diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 3a4d0d292748f1c8f7546468d8f8b4657c9d10c2..aeb18459f28e01c33c3c09a48dd8d9b9ee342822 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -342,7 +342,94 @@ The Handle Classes
A chain of one or more :class:`residues <ResidueHandle>`. Chains are always
part of an entity.
-
+
+ .. attribute:: atoms
+
+ Get list of all atoms of this chain. To access a single atom, use
+ :meth:`FindAtom`.
+
+ This property is read-only. Also available as :meth:`GetAtomList`
+
+ :type: :class:`AtomHandleList` (list of :class:`AtomHandle`)
+
+ .. attribute:: bounds
+
+ Axis-aligned bounding box of the chain. Read-only
+
+ :type: :class:`ost.geom.AlignedCuboid`
+
+ .. attribute:: center_of_atoms
+
+ Center of atoms (not mass weighted). Also available as
+ :meth:`GetCenterOfAtoms`.
+
+ :type: :class:`~ost.geom.Vec3`
+
+ .. attribute:: center_of_mass
+
+ Center of mass. Also available as :meth:`GetCenterOfMass`
+
+ :type: :class:`~ost.geom.Vec3`
+
+ .. attribute:: description
+
+ Details about the chain. Not categorised, just text.
+
+ .. attribute:: in_sequence
+
+ Whether the residue numbers are in ascending order. For example:
+
+ .. code-block:: python
+
+ chain=ent.FindChain("A")
+ print(chain.residues) # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
+ print(chain.in_sequence) # prints true
+
+ chain=ent.FindChain("B")
+ print(chain.residues) # [B.GLY1, B.GLY4, B.GLY3]
+ print(chain.in_sequence) # prints false
+
+ .. attribute:: is_oligosaccharide
+
+ Indicates if the chain is an oligosaccharide, a branched, non-linear entity
+ of multiple sugars. Also available as :meth:`IsOligosaccharide`.
+
+ :type: :class:`bool`
+
+ .. attribute:: is_polymer
+
+ Indicates if a chain is a polymer. True for polypeptides, polynucleotides,
+ polysaccharides, oligosaccharides and branched chains. Also available as
+ :meth:`IsPolymer`.
+
+ :type: :class:`bool`
+
+ .. attribute:: is_polynucleotide
+
+ Indicates if a chain is a nucleic acid. Also available as
+ :meth:`IsPolynucleotide`.
+
+ :type: :class:`bool`
+
+ .. attribute:: is_polypeptide
+
+ Indicates if a chain is a protein. Also available as :meth:`IsPolypeptide`.
+
+ :type: :class:`bool`
+
+ .. attribute:: is_polysaccharide
+
+ Indicates if a chain is a polysaccharide. Also available as
+ :meth:`IsPolysaccharide()`.
+
+ :type: :class:`bool`
+
+ .. attribute:: mass
+
+ The total mass of this chain in Dalton. Also available as :meth:`GetMass`
+
+ :type: float
+
.. attribute:: name
The chain name. The name uniquely identifies the chain in the entity. In
@@ -356,15 +443,11 @@ The Handle Classes
:type: str
- .. attribute:: type
-
- Describes the type of the chain.
-
- :type: :class:`ChainType`.
+ .. attribute:: residue_count
- .. attribute:: description
+ Number of residues. Read-only. See :meth:`GetResidueCount`.
- Details about the chain. Not categorised, just text.
+ :type: :class:`int`
.. attribute:: residues
@@ -387,59 +470,11 @@ The Handle Classes
:type: :class:`ResidueHandleList` (list of :class:`ResidueHandle`)
- .. attribute:: in_sequence
-
- Whether the residue numbers are in ascending order. For example:
-
- .. code-block:: python
-
- chain=ent.FindChain("A")
- print(chain.residues) # [A.GLY1, A.GLY2, A.GLY4A, A.GLY4B]
- print(chain.in_sequence) # prints true
-
- chain=ent.FindChain("B")
- print(chain.residues) # [B.GLY1, B.GLY4, B.GLY3]
- print(chain.in_sequence) # prints false
-
- .. attribute:: residue_count
-
- Number of residues. Read-only. See :meth:`GetResidueCount`.
-
- :type: :class:`int`
-
- .. attribute:: atoms
-
- Get list of all atoms of this chain. To access a single atom, use
- :meth:`FindAtom`.
