From a642facad90c4220a43470b317619a15871c2bff Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 25 Jul 2011 09:44:23 +0200
Subject: [PATCH] Revert MMCIF Parser to move to own branch
This reverts commit aac17c6cf70a13e6aa53792cf162b8d7a4022ef4.
---
modules/io/pymod/CMakeLists.txt | 1 -
modules/io/pymod/__init__.py | 101 +---
modules/io/pymod/export_mmcif_io.cc | 38 --
modules/io/pymod/wrap_io.cc | 2 -
modules/io/src/mol/CMakeLists.txt | 2 -
modules/io/src/mol/mmcif_reader.cc | 510 ------------------
modules/io/src/mol/mmcif_reader.hh | 197 -------
modules/io/src/mol/star_parser.cc | 71 +--
modules/io/src/mol/star_parser.hh | 34 +-
modules/io/tests/CMakeLists.txt | 1 -
modules/io/tests/test_mmcif_reader.cc | 233 --------
.../io/tests/testfiles/mmcif/atom_site.mmcif | 49 --
12 files changed, 4 insertions(+), 1235 deletions(-)
delete mode 100644 modules/io/pymod/export_mmcif_io.cc
delete mode 100644 modules/io/src/mol/mmcif_reader.cc
delete mode 100644 modules/io/src/mol/mmcif_reader.hh
delete mode 100644 modules/io/tests/test_mmcif_reader.cc
delete mode 100644 modules/io/tests/testfiles/mmcif/atom_site.mmcif
diff --git a/modules/io/pymod/CMakeLists.txt b/modules/io/pymod/CMakeLists.txt
index 023e000b8..902089f7f 100644
--- a/modules/io/pymod/CMakeLists.txt
+++ b/modules/io/pymod/CMakeLists.txt
@@ -1,7 +1,6 @@
set(OST_IO_PYMOD_SOURCES
wrap_io.cc
export_pdb_io.cc
- export_mmcif_io.cc
)
if (ENABLE_IMG)
diff --git a/modules/io/pymod/__init__.py b/modules/io/pymod/__init__.py
index 57a0464bb..74047dec0 100644
--- a/modules/io/pymod/__init__.py
+++ b/modules/io/pymod/__init__.py
@@ -88,7 +88,7 @@ def LoadPDB(filename, restrict_chains="", no_hetatms=None,
profile='DEFAULT', remote=False, dialect=None,
strict_hydrogens=None, seqres=False):
"""
- Load PDB file from disk and return one or more entities. Several options
+ Load PDB file from disk and returns one or more entities. Several options
allow to customize the exact behaviour of the PDB import. For more information
on these options, see :doc:`profile`.
@@ -264,105 +264,6 @@ def LoadCHARMMTraj(crd, dcd_file=None, profile='CHARMM',
raise ValueError("No DCD filename given")
return LoadCHARMMTraj_(crd, dcd_file, stride, lazy_load)
-def LoadMMCIF(filename, restrict_chains="", no_hetatms=None,
- fault_tolerant=None, load_multi=False, quack_mode=None,
- join_spread_atom_records=None, calpha_only=None,
- profile='DEFAULT', remote=False, strict_hydrogens=None,
- seqres=False):
- """
- Load MMCIF file from disk and return one or more entities. Several options
- allow to customize the exact behaviour of the MMCIF import. For more
- information on these options, see :doc:`profile`.
-
- Residues are flagged as ligand if they are mentioned in a HET record.
-
- :param restrict_chains: If not an empty string, only chains listed in the
- string will be imported.
-
- :param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides
- the value of :attr:`IOProfile.fault_tolerant`.
-
- :param no_hetatms: If set to True, HETATM records will be ignored. Overrides
- the value of :attr:`IOProfile.no_hetatms`
-
- :param load_multi: If set to True, a list of entities will be returned instead
- of only the first. This is useful when dealing with multi-PDB files.
-
- :param join_spread_atom_records: If set, overrides the value of
- :attr:`IOProfile.join_spread_atom_records`.
-
- :param remote: If set to true, the method tries to load the pdb from the
- remote pdb repository www.pdb.org. The filename is then interpreted as the
- pdb id.
-
- :rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is
- True.
-
- :param seqres: Whether to read SEQRES records. If set to true, the loaded
- entity and seqres entry will be returned as a tuple.
-
- :param strict_hydrogens: If set, overrides the value of
- :attr:`IOProfile.strict_hydrogens`.
-
- :raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous or
- inexistent file
- """
- def _override(val1, val2):
- if val2!=None:
- return val2
- else:
- return val1
- if isinstance(profile, str):
- prof = profiles[profile].Copy()
- else:
- prof = profile.Copy()
-
- prof.calpha_only=_override(prof.calpha_only, calpha_only)
- prof.no_hetatms=_override(prof.no_hetatms, no_hetatms)
- prof.quack_mode=_override(prof.quack_mode, quack_mode)
- prof.strict_hydrogens=_override(prof.strict_hydrogens, strict_hydrogens)
- prof.fault_tolerant=_override(prof.fault_tolerant, fault_tolerant)
- prof.join_spread_atom_records=_override(prof.join_spread_atom_records,
- join_spread_atom_records)
-
- if remote:
- output_dir = tempfile.gettempdir()
- if __GetModelFromPDB(filename, output_dir):
- filename = os.path.join(output_dir, 'pdb%s.ent.gz' % filename)
- else:
- raise IOError('Can not load PDB %s from www.pdb.org'%filename)
-
- conop_inst = conop.Conopology.Instance()
- builder = conop_inst.GetBuilder("DEFAULT")
-
- builder.strict_hydrogens = prof.strict_hydrogens
-
- try:
- #if load_multi:
- # ent_list=[]
- # while reader.HasNext():
- # ent=mol.CreateEntity()
- # reader.Import(ent, restrict_chains)
- # conop_inst.ConnectAll(builder, ent, 0)
- # ent_list.append(ent)
- # if len(ent_list)==0:
- # raise IOError("File doesn't contain any entities")
- # return ent_list
- #else:
- ent = mol.CreateEntity()
- reader = MMCifParser(filename, ent, prof)
- #reader.read_seqres = seqres
