diff --git a/include/nuri/algo/guess.h b/include/nuri/algo/guess.h
index 7b084b77..d9955fd5 100644
--- a/include/nuri/algo/guess.h
+++ b/include/nuri/algo/guess.h
@@ -6,6 +6,8 @@
 #ifndef NURI_ALGO_GUESS_H_
 #define NURI_ALGO_GUESS_H_
 
+#include <absl/base/attributes.h>
+
 #include "nuri/core/molecule.h"
 
 namespace nuri {
@@ -26,8 +28,9 @@ constexpr double kDefaultThreshold = 0.5;
  * If connectivity information is already present and is correct, consider using
  * guess_all_types().
  */
-extern bool guess_everything(MoleculeMutator &mut, int conf = 0,
-                             double threshold = kDefaultThreshold);
+ABSL_MUST_USE_RESULT extern bool
+guess_everything(MoleculeMutator &mut, int conf = 0,
+                 double threshold = kDefaultThreshold);
 
 /**
  * @brief Guess connectivity information of a molecule.
@@ -53,7 +56,7 @@ extern void guess_connectivity(MoleculeMutator &mut, int conf = 0,
  * and all atom/bond types and implicit hydrogen counts are incorrect. The
  * information present in the molecule could be overwritten by this function.
  */
-extern bool guess_all_types(Molecule &mol, int conf = 0);
+ABSL_MUST_USE_RESULT extern bool guess_all_types(Molecule &mol, int conf = 0);
 
 /**
  * @brief Guess formal charges of a molecule.
@@ -84,6 +87,10 @@ extern void guess_hydrogens_2d(Molecule &mol);
  * guess_hydrogens() in sequence.
  */
 extern void guess_fcharge_hydrogens_2d(Molecule &mol);
+
+namespace internal {
+  ABSL_MUST_USE_RESULT extern bool guess_update_subs(Molecule &mol);
+}  // namespace internal
 }  // namespace nuri
 
 #endif /* NURI_ALGO_GUESS_H_ */
diff --git a/include/nuri/fmt/base.h b/include/nuri/fmt/base.h
index 484ff581..23049fbb 100644
--- a/include/nuri/fmt/base.h
+++ b/include/nuri/fmt/base.h
@@ -129,7 +129,7 @@ class MoleculeReader {
    */
   virtual Molecule parse(const std::vector<std::string> &block) const = 0;
 
-  virtual bool sanitized() const = 0;
+  virtual bool bond_valid() const = 0;
 
   MoleculeStream<MoleculeReader> stream() { return { *this }; }
 };
diff --git a/include/nuri/fmt/mol2.h b/include/nuri/fmt/mol2.h
index da1602da..3f0b623e 100644
--- a/include/nuri/fmt/mol2.h
+++ b/include/nuri/fmt/mol2.h
@@ -31,7 +31,7 @@ class Mol2Reader: public DefaultReaderImpl<read_mol2> {
 
   bool getnext(std::vector<std::string> &block) override;
 
-  bool sanitized() const override { return false; }
+  bool bond_valid() const override { return true; }
 
 private:
   bool read_mol_header_ = false;
diff --git a/include/nuri/fmt/pdb.h b/include/nuri/fmt/pdb.h
index d18a29c4..1c0cdfbb 100644
--- a/include/nuri/fmt/pdb.h
+++ b/include/nuri/fmt/pdb.h
@@ -31,7 +31,7 @@ class PDBReader: public DefaultReaderImpl<read_pdb> {
 
   bool getnext(std::vector<std::string> &block) override;
 
-  bool sanitized() const override { return true; }
+  bool bond_valid() const override { return false; }
 
 private:
   std::vector<std::string> header_;
diff --git a/include/nuri/fmt/sdf.h b/include/nuri/fmt/sdf.h
index 4c06dd0d..84b0546e 100644
--- a/include/nuri/fmt/sdf.h
+++ b/include/nuri/fmt/sdf.h
@@ -31,7 +31,7 @@ class SDFReader: public DefaultReaderImpl<read_sdf> {
 
   bool getnext(std::vector<std::string> &block) override;
 
