diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index 1fa74533fa8039047f11f5d94c60b19de4bfd225..01e85e9cf5e605b142e1f032f30eb99e1776bf61 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -15,6 +15,7 @@ Changes in Release 2.5.0
flag to disable stereochemistry checks for lDDT, TMscore (including
associated chain mapping) computed by USalign, make residues/atoms uniquely
identifiable (also considering residue number insertion codes).
+ * Read atom charges if present from PDB/mmCIF/SDF files
* Several bug fixes and improvements.
Changes in Release 2.4.0
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 83aa5d857cd44b803c1de242cfeb5cdbe018624b..aa7daa5413e1039eb3ec3181d824caa050686f3a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -14,7 +14,7 @@ cmake_policy(SET CMP0060 NEW)
project(OpenStructure CXX C)
set (CMAKE_EXPORT_COMPILE_COMMANDS 1)
set (OST_VERSION_MAJOR 2)
-set (OST_VERSION_MINOR 4)
+set (OST_VERSION_MINOR 5)
set (OST_VERSION_PATCH 0)
set (OST_VERSION_STRING ${OST_VERSION_MAJOR}.${OST_VERSION_MINOR}.${OST_VERSION_PATCH} )
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake_support)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 3c33dceb50fa6378532e6066067283de524530ac..176cd5e1f6028c096d9b1bdc3dbd4b6f3fdce673 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -57,7 +57,6 @@ import os
import traceback
import ost
-from ost import conop
from ost import io
from ost.mol.alg import ligand_scoring
@@ -366,11 +365,24 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
if model_ligands is not None:
# Replace model ligand by path
- assert len(model_ligands) == len(scorer.model_ligands)
- # Map ligand => path
- model_ligands_map = {k: v for k, v in zip(scorer.model_ligands,
- args.model_ligands)}
- out["model_ligands"] = args.model_ligands
+ if len(model_ligands) == len(scorer.model_ligands):
+ # Map ligand => path
+ model_ligands_map = {k: v for k, v in zip(scorer.model_ligands,
+ args.model_ligands)}
+ out["model_ligands"] = args.model_ligands
+ elif len(model_ligands) < len(scorer.model_ligands):
+ # Multi-ligand SDF files were given
+ # Map ligand => path:idx
+ out["model_ligands"] = []
+ for ligand, filename in zip(model_ligands, args.model_ligands):
+ assert isinstance(ligand, ost.mol.EntityHandle)
+ for i, residue in enumerate(ligand.residues):
+ out["model_ligands"].append(f"{filename}:{i}")
+ else:
+ # This should never happen and would be a bug
+ raise RuntimeError("Fewer ligands in the model scorer "
+ "(%d) than given (%d)" % (
+ len(scorer.model_ligands), len(model_ligands)))
else:
model_ligands_map = {l: _QualifiedResidueNotation(l)
for l in scorer.model_ligands}
@@ -378,11 +390,25 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
if reference_ligands is not None:
# Replace reference ligand by path
- assert len(reference_ligands) == len(scorer.target_ligands)
- # Map ligand => path
- reference_ligands_map = {k: v for k, v in zip(scorer.target_ligands,
- args.reference_ligands)}
- out["reference_ligands"] = args.reference_ligands
+ if len(reference_ligands) == len(scorer.target_ligands):
+ # Map ligand => path
+ reference_ligands_map = {k: v for k, v in zip(scorer.target_ligands,
+ args.reference_ligands)}
+ out["reference_ligands"] = args.reference_ligands
+ elif len(reference_ligands) < len(scorer.target_ligands):
+ # Multi-ligand SDF files were given
+ # Map ligand => path:idx
+ out["reference_ligands"] = []
+ for ligand, filename in zip(reference_ligands, args.reference_ligands):
+ assert isinstance(ligand, ost.mol.EntityHandle)
+ for i, residue in enumerate(ligand.residues):
+ out["reference_ligands"].append(f"{filename}:{i}")
+ else:
+ # This should never happen and would be a bug
+ raise RuntimeError("Fewer ligands in the reference scorer "
+ "(%d) than given (%d)" % (
+ len(scorer.target_ligands), len(reference_ligands)))
+
else:
reference_ligands_map = {l: _QualifiedResidueNotation(l)
for l in scorer.target_ligands}
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 1975e401be9e21d7bcbee708b8ab5b5d068ebc5b..e019bcef45d8742129ea99819072b09b9baea6eb 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -2,7 +2,7 @@ FROM ubuntu:22.04
# ARGUMENTS
###########
-ARG OPENSTRUCTURE_VERSION="2.4.0"
+ARG OPENSTRUCTURE_VERSION="2.5.0"
ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=2
ARG OPENMM_VERSION="7.7.0"
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index a71c8db2ec2cbc978da9de73001857e8718da23d..8fd2dbab5d4be5f12cc6ae9c0443818fa20e8e44 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -23,7 +23,6 @@ You can compare two structures from the command line with the
interface to :class:`ost.mol.alg.scoring.Scorer`
.. warning::
-
``compare-structures`` underwent a complete rewrite in OpenStructure
release 2.4.0. The old version is still available as
``compare-structures-legacy`` with documentation available
@@ -412,4 +411,4 @@ Details on the usage (output of ``ost compare-ligand-structures --help``):
Additional information about the scores and output values is available in
:meth:`rmsd_details <ost.mol.alg.ligand_scoring.LigandScorer.rmsd_details>` and
-:meth:`lddt_pli_details <ost.mol.alg.ligand_scoring.LigandScorer.lddt_pli_details>`.
\ No newline at end of file
+:meth:`lddt_pli_details <ost.mol.alg.ligand_scoring.LigandScorer.lddt_pli_details>`.
diff --git a/modules/io/src/mol/mmcif_info.cc b/modules/io/src/mol/mmcif_info.cc
index 576e05912bb0073c9d93215d12ced3747353a2c8..ef44d4813fef36f2c709888b2acaef4d007342ee 100644
--- a/modules/io/src/mol/mmcif_info.cc
+++ b/modules/io/src/mol/mmcif_info.cc
@@ -207,6 +207,12 @@ void MMCifInfo::AddEntityBranchLink(String chain_name,
mol::AtomHandle atom2,
unsigned char bond_order)
{
+ if (!atom1.IsValid() || !atom2.IsValid()) {
+ /* Would love to give details about the atoms... but atom names are not
+ available at this point. */
+ LOG_WARNING("Invalid branch link found in chain '"+chain_name+"'.");
+ return;
+ }
// check if element already exists
MMCifInfoEntityBranchLinkMap::iterator blm_it =
entity_branches_.find(chain_name);
diff --git a/modules/io/src/mol/mmcif_reader.cc b/modules/io/src/mol/mmcif_reader.cc
index 7ddde3b2cf53f36807b659cb943f13207ed0a203..e550d96f83dfc160819f860055561534606b48fd 100644
--- a/modules/io/src/mol/mmcif_reader.cc
+++ b/modules/io/src/mol/mmcif_reader.cc
@@ -141,6 +141,7 @@ bool MMCifReader::OnBeginLoop(const StarLoopDesc& header)
indices_[AUTH_SEQ_ID] = header.GetIndex("auth_seq_id");
indices_[PDBX_PDB_INS_CODE] = header.GetIndex("pdbx_PDB_ins_code");
indices_[PDBX_PDB_MODEL_NUM] = header.GetIndex("pdbx_PDB_model_num");
+ indices_[FORMAL_CHARGE] = header.GetIndex("pdbx_formal_charge");
// post processing
if (category_counts_[category_] > 0) {
@@ -482,6 +483,7 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
return;
}
Real occ = 1.00f, temp = 0;
+ int charge = 0;
geom::Vec3 apos;
for (int i = CARTN_X; i <= CARTN_Z; ++i) {
@@ -505,6 +507,13 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
"atom_site.B_iso_or_equiv");
}
}
+ if (indices_[FORMAL_CHARGE] != -1) { // unit test
+ String charge_s = columns[indices_[FORMAL_CHARGE]].str();
+ if (charge_s != "?" && charge_s != ".") {
+ charge = this->TryGetInt(columns[indices_[FORMAL_CHARGE]],
+ "atom_site.pdbx_formal_charge");
+ }
+ }
// determine element
String s_ele(columns[indices_[TYPE_SYMBOL]].str());
@@ -665,6 +674,8 @@ void MMCifReader::ParseAndAddAtom(const std::vector<StringRef>& columns)
ah.SetOccupancy(occ);
+ ah.SetCharge(charge);
+
// record type
ah.SetHetAtom(indices_[GROUP_PDB] == -1 ? false :
columns[indices_[GROUP_PDB]][0]=='H');
diff --git a/modules/io/src/mol/mmcif_reader.hh b/modules/io/src/mol/mmcif_reader.hh
index 1f21c3928cac354f5f69197e763443d37a2dc9f6..f2f2d2dbd78069a778c6cd3ccab9d49abb7b0cb1 100644
--- a/modules/io/src/mol/mmcif_reader.hh
+++ b/modules/io/src/mol/mmcif_reader.hh
@@ -359,7 +359,7 @@ protected:
private:
/// \enum magic numbers of this class
typedef enum {
- MAX_ITEMS_IN_ROW=18 ///< count for possible items in a loop row
+ MAX_ITEMS_IN_ROW=19 ///< count for possible items in a loop row
} MMCifMagicNos;
/// \enum items of the atom_site category
@@ -381,7 +381,8 @@ private:
B_ISO_OR_EQUIV,
PDBX_PDB_INS_CODE,
GROUP_PDB, ///< record name
- PDBX_PDB_MODEL_NUM ///< model no. (especially NMR structures)
+ PDBX_PDB_MODEL_NUM,///< model no. (especially NMR structures)
+ FORMAL_CHARGE
} AtomSiteItems;
/// \enum items of the entity category
diff --git a/modules/io/src/mol/pdb_reader.cc b/modules/io/src/mol/pdb_reader.cc
index 3b69915de24795389f6566e5ce43e0cc487d9c8d..930ffbcf453f0563768d8aae0351f65fe6ac07bf 100644
--- a/modules/io/src/mol/pdb_reader.cc
+++ b/modules/io/src/mol/pdb_reader.cc
@@ -697,8 +697,11 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
atom_name, alt_loc, record_type, serial)) {
return;
}
- std::pair<bool, Real> charge, radius;
- std::pair<bool, Real> occ, temp;
+
+ std::pair<bool, Real> charge = std::make_pair(false, 0.0);
+ std::pair<bool, Real> radius = std::make_pair(false, 0.0);
+ std::pair<bool, Real> occ = std::make_pair(false, 0.0);
+ std::pair<bool, Real> temp = std::make_pair(false, 0.0);
geom::Vec3 apos;
for (int i=0;i<3; ++i) {
@@ -728,6 +731,20 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
if (line.length()>=66) {
temp=line.substr(60, 6).ltrim().to_float();
}
+ if (line.length()>=80) {
+ // example charge formatting: 1+, 2- etc.
+ charge = line.substr(78,1).trim().to_float();
+ if(charge.first) {
+ if(line[79] != '-' && line[79] != '+') {
+ std::stringstream ss;
+ ss << "error on line " << line_num << ": "
+ << "expect charge in format 1+, 2-, etc. got: "
+ << line.substr(78, 2);
+ throw IOException(ss.str());
+ }
+ if(line[79] == '-') charge.second *= (-1);
+ }
+ }
}
LOG_TRACE( "line: [" << line << "]" );
String s_ele;
@@ -838,6 +855,7 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
}
Real b=temp.first ? temp.second : 0.0;
Real o=occ.first ? occ.second : 1.0;
+
if (!profile_.quack_mode && alt_loc!=' ') {
// Check if there is already a atom with the same name.
mol::AtomHandle me=curr_residue_.FindAtom(aname);
@@ -869,16 +887,16 @@ void PDBReader::ParseAndAddAtom(const StringRef& line, int line_num,
ah=editor.InsertAtom(curr_residue_, aname, apos, s_ele);
++atom_count_;
}
- if(is_pqr_) {
- if (radius.first) {
- ah.SetRadius(radius.second);
- }
+
+ if (radius.first) {
+ ah.SetRadius(radius.second);
}
- ah.SetBFactor(b);
- ah.SetOccupancy(o);
if (charge.first) {
ah.SetCharge(charge.second);
}
+ ah.SetBFactor(b);
+ ah.SetOccupancy(o);
+
ah.SetHetAtom(record_type[0]=='H');
if(profile_.read_conect && serial != -1) {
this->amap_[serial] = ah;
diff --git a/modules/io/src/mol/sdf_reader.cc b/modules/io/src/mol/sdf_reader.cc
index 2db564c66de7d6c5990a9b78897d3420b5abfc12..3c28e279cb71a3f89575d5fe3bca70ce621c6c6f 100644
--- a/modules/io/src/mol/sdf_reader.cc
+++ b/modules/io/src/mol/sdf_reader.cc
@@ -159,6 +159,11 @@ void SDFReader::ParseAndAddHeader(const String& line, int line_num,
break;
case 4: // counts line
{
+ String version_str=line.substr(34, 5);
+ if (version_str != "V2000") {
+ String msg="Unsupported SDF version: %s.";
+ throw IOException(str(format(msg) % version_str));
+ }
String s_anum=line.substr(0,3);
try {
atom_count_=boost::lexical_cast<int>(boost::trim_copy(s_anum));
@@ -188,9 +193,15 @@ void SDFReader::ParseAndAddAtom(const String& line, int line_num,
LOG_TRACE( "line: [" << line << "]" );
if(line.length()<48 || line.length()>69) {
- String msg="Bad atom line %d: Not correct number of characters on the"
- " line: %i (should be between 48 and 69)";
- throw IOException(str(format(msg) % line_num % line.length()));
+ // Handle the case where we have trailing space characters
+ if (line.length()>69 && boost::trim_copy(line.substr(69)) == "") {
+ LOG_DEBUG( "Ignoring trailing space" );