- #if reader.HasNext():
- reader.Parse()
- conop_inst.ConnectAll(builder, ent, 0)
- #else:
- # raise IOError("File doesn't contain any entities")
- #if seqres:
- # return ent, reader.seqres
- return ent
- except:
- raise
-
## \example fft_li.py
#
# This scripts loads one or more images and shows their Fourier Transforms on
diff --git a/modules/io/pymod/export_mmcif_io.cc b/modules/io/pymod/export_mmcif_io.cc
deleted file mode 100644
index 4e0a47240..000000000
--- a/modules/io/pymod/export_mmcif_io.cc
+++ /dev/null
@@ -1,38 +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 <boost/python.hpp>
-using namespace boost::python;
-
-#include <ost/io/mol/io_profile.hh>
-#include <ost/io/mol/mmcif_reader.hh>
-using namespace ost;
-using namespace ost::io;
-using namespace ost::mol;
-
-void export_mmcif_io()
-{
- class_<MMCifParser, boost::noncopyable>("MMCifParser", init<const String&, EntityHandle&, const IOProfile&>())
- .def("Parse", &MMCifParser::Parse)
- .def("SetRestrictChains", &MMCifParser::SetRestrictChains)
- .add_property("restrict_chains",
- make_function(&MMCifParser::GetRestrictChains,
- return_value_policy<copy_const_reference>()),
- &MMCifParser::SetRestrictChains)
- ;
-}
diff --git a/modules/io/pymod/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index 1d9e3b936..af5087cd2 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -72,7 +72,6 @@ BOOST_PYTHON_FUNCTION_OVERLOADS(save_charmm_trj_ov,
}
void export_pdb_io();
-void export_mmcif_io();
#if OST_IMG_ENABLED
void export_map_io();
#endif
@@ -118,7 +117,6 @@ BOOST_PYTHON_MODULE(_ost_io)
def("LoadMAE", &LoadMAE);
export_pdb_io();
- export_mmcif_io();
#if OST_IMG_ENABLED
export_map_io();
#endif
diff --git a/modules/io/src/mol/CMakeLists.txt b/modules/io/src/mol/CMakeLists.txt
index db328bb9c..1201eb58f 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -15,14 +15,12 @@ chemdict_parser.cc
io_profile.cc
dcd_io.cc
star_parser.cc
-mmcif_reader.cc
PARENT_SCOPE
)
set(OST_IO_MOL_HEADERS
chemdict_parser.hh
star_parser.hh
-mmcif_reader.hh
io_profile.hh
dcd_io.hh
entity_io_crd_handler.hh
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
deleted file mode 100644
index 0a463ac24..000000000
--- a/modules/io/src/mol/mmcif_reader.cc
+++ /dev/null
@@ -1,510 +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 <ctype.h>
-
-//#include <boost/iostreams/filter/gzip.hpp>
-//#include <boost/filesystem/convenience.hpp>
-//#include <boost/algorithm/string.hpp>
-//#include <boost/algorithm/string/trim.hpp>
-
-//#include <boost/format.hpp>
-//#include <boost/lexical_cast.hpp>
-
-#include <ost/profile.hh>
-#include <ost/log.hh>
-#include <ost/mol/xcs_editor.hh>
-#include <ost/io/mol/mmcif_reader.hh>
-
-namespace ost { namespace io {
-
-MMCifParser::MMCifParser(std::istream& stream, mol::EntityHandle& ent_handle,
- const IOProfile& profile):
- StarParser(stream, true), profile_(profile), ent_handle_(ent_handle)
-{
- this->Init();
-}
-
-MMCifParser::MMCifParser(const String& filename, mol::EntityHandle& ent_handle,
- const IOProfile& profile):
- StarParser(filename, true), profile_(profile), ent_handle_(ent_handle)
-{
- this->Init();
-}
-
-void MMCifParser::Init()
-{
- warned_name_mismatch_ = false;
- category_ = DONT_KNOW;
- chain_count_ = 0;
- atom_count_ = 0;
- residue_count_ = 0;
- auth_chain_id_ = false;
- go_on_ = true;
- //memset(indices_, -1, MAX_ITEMS_IN_ROW * sizeof(int));
- restrict_chains_ = "";
- //curr_chain_ = mol::ChainHandle();
- //curr_residue_ = mol::ResidueHandle();
-}
-
-void MMCifParser::ClearState()
-{
- curr_chain_ = mol::ChainHandle();
- curr_residue_ = mol::ResidueHandle();
- chain_count_ = 0;
- residue_count_ = 0;
- atom_count_ = 0;
- category_ = DONT_KNOW;
- warned_name_mismatch_ = false;
-}
-
-void MMCifParser::SetRestrictChains(const String& restrict_chains)
-{
- restrict_chains_ = restrict_chains;
-}
-
-bool MMCifParser::IsValidPDBIdent(const StringRef& pdbid)
-{
- if (pdbid.length() == PDBID_LEN && isdigit(pdbid[0])) {
- return true;
- }
- return false;
-}
-
-bool MMCifParser::OnBeginData(const StringRef& data_name)
-{
- LOG_DEBUG("MCIFFReader: " << profile_);
- Profile profile_import("MMCifReader::OnBeginData");
-
- // check for PDB id
- if (!this->IsValidPDBIdent(data_name)) {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "No valid PDB id found for data block, read instead \'"
- + data_name.str() + "\'",
- this->GetCurrentLinenum()));
- }
-
- this->ClearState();
-
- go_on_ = true;
-
- return true;
-}
-
-bool MMCifParser::OnBeginLoop(const StarLoopDesc& header)
-{
- // set whole array to -1
- memset(indices_, -1, MAX_ITEMS_IN_ROW * sizeof(int));
- // walk through possible categories
- if (header.GetCategory() == "atom_site") {
- category_ = ATOM_SITE;
- // mandatory items
- this->TryStoreIdx(AUTH_ASYM_ID, "auth_asym_id", header);
- this->TryStoreIdx(ID, "id", header);
- this->TryStoreIdx(LABEL_ALT_ID, "label_alt_id", header);
- this->TryStoreIdx(LABEL_ASYM_ID, "label_asym_id", header);
- this->TryStoreIdx(LABEL_ATOM_ID, "label_atom_id", header);
- this->TryStoreIdx(LABEL_COMP_ID, "label_comp_id", header);
- this->TryStoreIdx(LABEL_ENTITY_ID, "label_entity_id", header);
- this->TryStoreIdx(LABEL_SEQ_ID, "label_seq_id", header);
- this->TryStoreIdx(TYPE_SYMBOL, "type_symbol", header);
- // assumed mandatory
