The Molecular Entity¶

This document describes the EntityHandle and the related classes.

The Handle Classes¶

CreateEntity()¶

Creates a new entity. The created entity is empty, that is, it does not contain any atoms, residues, chains, bonds or torsions. To populate the entity, use an entity editor.

Returns:	The newly created `EntityHandle`

class EntityHandle¶

The entity class represents a molecular structure. Such a structure is in general made up of one or more chains of residues, which in turn are formed by one or more atoms.

The interface of entities is tailored to biological macromolecules, but this does not prevent it to be used for molecules in general: An entity also represent a ligand or a collection of water molecules - hence the rather generic name.

chains¶

List of all chains of this entity. The chains are in the same order they have been added, for example the order they have been listed in a PDB file.

Also available as GetChainList(). To access a single chain, use FindChain().

This property is read-only.

residues¶

List of all residues of this entity. The returned residues are first sorted by chain and then from N- to C-terminus.

This property is read-only.

Example usage:

for res in ent.residues:
  print res.name, res.atom_count

Also available as GetResidueList(). To access a single residue, use FindResidue().

returns: A list of residue handles

atoms¶

Get list of all atoms of this entity. To access a single atom, use FindAtom().

This property is read-only. Also available as GetAtomList()

Type :	A list of `atom handles`

bounds¶

Axis-aligned bounding box of the entity. Read-only

Type :	`ost.geom.AlignedCuboid`

mass¶

The total mass of the entity in Dalton. Also available as GetMass().

Type :	float

center_of_mass¶

Center of mass. Also available as GetCenterOfMass()

Type :	`Vec3`

center_of_atoms¶

Center of atoms (not mass-weighted). Also available as GetCenterOfAtoms().

Type :	`Vec3`

FindChain(chain_name)¶

Get chain by name. See also chains

Parameters:	chain_name (str) – Chain identifier, e.g. “A”
Returns:	A valid `ChainHandle`, if the entity contains a chain with the given name, an invalid `ChainHandle` otherwise.

GetChainList()¶: See chains

FindResidue(chain_name, res_num)¶

Get residue by chain name and residue number. See also GetResidueList()

Parameters:	chain_name (str) – Chain identifier, e.g. “A” res_num (mol.ResNum) – residue number
Returns:	A valid `ResidueHandle` if the chain exists and the chain contains a residue of the given residue number, an invalid `ResidueHandle` otherwise.

GetResidueList()¶: See residues

FindAtom(chain_name, res_num, atom_name)¶

Get atom by chain name, residue number and atom name. See also atoms

Parameters:	chain_name (str) – Chain identifier, e.g. “A” res_num (mol.ResNum) – residue number atom_name (str) – atom name, e.g. CA
Returns:	A valid `AtomHandle` if an atom matching the parameters could be found, an invalid `AtomHandle` otherwise

GetAtomList()¶: See atoms

EditXCS([edit_mode=mol.EditMode.BUFFERED_EDIT])¶

Request XCSEditor for editing the external coordinate system. This call will fail when there are pending changes of the internal coordinate system.

Parameters:	edit_mode (mol.EditMode) – Must be EditMode.BUFFERED_EDIT or EditMode.UNBUFFERED_EDIT. For more details, see the editor documentation.
Returns:	`XCSEditor`

EditICS([edit_mode=mol.EditMode.BUFFERED_EDIT])¶

Request ICSEditor for editing the internal coordinate system, such as torsions, bond lengths and angle between two bonds. This call will fail when there are pending changes of the external coordinate system.

Parameters:	edit_mode (mol.EditMode) – Must be EditMode.BUFFERED_EDIT or EditMode.UNBUFFERED_EDIT. For more details, see the editor documentation.
Returns:	`ICSEditor`

Select(query, flags=0)¶

Perform a selection on the entity. The result of the selection is an EntityView which (usually) contains only a subset of chains, residues, atoms and bonds of the original entity.

