Skip to content
Snippets Groups Projects
Commit b98ccb08 authored by Gerardo Tauriello's avatar Gerardo Tauriello
Browse files

Doc update for Select queries.

parent 55a725c0
No related branches found
No related tags found
No related merge requests found
......@@ -508,15 +508,16 @@ 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
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.
.. 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`.
class `ChemType::IONS`, amino acids to `ChemType::AMINOACIDS`. The type is
only properly set if a compund library is used.
.. attribute:: sec_structure
......@@ -529,6 +530,10 @@ The Handle Classes
most likely not be set properly for all except PDB files coming from
pdb.org.
.. attribute:: index
Residue index (starting at 0) within chain.
.. method:: FindAtom(atom_name)
Get atom by atom name. See also :attr:`atoms`
......@@ -544,6 +549,12 @@ The Handle Classes
Get list of all atoms of this residue. To access a single atom, use
:meth:`FindAtom`.
.. method:: IsPeptideLinking()
:return: True, if residue can form peptide bonds (determined based on
:attr:`chem_class` set when loading the structure).
:rtype: :class:`bool`
.. method:: GetChain()
......@@ -568,6 +579,10 @@ The Handle Classes
.. method:: GetChemType()
See :attr:`chem_type`
.. method:: GetIndex()
See :attr:`index`
.. class:: AtomHandle
......@@ -668,6 +683,10 @@ The Handle Classes
:type: list of :class:`bond handles<BondHandle>`
.. attribute:: index
Atom index (starting at 0) within entity.
.. method:: FindBondToAtom(other_atom)
Finds and returns the bond formed between this atom and `other_atom`. If no
......@@ -731,7 +750,7 @@ The Handle Classes
.. method:: GetIndex()
Returns the index of the atom.
See :attr:`index`
:rtype: int
......@@ -1444,6 +1463,10 @@ The View Classes
:type: :class:`AtomViewList`
.. attribute:: index
Residue index (starting at 0) within chain view.
.. method:: RemoveAtom(atom_view)
Remove atom from residue and all associated bonds. If the atom is not part
......
......@@ -175,36 +175,40 @@ The following properties may be used in predicates. The type is given for each p
Properties of Chains
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**cname/chain** (str) :attr:`Chain name<ChainHandle.name>`
Properties of Residues
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**rname** (str): :attr:`Residue name<ResidueHandle.name>`
**rnum** (int): :attr:`Residue number<ResidueHandle.number>`. Currently only the numeric part is honored.
**rnum** (int): :attr:`Residue number<ResidueHandle.number>`. Currently only the
numeric part is honored.
**rtype** (str): Residue type as given by the DSSP code, i.e. H for helix, E for extended.
**rindex** (int): :attr:`Index<ResidueHandle.index>` of residue in chain. This
index is the same for views and handles.
**rtype** (str): Residue type as given by the DSSP code (e.g. "H" for alpha
helix, "E" for extended), "helix" for all helix types, "ext" or "strand" for
all beta sheets or "coil" for any type of coil.
**ishetatm** (bool): Whether the atom is a :attr:`heterogenous<AtomHandle.is_hetatm>` atom.
**rindex** (int): :attr:`Index<ResidueHandle.index>` of residue handle in chain.
This index is the same for views and handles.
**peptide** (bool): Whether the residue is a :meth:`peptide <ResidueHandle.IsPeptideLinking>`.
**peptide** (bool): Whether the residue is :meth:`peptide linking
<ResidueHandle.IsPeptideLinking>`.
**protein** (bool): Whether the residue is considered to be part of a protein.
This is set when loading a structure if the residue forms a feasible peptide
bond to the previous or next residue.
**rbfac** (float): average B (temperature) factor of residue
**ligand** (bool) Whether the residue is a ligand. For official PDB files, the ligand property is set based on HET records.
**ligand** (bool) Whether the residue is a :meth:`ligand
<ResidueHandle.is_ligand>`.
**water** (bool) Whether the residue is water.
Properties of Atoms
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**aname** (str): :attr:`Atom name<AtomHandle.name>`
**ele** (str): :attr:`Atom element<AtomHandle.element>`
......@@ -219,6 +223,14 @@ Properties of Atoms
**z** (float): :attr:`Z<AtomHandle.pos>` coordinate of atom.
**aindex** (int): :attr:`Atom index<AtomHandle.index>`
**ishetatm** (bool): Whether the atom is a :attr:`heterogenous
atom<AtomHandle.is_hetatom>`.
**acharge** (float): :attr:`Atom charge<AtomHandle.charge>`
Query API documentation
--------------------------------------------------------------------------------
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment