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Commit f779c422 authored by Gerardo Tauriello's avatar Gerardo Tauriello
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Added doc for ChemType, ChemClass and QueryFlag

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......@@ -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
......@@ -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)
......@@ -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';
......
......@@ -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',
......
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