+ }
+ else {
+ String msg="Bad atom line %d: Not correct number of characters on the"
+ " line: %i (should be between 48 and 69)";
+ throw IOException(str(format(msg) % line_num % line.length()));
+ }
}
int anum = line_num-4; // start at 1 on fifth line since first four lines are header
String s_posx=line.substr(0,10);
@@ -253,9 +264,15 @@ void SDFReader::ParseAndAddBond(const String& line, int line_num,
LOG_TRACE( "line: [" << line << "]" );
if(line.length()<9 || line.length()>21) {
- String msg="Bad bond line %d: Not correct number of characters on the"
- " line: %i (should be between 9 and 21)";
- throw IOException(str(format(msg) % line_num % line.length()));
+ // Handle the case where we have trailing space characters
+ if (line.length()>21 && boost::trim_copy(line.substr(21)) == "") {
+ LOG_DEBUG( "Ignoring trailing space" );
+ }
+ else {
+ String msg="Bad bond line %d: Not correct number of characters on the"
+ " line: %i (should be between 9 and 21)";
+ throw IOException(str(format(msg) % line_num % line.length()));
+ }
}
String s_first_name=line.substr(0,3);
diff --git a/modules/io/src/mol/sdf_writer.cc b/modules/io/src/mol/sdf_writer.cc
index 8deaf9a7819f0fff6c069b721af7b55e446a0245..e39444d0cdd394b568f82568622c6b4fbc006545 100644
--- a/modules/io/src/mol/sdf_writer.cc
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -50,7 +50,12 @@ namespace {
<< format("%10.4f") % atom.GetPos()[1]
<< format("%10.4f ") % atom.GetPos()[2]
<< format("%-3s") % SDFAtomWriter::FormatEle(atom.GetElement())
- << " 0 0 0 0 0 0"
+ << " 0" // Mass difference
+ << format("%-3s") % SDFAtomWriter::FormatCharge(atom.GetCharge()) // Charge
+ << " 0" // Atom stereo parity
+ << " 0" // Hydrogen count + 1
+ << " 0" // Stereo care box
+ << " 0" // Valence
<< std::endl;
return true;
}
@@ -66,6 +71,24 @@ namespace {
}
return return_ele;
}
+
+ static String FormatCharge(const Real& chg) {
+ // Format charge according to https://doi.org/10.1021/ci00007a012
+ // 0 = uncharged or value other than these, 1 = +3, 2 = +2, 3 = +1,
+ // 4 doublet (A), 5 = -1, 6 = -2, 7 = -3
+ // Doublet means radical. This function would never return 4.
+ if (chg == 0) {
+ return " 0";
+ }
+ else if (abs(chg) > 3) {
+ String msg = "SDF format only supports charges from -3 to +3, not %g";
+ throw IOException(str(format(msg) % chg));
+ }
+ else {
+ Real chg_sdf = 4 - chg;
+ return str(format("%3.0f") % chg_sdf);
+ }
+ }
private:
std::ostream& ostr_;
std::map<long, int>& atom_indices_;
diff --git a/modules/io/tests/test_io_sdf.py b/modules/io/tests/test_io_sdf.py
index 718ac0691192f24ddbc04c71d2ef71d15fa631cf..735158fc3c38f8ed2345415ae913143f8b7d1bf1 100644
--- a/modules/io/tests/test_io_sdf.py
+++ b/modules/io/tests/test_io_sdf.py
@@ -16,6 +16,28 @@ class TestSDF(unittest.TestCase):
ent = io.LoadSDF('testfiles/sdf/6d5w_rank1_crlf.sdf.gz')
self.assertEqual(len(ent.atoms), 21)
self.assertEqual(len(ent.bonds), 24)
+
+ def test_Charge(self):
+ ent = io.LoadSDF('testfiles/sdf/simple.sdf')
+ self.assertEqual(ent.FindAtom("00001_Simple Ligand", 1, "6").charge, 0)
+
+ # Write and read charges properly
+ for chg in range(-3, 4):
+ ent.FindAtom("00001_Simple Ligand", 1, "6").charge = chg
+ sdf_str = io.EntityToSDFStr(ent)
+ ent = io.SDFStrToEntity(sdf_str)