Example Usage:

Parameters:	query (string or `Query`) – The query to be executed. See `Query` for details. flags (int) – An ORed combination of `QueryFlags`.
Returns:	An `entity view`.
Raises :	`QueryError` when the query could not be executed due to syntactic errors.

CreateFullView()¶

Creates an entity view containing all chains, residues, atoms and bonds of this entity.

# these two lines are identical
full=ent.Select('')
full=ent.CreateFullView()

Returns:	`EntityView`

CreateEmptyView()¶

Creates an entity view pointing to this entity, but otherwise empty. This method is usually the starting point for manual entity view creation, e.g.:

view=ent.CreateEmtpyView()
for atom in ent.atoms:
  if ComplicatedPredicate(atom):
     view.AddAtom(atom)

Returns:	`EntityView`

Copy()¶

Creates a deep copy of the entity.

Returns:	A new `EntityHandle` that is an exact copy of this entity.

Note

alternative atom positions are not handled yet.

GetCenterOfAtoms()¶

Get center of atoms, that is the average atom position of the entity. Use GetCenterOfMass() to calculate the mass-weighted center of the entity.

Returns:	`Vec3`

GetCenterOfMass()¶

Calculates the center of mass of the entity. Use GetCenterOfAtoms() to calculate the non-mass-weighted center of the entity.

Returns:	`Vec3`

GetGeometricCenter()¶

Calculates the mid-point of the axis aligned bounding box of the entity.

Returns:	`Vec3`

GetMass()¶: See mass

FindWithin(pos, radius)¶

Find all atoms in sphere of given radius centred at pos. To turn the returned list of atoms into an EntityView, use CreateViewFromAtomList().

Parameters:	pos (`Vec3`) – Center of sphere radius (float) – The radius of the sphere
Returns:	A list of `atom handles`

class ChainHandle¶

A chain of one or more residues. Chains are always part of an entity.

name¶

The chain name. The name uniquely identifies the chain in the entity. In most cases, the chain name is one character. This is restriction of the PDB file format. However, you are free to use longer names as long as you don’t want to save them as PDB files

This property is read-only. To change the name, use an XCSEditor.

Also available as GetName()

Type :	str

type¶: Describes the type of the chain. See ChainType.

description¶: Details about the chain. Not categorised, just text.

residues¶

List of all residues of this chain. The residues are sorted from N- to C-terminus. Usually the residue numbers are in ascending order (see in_sequence).

This property is read-only.

Example usage:

chain=ent.FindChain("A")
for res in chain.residues:
  print res.name, res.atom_count

Also available as GetResidueList(). To access a single residue, use FindResidue().

Returns:	A list of `residue handles`

in_sequence¶

Whether the residue numbers are in ascending order. For example:

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

atoms¶

Get list of all atoms of this chain. To access a single atom, use FindAtom().

This property is read-only. Also available as GetAtomList()

Type :	A list of `atom handles`

bounds¶

Axis-aligned bounding box of the chain. Read-only

Type :	`ost.geom.AlignedCuboid`

mass¶

The total mass of this chain in Dalton. Also available as GetMass()

Type :	float

center_of_mass¶

Center of mass. Also available as GetCenterOfMass()

Type :	`Vec3`

center_of_atoms¶

Center of atoms (not mass weighted). Also available as GetCenterOfAtoms().

Type :	`Vec3`

FindResidue(res_num)¶

Get residue by residue number. See also residues

Parameters:	res_num (mol.ResNum) – residue number
Returns:	A valid `ResidueHandle` if the chain contains a residue with matching residue number, an invalid `ResidueHandle` otherwise.

GetResidueList()¶

Get list of all residues of this chain. For peptide chains, the residues are usually ordered from N- to C-terminus.To access a single residue, use FindResidue().