-  bool sanitized() const override { return false; }
+  bool bond_valid() const override { return true; }
 };
 
 class SDFReaderFactory: public DefaultReaderFactoryImpl<SDFReader> {
diff --git a/include/nuri/fmt/smiles.h b/include/nuri/fmt/smiles.h
index 8fd4cc7e..a21826eb 100644
--- a/include/nuri/fmt/smiles.h
+++ b/include/nuri/fmt/smiles.h
@@ -33,7 +33,7 @@ class SmilesReader: public DefaultReaderImpl<read_smiles> {
 
   bool getnext(std::vector<std::string> &block) override;
 
-  bool sanitized() const override { return false; }
+  bool bond_valid() const override { return true; }
 };
 
 class SmilesReaderFactory: public DefaultReaderFactoryImpl<SmilesReader> {
diff --git a/python/docs/conf.py.in b/python/docs/conf.py.in
index cdd0df8f..9a2d35df 100644
--- a/python/docs/conf.py.in
+++ b/python/docs/conf.py.in
@@ -8,9 +8,9 @@
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+import doctest
 import re
 
-import doctest
 from sphinx.ext import autodoc
 
 # -- Project information -----------------------------------------------------
@@ -61,10 +61,10 @@ html_static_path = ["@CMAKE_CURRENT_LIST_DIR@/_static"]
 if "@DOXYGEN_OUTPUT_DIR@":
     html_extra_path = ["@DOXYGEN_OUTPUT_DIR@/html"]
 html_css_files = [
-    "css/rtd-property.css" # workaround https://github.com/readthedocs/sphinx_rtd_theme/issues/1301
+    "css/rtd-property.css"  # workaround https://github.com/readthedocs/sphinx_rtd_theme/issues/1301
 ]
 html_theme_options = {
-    'navigation_depth': -1,
+    "navigation_depth": -1,
 }
 
 intersphinx_mapping = {
@@ -83,7 +83,8 @@ doctest_global_setup = "import nuri"
 class UnneededBaseStripDocumenter(autodoc.ClassDocumenter):
     _strip_re = re.compile(
         r"\s*Bases:\s*:py:class:"
-        r"`([^`]*?\bpybind11_[A-Za-z0-9_\.]+|object)`\s*")
+        r"`([^`]*?\bpybind11_[A-Za-z0-9_\.]+|object)`\s*"
+    )
 
     def add_line(self, line: str, source: str, *lineno: int):
         if self._strip_re.fullmatch(line):
diff --git a/python/src/nuri/fmt/fmt_module.cpp b/python/src/nuri/fmt/fmt_module.cpp
index 5d07b2c3..27463e7d 100644
--- a/python/src/nuri/fmt/fmt_module.cpp
+++ b/python/src/nuri/fmt/fmt_module.cpp
@@ -22,6 +22,7 @@
 #include <pybind11/pytypes.h>
 #include <pybind11/stl/filesystem.h>
 
+#include "nuri/algo/guess.h"
 #include "nuri/core/molecule.h"
 #include "nuri/fmt/base.h"
 #include "nuri/fmt/mol2.h"
@@ -38,7 +39,8 @@ class PyMoleculeReader {
 public:
   PyMoleculeReader(std::unique_ptr<std::istream> is, std::string_view fmt,
                    bool sanitize, bool skip_on_error)
-      : stream_(std::move(is)), skip_on_error_(skip_on_error) {
+      : stream_(std::move(is)), sanitize_(sanitize),
+        skip_on_error_(skip_on_error) {
     if (!*stream_)
       throw py::value_error(absl::StrCat("Invalid stream object"));
 
@@ -51,7 +53,7 @@ class PyMoleculeReader {
     if (!reader_)
       throw py::value_error(absl::StrCat("Failed to create reader for ", fmt));
 
-    sanitize_ = sanitize && !reader_->sanitized();
+    guess_ = sanitize && !reader_->bond_valid();
   }
 
   auto next() {
@@ -78,7 +80,16 @@ class PyMoleculeReader {
         continue;
       }
 
-      if (sanitize_ && !MoleculeSanitizer(mol).sanitize_all()) {
+      if (guess_ && mol.is_3d()) {
+        if (!internal::guess_update_subs(mol)) {
+          log_or_throw("Failed to guess molecule atom/bond types");
+          continue;
+        }
+      } else if (sanitize_ && !MoleculeSanitizer(mol).sanitize_all()) {
+        ABSL_LOG_IF(WARNING, guess_ && !mol.is_3d())
+            << "Reader might produce molecules with invalid bonds, but the "
+               "molecule is missing 3D coordinates; guessing is disabled.";
+
         log_or_throw("Failed to sanitize molecule");
         continue;
       }
@@ -102,6 +113,7 @@ class PyMoleculeReader {
   std::vector<std::string> block_;
   bool sanitize_;
   bool skip_on_error_;
+  bool guess_;
 };
 
 template <class F, class... Args>
@@ -146,9 +158,10 @@ Read a molecule from a file.
 
