diff --git a/modules/io/src/mol/sdf_writer.cc b/modules/io/src/mol/sdf_writer.cc
index 23f5d3ed4133a277865d7b6374fc468e2a15a5e9..c2db1ddb096925a67b02f542908c2a342010f2ef 100644
--- a/modules/io/src/mol/sdf_writer.cc
+++ b/modules/io/src/mol/sdf_writer.cc
@@ -29,7 +29,7 @@ using boost::format;
namespace {
- class SDFAtomWriter : public mol::EntityVisitor {
+ class SDFAtomWriter : public mol::EntityViewVisitor {
public:
SDFAtomWriter(std::ostream& ostream, std::map<long, int>& atom_indices)
: ostr_(ostream), atom_indices_(atom_indices), counter_(0) {
@@ -37,7 +37,7 @@ namespace {
}
private:
public:
- virtual bool VisitAtom(const mol::AtomHandle& atom) {
+ virtual bool VisitAtom(const mol::AtomView& atom) {
atom_indices_[atom.GetHashCode()] = ++counter_;
ostr_ << format("%10.4f") % atom.GetPos()[0]
<< format("%10.4f") % atom.GetPos()[1]
@@ -53,22 +53,22 @@ namespace {
int counter_;
};
- class SDFBondWriter : public mol::EntityVisitor {
+ class SDFBondWriter : public mol::EntityViewVisitor {
public:
SDFBondWriter(std::ostream& ostream, std::map<long, int>& atom_indices)
: ostr_(ostream), atom_indices_(atom_indices), counter_(0) {
}
private:
public:
- virtual bool VisitAtom(const mol::AtomHandle& atom) {
+ virtual bool VisitAtom(const mol::AtomView& atom) {
counter_++;
- mol::AtomHandleList atoms = atom.GetBondPartners();
- mol::AtomHandleList::iterator atom_iter = atoms.begin();
+ mol::AtomViewList atoms = atom.GetBondPartners();
+ mol::AtomViewList::iterator atom_iter = atoms.begin();
for(; atom_iter != atoms.end(); ++atom_iter) {
int atom_index = atom_indices_.find((*atom_iter).GetHashCode())->second;
if(atom_index > counter_) {
int type = 1;
- mol::BondHandle bond = atom.FindBondToAtom(*atom_iter);
+ mol::BondHandle bond = atom.GetHandle().FindBondToAtom(atom_iter->GetHandle());
if(bond.IsValid()) type = bond.GetBondOrder();
ostr_ << format("%3i") % counter_
<< format("%3i") % atom_index
@@ -105,11 +105,11 @@ void SDFWriter::Write(const mol::EntityView& ent) {
}
void SDFWriter::Write(const mol::EntityHandle& ent) {
- mol::EntityHandle non_const_handle = ent;
- non_const_handle.Apply(*this);
+ mol::EntityView non_const_view = ent.CreateFullView();
+ non_const_view.Apply(*this);
}
-bool SDFWriter::VisitChain(const mol::ChainHandle& chain) {
+bool SDFWriter::VisitChain(const mol::ChainView& chain) {
// print end of molecule line
if(counter_ != 0) {
ostr_ << "$$$$" << std::endl;
@@ -138,7 +138,7 @@ bool SDFWriter::VisitChain(const mol::ChainHandle& chain) {
// write atom block
SDFAtomWriter atom_writer(ostr_, atom_indices_);
- mol::ChainHandle non_const_chain = chain;
+ mol::ChainView non_const_chain = chain;
non_const_chain.Apply(atom_writer);
// write bond block
diff --git a/modules/io/src/mol/sdf_writer.hh b/modules/io/src/mol/sdf_writer.hh
index 62a365d491f303f6e0a5a01add5ce3af1636deba..76538f808f611dd8edb1a5979b2f9ad9ced66359 100644
--- a/modules/io/src/mol/sdf_writer.hh
+++ b/modules/io/src/mol/sdf_writer.hh
@@ -38,7 +38,7 @@
namespace ost { namespace io {
-class DLLEXPORT_OST_IO SDFWriter : public mol::EntityVisitor {
+class DLLEXPORT_OST_IO SDFWriter : public mol::EntityViewVisitor {
public:
SDFWriter(std::ostream& ostream);
SDFWriter(const String& filename);
@@ -48,7 +48,7 @@ public:
void Write(const mol::EntityHandle& ent);
private:
- virtual bool VisitChain(const mol::ChainHandle& chain);
+ virtual bool VisitChain(const mol::ChainView& chain);
std::ofstream outfile_;
std::ostream& ostr_;
diff --git a/modules/io/tests/test_io_sdf.cc b/modules/io/tests/test_io_sdf.cc
index 08ae8d80ccd475ed20d9c2c5dba3791609149ef7..f18f018bc48150ebb2776dea1f98d302db043ce5 100644
--- a/modules/io/tests/test_io_sdf.cc
+++ b/modules/io/tests/test_io_sdf.cc
@@ -151,6 +151,21 @@ BOOST_AUTO_TEST_CASE(write_sdf)
"testfiles/sdf/compound-out.sdf"));
}
+BOOST_AUTO_TEST_CASE(write_sdf_view)
+{
+ // this scope is required to force the writer stream to be closed before
+ // opening the file again in compare_files. Avoids a race condition.