+ self.assertEqual(ent.FindAtom("00001_Simple Ligand", 1, "6").charge, chg)
+
+ # Only -3 to +3 is supported
+ # If M CHG is implemented the following tests can be removed
+ with self.assertRaises(Exception):
+ ent.FindAtom("00001_Simple Ligand", 1, "6").charge = 4
+ io.EntityToSDFStr(ent)
+
+ with self.assertRaises(Exception):
+ ent.FindAtom("00001_Simple Ligand", 1, "6").charge = -4
+ io.EntityToSDFStr(ent)
+
if __name__== '__main__':
from ost import testutils
diff --git a/modules/io/tests/test_mmcif_info.cc b/modules/io/tests/test_mmcif_info.cc
index 5370d2ce1eeb733bbba23b2ff52fadaf2cd22274..faf5cc10379e88b73db25e58be05bbf64a34ce6b 100644
--- a/modules/io/tests/test_mmcif_info.cc
+++ b/modules/io/tests/test_mmcif_info.cc
@@ -341,16 +341,23 @@ BOOST_AUTO_TEST_CASE(mmcif_info)
mol::ResidueHandle res11 = editor.AppendResidue(ch1, "NAG");
mol::ResidueHandle res12 = editor.AppendResidue(ch1, "NAG");
// create AtomHandles for testing
- mol::AtomHandle atom11 = editor.InsertAtom(res12, "C1",geom::Vec3());
- mol::AtomHandle atom12 = editor.InsertAtom(res11, "O4",geom::Vec3());
+ mol::AtomHandle atom11 = editor.InsertAtom(res12, "C1", geom::Vec3());
+ mol::AtomHandle atom12 = editor.InsertAtom(res11, "O4", geom::Vec3());
mol::ChainHandle ch2 = editor.InsertChain("B");
mol::ResidueHandle res21 = editor.AppendResidue(ch2, "BMA");
mol::ResidueHandle res22 = editor.AppendResidue(ch2, "MAN");
// create AtomHandles for testing
- mol::AtomHandle atom21 = editor.InsertAtom(res22, "C1",geom::Vec3());
- mol::AtomHandle atom22 = editor.InsertAtom(res21, "O3",geom::Vec3());
+ mol::AtomHandle atom21 = editor.InsertAtom(res22, "C1", geom::Vec3());
+ mol::AtomHandle atom22 = editor.InsertAtom(res21, "O3", geom::Vec3());
+ // create invalid AtomHandle pairs for testing
+ mol::AtomHandle atom_invalid;
info.AddEntityBranchLink(ch1.GetName(), atom11, atom12, 1);
info.AddEntityBranchLink(ch2.GetName(), atom21, atom22, 1);
+ /* Sometimes branched PDB entries link two atoms which are available in the
+ compound's definition but not resolved (missing) in the coordinates, e.g.
+ RCSB entry 7zim. Check that in case of invalid atom, no link is created. */
+ info.AddEntityBranchLink(ch2.GetName(), atom11, atom_invalid, 1);
+ info.AddEntityBranchLink(ch2.GetName(), atom_invalid, atom12, 1);
std::vector<MMCifInfoEntityBranchLink> blinks = info.GetEntityBranchLinks();
BOOST_CHECK(blinks.size() == 2);
diff --git a/modules/io/tests/test_mmcif_reader.cc b/modules/io/tests/test_mmcif_reader.cc
index e03eb0073be2133e959420e390e3c6f07ec07fde..6d81b46033ab1143be596f7464020706a4645abd 100644
--- a/modules/io/tests/test_mmcif_reader.cc
+++ b/modules/io/tests/test_mmcif_reader.cc
@@ -1616,5 +1616,22 @@ BOOST_AUTO_TEST_CASE(mmcif_atom_site_B_iso_or_equiv_tests)
BOOST_TEST_MESSAGE(" done.");
}
+BOOST_AUTO_TEST_CASE(mmcif_formal_charge)
+{
+ mol::EntityHandle eh = mol::CreateEntity();
+ std::ifstream s("testfiles/mmcif/4C79_charged.cif");
+ IOProfile profile;
+ MMCifReader mmcif_p(s, eh, profile);
+ mmcif_p.Parse();
+
+ BOOST_CHECK_EQUAL(eh.FindAtom("A", 49, "OE2").GetCharge(), -1);
+ BOOST_CHECK_EQUAL(eh.FindAtom("A", 49, "OE1").GetCharge(), 0); // '?'
+ BOOST_CHECK_EQUAL(eh.FindAtom("A", 49, "CA").GetCharge(), 0); // Explicit 0
+ BOOST_CHECK_EQUAL(eh.FindAtom("A", 49, "CB").GetCharge(), 0); // '.'
+ BOOST_CHECK_EQUAL(eh.FindAtom("C", 1, "ZN").GetCharge(), 2);
+ BOOST_CHECK_EQUAL(eh.FindAtom("D", 1, "NA").GetCharge(), 1);
+
+}
+
BOOST_AUTO_TEST_SUITE_END();
diff --git a/modules/io/tests/testfiles/mmcif/4C79_charged.cif b/modules/io/tests/testfiles/mmcif/4C79_charged.cif
new file mode 100644
index 0000000000000000000000000000000000000000..c5089608ff706068345942fb2240a2f7394c5a52
--- /dev/null
+++ b/modules/io/tests/testfiles/mmcif/4C79_charged.cif
@@ -0,0 +1,289 @@
+data_4C79
+# taken and modified from 4C79.cif
+_entry.id 4C79
+#
+loop_
+_entity.id
+_entity.type
+_entity.src_method
+_entity.pdbx_description
+_entity.formula_weight
+_entity.pdbx_number_of_molecules
+_entity.pdbx_ec
+_entity.pdbx_mutation
+_entity.pdbx_fragment
+_entity.details
+1 polymer man SMOOTHENED 22144.174 2 ? ? 'CYSTEINE-RICH DOMAIN (CRD), RESIDUES 28-210' ?
+2 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ?
+3 non-polymer syn 'SODIUM ION' 22.990 2 ? ? ? ?
+4 water nat water 18.015 48 ? ? ? ?
+#
+_entity_poly.entity_id 1
+_entity_poly.type 'polypeptide(L)'
+_entity_poly.nstd_linkage no
+_entity_poly.nstd_monomer no
+_entity_poly.pdbx_seq_one_letter_code
+;MAVILHPNETIFNDFCKKSTTCEVLKYNTCLGSPLPYTHTSLILAEDSETQEEAFEKLAMWSGLRNAPRCWAVIQPLLCA
+VYMPKCENGKVELPSQHLCQATRNPCSIVERERGWPNFLKCENKEQFPKGCQNEVQKLKFNTSGQCEAPLVKTDIQASWY
+KDVEGCGIQCDNPLFTEDEHSDMHKLEHHHHHH
+;
+_entity_poly.pdbx_seq_one_letter_code_can
+;MAVILHPNETIFNDFCKKSTTCEVLKYNTCLGSPLPYTHTSLILAEDSETQEEAFEKLAMWSGLRNAPRCWAVIQPLLCA
+VYMPKCENGKVELPSQHLCQATRNPCSIVERERGWPNFLKCENKEQFPKGCQNEVQKLKFNTSGQCEAPLVKTDIQASWY
+KDVEGCGIQCDNPLFTEDEHSDMHKLEHHHHHH
+;
+_entity_poly.pdbx_strand_id A
+_entity_poly.pdbx_target_identifier ?
+#
+loop_
+_entity_poly_seq.entity_id
+_entity_poly_seq.num
+_entity_poly_seq.mon_id
+_entity_poly_seq.hetero
+1 1 MET n
+1 2 ALA n
+1 3 VAL n
+1 4 ILE n
+1 5 LEU n
+1 6 HIS n
+1 7 PRO n
+1 8 ASN n
+1 9 GLU n
+1 10 THR n
+1 11 ILE n
+1 12 PHE n
+1 13 ASN n
+1 14 ASP n
+1 15 PHE n
+1 16 CYS n
+1 17 LYS n
+1 18 LYS n
+1 19 SER n
+1 20 THR n
+1 21 THR n
+1 22 CYS n
+1 23 GLU n
+1 24 VAL n
+1 25 LEU n
+1 26 LYS n
+1 27 TYR n
+1 28 ASN n
+1 29 THR n
+1 30 CYS n
+1 31 LEU n
+1 32 GLY n
+1 33 SER n
+1 34 PRO n
+1 35 LEU n
+1 36 PRO n
+1 37 TYR n
+1 38 THR n
+1 39 HIS n
+1 40 THR n
+1 41 SER n
+1 42 LEU n
+1 43 ILE n
+1 44 LEU n
+1 45 ALA n
+1 46 GLU n
+1 47 ASP n
+1 48 SER n
+1 49 GLU n
+1 50 THR n
+1 51 GLN n
+1 52 GLU n
+1 53 GLU n
+1 54 ALA n
+1 55 PHE n
+1 56 GLU n
+1 57 LYS n
+1 58 LEU n
+1 59 ALA n
+1 60 MET n
+1 61 TRP n
+1 62 SER n
+1 63 GLY n
+1 64 LEU n
+1 65 ARG n
+1 66 ASN n
+1 67 ALA n
+1 68 PRO n
+1 69 ARG n
+1 70 CYS n
+1 71 TRP n
+1 72 ALA n
+1 73 VAL n
+1 74 ILE n
+1 75 GLN n
+1 76 PRO n
+1 77 LEU n
+1 78 LEU n
+1 79 CYS n
+1 80 ALA n
+1 81 VAL n
+1 82 TYR n
+1 83 MET n
+1 84 PRO n
+1 85 LYS n
+1 86 CYS n
+1 87 GLU n
+1 88 ASN n
+1 89 GLY n
+1 90 LYS n
+1 91 VAL n
+1 92 GLU n
+1 93 LEU n
+1 94 PRO n
+1 95 SER n
+1 96 GLN n
+1 97 HIS n
+1 98 LEU n
+1 99 CYS n
+1 100 GLN n
+1 101 ALA n
+1 102 THR n
+1 103 ARG n
+1 104 ASN n
+1 105 PRO n
+1 106 CYS n
+1 107 SER n
+1 108 ILE n
+1 109 VAL n
+1 110 GLU n
+1 111 ARG n
+1 112 GLU n
+1 113 ARG n
+1 114 GLY n
+1 115 TRP n
+1 116 PRO n
+1 117 ASN n
+1 118 PHE n
+1 119 LEU n
+1 120 LYS n
+1 121 CYS n
+1 122 GLU n
+1 123 ASN n
+1 124 LYS n
+1 125 GLU n
+1 126 GLN n
+1 127 PHE n
+1 128 PRO n
+1 129 LYS n
+1 130 GLY n
+1 131 CYS n
+1 132 GLN n
+1 133 ASN n
+1 134 GLU n
+1 135 VAL n
+1 136 GLN n
+1 137 LYS n
+1 138 LEU n
+1 139 LYS n
+1 140 PHE n
+1 141 ASN n
+1 142 THR n
+1 143 SER n
+1 144 GLY n
+1 145 GLN n
+1 146 CYS n
+1 147 GLU n
+1 148 ALA n
+1 149 PRO n
+1 150 LEU n
+1 151 VAL n
+1 152 LYS n
+1 153 THR n
+1 154 ASP n
+1 155 ILE n
+1 156 GLN n
+1 157 ALA n
+1 158 SER n
+1 159 TRP n
+1 160 TYR n
+1 161 LYS n
+1 162 ASP n
+1 163 VAL n
+1 164 GLU n
+1 165 GLY n
+1 166 CYS n
+1 167 GLY n
+1 168 ILE n
+1 169 GLN n
+1 170 CYS n
+1 171 ASP n
+1 172 ASN n
+1 173 PRO n
+1 174 LEU n
+1 175 PHE n
+1 176 THR n
+1 177 GLU n
+1 178 ASP n
+1 179 GLU n
+1 180 HIS n
+1 181 SER n
+1 182 ASP n
+1 183 MET n
+1 184 HIS n
+1 185 LYS n
+1 186 LEU n
+1 187 GLU n
+1 188 HIS n
+1 189 HIS n
+1 190 HIS n
+1 191 HIS n
+1 192 HIS n
+1 193 HIS n
+#
+_struct.entry_id 4C79
+_struct.title 'Crystal structure of the Smoothened CRD, native'
+_struct.pdbx_descriptor SMOOTHENED
+_struct.pdbx_model_details ?
+_struct.pdbx_CASP_flag ?
+_struct.pdbx_model_type_details ?
+#
+_struct_keywords.entry_id 4C79
+_struct_keywords.pdbx_keywords 'SIGNALING PROTEIN'
+_struct_keywords.text 'SIGNALING PROTEIN'
+#
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 262 N N . GLU A 1 49 ? -25.812 5.207 -4.954 1.00 35.58 ? 75 GLU A N 1
+ATOM 263 C CA . GLU A 1 49 ? -26.815 4.149 -4.979 1.00 36.58 0 75 GLU A CA 1
+ATOM 264 C C . GLU A 1 49 ? -27.600 4.155 -6.288 1.00 35.91 ? 75 GLU A C 1
+ATOM 265 O O . GLU A 1 49 ? -28.206 3.150 -6.663 1.00 35.94 ? 75 GLU A O 1
+ATOM 266 C CB . GLU A 1 49 ? -27.774 4.284 -3.794 1.00 38.91 . 75 GLU A CB 1
+ATOM 267 C CG . GLU A 1 49 ? -27.114 4.163 -2.426 1.00 40.64 ? 75 GLU A CG 1
+ATOM 268 C CD . GLU A 1 49 ? -26.931 2.725 -1.965 1.00 42.04 ? 75 GLU A CD 1
+ATOM 269 O OE1 . GLU A 1 49 ? -26.905 1.807 -2.812 1.00 42.07 ? 75 GLU A OE1 1
+ATOM 270 O OE2 . GLU A 1 49 ? -26.811 2.516 -0.740 1.00 42.97 -1 75 GLU A OE2 1
+HETATM 1881 ZN ZN . ZN C 2 . ? -29.714 -4.622 -22.478 1.00 31.76 2 1159 ZN A ZN 1
+HETATM 1882 NA NA . NA D 3 . ? -23.050 1.721 -4.584 1.00 26.51 1 1160 NA A NA 1
+#
+loop_
+_pdbx_entity_nonpoly.entity_id
+_pdbx_entity_nonpoly.name
+_pdbx_entity_nonpoly.comp_id
+2 'ZINC ION' ZN
+3 'SODIUM ION' NA
+4 water HOH
+#
diff --git a/modules/mol/alg/doc/lddt_deprecated.rst b/modules/mol/alg/doc/lddt_deprecated.rst
index 4293046fd7e9359808d394a815366b1696277453..173bcb5ed5b3d8adbdc5abec02df9f2bc580b765 100644
--- a/modules/mol/alg/doc/lddt_deprecated.rst
+++ b/modules/mol/alg/doc/lddt_deprecated.rst
@@ -3,6 +3,11 @@
lDDT (deprecated)
================================================================================
+.. warning::
+
+ These functions in `ost.mol.alg` are deprecated. Consider using the newer
+ implementation in :class:`ost.mol.alg.lDDTScorer` instead.
+
.. function:: LocalDistDiffTest(model, distance_list, tolerance_list, \
sequence_separation=0, \
local_lddt_property_string="")
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index bf451df52b20b045f3a0a1e5e82d793cd537847b..3a43ea5de90b8b5bf14393c15754b09b6e2d37d4 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -7,14 +7,14 @@
Local Distance Test scores (lDDT, DRMSD)
--------------------------------------------------------------------------------
-.. warning::
+.. note::
- The code that comes with
+ This is a new implementation of lDDT, introduced in OpenStructure 2.4 with
+ focus on supporting quaternary structure and compounds beyond the 20
+ standard proteinogenic amino acids.
+ The :doc:`previous lDDT code <lddt_deprecated>` that comes with
`Mariani et al. <https://dx.doi.org/10.1093/bioinformatics/btt473>`_ is
- considered deprecated. lDDT has been re-implemented with a focus on
- supporting quaternary structure and compounds beyond the 20 standard
- proteinogenic amino acids. The old code is still available and documented
- :doc:`here <lddt_deprecated>`.
+ considered deprecated.
.. note::
@@ -135,16 +135,16 @@ Local Distance Test scores (lDDT, DRMSD)
.. currentmodule:: ost.mol.alg
-:mod:`qsscoring <ost.mol.alg.qsscore>` -- QS score implementation
+:mod:`qsscore <ost.mol.alg.qsscore>` -- New QS score implementation
--------------------------------------------------------------------------------
-.. warning::
+.. note::
- The code that comes with
+ This is a new implementation of QS Score, introduced in OpenStructure 2.4 and
+ tightly integrated with the chain mapping algorithms.
+ The :doc:`previous qsscoring code <qsscoring_deprecated>` that comes with
`Bertoni et al. <https://www.nature.com/articles/s41598-017-09654-8>`_ is
- considered deprecated. QS score has been re-implemented to be tightly
- integrated with the chain mapping algorithms. The old code is still available
- and documented :doc:`here <qsscoring_deprecated>`.
+ considered deprecated.
.. automodule:: ost.mol.alg.qsscore
:members:
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index b47aa4e76e1544ba28caa18482253833b57106c9..8928646b98283584f2f5e5b82a0b4b8e0b49715d 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -2,6 +2,11 @@
Scoring of quaternary structures (QS). The QS scoring is according to the paper
by `Bertoni et al. <https://dx.doi.org/10.1038/s41598-017-09654-8>`_.
+.. warning::
+
+ The `qsscoring` module is deprecated. Consider using the newer implementation
+ in :mod:`~ost.mol.alg.qsscore` instead.
+
.. note ::
Requirements for use:
diff --git a/singularity/Singularity b/singularity/Singularity
index 1d1a0da33345fc2415fca5d32643f7a15b1bad5a..71f2c00fcad8ca8a2be1939865a2e7254ef0b486 100644
--- a/singularity/Singularity
+++ b/singularity/Singularity
@@ -1,5 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/openstructure:2.4.0-jammy
+From: registry.scicore.unibas.ch/schwede/openstructure:2.5.0-jammy
%post
##############################################################################
# POST