Returns:	A list of `residue handles`

FindAtom(res_num, atom_name)¶

Get atom by residue number and atom name. See also atoms

Parameters:	res_num (mol.ResNum) – residue number atom_name (str) – atom name, e.g. CA
Returns:	A valid `AtomHandle` if an atom matching the parameters could be found, an invalid `AtomHandle` otherwise

GetAtomList()¶: See atoms

GetName()¶: See name

GetType()¶: See type

GetDescription()¶: See description

class ResidueHandle¶

The residue is either used to represent complete molecules or building blocks in a polymer, e.g. in a protein, DNA or RNA. A residue consists of one or more atoms. Residues are always part of a ChainHandle, even if they are ligands or water molecules where the concept of a chain does not apply.

name¶

The residue name is usually a str of 3 characters, e.g. GLY for glycine or ALA for alanine, but may be shorter, e.g. G for guanosine, or longer for structures loaded from formats other than PDB.

This property is read-only. To change the name of the residue, use EditorBase.SetResidueName().

number¶

The number of this residue. The residue number has a numeric part and an insertion-code. This property is read-only. Also available as GetNumber().

Type :	`ResNum`

one_letter_code¶

For amino acids, and nucleotides the one_letter_code is an alpha-numeric character. For unknown or more exotic residues, the one letter code is set to ‘?’.

Example

This code-snippet shows how to get the sequence string from a list of residues.

print ''.join([r.one_letter_code for r in chain.residues])

Type :	str

bounds¶

Axis-aligned bounding box of the residue. Read-only.

Type :	`ost.geom.AlignedCuboid`

mass¶

The total mass of this residue in Dalton. Also available as GetMass().

Type :	float

center_of_mass¶

Center of mass. Also available as GetCenterOfMass()

Type :	`Vec3`

center_of_atoms¶

Center of atoms (not mass weighted). Also available as GetCenterOfAtoms().

Type :	`Vec3`

chain¶

The chain this residue belongs to. Read-only. Also available as GetChain()

Type :	`ChainHandle`

phi_torsion¶

The PHI dihedral angle between this residue and the next. For residues that are not amino acids, residues that do not have all atoms required or residues that do not have bonds between the four atoms involved in the torsion, the PHI torsion is an invalid handle.

Read-only. Also available as GetPhiTorsion()

Type :	`TorsionHandle`

psi_torsion¶

The PSI dihedral angle between this residue and the previous. For residues that are not amino acids, residues that do not have all atoms required or residues that do not have bonds between the four atoms involved in the torsion, the PSI torsion is an invalid handle.

Read-only. Also available as GetPsiTorsion()

Type :	`TorsionHandle`

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.

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.

sec_structure¶: The secondary structure of the residue.

is_ligand¶: Whether the residue is a ligand. When loading PDB structures, this property is set based on the HET records. This also means, that this property will most likely not be set properly for all except PDB files coming from pdb.org.

FindAtom(atom_name)¶

Get atom by atom name. See also atoms

Parameters:	atom_name (str) – atom name, e.g. CA
Returns:	A valid `AtomHandle` if an atom with the given name could be found, an invalid `AtomHandle` otherwise

GetAtomList()¶: Get list of all atoms of this residue. To access a single atom, use FindAtom().

GetChain()¶: See chain

GetCenterOfAtoms()¶: See center_of_atoms

GetCenterOfMass()¶: See center_of_mass

GetPhiTorsion()¶: See phi_torsion

GetPsiTorsion()¶: See psi_torsion

GetChemType()¶: See chem_type

class AtomHandle¶

Represents an atom in a molecular structure. Atoms are always part of a residue.

name¶

The atom name, usually a capitalized string consisting of the element and an position indicator, e.g. G1. In general, the atom name uniquely identifies an atom within a residue. However, this is not enforced and there may be more than one atoms with the same name.

Type :	str

qualified_name¶

The qualified name consists of the atom name as well as a unique residue identifier and chain name. For CA of a glycine with residue number 2 of chain A, the qualified name is “A.GLY2.CA”.

Type :	str

element¶

The atom’s element. Note that this may return an empty string. Also available as GetElement(). Read-only.

Type :	str

mass¶

The atom’s mass in Dalton. Also available as GetMass(). Read-only.

Type :	float

pos¶

The atom’s position in global coordinates, transformed by the entity transformation. Also available as GetPos().

Read-only.

Type :	`Vec3`

original_pos¶

The atom’s untransformed position in global coordinates. Also available as GetOriginalPos().

Read-only.

Type :	`Vec3`

radius¶

The van-der-Waals radius of the atom. Also available as GetRadius(). Read/write.

Type :	float

occupancy¶: The atom’s occupancy in the range 0 to 1. Read/write. Also available as meth:GetOccupancy, SetOccupancy(). :type: float

b_factor¶

The atom’s temperature factor. Read/write. Also available as GetBFactor(), SetBFactor().

Type :	float

charge¶

The atom’s charge. Also available as GetCharge(), SetCharge().

Type :	float

residue¶

The residue this atom belongs to. Read-only.

Type :	`ResidueHandle`

is_hetatom¶: Indicates whether this atom is a HETATM. When loading a structure from a PDB file, all non-standard aminoacid and nucleotide atoms as well as ligands are marked as HETATM.

bonds¶

List of bonds this atom is involved in. The bonds are in no particular order. Also available as GetBondList().

Type :	list of `bond handles`

FindBondToAtom(other_atom)¶

Finds and returns the bond formed between this atom and other_atom. If no bond exists between the two atoms, an invalid BondHandle is returned.

Parameters:	other_atom (`AtomHandle`) – The other atom
Return type:	`BondHandle`

GetBondCount()¶

Return type:	int

GetBondList()¶

See bonds

Return type:	`BondHandleList`

GetBondPartners()¶

Get list of atoms this atom is bonded with. This method exists as a shortcut to determine all the bonding partners of an atom and avoids code like this:

bond_parters=[]
for bond in atom.bonds:
  if bond.first==atom:
    bond_partners.append(bond.second)
  else:
    bond_partners.append(bond.first)

Return type:	`AtomHandleList`

GetCharge()¶

See charge

Return type:	float

GetElement()¶

See element

Return type:	str

GetEntity()¶

The entity this atom belongs to

Return type:	`EntityHandle`

GetHashCode()¶: Returns a unique identifier for this atom. :rtype: int

GetIndex()¶

Returns the index of the atom.

Return type:	int

GetMass()¶

See mass

Return type:	float

GetName()¶

See name

Return type:	str

GetOriginalPos()¶

Return type:	`Vec3`

GetPos()¶

See pos

Return type:	`Vec3`

GetQualifiedName()¶

See qualified_name

Return type:	str

GetRadius()¶

See radius

Return type:	float

GetResidue()¶

See residue

Return type:	`ResidueHandle`

IsHetAtom()¶

See is_hetatom

Return type:	bool

IsValid()¶

See valid

Return type:	bool

The View Classes¶

class EntityView¶

An entity view represents a structural subset of an EntityHandle. For an introduction ,see Introduction to the mol Module.

chains¶

List of all chains of this entity. The chains are in the same order they have been added.

Also available as GetChainList(). To access a single chain, use FindChain().

This property is read-only.

residues¶

List of all residues of this entity. The returned residues are first sorted by chain and then from N- to C-terminus.

This property is read-only.

Example usage:

for res in ent.residues:
  print res.name, res.atom_count

Also available as GetResidueList(). To access a single residue, use FindResidue().

Type :	A list of `ResidueViews`

atoms¶

Get list of all atoms of this entity. To access a single atom, use FindAtom().

This property is read-only. Also available as GetAtomList()

Type :	A list of `AtomViews`

bounds¶

Axis-aligned bounding box of the entity view. Read-only.

Type :	`ost.geom.AlignedCuboid`

handle¶

The underlying handle of the entity view. Also available as GetHandle().

Type :	`EntityHandle`

CreateEmptyView()¶

See EntityHandle.CreateEmptyView()

Return type:	EntityView

CreateFullView()¶

Returns a copy of this entity. Provided for duck-typing <http://en.wikipedia.org/wiki/Duck_typing> purposes.

Return type:	`EntityView`

AddChain(chain_handle[, view_add_flags])¶

Add chain to view. By default, only the chain is added to the view, but not its residues and atoms. This behaviour can be changed by passing in an appropriate set of view_add_flags.

The following example just adds a chain without residues and atoms:

pdb = ost.io.LoadPDB(<PDB file name>)
v = pdb.CreateEmptyView()
v.AddChain(pdb.chains[0])

To copy a whole chain, go like:

pdb = ost.io.LoadPDB(<PDB file name>)
v = pdb.CreateEmptyView()
v.AddChain(pdb.chains[0], ost.mol.INCLUDE_ALL)

Parameters:	chain_handle (`ChainHandle`) – The chain handle to be added. view_add_flags (`int`) – An ORed together combination of ViewAddFlags.
Return type:	`ChainView`

AddResidue(residue_handle[, view_add_flags])¶

Add residue to view. If the residue’s chain is not already part of the view, it will be added. By default, only the residue is added, but not its atoms. This behaviour can be modified by passing in an appropriate combination of ViewAddFlags.

Parameters:	residue_handle (`ResidueHandle`) – The residue handle to be added view_add_flags (`int`) – An ORed together combination of ViewAddFlags
Return type:	`ResidueView`

AddAtom(atom_handle[, view_add_flags])¶

Add the atom to view. The chain and residue of the atom are added to the view if they haven’t already been added.

Parameters:	atom_handle (`AtomHandle`) – The atom handle view_add_flags (`int`) – An ORed together combination of ViewAddFlags
Return type:	`AtomView`

AddBond(bond_handle)¶

Add bond to the view.

Parameters:	bond_handle (BondHandle) – Bond to be added
Returns:	True if the bond has been added, false if the bond was already present in the view.
Return type:	bool

AddAllInclusiveBonds()¶: Convenience method to add all bonds to the view for which both of the bond partners are in the view. This method is useful when manually assembling views.

RemoveChain(chain)¶

Remove chain and all its residues from the entity view.

Parameters:	chain (ChainView) – The chain to be removed. May be invalid

RemoveResidue(residue)¶

Remove residue from view.

Parameters:	residue (ResidueView) – The residue to be removed. May be invalid

RemoveAtom(atom)¶

Remove atom from view

Parameters:	atom (AtomView) – The atom to be removed. May be invalid

GetAngle(atom1, atom2, atom3)¶

Parameters:	atom1 (AtomHandle) – atom2 (AtomHandle) – atom3 (AtomHandle) –
Return type:	float

FindWithin(pos, radius)¶

Find all atoms that are within radius of the given position. See EntityHandle.FindWithin().

Parameters:	pos (`Vec3`) – radius (float) –
Return type:	class:AtomViewList

FindChain(chain_name)¶

Find chain by name.

Parameters:	chain_name (str) –
Returns:	The chain if present in the view, an invalid `ChainView` otherwise
Return type:	class:ChainView

FindResidue(residue)¶

Find residue view of pointing to the given handle.

Parameters:	residue (ResidueHandle) – Residue handle
Returns:	The residue view pointing the the handle, or an invalid handle if the residue is not part of the view
Return type:	class:ResidueView

FindAtom(chain_name, res_num, atom_name)¶

Parameters:	chain_name (str) – The chain name res_num (ResNum or int) – The residue number atom_name (str) – The name of the atom
Return type:	class:AtomView

Select(query[, flags])¶

Perform selection on entity view. See EntityHandle.Select().

Parameters:	query ((`Query` or str)) – The query flags (int) – An ORed together combination of ViewAddFlags
Return type:	EntityView

Copy()¶

Returns a deep copy of the entity view. The effect is identical to calling

the_copy=view.Select(')

Return type:	EntityView

GetMass()¶

Get total mass of view.

Return type:	float

GetCenterOfMass()¶

Get the center of mass. For a non-mass-weighted center, see GetCenterOfAtoms().

Return type:	`Vec3`

GetGeometricCenter()¶

Get the geometric center (the center of the axis-aligned bounding box).

Return type:	`Vec3`

GetGeometricStart()¶

Return type:	`Vec3`

chain_count¶

Number of chains. Read-only. See GetChainCount().

Type :	int

residue_count¶

Number of residues. Read-only. See GetResidueCount().

Type :	int

atom_count¶

Number of atoms. Read-only. See GetAtomCount().

Type :	int

GetCenterOfAtoms()¶

Calculates the center of atoms. For a mass-weighted center, use GetCenterOfMass().

Return type:	`Vec3`

GetAtomList()¶

See atoms

Return type:	class:AtomViewList

GetBondCount()¶: Get number of bonds :rtype: int

GetChainCount()¶

Get number chains. See chain_count

Return type:	int

GetResidueCount()¶

See residue_count

Return type:	int

GetBondList()¶

See bonds

Return type:	`BondHandleList`

GetHandle()¶

See handle

Return type:	class:EntityHandle

GetResidueList()¶

Return type:	class:ResidueViewList

GetGeometricEnd()¶

Return type:	`Vec3`

GetChainList()¶

See chains

Return type:	class:ChainViewList

GetAtomCount()¶: Get number of atoms. See :attr`atom_count`. :rtype: int

class ChainView¶

name¶

This property is read-only. To change the name, use an XCSEditor.

Also available as GetName()

Type :	str

residues¶

List of all residues of this chain. The residues are sorted from N- to C-terminus. Usually the residue numbers are in ascending order (see in_sequence).

This property is read-only.

Example usage:

chain=ent.FindChain("A")
for res in chain.residues:
  print res.name, res.atom_count

Also available as GetResidueList(). To access a single residue, use FindResidue().

Type :	A list of `residue views`

in_sequence¶

Whether the residue numbers are in ascending order. For example:

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

atoms¶

Get list of all atoms of this chain. To access a single atom, use FindAtom().

This property is read-only. Also available as GetAtomList()

Type :	A list of `atom handles`

bounds¶

Axis-aligned bounding box of the chain. Read-only

Type :	`ost.geom.AlignedCuboid`

mass¶

The total mass of this chain in Dalton. Also available as GetMass()

Type :	float

center_of_mass¶

Center of mass. Also available as GetCenterOfMass()

Type :	`Vec3`

center_of_atoms¶

Center of atoms (not mass weighted). Also available as GetCenterOfAtoms().

Type :	`Vec3`

handle¶

The chain handle this view points to. Also available as GetHandle().

Type :	`ChainHandle`

in_sequence

Whether the residue numbers are in ascending order. Note that the value of in_sequence is independent from the value of ChainHandle.in_sequence.

Type :	bool

AddAtom(atom_handle[, view_add_flags])¶

Add atom to the view. If the residue of the atom is not already part of the view, it will be added. If the atom does not belong to chain, the result is undefined. Foo

Parameters:	atom_handle (`AtomHandle`) – The atom to be added view_add_flags (`int`) – An ORed together combination of ViewAddFlags
Return type:	`AtomView`

AddResidue(residue_handle[, view_add_flags])¶

Add residue to the view. If the atom does not belong to chain, the result is undefined. By default, only the residue, but no atoms are added to the view. To change the behavior, pass in a suitable combination of ViewAddFlags.

Parameters:	residue_handle (`ResidueHandle`) – The residue handle to be added. view_add_flags (`int`) – An ORed together combination of ViewAddFlags
Return type:	`ResidueView`

FindAtom(res_num, atom_name)¶

Find atom with the given residue number and atom name.

Parameters:	res_num (`ResNum`) – The residue number atom_name (str) – The atom name
Returns:	The atom view, or an invalid atom view if no atom with the given parameters is part of the view.
Return type:	`AtomView`

FindResidue(res_num)¶

Find residue by residue number.

Parameters:	res_num (`ResNum`) –
Return type:	`ResidueView`
Returns:	The residue view, or an invalid residue view if no residue with the given residue number is in the view.

GetCenterOfAtoms()¶: See center_of_atoms

GetCenterOfMass()¶: See center_of_mass

GetEntity()¶: See entity

GetGeometricCenter()¶: See geometric_center

GetHandle()¶: See handle

GetMass()¶: See mass

GetName()¶: See name

GetResidueByIndex(index)¶

Returns the residue view at index. If index is negative or bigger than the number of residues minus one, an invalid ResidueView is returned.

Parameters:	index (int) – The index
Return type:	`ResidueView`

GetResidueList()¶

See residues

Return type:	bool

InSequence()¶: See in_sequence

IsValid()¶: See valid

RemoveResidue(residue)¶

Remove residue from chain. If the residue is not part of the view, the chain is left unchanged.

Parameters:	residue (`ResidueView`) – The residue view. May be invalid
Return type:	None

RemoveResidues()¶: Remove all residues from this chain view

Select(query[, flags])¶

Perform query on chain. This will return an entity view containing atoms and bonds of the residue view that match the residue. In case no atom matches the predicate, an empty view is returned.

Parameters:	query (`Query` or str) – The query flags (int) – An ORed together combination of query flags
Return type:	`EntityView`

class ResidueView¶

handle¶

The residue handle this view points to. Also available as GetHandle().

Type :	`ResidueHandle`

name¶

The residue name is usually a str of 3 characters, e.g. GLY for glycine or ALA for alanine, but may be shorter, e.g. G for guanosine, or longer for structures loaded from formats other than PDB.

This property is read-only. To change the name of the residue, use EditorBase.SetResidueName().

number¶

The number of this residue. The residue number has a numeric part and an insertion-code. This property is read-only. Also available as GetNumber().

Type :	`ResNum`

one_letter_code¶

For amino acids, and nucleotides the one_letter_code is an alpha-numeric character. For unknown or more exotic residues, the one letter code is set to ‘?’.

Example

This code-snippet shows how to get the sequence string from a list of residues.

print ''.join([r.one_letter_code for r in chain.residues])

Type :	str

bounds¶

Axis-aligned bounding box of the residue view. Read-only

Type :	`ost.geom.AlignedCuboid`

mass¶

The total mass of this residue in Dalton. Also available as GetMass().

Type :	float

center_of_mass¶

Center of mass. Also available as GetCenterOfMass()

Type :	`Vec3`

center_of_atoms¶

Center of atoms (not mass weighted). Also available as GetCenterOfAtoms().

Type :	`Vec3`

chain¶

The chain this residue belongs to. Read-only. Also available as GetChain()

Type :	`ChainView`

handle

The residue handle this view points to

Type :	`ResidueHandle`

RemoveAtom(atom_view)¶

Remove atom from residue and all associated bonds. If the atom is not part of the view, the residue view is left unchanged.

Parameters:	atom_view (`AtomView`) – The atom to be removed. May be an invalid handle
Return type:	None

GetHandle()¶: See handle

GetMass()¶: See mass

GetChain()¶: See chain

FindAtom(atom_name)¶

Find atom by name. Returns the atom, or an invalid atom if no atoms with the given name is part of the view.

Parameters:	atom_name (str) –
Return type:	`AtomView`

GetIndex()¶: See index

GetCenterOfMass()¶: See center_of_mass

IsAtomIncluded(atom_handle)¶

Returns true if the given atom is part of the view, false if not.

Parameters:	atom_handle (`AtomHandle`) –
Return type:	bool

GetGeometricCenter()¶: See geometric_center

AddAtom(atom_handle[, flags])¶

Add atom to the view.

Parameters:	atom_handle (`AtomHandle`) – Atom handle to be added flags (`int`) – An ORed together combination of ViewAddFlags
Return type:	`AtomView`

GetCenterOfAtoms()¶: See center_of_atoms

GetAtomList()¶: See atoms

Select(query[, flags])¶

Perform selection on residue view. This method will return an entity view containing all atoms and bonds of the residue matching the predicate. In case no atom matches the predicate, this will return an empty view.

Parameters:	query (`Query` or str) – The query flags (int) – An ORed together combination of query flags
Return type:	`EntityView`

Functions¶

Boolean Operators¶

Intersection(view_a, view_b)¶

Calculates and returns the intersection of view_a and view_b. view_a and view_b must be views of the same entity.