+ {
+ mol::EntityHandle eh = mol::CreateEntity();
+ EntityIOSDFHandler sdfh;
+ sdfh.Import(eh,"testfiles/sdf/compound.sdf");
+ mol::EntityView ev = eh.Select("(ele=C or ele=N) and aname!='1'");
+ SaveEntity(ev, "testfiles/sdf/compound-view-out.sdf");
+ }
+ BOOST_CHECK(compare_files("testfiles/sdf/compound-view.sdf",
+ "testfiles/sdf/compound-view-out.sdf"));
+}
+
BOOST_AUTO_TEST_CASE(nonexisting_file)
{
mol::EntityHandle eh=mol::CreateEntity();
diff --git a/modules/io/tests/testfiles/sdf/compound-view.sdf b/modules/io/tests/testfiles/sdf/compound-view.sdf
new file mode 100644
index 0000000000000000000000000000000000000000..0902b1232e979e69f500f1ff5c9c5a93fbf2994b
--- /dev/null
+++ b/modules/io/tests/testfiles/sdf/compound-view.sdf
@@ -0,0 +1,440 @@
+Test Ligand
+
+
+ 21 23 0 0 0 0 999 V2000
+ 33.9561 6.2475 23.4088 C 0 0 0 0 0 0
+ 32.6324 6.6232 23.1367 C 0 0 0 0 0 0
+ 34.5295 6.5843 24.6557 C 0 0 0 0 0 0
+ 31.8762 7.3329 24.0856 C 0 0 0 0 0 0
+ 33.7671 7.2733 25.6188 C 0 0 0 0 0 0
+ 32.4286 7.6460 25.3459 C 0 0 0 0 0 0
+ 31.5951 8.3119 26.3710 C 0 0 0 0 0 0
+ 31.3314 7.9140 27.6484 C 0 0 0 0 0 0
+ 31.8735 6.7525 28.4344 C 0 0 0 0 0 0
+ 30.4351 8.7885 28.2094 N 0 0 0 0 0 0
+ 31.7811 6.9129 29.7679 N 0 0 0 0 0 0
+ 30.1110 9.7809 27.3482 N 0 0 0 0 0 0
+ 32.3829 6.0325 30.7674 C 0 0 0 0 0 0
+ 30.7767 9.4820 26.2306 C 0 0 0 0 0 0
+ 31.3859 4.9676 31.2295 C 0 0 0 0 0 0
+ 30.7144 10.3135 25.0185 C 0 0 0 0 0 0
+ 31.9150 10.8059 24.4681 C 0 0 0 0 0 0
+ 31.8995 11.6150 23.3143 C 0 0 0 0 0 0
+ 30.6694 11.9024 22.6787 C 0 0 0 0 0 0
+ 29.4673 11.4261 23.2329 C 0 0 0 0 0 0
+ 29.4821 10.6385 24.4075 C 0 0 0 0 0 0
+ 1 2 1 0 0 0
+ 1 3 2 0 0 0
+ 2 4 2 0 0 0
+ 3 5 1 0 0 0
+ 4 6 1 0 0 0
+ 5 6 2 0 0 0
+ 6 7 1 0 0 0
+ 7 8 2 0 0 0
+ 7 14 1 0 0 0
+ 8 9 1 0 0 0
+ 8 10 1 0 0 0
+ 9 11 1 0 0 0
+ 10 12 1 0 0 0
+ 11 13 1 0 0 0
+ 12 14 2 0 0 0
+ 13 15 1 0 0 0
+ 14 16 1 0 0 0
+ 16 17 1 0 0 0
+ 16 21 2 0 0 0
+ 17 18 2 0 0 0
+ 18 19 1 0 0 0
+ 19 20 2 0 0 0
+ 20 21 1 0 0 0
+M END
+> <i_i_glide_confnum>
+2
+
+> <i_i_glide_lignum>
+1
+
+> <i_i_glide_posenum>
+352
+
+> <r_i_docking_score>
+-8.84426
+