 :param fmt: The format of the file.
 :param path: The path to the file.
-:param sanitize: Whether to sanitize the produced molecule. Note that if the
-  underlying reader produces a sanitized molecule, this option is ignored and
-  the molecule is always sanitized.
+:param sanitize: Whether to sanitize the produced molecule. For formats that is
+  known to produce molecules with insufficient bond information (e.g. PDB), this
+  option will trigger guessing based on the 3D coordinates
+  (:func:`nuri.algo.guess_everything()`).
 :param skip_on_error: Whether to skip a molecule if an error occurs, instead of
   raising an exception.
 :raises OSError: If any file-related error occurs.
@@ -171,9 +184,10 @@ Read a molecule from string.
 
 :param fmt: The format of the file.
 :param data: The string to read.
-:param sanitize: Whether to sanitize the produced molecule. Note that if the
-  underlying reader produces a sanitized molecule, this option is ignored and
-  the molecule is always sanitized.
+:param sanitize: Whether to sanitize the produced molecule. For formats that is
+  known to produce molecules with insufficient bond information (e.g. PDB), this
+  option will trigger guessing based on the 3D coordinates
+  (:func:`nuri.algo.guess_everything()`).
 :param skip_on_error: Whether to skip a molecule if an error occurs, instead of
   raising an exception.
 :raises ValueError: If the format is unknown or sanitization fails, unless
diff --git a/src/algo/guess/3d.cpp b/src/algo/guess/3d.cpp
index d3922134..51d8f7c8 100644
--- a/src/algo/guess/3d.cpp
+++ b/src/algo/guess/3d.cpp
@@ -2170,4 +2170,19 @@ bool guess_all_types(Molecule &mol, int conf) {
   reset_bonds(mol);
   return guess_types_common(mol, mol.confs()[conf]);
 }
+
+namespace internal {
+  bool guess_update_subs(Molecule &mol) {
+    bool ret;
+    {
+      auto mut = mol.mutator();
+      ret = guess_everything(mut);
+    }
+
+    for (auto &sub: mol.substructures())
+      sub.refresh_bonds();
+
+    return ret;
+  }
+}  // namespace internal
 }  // namespace nuri
diff --git a/src/fmt/pdb.cpp b/src/fmt/pdb.cpp
index b542791b..fc29455d 100644
--- a/src/fmt/pdb.cpp
+++ b/src/fmt/pdb.cpp
@@ -19,9 +19,7 @@
 #include <utility>
 #include <vector>
 
-#include <absl/algorithm/container.h>
 #include <absl/base/optimization.h>
-#include <absl/container/fixed_array.h>
 #include <absl/container/flat_hash_map.h>
 #include <absl/container/flat_hash_set.h>
 #include <absl/log/absl_check.h>
@@ -34,7 +32,6 @@
 #include <Eigen/Dense>
 
 #include "nuri/eigen_config.h"
-#include "nuri/algo/guess.h"
 #include "nuri/core/element.h"
 #include "nuri/core/graph.h"
 #include "nuri/core/molecule.h"
@@ -487,9 +484,9 @@ std::string read_model_line(std::string_view line) {
   line.remove_prefix(5);
   return std::string(absl::StripAsciiWhitespace(line));
 }
-}  // namespace
 
-namespace {
+// TODO(jnooree): move to separate file and provide a more general interface
+/*
 struct PDBAtomInfoTemplate {
   std::string_view name;
   int atomic_number;
@@ -1563,6 +1560,7 @@ const absl::flat_hash_map<std::string_view, AminoAcid> kAAData {
   } },
 };
 // clang-format on
+*/
 
 std::pair<int, bool> parse_serial(std::string_view line) {
   int serial;
@@ -1913,11 +1911,6 @@ void read_connect_line(std::string_view line, const int src,
       continue;
     }
 