-
- This property is read-only. Also available as :meth:`GetAtomList`
-
- :type: :class:`AtomHandleList` (list of :class:`AtomHandle`)
-
- .. attribute:: bounds
-
- Axis-aligned bounding box of the chain. Read-only
-
- :type: :class:`ost.geom.AlignedCuboid`
-
- .. attribute:: mass
-
- The total mass of this chain in Dalton. Also available as :meth:`GetMass`
-
- :type: float
+ .. attribute:: type
- .. attribute:: center_of_mass
+ Describes the type of the chain.
- Center of mass. Also available as :meth:`GetCenterOfMass`
-
- :type: :class:`~ost.geom.Vec3`
-
- .. attribute:: center_of_atoms
-
- Center of atoms (not mass weighted). Also available as
- :meth:`GetCenterOfAtoms`.
-
- :type: :class:`~ost.geom.Vec3`
+ :type: :class:`ChainType`.
.. attribute:: valid
@@ -491,6 +526,26 @@ The Handle Classes
See :attr:`type`
+ .. method:: IsOligosaccharide()
+
+ See :attr:`is_oligosaccharide`
+
+ .. method:: IsPolymer()
+
+ See :attr:`is_polymer`
+
+ .. method:: IsPolynucleotide()
+
+ See :attr:`is_polynucleotide`
+
+ .. method:: IsPolypeptide()
+
+ See :attr:`is_polypeptide`
+
+ .. method:: IsPolysaccharide()
+
+ See :attr:`is_polysaccharide`
+
.. method:: GetDescription()
See :attr:`description`
diff --git a/modules/mol/base/pymod/export_chain.cc b/modules/mol/base/pymod/export_chain.cc
index 1664c13a33ed03c1fbdc404bbac9b081522c8e4a..b5ce6d91cba30b6a3dab3a83a066f044139e1d41 100644
--- a/modules/mol/base/pymod/export_chain.cc
+++ b/modules/mol/base/pymod/export_chain.cc
@@ -58,10 +58,12 @@ void export_Chain()
.def("IsPolypeptide", &ChainBase::IsPolypeptide)
.def("IsPolynucleotide", &ChainBase::IsPolynucleotide)
.def("IsPolysaccharide", &ChainBase::IsPolysaccharide)
+ .def("IsOligosaccharide", &ChainBase::IsOligosaccharide)
.def("IsPolymer", &ChainBase::IsPolymer)
.add_property("is_polypeptide", &ChainBase::IsPolypeptide)
.add_property("is_polynucleotide", &ChainBase::IsPolynucleotide)
.add_property("is_polysaccharide", &ChainBase::IsPolysaccharide)
+ .add_property("is_oligosaccharide", &ChainBase::IsOligosaccharide)
.add_property("is_polymer", &ChainBase::IsPolymer)
.add_property("type", &ChainBase::GetType)
.add_property("description", &ChainBase::GetDescription)
diff --git a/modules/mol/base/src/chain_base.cc b/modules/mol/base/src/chain_base.cc
index 4114a1462be137b7ea2e84cac6618df2309849e3..2b693b7fc031d07bf3da2492a1644db649557b30 100644
--- a/modules/mol/base/src/chain_base.cc
+++ b/modules/mol/base/src/chain_base.cc
@@ -81,6 +81,13 @@ bool ChainBase::IsPolysaccharide() const
}
+bool ChainBase::IsOligosaccharide() const
+{
+ this->CheckValidity();
+ return impl_->IsOligosaccharide();
+
+}
+
bool ChainBase::IsPolypeptide() const
{
this->CheckValidity();
diff --git a/modules/mol/base/src/chain_base.hh b/modules/mol/base/src/chain_base.hh
index 5463ef0a8627eac578b12e801618da69bc74c898..0ab82a3dbaf784193d3ba09fe1e687af4f96eaeb 100644
--- a/modules/mol/base/src/chain_base.hh
+++ b/modules/mol/base/src/chain_base.hh
@@ -82,7 +82,10 @@ public:
/// \brief whether the chain is a polysaccharide
bool IsPolysaccharide() const;
-
+
+ /// \brief whether the chain is an oligsaccharide (branched mmCIF entity)
+ bool IsOligosaccharide() const;
+
/// \brief whether the chain is a polypeptide
bool IsPolypeptide() const;
diff --git a/modules/mol/base/src/impl/chain_impl.hh b/modules/mol/base/src/impl/chain_impl.hh
index a3a7a97dcec720f024c39a2bcf73ff0bc108e9b6..e5bc7aac338d1d3c82c81730b9b5709eba7cf569 100644
--- a/modules/mol/base/src/impl/chain_impl.hh
+++ b/modules/mol/base/src/impl/chain_impl.hh