- this->TryStoreIdx(CARTN_X, "Cartn_x", header);
- this->TryStoreIdx(CARTN_Y, "Cartn_y", header);
- this->TryStoreIdx(CARTN_Z, "Cartn_z", header);
- // optional
- indices_[OCCUPANCY] = header.GetIndex("occupancy");
- indices_[B_ISO_OR_EQUIV] = header.GetIndex("B_iso_or_equiv");
- indices_[GROUP_PDB] = header.GetIndex("group_PDB");
- return true;
- } /*else if (header.GetCategory()=="entity_poly") {
- } else if (header.GetCategory()=="pdbx_poly_seq_scheme") {
- } else if (header.GetCategory()=="pdbx_struct_assembly") {
- } else if (header.GetCategory()=="struct_conf") {
- }*/
- return false;
-}
-
-mol::ResNum to_res_num(int num, char ins_code)
-{
- return mol::ResNum(num, ins_code==' ' ? '\0' : ins_code);
-}
-
-bool MMCifParser::ParseAtomIdent(const std::vector<StringRef>& columns,
- String& chain_name,
- StringRef& res_name,
- mol::ResNum& resnum,
- StringRef& atom_name,
- char& alt_loc)
-{
- // ATOM name
- atom_name = columns[indices_[LABEL_ATOM_ID]];
- if (profile_.calpha_only) { // unit test profile
- if (atom_name != StringRef("CA", 2)) {
- return false;
- }
- }
- // CHAIN ID
- if (auth_chain_id_) { // unit test different IDs
- chain_name = columns[indices_[AUTH_ASYM_ID]].str();
- } else {
- chain_name = columns[indices_[LABEL_ASYM_ID]].str();
- }
- if (restrict_chains_.size() > 0 && // unit test
- restrict_chains_.find(chain_name) == String::npos) { // unit test
- return false;
- }
-
- std::pair<bool, int> a_num = this->TryGetInt(columns[indices_[ID]],
- "_atom_site.id",
- profile_.fault_tolerant); // unit test
-
- alt_loc = columns[indices_[LABEL_ALT_ID]][0];
- res_name = columns[indices_[LABEL_COMP_ID]];
- std::pair<bool, int> res_num =this->TryGetInt(columns[indices_[LABEL_SEQ_ID]],
- "_atom_site.label_seq_id",
- profile_.fault_tolerant); // unit test
- if (!res_num.first) { // unit test
- if (profile_.fault_tolerant) {
- return false;
- }
- }
-
- resnum=to_res_num(res_num.second, ' ');
-
- return true;
-}
-
-void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
-{
- mol::XCSEditor editor=ent_handle_.EditXCS(mol::BUFFERED_EDIT); // potbl
- char alt_loc=0;
- String chain_name;
- StringRef res_name, atom_name;
- mol::ResNum res_num(0);
- if (!this->ParseAtomIdent(columns,
- chain_name,
- res_name,
- res_num,
- atom_name,
- alt_loc)) {
- return;
- }
- Real occ = 1.00f, temp = 0;
- geom::Vec3 apos;
-
- for (int i = CARTN_X; i <= CARTN_Z; ++i) {
- std::pair<bool, float> result = this->TryGetFloat(columns[indices_[i]],
- "atom_site.cartn_[xyz]",
- profile_.fault_tolerant);
- if (!result.first) { // unit test
- if (profile_.fault_tolerant) { // unit test
- return;
- }
- }
- apos[i - CARTN_X] = result.second;
- }
-
- if (indices_[OCCUPANCY] != -1) { // unit test
- occ = this->TryGetReal(columns[indices_[OCCUPANCY]], "atom_site.occupancy");
- }
- if (indices_[B_ISO_OR_EQUIV] != -1) { // unit test
- temp = this->TryGetReal(columns[indices_[B_ISO_OR_EQUIV]],
- "atom_site.B_iso_or_equiv");
- }
-
- // determine element
- String s_ele(columns[indices_[TYPE_SYMBOL]].str());
-
- String aname(atom_name.str());
- // some postprocessing
- LOG_TRACE( "s_chain: [" << chain_name << "]" );
-
- // determine chain and residue update
- bool update_chain=false;
- bool update_residue=false;
- if(!curr_chain_) { // unit test
- update_chain=true;
- update_residue=true;
- } else if(curr_chain_.GetName() != chain_name) { // unit test
- update_chain=true;
- update_residue=true;
- }
-
- if(!curr_residue_) { // unit test
- update_residue=true;
- } else if(curr_residue_.GetNumber() != res_num) { // unit test
- update_residue=true;
- }
-
- if(update_chain) { // unit test
- curr_chain_ = ent_handle_.FindChain(chain_name);
- if(!curr_chain_.IsValid()) { // unit test
- LOG_DEBUG("new chain " << chain_name);
- curr_chain_=editor.InsertChain(chain_name);
- ++chain_count_;
- }
- assert(curr_chain_.IsValid());
- }
-
- if(update_residue) { // unit test
- curr_residue_=mol::ResidueHandle();
- if (profile_.join_spread_atom_records) { // unit test
- curr_residue_=curr_chain_.FindResidue(res_num);
- }
- if (!curr_residue_.IsValid()) { // unit test
- LOG_DEBUG("new residue " << res_name << " " << res_num);
- curr_residue_ =editor.AppendResidue(curr_chain_, res_name.str(), res_num);
- warned_name_mismatch_=false;
- ++residue_count_;
- }
- assert(curr_residue_.IsValid());
- }
-
- // finally add atom
- LOG_DEBUG("adding atom " << aname << " (" << s_ele << ") @" << apos);
- mol::AtomHandle ah;
- if (curr_residue_.GetName()!=res_name.str()) { // unit test
- if (!profile_.fault_tolerant && alt_loc=='.') { // unit test
- std::stringstream ss;
- ss << "Residue with number " << res_num << " has more than one name.";
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- ss.str(),
- this->GetCurrentLinenum()));
- }
- if (!warned_name_mismatch_) { // unit test
- if (alt_loc=='.') { // unit test
- LOG_WARNING("Residue with number " << res_num << " has more than one "
- "name. Ignoring atoms for everything but the first");
- } else {
- LOG_WARNING("Residue with number " << res_num
- << " contains a microheterogeneity. Everything but atoms "
- "for the residue '" << curr_residue_.GetName()
- << "' will be ignored");
- }
- }
- warned_name_mismatch_=true;
- return;
- }
- if (alt_loc!='.') { // unit test
- // Check if there is already a atom with the same name.
