diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst
index 6d036a70bf3e287cad950c7b55734d6e915f75fb..7d5bfd7f749b6b17c4341751bcdb3c9ec7aa759f 100644
--- a/modules/mol/base/doc/entity.rst
+++ b/modules/mol/base/doc/entity.rst
@@ -520,16 +520,16 @@ The Handle Classes
.. attribute:: chem_class
- The chemical class of a residue is used to broadly categorize residues based
- on their chemical properties. For example, peptides belong to the
- `L_PEPTIDE_LINKING` or `D_PEPTIDE_LINKING` classes.
+ The chemical class of the residue.
+
+ :type: :class:`ChemClass`
.. attribute:: chem_type
- The chemical type of a residue is a classification of all compounds
- obtained from the PDB component dictionary. For example, ions belong to the
- class `ChemType::IONS`, amino acids to `ChemType::AMINOACIDS`. The type is
- only properly set if a compund library is used.
+ The chemical type of the residue. The type is only properly set if a
+ compound library is used.
+
+ :type: :class:`ChemType`
.. attribute:: sec_structure
@@ -1835,11 +1835,116 @@ SecStructure
.. hlist::
:columns: 2
- * ALPHA_HELIX = 'H'
- * PI_HELIX = 'I'
- * THREE_TEN_HELIX = 'G'
- * EXTENDED = 'E'
- * BETA_BRIDGE = 'B'
- * TURN = 'T'
- * BEND = 'S'
- * COIL = 'C'
+ * ``ALPHA_HELIX`` = 'H'
+ * ``PI_HELIX`` = 'I'
+ * ``THREE_TEN_HELIX`` = 'G'
+ * ``EXTENDED`` = 'E'
+ * ``BETA_BRIDGE`` = 'B'
+ * ``TURN`` = 'T'
+ * ``BEND`` = 'S'
+ * ``COIL`` = 'C'
+
+
+ChemClass
+--------------------------------------------------------------------------------
+
+.. class:: ChemClass(chem_class)
+
+ The chemical class is used to broadly categorize residues based on their
+ chemical properties. For example, peptides belong to some PEPTIDE_LINKING
+ class. Possible values as constant variable names and as characters:
+
+ .. hlist::
+ :columns: 2
+
+ * ``PEPTIDE_LINKING`` = 'P'
+ * ``D_PEPTIDE_LINKING`` = 'D'
+ * ``L_PEPTIDE_LINKING`` = 'L'
+ * ``RNA_LINKING`` = 'R'
+ * ``DNA_LINKING`` = 'S'
+ * ``NON_POLYMER`` = 'N'
+ * ``L_SACCHARIDE`` = 'X'
+ * ``D_SACCHARIDE`` = 'Y'
+ * ``SACCHARIDE`` = 'Z'
+ * ``WATER`` = 'W'
+ * ``UNKNOWN`` = 'U'
+
+ Python can implicitly convert characters to objects of this type.
+
+ :param chem_class: Chemical class to set.
+ :type chem_class: :class:`str`
+
+ .. method:: IsPeptideLinking
+
+ :return: True, if set class is PEPTIDE_LINKING, D_PEPTIDE_LINKING or
+ L_PEPTIDE_LINKING
+
+ .. method:: IsNucleotideLinking
+
+ :return: True, if set class is RNA_LINKING or DNA_LINKING
+
+
+ChemType
+--------------------------------------------------------------------------------
+
+.. class:: ChemType
+
+ The chemical type of a residue is a classification of all compounds obtained
+ from the PDB component dictionary. For example, ions belong to the class IONS,
+ amino acids to AMINOACIDS. Possible values as constant variable names and as
+ characters:
+
+ .. hlist::
+ :columns: 2
+
+ * ``IONS`` = 'I'
+ * ``NONCANONICALMOLS`` = 'M'
+ * ``SACCHARIDES`` = 'S'
+ * ``NUCLEOTIDES`` = 'N'
+ * ``AMINOACIDS`` = 'A'
+ * ``COENZYMES`` = 'E'
+ * ``WATERCOORDIONS`` = 'C'
+ * ``DRUGS`` = 'D'
+ * ``WATERS`` = 'W'
+ * ``UNKNOWN`` = 'U'
+
+ Python can implicitly convert characters to objects of this type.