+> <r_i_glide_ecoul>
+-16.1644
+
+> <r_i_glide_einternal>
+6.78671
+
+> <r_i_glide_emodel>
+-96.9661
+
+> <r_i_glide_energy>
+-62.2146
+
+> <r_i_glide_erotb>
+0.517993
+
+> <r_i_glide_esite>
+-0.0291388
+
+> <r_i_glide_evdw>
+-46.0502
+
+> <r_i_glide_gscore>
+-8.84426
+
+> <r_i_glide_hbond>
+-0.960751
+
+> <r_i_glide_ligand_efficiency>
+-0.327565
+
+> <r_i_glide_ligand_efficiency_ln>
+-2.0588
+
+> <r_i_glide_ligand_efficiency_sa>
+-0.982695
+
+> <r_i_glide_lipo>
+-2.84534
+
+> <r_i_glide_metal>
+-0
+
+> <r_i_glide_rewards>
+-0.799851
+
+> <r_i_glide_rmsd>
+0.6819
+
+$$$$
+Test Ligand
+
+
+ 21 23 0 0 0 0 999 V2000
+ 34.1450 6.3862 23.4047 C 0 0 0 0 0 0
+ 34.6745 6.7394 24.6654 C 0 0 0 0 0 0
+ 32.7998 6.7274 23.0916 C 0 0 0 0 0 0
+ 33.8742 7.4015 25.6120 C 0 0 0 0 0 0
+ 32.0035 7.3913 24.0448 C 0 0 0 0 0 0
+ 32.5275 7.7230 25.3191 C 0 0 0 0 0 0
+ 31.6607 8.3431 26.3377 C 0 0 0 0 0 0
+ 31.4133 7.9370 27.6169 C 0 0 0 0 0 0
+ 31.9782 6.7689 28.3776 C 0 0 0 0 0 0
+ 30.5206 8.8053 28.2099 N 0 0 0 0 0 0
+ 32.0029 6.9625 29.7121 N 0 0 0 0 0 0
+ 30.1677 9.8050 27.3570 N 0 0 0 0 0 0
+ 32.5238 6.0208 30.6934 C 0 0 0 0 0 0
+ 30.8244 9.5086 26.2225 C 0 0 0 0 0 0
+ 31.3863 5.1079 31.1861 C 0 0 0 0 0 0
+ 30.7465 10.3438 25.0101 C 0 0 0 0 0 0
+ 31.9316 10.8558 24.4417 C 0 0 0 0 0 0
+ 31.8920 11.6586 23.2829 C 0 0 0 0 0 0
+ 30.6518 11.9231 22.6600 C 0 0 0 0 0 0
+ 29.4612 11.4393 23.2345 C 0 0 0 0 0 0
+ 29.4978 10.6576 24.4073 C 0 0 0 0 0 0
+ 1 2 1 0 0 0
+ 1 3 2 0 0 0
+ 2 4 2 0 0 0
+ 3 5 1 0 0 0
+ 4 6 1 0 0 0
+ 5 6 2 0 0 0
+ 6 7 1 0 0 0
+ 7 8 2 0 0 0
+ 7 14 1 0 0 0
+ 8 9 1 0 0 0
+ 8 10 1 0 0 0
+ 9 11 1 0 0 0
+ 10 12 1 0 0 0
+ 11 13 1 0 0 0
+ 12 14 2 0 0 0
+ 13 15 1 0 0 0
+ 14 16 1 0 0 0
+ 16 17 1 0 0 0
+ 16 21 2 0 0 0
+ 17 18 2 0 0 0
+ 18 19 1 0 0 0
+ 19 20 2 0 0 0
+ 20 21 1 0 0 0
+M END
+> <i_i_glide_confnum>
+14
+
+> <i_i_glide_lignum>
+1
+
+> <i_i_glide_posenum>
+302
+
+> <r_i_docking_score>
+-8.79327
+
+> <r_i_glide_ecoul>
+-16.9687
+
+> <r_i_glide_einternal>
+5.76514
+
+> <r_i_glide_emodel>
+-98.4298
+
+> <r_i_glide_energy>
+-63.3874
+
+> <r_i_glide_erotb>
+0.517993
+
+> <r_i_glide_esite>
+-0.00975737
+
+> <r_i_glide_evdw>
+-46.4187
+
+> <r_i_glide_gscore>
+-8.79327
+
+> <r_i_glide_hbond>
+-0.966475
+
+> <r_i_glide_ligand_efficiency>
+-0.325677
+
+> <r_i_glide_ligand_efficiency_ln>
+-2.04693
+
+> <r_i_glide_ligand_efficiency_sa>
+-0.97703
+
+> <r_i_glide_lipo>
+-2.69167
+
+> <r_i_glide_metal>
+-0
+
+> <r_i_glide_rewards>
+-0.777126
+
+> <r_i_glide_rmsd>
+0.605551
+
+$$$$
+Test Ligand
+
+
+ 21 23 0 0 0 0 999 V2000
+ 34.2768 6.4601 23.4276 C 0 0 0 0 0 0
+ 34.7199 6.6807 24.7535 C 0 0 0 0 0 0
+ 32.9608 6.8443 23.0740 C 0 0 0 0 0 0
+ 33.8637 7.2655 25.7079 C 0 0 0 0 0 0
+ 32.1001 7.4207 24.0338 C 0 0 0 0 0 0
+ 32.5448 7.6388 25.3572 C 0 0 0 0 0 0
+ 31.6578 8.2493 26.3632 C 0 0 0 0 0 0
+ 31.3829 7.8493 27.6381 C 0 0 0 0 0 0
+ 31.8957 6.6637 28.4136 C 0 0 0 0 0 0
+ 30.4903 8.7246 28.2064 N 0 0 0 0 0 0
+ 31.7656 6.7961 29.7467 N 0 0 0 0 0 0
+ 30.1647 9.7304 27.3526 N 0 0 0 0 0 0
+ 32.1947 5.8187 30.7363 C 0 0 0 0 0 0
+ 30.8430 9.4334 26.2330 C 0 0 0 0 0 0
+ 33.6957 5.9781 31.0077 C 0 0 0 0 0 0
+ 30.7874 10.2877 25.0301 C 0 0 0 0 0 0
+ 31.9854 10.7833 24.4695 C 0 0 0 0 0 0
+ 31.9583 11.6080 23.3306 C 0 0 0 0 0 0
+ 30.7247 11.9044 22.7018 C 0 0 0 0 0 0
+ 29.5221 11.4297 23.2588 C 0 0 0 0 0 0
+ 29.5448 10.6400 24.4309 C 0 0 0 0 0 0
+ 1 2 1 0 0 0
+ 1 3 2 0 0 0
+ 2 4 2 0 0 0
+ 3 5 1 0 0 0
+ 4 6 1 0 0 0
+ 5 6 2 0 0 0
+ 6 7 1 0 0 0
+ 7 8 2 0 0 0
+ 7 14 1 0 0 0
+ 8 9 1 0 0 0
+ 8 10 1 0 0 0
+ 9 11 1 0 0 0
+ 10 12 1 0 0 0
+ 11 13 1 0 0 0
+ 12 14 2 0 0 0
+ 13 15 1 0 0 0
+ 14 16 1 0 0 0
+ 16 17 1 0 0 0
+ 16 21 2 0 0 0
+ 17 18 2 0 0 0
+ 18 19 1 0 0 0
+ 19 20 2 0 0 0
+ 20 21 1 0 0 0
+M END
+> <i_i_glide_confnum>
+1
+
+> <i_i_glide_lignum>
+1
+
+> <i_i_glide_posenum>
+177
+
+> <r_i_docking_score>
+-8.70173
+
+> <r_i_glide_ecoul>
+-15.8862
+
+> <r_i_glide_einternal>
+1.84397
+
+> <r_i_glide_emodel>
+-99.0481
+
+> <r_i_glide_energy>
+-62.44
+
+> <r_i_glide_erotb>
+0.517993
+
+> <r_i_glide_esite>
+-0.0274759
+
+> <r_i_glide_evdw>
+-46.5538
+
+> <r_i_glide_gscore>
+-8.70173
+
+> <r_i_glide_hbond>
+-0.97397
+
+> <r_i_glide_ligand_efficiency>
+-0.322286
+
+> <r_i_glide_ligand_efficiency_ln>