- mol::AtomHandle me=curr_residue_.FindAtom(aname);
- if (me.IsValid()) { // unit test
- try {
- editor.AddAltAtomPos(String(1, alt_loc), me, apos);
- } catch (Error) {
- LOG_INFO("Ignoring atom alt location since there is already an atom "
- "with name " << aname << ", but without an alt loc");
- return;
- }
- return;
- } else {
- ah = editor.InsertAltAtom(curr_residue_, aname,
- String(1, alt_loc), apos, s_ele);
- ++atom_count_;
- }
- } else {
- mol::AtomHandle atom=curr_residue_.FindAtom(aname);
- if (atom.IsValid() && !profile_.quack_mode) { // unit test
- if (profile_.fault_tolerant) { // unit test
- LOG_WARNING("duplicate atom '" << aname << "' in residue "
- << curr_residue_);
- return;
- }
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "Duplicate atom '"+aname+
- "' in residue "+
- curr_residue_.GetQualifiedName(),
- this->GetCurrentLinenum()));
- }
- ah = editor.InsertAtom(curr_residue_, aname, apos, s_ele);
- ++atom_count_;
- }
- ah.SetBFactor(temp);
-
- ah.SetOccupancy(occ);
-
- // record type
- ah.SetHetAtom(indices_[GROUP_PDB] == -1 ? false :
- columns[indices_[GROUP_PDB]][0]=='H');
-
-}
-
-void MMCifParser::OnDataRow(const StarLoopDesc& header,
- const std::vector<StringRef>& columns)
-{
- switch(category_) {
- case ATOM_SITE:
- LOG_TRACE("processing atom_site entry");
- this->ParseAndAddAtom(columns);
- break;
- default:
- return;
- }
-}
-
- /*
-void PDBReader::Import(mol::EntityHandle& ent,
- const String& restrict_chains)
-{
- do {
- switch(curr_line[0]) {
- case 'A':
- case 'a':
- if (IEquals(curr_line.substr(0, 6), StringRef("ANISOU", 6))) {
- if (!charmm_style_) {
- LOG_TRACE("processing ANISOU entry");
- this->ParseAnisou(curr_line, line_num_, ent);
- }
- }
- break;
- case 'C':
- case 'c':
- if (curr_line.size()<20) {
- LOG_TRACE("skipping entry");
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("COMPND", 6))) {
- LOG_TRACE("processing COMPND entry");
- this->ParseCompndEntry(curr_line, line_num_);
- }
- break;
- case 'E':
- case 'e':
- if (curr_line.size()<3) {
- continue;
- }
- if (IEquals(curr_line.rtrim(), StringRef("END", 3))) {
- hard_end_=true;
- go_on=false;
- break;
- }
- if (curr_line.size()<6) {
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("ENDMDL", 6))) {
- go_on=false;
- num_model_records_=0;
- break;
- }
- case 'H':
- case 'h':
- if (curr_line.size()<6) {
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("HETATM", 6))) {
- if (profile_.no_hetatms)
- continue;
- LOG_TRACE("processing HETATM entry");
- this->ParseAndAddAtom(curr_line, line_num_, ent,
- StringRef("HETATM", 6));
- } else if (IEquals(curr_line.substr(0, 6), StringRef("HELIX ", 6))) {
- if (!charmm_style_) {
- this->ParseHelixEntry(curr_line);
- }
- } else if (IEquals(curr_line.substr(0, 6), StringRef("HET ", 6))) {
- // remember het entry to mark the residues as ligand during ATOM import
- char chain=curr_line[12];
- std::pair<bool, int> num=curr_line.substr(13, 4).ltrim().to_int();
- if (!num.first) {
- if (profile_.fault_tolerant) {
- LOG_WARNING("Invalid HET entry on line " << line_num_);
- continue;
- } else {
- String msg=str(format("Invalid HET entry on line %d")%line_num_);
- throw IOException(msg);
- }
- }
- hets_.push_back(HetEntry(chain, to_res_num(num.second,
- curr_line[17])));
- }
- break;
- case 'M':
- case 'm':
- if (curr_line.size()<6) {
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("MODEL ", 6))) {
- ++num_model_records_;
- if (num_model_records_<2) {
- continue;
- }
- if (profile_.fault_tolerant) {
- go_on=false;
- num_model_records_=1;
- break;
- }
- String msg=str(format("MODEL record without matching ENDMDL on line %d")%line_num_);
- throw IOException(msg);
- }
- break;
- case 'S':
- case 's':
- if (curr_line.size()<6) {
- continue;
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("SHEET ", 6))) {
- if (!charmm_style_) {
- this->ParseStrandEntry(curr_line);
- }
- }
- if (IEquals(curr_line.substr(0, 6), StringRef("SEQRES", 6))) {
- if (read_seqres_) {
- this->ParseSeqRes(curr_line, line_num_);
- }
- }
- break;
- default:
- break;
- }
- } while (std::getline(in_, curr_line_) && ++line_num_ && go_on);
- LOG_INFO("imported "
- << chain_count_ << " chains, "
- << residue_count_ << " residues, "
- << atom_count_ << " atoms; with "
- << helix_list_.size() << " helices and "
- << strand_list_.size() << " strands");
- this->AssignSecStructure(ent);
- this->AssignMolIds(ent);
- for (HetList::const_iterator i=hets_.begin(), e=hets_.end(); i!=e; ++i) {
- mol::ResidueHandle res=ent.FindResidue(String(1, i->chain), i->num);
- if (res.IsValid()) {
- res.SetIsLigand(true);
- }
- }
-}
- */
-
-
- /*
- virtual void OnEndLoop() { }
-
- virtual void OnDataItem(const StarDataItem& item) { }
-
- };*/
-
-void MMCifParser::OnEndData()
-{
- LOG_INFO("imported "
- << chain_count_ << " chains, "
- << residue_count_ << " residues, "
- << atom_count_ << " atoms;");
-}
-
-}}
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
deleted file mode 100644
index 6f933ae12..000000000
--- a/modules/io/src/mol/mmcif_reader.hh
+++ /dev/null
@@ -1,197 +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_MMCIF_PARSER_HH
-#define OST_MMCIF_PARSER_HH
-
-//#include <boost/iostreams/filtering_stream.hpp>
-//#include <boost/filesystem/fstream.hpp>
-
-#include <ost/mol/residue_handle.hh>
-#include <ost/io/mol/io_profile.hh>
-#include <ost/io/io_exception.hh>
-#include <ost/io/mol/star_parser.hh>
-
-namespace ost { namespace io {
-
-/// \brief reader for the mmcif file format
-///
-/// \section mmcif_format mmcif format description/ coverage
-///
-/// mmcif is an instance of the \link StarParser STAR format\endlink to store
-/// entries of the PDB. The following data categories should be covered by this
-/// parser:
-///
-/// \li atom_site
-class DLLEXPORT_OST_IO MMCifParser : public StarParser {
-public:
- /// \brief create a MMCifParser
- ///
- /// \param stream input stream
- MMCifParser(std::istream& stream, mol::EntityHandle& ent_handle,
- const IOProfile& profile);
-
- /// \brief create a MMCifParser
- ///
- /// \param filename input file
- MMCifParser(const String& filename, mol::EntityHandle& ent_handle,
- const IOProfile& profile);
-
- /// \brief Initialise the parser.
