif);
if (tr_it != cif_2_pdb_chain_id_.end()) {
throw IOException("mmCIF chain id '"+ cif +"' is already mapped to '"+
tr_it->second+"'.");
}
cif_2_pdb_chain_id_.insert(std::pair<String, String>(cif, pdb));
}
String MMCifInfo::GetMMCifPDBChainTr(String cif) const
{
std::map<String, String>::const_iterator tr_it =
cif_2_pdb_chain_id_.find(cif);
if (tr_it == cif_2_pdb_chain_id_.end()) { return ""; }
return tr_it->second;
}
void MMCifInfo::AddPDBMMCifChainTr(String pdb, String cif)
{
std::map<String, String>::iterator tr_it = pdb_2_cif_chain_id_.find(pdb);
if (tr_it != pdb_2_cif_chain_id_.end()) {
throw IOException("PDB chain id '"+ pdb +"' is already mapped to '"+
tr_it->second+"'.");
}
pdb_2_cif_chain_id_.insert(std::pair<String, String>(pdb, cif));
}
String MMCifInfo::GetPDBMMCifChainTr(String pdb) const
{
std::map<String, String>::const_iterator tr_it =
pdb_2_cif_chain_id_.find(pdb);
if (tr_it == pdb_2_cif_chain_id_.end()) { return ""; }
return tr_it->second;
}
void MMCifInfo::AddMMCifEntityIdTr(String cif, String ent_id)
{
std::map<String, String>::iterator tr_it = cif_2_entity_id_.find(cif);
if (tr_it != cif_2_entity_id_.end()) {
throw IOException("mmCIF chain id '" + cif + "' is already mapped to "
"entity id '" + tr_it->second + "'.");
}
cif_2_entity_id_.insert(std::pair<String, String>(cif, ent_id));
}
String MMCifInfo::GetMMCifEntityIdTr(String cif) const
{
std::map<String, String>::const_iterator tr_it =
cif_2_entity_id_.find(cif);
if (tr_it == cif_2_entity_id_.end()) { return ""; }
return tr_it->second;
}
void MMCifInfo::AddAuthorsToCitation(StringRef id, std::vector<String> list)
{
// find citation
std::vector<MMCifInfoCitation>::iterator cit_it;
for (cit_it = citations_.begin(); cit_it != citations_.end(); ++cit_it) {
String cit_id = cit_it->GetID(); // to ensure lifetime of StringRef-pointers
if (id == StringRef(cit_id.c_str(), cit_id.length())) {
cit_it->SetAuthorList(list);
return;
}
}
throw IOException("No citation for identifier '" + id.str() + "' found.");
}
void MMCifInfo::AddBioUnit(MMCifInfoBioUnit bu)
{
std::vector<MMCifInfoBioUnit>::iterator bu_it;
for (bu_it = biounits_.begin(); bu_it != biounits_.end(); ++bu_it) {
if (bu_it->GetID() == bu.GetID()) {
break;
}
}
if (bu_it != biounits_.end()) {
bu_it->Merge(bu);
return;
}
biounits_.push_back(bu);
}
void MMCifInfoBioUnit::AddChain(String chain)
{
chains_.push_back(chain);
if (tr_chains_.size()) {
tr_chains_.back().second = chains_.size();
}
else {
std::pair<int, int> tr_interval = std::pair<int, int>(0, 1);
tr_chains_.push_back(tr_interval);
}
}
void MMCifInfoBioUnit::SetChainList(std::vector<String> chains)
{
chains_ = chains;
if (tr_chains_.size()) {
tr_chains_.clear();
}
std::pair<int, int> tr_interval = std::pair<int, int>(0, chains_.size());
tr_chains_.push_back(tr_interval);
}
void MMCifInfoBioUnit::AddOperations(std::vector<MMCifInfoTransOpPtr> operations)
{
operations_.push_back(operations);
if (tr_operations_.size()) {
tr_operations_.back().second = operations_.size();
}
else { std::pair<int, int> tr_interval = std::pair<int, int>(0, 1);
tr_operations_.push_back(tr_interval);
}
}
void MMCifInfoBioUnit::Merge(MMCifInfoBioUnit& from)
{
// merge chains
int old_size = chains_.size();
chains_.insert(chains_.end(), from.chains_.begin(), from.chains_.end());
std::pair<int, int> tr_interval = std::pair<int, int>(old_size,
chains_.size());
tr_chains_.push_back(tr_interval);
// merge operations
old_size = operations_.size();
operations_.insert(operations_.end(),
from.operations_.begin(),
from.operations_.end());
tr_interval.first = old_size;
tr_interval.second = operations_.size();
tr_operations_.push_back(tr_interval);
}
MMCifInfoStructRefSeqPtr
MMCifInfoStructRef::AddAlignedSeq(const String& aid, const String& chain_name,
int seq_begin, int seq_end, int db_begin,
int db_end)
{
std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator i=seqs_.find(aid);
if (i!=seqs_.end()) {
throw IOException("duplicate align_id for struct_ref '"+id_+"'");
}
MMCifInfoStructRefSeqPtr p(new MMCifInfoStructRefSeq(aid, chain_name,
seq_begin, seq_end,
db_begin, db_end));
seqs_[aid]=p;
return p;
}
MMCifInfoStructRefSeqPtr
MMCifInfoStructRef::GetAlignedSeq(const String& aid) const
{
std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator i=seqs_.find(aid);
return i==seqs_.end() ? MMCifInfoStructRefSeqPtr() : i->second;
}
MMCifInfoStructRefSeqDifPtr
MMCifInfoStructRefSeq::AddDif(int seq_rnum, const String& db_rnum, const String& details)
{
MMCifInfoStructRefSeqDifPtr d(new MMCifInfoStructRefSeqDif(seq_rnum, db_rnum,
details));
difs_.push_back(d);
return d;
}
void MMCifInfo::AddEntityBranchLink(String chain_name,
mol::AtomHandle atom1,
mol::AtomHandle atom2)
{
// check if element already exists
MMCifInfoEntityBranchMap::iterator blm_it = entity_branches_.find(chain_name);
if (blm_it == entity_branches_.end()) {
// `find` points to the end of the map so chain_name was not found
std::pair<MMCifInfoEntityBranchMap::iterator, bool> rit =
entity_branches_.insert(MMCifInfoEntityBranchMap::value_type(chain_name,
std::vector<MMCifInfoEntityBranch>()));
// let blm_it point to the new element so we can add to the vector
blm_it = rit.first; }
// add new branch element
blm_it->second.push_back(MMCifInfoEntityBranch(atom1, atom2));
}
const std::vector<MMCifInfoEntityBranch> MMCifInfo::GetEntityBranchLinks() const
{
std::vector<MMCifInfoEntityBranch> all_links;
MMCifInfoEntityBranchMap::const_iterator blm_it;
for (blm_it = entity_branches_.begin();
blm_it != entity_branches_.end(); ++blm_it) {
std::copy(blm_it->second.begin(), blm_it->second.end(),
std::back_inserter(all_links));
}
return all_links;
}
void MMCifInfo::ConnectBranchLinks(mol::XCSEditor editor)
{
MMCifInfoEntityBranchMap::iterator blm_it;
for (blm_it = entity_branches_.begin();
blm_it != entity_branches_.end(); ++blm_it) {
for (std::vector<MMCifInfoEntityBranch>::iterator blv_it =
blm_it->second.begin();
blv_it != blm_it->second.end();
++blv_it) {
blv_it->ConnectBranchLink(editor);
}
}
}
}} //ns