From aac17c6cf70a13e6aa53792cf162b8d7a4022ef4 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 20 Jul 2011 12:12:48 +0200
Subject: [PATCH] First version of a MMCIF Parser, early stage (experimental)
---
modules/io/pymod/CMakeLists.txt | 1 +
modules/io/pymod/__init__.py | 101 +++-
modules/io/pymod/wrap_io.cc | 2 +
modules/io/src/mol/CMakeLists.txt | 2 +
modules/io/src/mol/mmcif_reader.cc | 550 ++++++++++++++++++
modules/io/src/mol/mmcif_reader.hh | 208 +++++++
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 ++
11 files changed, 1248 insertions(+), 4 deletions(-)
create mode 100644 modules/io/src/mol/mmcif_reader.cc
create mode 100644 modules/io/src/mol/mmcif_reader.hh
create mode 100644 modules/io/tests/test_mmcif_reader.cc
create 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 902089f7f..023e000b8 100644
--- a/modules/io/pymod/CMakeLists.txt
+++ b/modules/io/pymod/CMakeLists.txt
@@ -1,6 +1,7 @@
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 74047dec0..57a0464bb 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 returns one or more entities. Several options
+ Load PDB file from disk and return 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`.
@@ -264,6 +264,105 @@ 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/wrap_io.cc b/modules/io/pymod/wrap_io.cc
index af5087cd2..1d9e3b936 100644
--- a/modules/io/pymod/wrap_io.cc
+++ b/modules/io/pymod/wrap_io.cc
@@ -72,6 +72,7 @@ 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
@@ -117,6 +118,7 @@ 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 1201eb58f..db328bb9c 100644
--- a/modules/io/src/mol/CMakeLists.txt
+++ b/modules/io/src/mol/CMakeLists.txt
@@ -15,12 +15,14 @@ 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
new file mode 100644
index 000000000..535aedbfa
--- /dev/null
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -0,0 +1,550 @@
+//------------------------------------------------------------------------------
+// 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;
+ record_type_ = "";
+ 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;
+ record_type_ = "";
+ 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_[PDBX_PDB_INS_CODE] = header.GetIndex("pdbx_PDB_ins_code");
+ 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;
+}
+
+bool MMCifParser::EnsureEnoughColumns(const std::vector<StringRef>& columns,
+ size_t size)
+{
+ if (columns.size() < size) {
+ if (profile_.fault_tolerant) {
+ return false;
+ }
+ throw IOException(this->FormatDiagnostic(STAR_DIAG_ERROR,
+ "Not enough data fields",
+ this->GetCurrentLinenum()));
+ }
+ return true;
+}
+
+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)
+{
+ // is checking really neccessary? just by using OnBeginData, enough columns
+ // should be available!
+ if (!this->EnsureEnoughColumns(columns, 12)) {
+ return false;
+ }
+ // 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;
+ }
+ }
+
+ if (indices_[PDBX_PDB_INS_CODE] != -1) { // unit test
+ resnum=to_res_num(res_num.second, columns[indices_[PDBX_PDB_INS_CODE]][0]);
+ }
+ else {
+ resnum=to_res_num(res_num.second, ' ');
+ }
+
+ return true;
+}
+
+void MMCifParser::ParseAndAddAtom(const std::vector<StringRef>& columns)
+{
+ if (!this->EnsureEnoughColumns(columns, 12)) {
+ return;
+ }
+ 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, temp;
+ 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");
+ } else {
+ occ = 1.00f;
+ }
+ if (indices_[B_ISO_OR_EQUIV] != -1) { // unit test
+ temp = this->TryGetReal(columns[indices_[B_ISO_OR_EQUIV]],
+ "atom_site.B_iso_or_equiv");
+ } else {
+ temp = 0;
+ }
+
+ // 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_;
+ }
+ if (indices_[B_ISO_OR_EQUIV] != -1) {// unit test
+ ah.SetBFactor(temp);
+ }
+ if (indices_[OCCUPANCY] != -1) {// unit test
+ ah.SetOccupancy(occ);
+ }
+
+ // record type
+ if (indices_[GROUP_PDB] != -1) {
+ record_type_ = columns[indices_[GROUP_PDB]].str();
+ } else {
+ record_type_ = "ATOM";
+ }
+ ah.SetHetAtom(record_type_[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
new file mode 100644
index 000000000..20f7bacd9
--- /dev/null
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -0,0 +1,208 @@
+//------------------------------------------------------------------------------
+// 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 {
+
+/// \enum categories of the mmcif format
+typedef enum {
+ ATOM_SITE,
+ DONT_KNOW
+} MMCifCategory;
+
+
+/// \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 Check no. of columns available.
+ ///
+ /// \param columns fields
+ /// \param size required no. of columns
+ ///
+ /// \return true if there are enough columns, false otherwise
+ bool EnsureEnoughColumns(const std::vector<StringRef>& columns, size_t size);
+
+ /// \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 ||
+ PDBX_PDB_INS_CODE,
+ OCCUPANCY,
+ B_ISO_OR_EQUIV,
+ GROUP_PDB ///< record name
+ } AtomSiteItems;
+
+ // 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_;
+ String record_type_;
+ 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 33e235d09..d0440904e 100644
--- a/modules/io/src/mol/star_parser.cc
+++ b/modules/io/src/mol/star_parser.cc
@@ -20,28 +20,40 @@
/*
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):
- stream_(stream), filename_("<stream>"), line_num_(0),
+ 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()), stream_(fstream_), filename_(filename),
+ fstream_(filename.c_str()), 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,
@@ -66,6 +78,18 @@ 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();
@@ -78,6 +102,28 @@ 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();
@@ -90,6 +136,27 @@ 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 96da40e73..75feb7adf 100644
--- a/modules/io/src/mol/star_parser.hh
+++ b/modules/io/src/mol/star_parser.hh
@@ -23,6 +23,8 @@
/*
Author: Marco Biasini
*/
+#include <boost/iostreams/filtering_stream.hpp>
+
#include <iostream>
#include <fstream>
#include <vector>
@@ -148,6 +150,14 @@ 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
@@ -156,6 +166,17 @@ 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
@@ -164,6 +185,17 @@ 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
@@ -238,7 +270,7 @@ private:
void DiagnoseUnknown();
bool ParseMultilineValue(String& value, bool skip=false);
std::ifstream fstream_;
- std::istream& stream_;
+ boost::iostreams::filtering_stream<boost::iostreams::input> 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 f10be7bc4..bcad4b24e 100644
--- a/modules/io/tests/CMakeLists.txt
+++ b/modules/io/tests/CMakeLists.txt
@@ -8,6 +8,7 @@ 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
new file mode 100644
index 000000000..09541ca29
--- /dev/null
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -0,0 +1,233 @@
+//------------------------------------------------------------------------------
+// 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
new file mode 100644
index 000000000..6c9a29637
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/atom_site.mmcif
@@ -0,0 +1,49 @@
+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 - - - -
--
GitLab