-    if (mut.mol().atom(*dst).data().element().type() == Element::Type::kMetal) {
-      ABSL_LOG(INFO) << "ignoring CONECT record to metal atom " << serial;
-      continue;
-    }
-
     auto [_, added] = mut.add_bond(src, *dst, BondData(constants::kSingleBond));
     if (added)
       ABSL_VLOG(1) << "Added bond " << src << " -> " << *dst << " from CONECT";
@@ -1954,11 +1947,6 @@ void read_connect_section(Iterator &it, const Iterator end,
       continue;
     }
 
-    if (mut.mol().atom(*idx).data().element().type() == Element::Type::kMetal) {
-      ABSL_LOG(INFO) << "ignoring CONECT record to metal atom " << serial;
-      continue;
-    }
-
     read_connect_line(line, *idx, mut, serial_to_idx);
   }
 }
@@ -2065,9 +2053,10 @@ void update_confs(Molecule &mol, const std::vector<PDBAtomData> &atom_data) {
 
 constexpr int kChainIdx = 0;
 
-void update_substructures(Molecule &mol, std::vector<Substructure> &subs,
-                          PDBResidueData &residue_data,
+void update_substructures(Molecule &mol, PDBResidueData &residue_data,
                           const std::vector<PDBAtomData> &atom_data) {
+  auto &subs = mol.substructures();
+
   std::vector<std::pair<char, std::vector<int>>> chains;
 
   for (int i = 0; i < atom_data.size(); ++i) {
@@ -2088,14 +2077,14 @@ void update_substructures(Molecule &mol, std::vector<Substructure> &subs,
 
   auto sit = subs.begin();
   for (int i = 0; i < residue_data.size(); ++i, ++sit) {
-    auto &[id, resname, idxs] = residue_data[i];
+    auto &data = residue_data[i];
 
-    sit->update(std::move(idxs), {});
-    sit->name() = std::string(resname);
-    sit->set_id(id.seqnum);
-    sit->add_prop("chain", std::string(1, id.chain));
-    if (id.icode != ' ')
-      sit->add_prop("icode", std::string(1, id.icode));
+    sit->update(std::move(data.idxs), {});
+    sit->name() = std::string(data.resname);
+    sit->set_id(data.id.seqnum);
+    sit->add_prop("chain", std::string(1, data.id.chain));
+    if (data.id.icode != ' ')
+      sit->add_prop("icode", std::string(1, data.id.icode));
 
     ABSL_DCHECK(sit->props()[kChainIdx].first == "chain");
   }
@@ -2107,81 +2096,6 @@ void update_substructures(Molecule &mol, std::vector<Substructure> &subs,
     sit->set_id(i);
   }
 }
-
-void update_std_atoms(Molecule &mol, const std::vector<Substructure> &subs) {
-  for (const Substructure &sub: subs) {
-    if (sub.category() != SubstructCategory::kResidue)
-      continue;
-
-    std::string_view resname = sub.name();
-    auto ait = kAAData.find(resname);
-    if (ait == kAAData.end())
-      continue;
-
-    const AminoAcid &aa = ait->second;
-    aa.update_atoms(mol, sub.atom_ids());
-  }
-}
-
-// Typically 1.32 Angstroms
-constexpr double kMaxPepBondLSq = 2.0 * 2.0;
-
-void add_inter_res_bond(MoleculeMutator &mut, const int prev_cterm,
-                        const int nterm) {
-  double lsq = mut.mol().distsq(prev_cterm, nterm);
-  if (lsq > kMaxPepBondLSq) {
-    ABSL_VLOG(1) << "Peptide bond between atoms " << prev_cterm << " and "
-                 << nterm << " is too long (" << std::sqrt(lsq)
-                 << " Angstroms), missing residues?";
-    return;
-  }
-
-  auto [bit, added] = mut.add_bond(prev_cterm, nterm, {});
-  if (!added) {
-    ABSL_LOG(INFO) << "Duplicate peptide bond between atoms " << prev_cterm
-                   << " and " << nterm << "; ignoring";
-    return;
-  }
-
-  BondData &bd = bit->data();
-  bd.set_conjugated(true);
-
-  AtomData &ad = mut.mol().atom(nterm).data();
-  ad.set_hybridization(constants::kSP2);
-  ad.set_conjugated(true);
-  ad.set_implicit_hydrogens(nonnegative(ad.implicit_hydrogens() - 1));
-}
-
-void add_std_bonds(MoleculeMutator &mut,
-                   const std::vector<Substructure> &subs) {
-  char prev_chain = '\0';
-  int prev_cterm = -1;
-
-  for (const Substructure &sub: subs) {
-    if (sub.category() != SubstructCategory::kResidue)
-      continue;
-
-    std::string_view resname = sub.name();
-    auto ait = kAAData.find(resname);
-    if (ait == kAAData.end()) {
-      prev_cterm = -1;
-      continue;
-    }
-
-    const AminoAcid &aa = ait->second;
-    auto [nterm, cterm] = aa.add_bonds(mut, sub.atom_ids());
-    const char chain = sub.props()[kChainIdx].second[0];
-    ABSL_DCHECK(sub.props()[kChainIdx].first == "chain");
-
-    if (prev_chain == chain && prev_cterm >= 0 && nterm >= 0) {
-      ABSL_DCHECK(prev_cterm != nterm);
-      add_inter_res_bond(mut, prev_cterm, nterm);
-    }
-
-    prev_chain = chain;
-    prev_cterm = cterm;
-  }
-}
 }  // namespace
 
 Molecule read_pdb(const std::vector<std::string> &pdb) {
@@ -2252,37 +2166,19 @@ Molecule read_pdb(const std::vector<std::string> &pdb) {
     return mol;
   }
 
-  std::vector<Substructure> subs;
-
   {
     auto mut = mol.mutator();
     for (PDBAtomData &pd: atom_data)
       mut.add_atom(pd.to_standard());
 
-    update_substructures(mol, subs, residue_data, atom_data);
     update_confs(mol, atom_data);
 
-    bool guess_ok = guess_everything(mut);
-    if (!guess_ok) {
-      ABSL_LOG(WARNING) << "Failed to guess atom/bond types; the resulting "
-                           "molecule might be invalid";
-      mut.clear_bonds();
-      update_std_atoms(mol, subs);
-      add_std_bonds(mut, subs);
-
-      int connect_bonds_start = mol.num_bonds();
-      read_connect_section(it, end, mut, serial_to_idx);
-      if (mol.num_bonds() != connect_bonds_start)
-        remove_hbonds(mut);
-
-      // TODO(jnooree): handle stereochemistry correctly
-    }
+    read_connect_section(it, end, mut, serial_to_idx);
+    if (!mol.bond_empty())
+      remove_hbonds(mut);
   }
 
-  for (Substructure &sub: subs)
-    sub.refresh_bonds();
-
-  mol.substructures() = std::move(subs);
+  update_substructures(mol, residue_data, atom_data);
 
   return mol;
 }
diff --git a/test/algo/guess_test.cpp b/test/algo/guess_test.cpp
index 65079562..8bf23b99 100644
--- a/test/algo/guess_test.cpp
+++ b/test/algo/guess_test.cpp
@@ -1058,6 +1058,8 @@ TEST(GuessSelectedMolecules, GH358) {
   int i = 0;
   for (; i < smiles_answers.size() && reader.getnext(blk); ++i) {
     Molecule mol = reader.parse(blk);
+    EXPECT_TRUE(internal::guess_update_subs(mol));
+
     std::string smi;
     write_smiles(smi, mol);
     absl::StripAsciiWhitespace(&smi);
@@ -1098,6 +1100,8 @@ TEST(GuessSelectedMolecules, GH367) {
   int i = 0;
   for (; i < smiles_answers.size() && reader.getnext(blk); ++i) {
     Molecule mol = reader.parse(blk);
+    EXPECT_TRUE(internal::guess_update_subs(mol));
+
     std::string smi;
     write_smiles(smi, mol);
     absl::StripAsciiWhitespace(&smi);
diff --git a/test/fmt/base_test.cpp b/test/fmt/base_test.cpp
index b85342ea..80880d05 100644
--- a/test/fmt/base_test.cpp
+++ b/test/fmt/base_test.cpp
@@ -117,7 +117,7 @@ class DummyReader: public MoleculeReader {
     return {};
   }
 