+-2.02562
+
+> <r_i_glide_ligand_efficiency_sa>
+-0.966858
+
+> <r_i_glide_lipo>
+-2.74283
+
+> <r_i_glide_metal>
+-0
+
+> <r_i_glide_rewards>
+-0.764823
+
+> <r_i_glide_rmsd>
+0.543804
+
+$$$$
+Test Ligand
+
+
+ 21 23 0 0 0 0 999 V2000
+ 34.5144 6.6833 23.3611 C 0 0 0 0 0 0
+ 33.1880 6.9515 22.9860 C 0 0 0 0 0 0
+ 34.9381 7.0224 24.6610 C 0 0 0 0 0 0
+ 32.2870 7.5460 23.8905 C 0 0 0 0 0 0
+ 34.0422 7.6076 25.5720 C 0 0 0 0 0 0
+ 32.7085 7.8735 25.1943 C 0 0 0 0 0 0
+ 31.7655 8.4568 26.1623 C 0 0 0 0 0 0
+ 31.4563 8.0176 27.4151 C 0 0 0 0 0 0
+ 31.9612 6.8234 28.1735 C 0 0 0 0 0 0
+ 30.4991 8.8399 27.9505 N 0 0 0 0 0 0
+ 31.7656 6.8973 29.5011 N 0 0 0 0 0 0
+ 30.1623 9.8254 27.0921 N 0 0 0 0 0 0
+ 32.1790 5.9073 30.4826 C 0 0 0 0 0 0
+ 30.8968 9.5864 26.0023 C 0 0 0 0 0 0
+ 33.4739 6.3765 31.1528 C 0 0 0 0 0 0
+ 30.8088 10.4312 24.8021 C 0 0 0 0 0 0
+ 31.9800 11.0176 24.2785 C 0 0 0 0 0 0
+ 31.9238 11.8291 23.1331 C 0 0 0 0 0 0
+ 30.6968 12.0157 22.4634 C 0 0 0 0 0 0
+ 29.5186 11.4761 23.0060 C 0 0 0 0 0 0
+ 29.5649 10.7043 24.1795 C 0 0 0 0 0 0
+ 1 2 1 0 0 0
+ 1 3 2 0 0 0
+ 2 4 2 0 0 0
+ 3 5 1 0 0 0
+ 4 6 1 0 0 0
+ 5 6 2 0 0 0
+ 6 7 1 0 0 0
+ 7 8 2 0 0 0
+ 7 14 1 0 0 0
+ 8 9 1 0 0 0
+ 8 10 1 0 0 0
+ 9 11 1 0 0 0
+ 10 12 1 0 0 0
+ 11 13 1 0 0 0
+ 12 14 2 0 0 0
+ 13 15 1 0 0 0
+ 14 16 1 0 0 0
+ 16 17 1 0 0 0
+ 16 21 2 0 0 0
+ 17 18 2 0 0 0
+ 18 19 1 0 0 0
+ 19 20 2 0 0 0
+ 20 21 1 0 0 0
+M END
+> <i_i_glide_confnum>
+9
+
+> <i_i_glide_lignum>
+1
+
+> <i_i_glide_posenum>
+294
+
+> <r_i_docking_score>
+-8.69162
+
+> <r_i_glide_ecoul>
+-14.7519
+
+> <r_i_glide_einternal>
+5.89466
+
+> <r_i_glide_emodel>
+-97.7232
+
+> <r_i_glide_energy>
+-63.1839
+
+> <r_i_glide_erotb>
+0.517993
+
+> <r_i_glide_esite>
+-0.0119369
+
+> <r_i_glide_evdw>
+-48.432
+
+> <r_i_glide_gscore>
+-8.69162
+
+> <r_i_glide_hbond>
+-0.870172
+
+> <r_i_glide_ligand_efficiency>
+-0.321912
+
+> <r_i_glide_ligand_efficiency_ln>
+-2.02327
+
+> <r_i_glide_ligand_efficiency_sa>
+-0.965735
+
+> <r_i_glide_lipo>
+-2.92829
+
+> <r_i_glide_metal>
+-0
+
+> <r_i_glide_rewards>
+-0.764823
+
+> <r_i_glide_rmsd>
+0.463026
+
+$$$$