- ///
- /// \param loc Location of the file
- void Init();
-
- /// \brief Set up a fresh instance
- void ClearState();
-
- /// \brief Set names of restricted chains for the parser.
- ///
- /// \param restrict_chains chain name
- void SetRestrictChains(const String& restrict_chains);
-
- const String& GetRestrictChains() const
- {
- return restrict_chains_;
- }
-
- /// \brief check mmcif input to be read. Substitutional function for
- /// \link StarParser StarParser\endlink.
- ///
- /// \param data_name value of the data_ tag
- ///
- /// \return true, if the blockcode (PDB id) is valid, false otherwise
- virtual bool OnBeginData(const StringRef& data_name);
-
- /// \brief check if a current loop is to be parsed
- ///
- /// \param header categories of the upcoming loop block
- ///
- /// \return bool
- virtual bool OnBeginLoop(const StarLoopDesc& header);
-
- /// \brief read a row of data
- ///
- /// \param header categories and items
- /// \param columns data
- virtual void OnDataRow(const StarLoopDesc& header,
- const std::vector<StringRef>& columns);
-
- /// \brief Finalise parsing.
- virtual void OnEndData();
-
- protected:
- /// \brief Store an item index from loop header in preparation for reading a
- /// row. Throws an exception if the item does not exist.
- ///
- /// \param mapping position the item index is stored at
- /// \param item exact item name to fetch
- /// \param header loop header to pull index from
- void TryStoreIdx(const int mapping,
- const String& item,
- const StarLoopDesc& header)
- {
- indices_[mapping] = header.GetIndex(item);
-
- if (indices_[mapping] == -1) {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "No item '" + item +
- "' found in '" +
- header.GetCategory()+
- "' header",
- this->GetCurrentLinenum()));
- }
- }
-
- /// \brief Check a PDB id to be of length 4 and start with a digit
- ///
- /// \param pdbid putative PDB id
- ///
- /// \return true for a valid id, false otherwise
- bool IsValidPDBIdent(const StringRef& pdbid);
-
- /// \brief ...
- ///
- /// \param columns data row
- /// \param atom_name corresponds to label_atom_id
- bool ParseAtomIdent(const std::vector<StringRef>& columns,
- String& chain_name,
- StringRef& res_name,
- mol::ResNum& resnum,
- StringRef& atom_name,
- char& alt_loc);
-
- /// \brief Fetch atom information and store it.
- ///
- /// \param columns data row
- void ParseAndAddAtom(const std::vector<StringRef>& columns);
-
-private:
- /// \enum magic numbers of this class
- typedef enum {
- PDBID_LEN=4, ///< length of a PDB id
- MAX_ITEMS_IN_ROW=16 ///< count for possible items in a loop row
- } MMCifMagicNos;
-
- /// \enum items of the atom_site category
- typedef enum {
- AUTH_ASYM_ID, ///< chain name by author as in PDB
- ID, ///< atom serial id
- LABEL_ALT_ID, ///< AltLoc
- LABEL_ASYM_ID, ///< chain name by PDB
- LABEL_ATOM_ID,
- LABEL_COMP_ID,
- LABEL_ENTITY_ID,
- LABEL_SEQ_ID, ///< residue no.
- TYPE_SYMBOL, ///< chemical element
- CARTN_X, ///< Coordinates ||IMPORTANT: This 3 entries have to stay
- CARTN_Y, ///< Coordinates ||together for the parser to work!
- CARTN_Z, ///< Coordinates ||
- OCCUPANCY,
- B_ISO_OR_EQUIV,
- GROUP_PDB ///< record name
- } AtomSiteItems;
-
- /// \enum categories of the mmcif format
- typedef enum {
- ATOM_SITE,
- DONT_KNOW
- } MMCifCategory;
-
- // members
- MMCifCategory category_;
- int indices_[MAX_ITEMS_IN_ROW]; ///< map items to values in loops
- const IOProfile& profile_;
- mol::EntityHandle& ent_handle_;
- String restrict_chains_;
- bool auth_chain_id_; ///< use chain IDs given by authors rather than pdb
- mol::ChainHandle curr_chain_;
- mol::ResidueHandle curr_residue_;
- int chain_count_;
- int residue_count_;
- int atom_count_;
- bool warned_name_mismatch_;
- bool go_on_; ///< flow control within the parser hooks
- //from pdbdreader
- //entity als member, fill in ondatarow
- //import function
-};
-
-}}
-
-#endif
diff --git a/modules/io/src/mol/star_parser.cc b/modules/io/src/mol/star_parser.cc
index d0440904e..33e235d09 100644
--- a/modules/io/src/mol/star_parser.cc
+++ b/modules/io/src/mol/star_parser.cc
@@ -20,40 +20,28 @@
/*
Author: Marco Biasini
*/
-#include <boost/iostreams/filter/gzip.hpp>
-
#include <cassert>
#include <sstream>
-#include <ost/log.hh>
#include <ost/io/io_exception.hh>
#include <ost/io/mol/star_parser.hh>
namespace ost { namespace io {
StarParser::StarParser(std::istream& stream, bool items_as_row):
- filename_("<stream>"), line_num_(0),
+ stream_(stream), filename_("<stream>"), line_num_(0),
has_current_line_(false), current_line_(),
items_row_header_(), items_row_columns_(),
items_row_values_()
{
items_as_row_ = items_as_row;
-
- stream_.push(stream);
}
StarParser::StarParser(const String& filename, bool items_as_row):
- fstream_(filename.c_str()), filename_(filename),
+ fstream_(filename.c_str()), stream_(fstream_), filename_(filename),
line_num_(0), has_current_line_(false), current_line_(),
items_row_header_(), items_row_columns_(), items_row_values_()
{
items_as_row_ = items_as_row;
-
- if (filename.length() >= 3 &&
- filename.substr(filename.length() - 3) == ".gz") {
- stream_.push(boost::iostreams::gzip_decompressor());
- }
-
- stream_.push(fstream_);
}
String StarParser::FormatDiagnostic(StarDiagType type, const String& message,
@@ -78,18 +66,6 @@ String StarParser::FormatDiagnostic(StarDiagType type, const String& message,
return ss.str();
}
-Real StarParser::TryGetReal(const StringRef& data, const String& name) const
-{
- std::pair<bool, Real> value = data.to_float();
- if (!value.first) {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "Expecting real number for " +
- name + ", found '" + data.str() +
- "' instead.", line_num_));
- }
- return value.second;
-}
-
float StarParser::TryGetFloat(const StringRef& data, const String& name) const
{
std::pair<bool, float> value = data.to_float();
@@ -102,28 +78,6 @@ float StarParser::TryGetFloat(const StringRef& data, const String& name) const
return value.second;
}
-std::pair<bool, float> StarParser::TryGetFloat(const StringRef& data,
- const String& name,
- bool may_fail) const
-{
- std::pair<bool, float> value = data.to_float();
- if (!value.first) {
- if (!may_fail) {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "Expecting floating point value for " +
- name + ", found '" + data.str() +
- "' instead.", line_num_));
- }
- else {
- LOG_WARNING(this->FormatDiagnostic(STAR_DIAG_WARNING,
- "Expecting floating point value for " +
- name + ", found '" + data.str() +
- "' instead.", line_num_));
- }
- }
- return value;
-}
-
int StarParser::TryGetInt(const StringRef& data, const String& name) const
{
std::pair<bool, int> value = data.to_int();
@@ -136,27 +90,6 @@ int StarParser::TryGetInt(const StringRef& data, const String& name) const
return value.second;
}
-std::pair<bool, int> StarParser::TryGetInt(const StringRef& data,
- const String& name,
- bool may_fail) const
-{
- std::pair<bool, int> value = data.to_int();
- if (!value.first) {
- if (!may_fail) {
- throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
- "Expecting integer value for " +
- name + ", found '" + data.str() +
- "' instead.", line_num_));
- } else {
- LOG_WARNING(this->FormatDiagnostic(STAR_DIAG_WARNING,
- "Expecting integer value for " +
- name + ", found '" + data.str() +
- "' instead.", line_num_));
- }
- }
- return value;
-}
-
bool StarParser::TryGetBool(const StringRef& data, const String& name) const
{
if (data.length() == 1) {
diff --git a/modules/io/src/mol/star_parser.hh b/modules/io/src/mol/star_parser.hh
index 75feb7adf..96da40e73 100644
--- a/modules/io/src/mol/star_parser.hh
+++ b/modules/io/src/mol/star_parser.hh
@@ -23,8 +23,6 @@
/*
Author: Marco Biasini
*/
-#include <boost/iostreams/filtering_stream.hpp>
-
#include <iostream>
#include <fstream>
#include <vector>
@@ -150,14 +148,6 @@ public:
/// OnBeginData() returned true.
virtual void OnEndData() { }
- /// \brief try to convert a value to Real, on failure raise an exception.
- ///
- /// \param data value to be converted
- /// \param name to be included in the message
- ///
- /// \return converted value
- Real TryGetReal(const StringRef& data, const String& name) const;
-
/// \brief try to convert a value to float, on failure raise an exception.
///
/// \param data value to be converted
@@ -166,17 +156,6 @@ public:
/// \return converted value
float TryGetFloat(const StringRef& data, const String& name) const;
- /// \brief try to convert a value to float, on failure raise an exception.
- ///
- /// \param data value to be converted
- /// \param name to be included in the message
- /// \param may_fail decides if an exception is raised (false) or not (true)
- ///
- /// \return converted value
- std::pair<bool, float> TryGetFloat(const StringRef& data,
- const String& name,
- bool may_fail) const;
-
/// \brief try to convert a value to integer, on failure raise an exception.
///
/// \param data value to be converted
@@ -185,17 +164,6 @@ public:
/// \return converted value
int TryGetInt(const StringRef& data, const String& name) const;
- /// \brief try to convert a value to integer, exception can be turned off.
- ///
- /// \param data value to be converted
- /// \param name to be included in the message
- /// \param may_fail decides if an exception is raised (false) or not (true)
- ///
- /// \return pair with value and indicator if conversion worked
- std::pair<bool, int> TryGetInt(const StringRef& data,
- const String& name,
- bool may_fail) const;
-
/// \brief try to convert a value to bool, on failure raise an exception.
