The Molecular Entity¶

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¶

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

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¶

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.

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