+
+ :param chem_type: Chemical type to set.
+ :type chem_type: :class:`str`
+
+ .. method:: IsIon
+
+ :return: True, if set type is IONS or WATERCOORDIONS
+
+ .. method:: IsNucleotide
+
+ :return: True, if set type is NUCLEOTIDES
+
+ .. method:: IsSaccharide
+
+ :return: True, if set type is SACCHARIDES
+
+ .. method:: IsAminoAcid
+
+ :return: True, if set type is AMINOACIDS
+
+ .. method:: IsCoenzyme
+
+ :return: True, if set type is COENZYMES
+
+ .. method:: IsDrug
+
+ :return: True, if set type is DRUGS
+
+ .. method:: IsNonCanonical
+
+ :return: True, if set type is NONCANONICALMOLS
+
+ .. method:: IsWater
+
+ :return: True, if set type is WATERS
+
+ .. method:: IsKnown
+
+ :return: True, if set type is not UNKNOWN
diff --git a/modules/mol/base/doc/query.rst b/modules/mol/base/doc/query.rst
index 8d5a6328658829756c9d227e76061c3efd043d55..54380f93f0f8b952934e31ef8aea865b1b89cbd8 100644
--- a/modules/mol/base/doc/query.rst
+++ b/modules/mol/base/doc/query.rst
@@ -273,3 +273,13 @@ In the following, the interface of the query class is described. In general, you
.. method:: IsResidueSelected(residue)
Returns true, when at least one atom of the residue matches the predicates.
+
+.. class:: QueryFlag
+
+ Defines flags to change default behaviour of Select queries. Possible values:
+
+ * ``EXCLUSIVE_BONDS`` - adds bonds to the :class:`EntityView` when at least
+ one of the two bonded atoms was selected (by default both must be selected)
+ * ``NO_BONDS`` - do not include any bonds (by default bonds are included)
+ * ``MATCH_RESIDUES`` - include all atoms of a residue if any of its atoms is
+ selected (by default only selected atoms are included)
diff --git a/modules/mol/base/src/chem_class.hh b/modules/mol/base/src/chem_class.hh
index 73ff48698baf5997d86284f0863be6d2358b8324..97f80f23e393d04c86cd377966b6bc7bb46e41a5 100644
--- a/modules/mol/base/src/chem_class.hh
+++ b/modules/mol/base/src/chem_class.hh
@@ -29,11 +29,11 @@ struct DLLEXPORT ChemClass {
const static char PEPTIDE_LINKING ='P';
const static char D_PEPTIDE_LINKING ='D';
const static char L_PEPTIDE_LINKING ='L';
- const static char RNA_LINKING ='R';
- const static char DNA_LINKING ='S';
+ const static char RNA_LINKING ='R';
+ const static char DNA_LINKING ='S';
const static char NON_POLYMER ='N';
const static char L_SACCHARIDE ='X';
- const static char D_SACCHARIDE ='Y';
+ const static char D_SACCHARIDE ='Y';
const static char SACCHARIDE ='Z';
const static char WATER ='W';
const static char UNKNOWN ='U';
diff --git a/modules/mol/base/src/sec_structure.hh b/modules/mol/base/src/sec_structure.hh
index 22779ed8118bdd9743e2f602b9a30d96c3ef1d72..f76b0e5f9c4508d76ed52f2efd41bc2f7c5a3aec 100644
--- a/modules/mol/base/src/sec_structure.hh
+++ b/modules/mol/base/src/sec_structure.hh
@@ -28,10 +28,10 @@ namespace ost { namespace mol {
/// format.
struct DLLEXPORT_OST_MOL SecStructure {
typedef enum {
- ALPHA_HELIX ='H',
- PI_HELIX ='I',
+ ALPHA_HELIX ='H',
+ PI_HELIX ='I',
THREE_TEN_HELIX ='G',
- TURN ='T',
+ TURN ='T',
EXTENDED ='E',
BETA_BRIDGE ='B',
BEND ='S',