///
/// \param data value to be converted
@@ -270,7 +238,7 @@ private:
void DiagnoseUnknown();
bool ParseMultilineValue(String& value, bool skip=false);
std::ifstream fstream_;
- boost::iostreams::filtering_stream<boost::iostreams::input> stream_;
+ std::istream& stream_;
String filename_;
int line_num_;
bool has_current_line_;
diff --git a/modules/io/tests/CMakeLists.txt b/modules/io/tests/CMakeLists.txt
index bcad4b24e..f10be7bc4 100644
--- a/modules/io/tests/CMakeLists.txt
+++ b/modules/io/tests/CMakeLists.txt
@@ -8,7 +8,6 @@ set(OST_IO_UNIT_TESTS
test_iomanager.cc
tests.cc
test_star_parser.cc
- test_mmcif_reader.cc
)
if (ENABLE_IMG)
list(APPEND OST_IO_UNIT_TESTS test_io_img.cc)
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
deleted file mode 100644
index 09541ca29..000000000
--- a/modules/io/tests/test_mmcif_reader.cc
+++ /dev/null
@@ -1,233 +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 <fstream>
-#include <ost/io/io_exception.hh>
-#include <ost/io/mol/mmcif_reader.hh>
-
-#define BOOST_AUTO_TEST_DYN_LINK
-#include <boost/test/unit_test.hpp>
-
-
-using namespace ost;
-using namespace ost::io;
-
-class TestMMCifParserProtected : MMCifParser {
-public:
- TestMMCifParserProtected(std::istream& stream, mol::EntityHandle& ent_handle):
- MMCifParser(stream, ent_handle, IOProfile())
- { }
-
- TestMMCifParserProtected(std::istream& stream, mol::EntityHandle& ent_handle,
- const IOProfile& profile):
- MMCifParser(stream, ent_handle, profile)
- { }
-
- using MMCifParser::IsValidPDBIdent;
- using MMCifParser::ParseAtomIdent;
- using MMCifParser::ParseAndAddAtom;
- using MMCifParser::EnsureEnoughColumns;
- using MMCifParser::TryStoreIdx;
-};
-
-BOOST_AUTO_TEST_SUITE( io );
-
-BOOST_AUTO_TEST_CASE(mmcif_isvalidpdbid)
-{
- mol::EntityHandle eh=mol::CreateEntity();
-
- // on changing the tests for a PDB id in mmcif files, extend this unit test
- BOOST_MESSAGE(" Running mmcif_isvalidpdbid tests...");
- std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- TestMMCifParserProtected tmmcif_p(s, eh);
- StringRef id = StringRef("1FOO", 4);
- BOOST_MESSAGE(" Testing valid id ('"+ id.str() +"')...");
- BOOST_CHECK(tmmcif_p.IsValidPDBIdent(id));
- BOOST_MESSAGE(" done.");
- id = StringRef("this is to long for a PDB id", 28);
- BOOST_MESSAGE(" Testing oversized PDB id ('"+ id.str() +"')...");
- BOOST_CHECK(!tmmcif_p.IsValidPDBIdent(id));
- BOOST_MESSAGE(" done.");
- id = StringRef("nFOO", 4);
- BOOST_MESSAGE(" Testing PDB id with missing number ('"+ id.str() +"')...");
- BOOST_CHECK(!tmmcif_p.IsValidPDBIdent(id));
- BOOST_MESSAGE(" done.");
-}
-
-BOOST_AUTO_TEST_CASE(mmcif_trystoreidx)
-{
- mol::EntityHandle eh = mol::CreateEntity();
-
- BOOST_MESSAGE(" Running mmcif_trystoreidx tests...");
- std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- TestMMCifParserProtected tmmcif_p(s, eh, IOProfile());
- StarLoopDesc mmcif_h;
- mmcif_h.SetCategory(StringRef("Foo", 3));
- // negative
- BOOST_CHECK_THROW(tmmcif_p.TryStoreIdx(0, "bar", mmcif_h), IOException);
- // positive
- mmcif_h.Add(StringRef("bar", 3));
- BOOST_CHECK_NO_THROW(tmmcif_p.TryStoreIdx(0, "bar", mmcif_h));
-}
-
-BOOST_AUTO_TEST_CASE(mmcif_atom_site_header)
-{
- mol::EntityHandle eh=mol::CreateEntity();
-
- BOOST_MESSAGE(" Running mmcif_atom_site_header tests...");
- std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- MMCifParser mmcif_p(s, eh, IOProfile());
- StarLoopDesc mmcif_h;
- mmcif_h.SetCategory(StringRef("atom_site", 9));
- BOOST_MESSAGE(" auth_asym_id");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("auth_asym_id", 12));
- BOOST_MESSAGE(" id");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("id", 2));
- BOOST_MESSAGE(" label_alt_id");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("label_alt_id", 12));
- BOOST_MESSAGE(" label_asym_id");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("label_asym_id", 13));
- BOOST_MESSAGE(" label_atom_id");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("label_atom_id", 13));
- BOOST_MESSAGE(" label_comp_id");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("label_comp_id", 13));
- BOOST_MESSAGE(" label_entity_id");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("label_entity_id", 15));
- BOOST_MESSAGE(" label_seq_id");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("label_seq_id", 12));
- BOOST_MESSAGE(" type_symbol");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("type_symbol", 11));
- BOOST_MESSAGE(" Cartn_x");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("Cartn_x", 7));
- BOOST_MESSAGE(" Cartn_y");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("Cartn_y", 7));
- BOOST_MESSAGE(" Cartn_z");
- BOOST_CHECK_THROW(mmcif_p.OnBeginLoop(mmcif_h), IOException);
- mmcif_h.Add(StringRef("Cartn_z", 7));
- BOOST_MESSAGE(" done.");
-}
-
-BOOST_AUTO_TEST_CASE(mmcif_ensureenoughcolumns)
-{
- mol::EntityHandle eh=mol::CreateEntity();
-
- BOOST_MESSAGE(" Running mmcif_ensureenoughcolumns tests...");
- std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- IOProfile profile;
- TestMMCifParserProtected tmmcif_p(s, eh, profile);
- std::vector<StringRef> cols;
- BOOST_MESSAGE(" testing short atom_site entry");
- cols.push_back(StringRef("ATOM", 4));
- BOOST_CHECK_THROW(tmmcif_p.EnsureEnoughColumns(cols, 2), IOException);