@@ -69,14 +69,20 @@ public:
{
return type_==CHAINTYPE_POLY || this->IsPolypeptide() ||
this->IsPolynucleotide() || this->IsPolysaccharide() ||
- type_==CHAINTYPE_POLY_PEPTIDE_DN_RN ||
- type_==CHAINTYPE_OLIGOSACCHARIDE;
+ this->IsOligosaccharide() ||
+ type_==CHAINTYPE_POLY_PEPTIDE_DN_RN || type_==CHAINTYPE_BRANCHED;
}
/// \brief whether the chain is a polysaccharide
bool IsPolysaccharide() const
{
return type_==CHAINTYPE_POLY_SAC_D || type_==CHAINTYPE_POLY_SAC_L;
}
+
+ /// \brief whether the chain is a polysaccharide
+ bool IsOligosaccharide() const
+ {
+ return type_==CHAINTYPE_OLIGOSACCHARIDE;
+ }
/// \brief whether the chain is a polypeptide
bool IsPolypeptide() const
{
diff --git a/modules/mol/base/tests/test_chain.cc b/modules/mol/base/tests/test_chain.cc
index 2154bdeab94555e73c89892847e6f9cac1759af4..f965fced69eb87d610baec27f4830e8d82202369 100644
--- a/modules/mol/base/tests/test_chain.cc
+++ b/modules/mol/base/tests/test_chain.cc
@@ -235,59 +235,69 @@ BOOST_AUTO_TEST_CASE(chain_type)
BOOST_CHECK(ch1.GetType() == CHAINTYPE_UNKNOWN);
BOOST_CHECK(!ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
e.SetChainType(ch1, CHAINTYPE_POLY);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
e.SetChainType(ch1, CHAINTYPE_NON_POLY);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_NON_POLY);
BOOST_CHECK(!ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
e.SetChainType(ch1, CHAINTYPE_WATER);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_WATER);
BOOST_CHECK(!ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_D);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_PEPTIDE_D);
e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_L);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_PEPTIDE_L);
e.SetChainType(ch1, CHAINTYPE_POLY_DN);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(ch1.IsPolynucleotide());
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_DN);
e.SetChainType(ch1, CHAINTYPE_POLY_RN);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(ch1.IsPolynucleotide());
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_RN);
e.SetChainType(ch1, CHAINTYPE_POLY_SAC_D);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_SAC_D);
e.SetChainType(ch1, CHAINTYPE_POLY_SAC_L);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_SAC_L);
@@ -295,6 +305,7 @@ BOOST_AUTO_TEST_CASE(chain_type)
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_DN_RN);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(ch1.IsPolynucleotide());
e.SetChainType(ch1, CHAINTYPE_N_CHAINTYPES);
@@ -305,30 +316,35 @@ BOOST_AUTO_TEST_CASE(chain_type)
BOOST_CHECK(ch1.GetType() == CHAINTYPE_MACROLIDE);
BOOST_CHECK(!ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
e.SetChainType(ch1, CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
e.SetChainType(ch1, CHAINTYPE_POLY_PEPTIDE_DN_RN);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_POLY_PEPTIDE_DN_RN);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
e.SetChainType(ch1, CHAINTYPE_BRANCHED);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_BRANCHED);
- BOOST_CHECK(!ch1.IsPolymer());
+ BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(!ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());
e.SetChainType(ch1, CHAINTYPE_OLIGOSACCHARIDE);
BOOST_CHECK(ch1.GetType() == CHAINTYPE_OLIGOSACCHARIDE);
BOOST_CHECK(ch1.IsPolymer());
BOOST_CHECK(!ch1.IsPolysaccharide());
+ BOOST_CHECK(ch1.IsOligosaccharide());
BOOST_CHECK(!ch1.IsPolypeptide());
BOOST_CHECK(!ch1.IsPolynucleotide());