Parameters:	view_a (EntityView) – first view view_b (EntityView) – second view

Difference(view_a, view_b)¶

Calculates and returns the difference between view_a and view_b. view_a and view_b must be views of the same entity.The returned view will contain atoms, residues, chains and bonds that are in view_a and not in view_b.

Parameters:	view_a (EntityView) – first view view_b (EntityView) – second view

Union(view_a, view_b)¶

Calculates and returns the union of view_a and view_b. view_a and view_b must be views of the same entity.The returned view will contain all atoms, residues, chains and bonds that are either in view_a, view_b or part of both views.

Parameters:	view_a (EntityView) – first view view_b (EntityView) – second view

Other Entity-Related Functions¶

CreateViewFromAtomList(atom_list)¶

Returns a view made up of the atoms in atom_list. All atoms are required to be atoms of the same entity. Duplicate atoms are only added to the view once.

Parameters:	atom_list (`AtomHandleList` or `AtomViewList`) – the atoms
Raises :	`IntegrityError` if atoms of different entities are encountered
Returns:	`EntityView`

CreateEntityFromView(view, include_exlusive_atoms, handle=EntityHandle())¶

This function behaves exactly like EntityHandle.Copy(), except that only atoms, residues, chains and bonds that are present in the view will be copied.

Parameters:

view – is the view to be converted to a handle
include_exlusive_atoms – if true, atoms that are part of an exclusive bond (only one bond partner is included in the view) will also be included in the new entity handle.
handle – If invalid a new entity will be created. If valid, the atoms, residues, chains, bonds and torsions will be added to handle. This is useful to combine several entities into one.

:returns EntityHandle

ChainType¶

A ChainType fills the ChainHandle.type attribute. Different types are described in the ChainType enum. Functions for setting a type belong to the EditorBase class, getting is provided by the ChainHandle class, further convenience functions are described here.

The ChainType enum¶

The ChainType enum enumerates all types defined by the PDB for the MMCif file format. Following values are supported:

CHAINTYPE_POLY, CHAINTYPE_NON_POLY, CHAINTYPE_WATER, CHAINTYPE_POLY_PEPTIDE_D, CHAINTYPE_POLY_PEPTIDE_L, CHAINTYPE_POLY_DN, CHAINTYPE_POLY_RN, CHAINTYPE_POLY_SAC_D, CHAINTYPE_POLY_SAC_L, CHAINTYPE_POLY_DN_RN, CHAINTYPE_UNKNOWN, CHAINTYPE_N_CHAINTYPES

Where CHAINTYPE_N_CHAINTYPES holds the number of different types available.

Setter & Getter functions¶

EditorBase.SetChainType(), ChainHandle.GetType()

ChainType functions¶

ChainTypeFromString(identifier)¶

Create a ChainType item for a given string.

Parameters:	identifier (`str`) – String to request a type for.
Raises :	`runtime_error` if identifier is unrecognised.
Returns:	`ChainType`

StringFromChainType(type)¶

Return the String identifier for a given type.

Parameters:	type (`ChainType`) – To be translated
Raises :	`runtime_error` if type is unrecognised.
Returns:	`str`

ViewAddFlags¶

Those are the flags controlling behaviour of routines adding handles to views.

INCLUDE_ATOMS - Include all atoms when adding a residue handle to a view
INCLUDE_RESIDUES - Include all residues when adding a chain to a view
INCLUDE_CHAINS - Include all chains when creating a new entity view
INCLUDE_ALL = INCLUDE_ATOMS | INCLUDE_RESIDUES | INCLUDE_CHAINS - Convenience flags to include all substructures
CHECK_DUPLICATES - If set, it will be checked that no duplicates are created when adding a new handle

The Molecular Entity¶

The Handle Classes¶

The View Classes¶

Functions¶

Boolean Operators¶

ChainType¶

The ChainType enum¶

Setter & Getter functions¶

ChainType functions¶

ViewAddFlags¶

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