-  bool sanitized() const override { return true; }
+  bool bond_valid() const override { return true; }
 };
 
 class DummyReaderFactory: public DefaultReaderFactoryImpl<DummyReader> { };
diff --git a/test/fmt/pdb_test.cpp b/test/fmt/pdb_test.cpp
index 630aa8df..f74d77b3 100644
--- a/test/fmt/pdb_test.cpp
+++ b/test/fmt/pdb_test.cpp
@@ -16,17 +16,25 @@
 
 #include "fmt_test_common.h"
 #include "test_utils.h"
+#include "nuri/algo/guess.h"
 #include "nuri/core/molecule.h"
 #include "nuri/fmt/base.h"
 
 namespace nuri {
 namespace {
-using PDBTest = internal::FileFormatTest<PDBReader>;
+class PDBTest: public internal::FileFormatTest<PDBReader> {
+  using Parent = internal::FileFormatTest<PDBReader>;
+
+public:
+  bool advance_and_guess() {
+    return advance() && internal::guess_update_subs(mol());
+  }
+};
 
 TEST_F(PDBTest, BasicParsing) {
   set_test_file("dummy.pdb");
 
-  ASSERT_TRUE(advance());
+  ASSERT_TRUE(advance_and_guess());
 
   EXPECT_EQ(mol().num_atoms(), 88);
   EXPECT_EQ(mol().num_bonds(), 87);
@@ -57,14 +65,10 @@ TEST_F(PDBTest, HandleInvalidCoordinates) {
   set_test_file("invalid.pdb");
 
   ASSERT_TRUE(advance());
+  EXPECT_NO_FATAL_FAILURE(
+      static_cast<void>(internal::guess_update_subs(mol())));
 
   EXPECT_EQ(mol().num_atoms(), 90);
-  EXPECT_EQ(mol().num_bonds(), 89);
-
-  // Peptide + H2O
-  EXPECT_EQ(mol().num_fragments(), 2);
-  // Ring from PHE
-  EXPECT_EQ(mol().ring_groups().size(), 1);
 
   // 11 residues + 1 chain
   EXPECT_EQ(mol().num_substructures(), 12);
@@ -79,17 +83,12 @@ TEST_F(PDBTest, HandleInvalidCoordinates) {
   auto atom = mol().atom(25);
   EXPECT_EQ(atom.data().get_name(), "N");
   EXPECT_EQ(atom.data().atomic_number(), 7);
-  EXPECT_EQ(atom.data().hybridization(), constants::kSP2);
-  EXPECT_TRUE(atom.data().is_conjugated());
-
-  EXPECT_NE(mol().find_bond(87, 88), mol().bond_end());
-  EXPECT_NE(mol().find_bond(87, 89), mol().bond_end());
 }
 
 TEST_F(PDBTest, HandleCleanPDB) {
   set_test_file("1ubq.pdb");
 
-  ASSERT_TRUE(advance());
+  ASSERT_TRUE(advance_and_guess());
 
   EXPECT_EQ(mol().name(), "1UBQ");
   EXPECT_EQ(mol().num_atoms(), 660);
@@ -114,7 +113,7 @@ TEST_F(PDBTest, HandleCleanPDB) {
 TEST_F(PDBTest, HandleMultipleModels) {
   set_test_file("3cye_part.pdb");
 
-  ASSERT_TRUE(advance());
+  ASSERT_TRUE(advance_and_guess());
   EXPECT_EQ(mol().name(), "3CYE");
 
   EXPECT_EQ(mol().num_atoms(), 55);
@@ -134,7 +133,7 @@ TEST_F(PDBTest, HandleMultipleModels) {
   EXPECT_EQ(mol().get_substructure(0).name(), "VAL");
   EXPECT_EQ(mol().get_substructure(0).num_atoms(), 7);
 
-  ASSERT_TRUE(advance());
+  ASSERT_TRUE(advance_and_guess());
   EXPECT_EQ(mol().name(), "3CYE");
 
   EXPECT_EQ(mol().num_atoms(), 36);
@@ -204,6 +203,7 @@ class PDB1alxTest: public testing::Test {
     MoleculeStream<PDBReader> ms(reader);
 
     ASSERT_TRUE(ms.advance());
+    EXPECT_TRUE(internal::guess_update_subs(ms.current()));
 
     mol_ = std::move(ms.current());
     ASSERT_EQ(mol_.name(), "1ALX");