- BOOST_MESSAGE(" testing correct number");
- BOOST_CHECK(tmmcif_p.EnsureEnoughColumns(cols, 1));
- BOOST_MESSAGE(" testing fault tolerant profile");
- profile.fault_tolerant = true;
- BOOST_CHECK(!tmmcif_p.EnsureEnoughColumns(cols, 2));
- BOOST_MESSAGE(" done.");
-}
-
-BOOST_AUTO_TEST_CASE(mmcif_parseatomident)
-{
- mol::EntityHandle eh = mol::CreateEntity();
-
- BOOST_MESSAGE(" Running mmcif_parseatomident tests...");
- std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- IOProfile profile;
- TestMMCifParserProtected tmmcif_p(s, eh, profile);
- std::vector<StringRef> cols;
- String chain_name;
- StringRef res_name;
- mol::ResNum resnum(0);
- StringRef atom_name;
- char alt_loc;
-
- BOOST_MESSAGE(" testing short atom_site entry");
- // negative
- cols.push_back(StringRef("ATOM", 4));
- BOOST_CHECK_THROW(tmmcif_p.ParseAtomIdent(cols,
- chain_name,
- res_name,
- resnum,
- atom_name,
- alt_loc), IOException);
- // positive
- StarLoopDesc tmmcif_h;
- tmmcif_h.SetCategory(StringRef("atom_site", 9));
- // build header
- //mmcif_h.Add(StringRef("AUTH_ASYM_ID", 12));
- /*
- this->TryStoreIdx(AUTH_ASYM_ID, "auth_asym_id", header);
- this->TryStoreIdx(ID, "id", header);
- this->TryStoreIdx(LABEL_ALT_ID, "label_alt_id", header);
- this->TryStoreIdx(LABEL_ASYM_ID, "label_asym_id", header);
- this->TryStoreIdx(LABEL_ATOM_ID, "label_atom_id", header);
- this->TryStoreIdx(LABEL_COMP_ID, "label_comp_id", header);
- this->TryStoreIdx(LABEL_ENTITY_ID, "label_entity_id", header);
- this->TryStoreIdx(LABEL_SEQ_ID, "label_seq_id", header);
- this->TryStoreIdx(TYPE_SYMBOL, "type_symbol", header);
- this->TryStoreIdx(CARTN_X, "Cartn_x", header);
- this->TryStoreIdx(CARTN_Y, "Cartn_y", header);
- this->TryStoreIdx(CARTN_Z, "Cartn_z", header);
-*/
-
- BOOST_MESSAGE(" done.");
-}
-
-BOOST_AUTO_TEST_CASE(mmcif_parseandaddatom)
-{
- mol::EntityHandle eh = mol::CreateEntity();
-
- BOOST_MESSAGE(" Running mmcif_parseandaddatom tests...");
- std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- TestMMCifParserProtected tmmcif_p(s, eh, IOProfile());
- std::vector<StringRef> cols;
-
- BOOST_MESSAGE(" testing short atom_site entry");
- cols.push_back(StringRef("ATOM", 4));
- BOOST_CHECK_THROW(tmmcif_p.ParseAndAddAtom(cols), IOException);
- BOOST_MESSAGE(" done.");
-}
-
-BOOST_AUTO_TEST_CASE(mmcif_testreader)
-{
- mol::EntityHandle eh = mol::CreateEntity();
- std::ifstream s("testfiles/mmcif/atom_site.mmcif");
- IOProfile profile;
- MMCifParser mmcif_p(s, eh, profile);
-
- mmcif_p.Parse();
-
- BOOST_REQUIRE_EQUAL(eh.GetChainCount(), 2);
- BOOST_REQUIRE_EQUAL(eh.GetResidueCount(), 4);
- BOOST_REQUIRE_EQUAL(eh.GetAtomCount(), 25);
-}
-
-BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/testfiles/mmcif/atom_site.mmcif b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
deleted file mode 100644
index 6c9a29637..000000000
--- a/modules/io/tests/testfiles/mmcif/atom_site.mmcif
+++ /dev/null
@@ -1,49 +0,0 @@
-data_1BAR
-
-loop_
-_atom_site.group_PDB
-_atom_site.type_symbol
-_atom_site.label_atom_id
-_atom_site.label_comp_id
-_atom_site.label_asym_id
-_atom_site.label_seq_id
-_atom_site.label_alt_id
-_atom_site.label_entity_id
-_atom_site.Cartn_x
-_atom_site.Cartn_y
-_atom_site.Cartn_z
-_atom_site.occupancy
-_atom_site.B_iso_or_equiv
-_atom_site.footnote_id
-_atom_site.auth_seq_id
-_atom_site.id
-_atom_site.auth_asym_id
-ATOM N N VAL A 11 . 1 25.369 30.691 11.795 1.00 17.93 . 11 1 A
-ATOM C CA VAL A 11 . 1 25.970 31.965 12.332 1.00 17.75 . 11 2 A
-ATOM C C VAL A 11 . 1 25.569 32.010 13.808 1.00 17.83 . 11 3 A
-ATOM O O VAL A 11 . 1 24.735 31.190 14.167 1.00 17.53 . 11 4 A
-ATOM C CB VAL A 11 . 1 25.379 33.146 11.540 1.00 17.66 . 11 5 A
-ATOM C CG1 VAL A 11 . 1 25.584 33.034 10.030 1.00 18.86 . 11 6 A
-ATOM C CG2 VAL A 11 . 1 23.933 33.309 11.872 1.00 17.12 . 11 7 A
-ATOM N N THR A 12 . 1 26.095 32.930 14.590 1.00 18.97 4 12 8 A
-ATOM C CA THR A 12 . 1 25.734 32.995 16.032 1.00 19.80 4 12 9 A
-ATOM C C THR A 12 . 1 24.695 34.106 16.113 1.00 20.92 4 12 10 A
-ATOM O O THR A 12 . 1 24.869 35.118 15.421 1.00 21.84 4 12 11 A
-ATOM C CB THR A 12 . 1 26.911 33.346 17.018 1.00 20.51 4 12 12 A
-ATOM O OG1 THR A 12 3 1 27.946 33.921 16.183 0.50 20.29 4 12 13 A
-ATOM O OG1 THR A 12 4 1 27.769 32.142 17.103 0.50 20.59 4 12 14 A
-ATOM C CG2 THR A 12 3 1 27.418 32.181 17.878 0.50 20.47 4 12 15 A
-ATOM C CG2 THR A 12 4 1 26.489 33.778 18.426 0.50 20.00 4 12 16 A
-ATOM N N ILE A 13 . 1 23.664 33.855 16.884 1.00 22.08 . 13 17 A
-ATOM C CA ILE A 13 . 1 22.623 34.850 17.093 1.00 23.44 . 13 18 A
-ATOM C C ILE A 13 . 1 22.657 35.113 18.610 1.00 25.77 . 13 19 A
-ATOM O O ILE A 13 . 1 23.123 34.250 19.406 1.00 26.28 . 13 20 A
-ATOM C CB ILE A 13 . 1 21.236 34.463 16.492 1.00 22.67 . 13 21 A
-ATOM C CG1 ILE A 13 . 1 20.478 33.469 17.371 1.00 22.14 . 13 22 A
-ATOM C CG2 ILE A 13 . 1 21.357 33.986 15.016 1.00 21.75 . 13 23 A
-# - - - - data truncated for brevity - - - -
-HETATM C C1 APS C 14 1 1 4.171 29.012 7.116 0.58 17.27 1 300 101 A
-HETATM C C2 APS C 14 1 1 4.949 27.758 6.793 0.58 16.95 1 300 102 A
-HETATM O O3 APS C 14 1 1 4.800 26.678 7.393 0.58 16.85 1 300 103 A
-HETATM N N4 APS C 14 1 1 5.930 27.841 5.869 0.58 16.43 1 300 104 A
-# - - - - data truncated for brevity - - - -
--
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