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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.

Type:ChainHandleList (list of ChainHandle)
chain_count

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

Type:int
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:ResidueHandleList (list of ResidueHandle)
residue_count

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

Type:int
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:AtomHandleList (list of AtomHandle)
atom_count

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

Type:int
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
positions

Equivalent to calling GetPositions() with sort_by_index = True. This property is read-only and only available if OpenStructure was compiled with an enabled USE_NUMPY flag (see here for details).

Type:numpy.array
GetName()
Returns:Name associated to this entity.
Return type:str
SetName(name)
Parameters:name (str) – Sets this as new name to be associated to this entity.
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

GetChainCount()

See chain_count

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 (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

GetResidueCount()

See residue_count

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 (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

GetAtomCount()

See atom_count

EditXCS([edit_mode=mol.EditMode.UNBUFFERED_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.UNBUFFERED_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:

# select calpha atoms of peptides
calphas = ent.Select('aname=CA and peptide=true')

# select atoms in a box of size 10, centred at the origin
in_box = ent.Select('x=-5:5 and y=-5:5 and z=-5:5')
Parameters:
  • query (Query / str) – The query to be executed.
  • flags (int / QueryFlag) – An ORed together combination of QueryFlag
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

GetPositions(sort_by_index=True)
Returns:Array of atom positions for this entity.
Return type:numpy.array (shape [atom_count, 3])
Parameters:sort_by_index – If True, the atoms are sorted by their index. Otherwise, they are sorted as they appear in the atoms list.

This method is only available if OpenStructure was compiled with an enabled USE_NUMPY flag (see here for details).

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:

AtomHandleList (list of AtomHandle)

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.

Type: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().

Type:ResidueHandleList (list of ResidueHandle)
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:AtomHandleList (list of AtomHandle)
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 (ResNum) – residue number
Returns:A valid ResidueHandle if the chain contains a residue with matching residue number, an invalid ResidueHandle otherwise.
GetResidueList()

See residues.

FindAtom(res_num, atom_name)

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

Parameters:
  • res_num (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
atoms

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

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

Type:AtomHandleList (list of AtomHandle)
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 the residue.

Type:ChemClass
chem_type

The chemical type of the residue. The type is only properly set if a compound library is used.

Type:ChemType
sec_structure

The secondary structure of the residue.

Type:SecStructure
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. Also available as IsLigand(), SetIsLigand().

is_protein

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 (see IsBondFeasible()). Also available as IsProtein(), SetIsProtein(). In contrast to IsPeptideLinking() this excludes residues which are not connected to neighbouring residues such as CA-only residues or badly positioned ones.

peptide_linking

Whether residue can form peptide bonds. This is determined based on chem_class which is set when loading the structure.

Type:bool
index

Residue index (starting at 0) within chain.

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()

See atoms

IsPeptideLinking()

See peptide_linking

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

GetIndex()

See index

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 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
index

Atom index (starting at 0) within entity.

Type:int
hash_code

A unique identifier for this atom. Note that a deep copy of an entity (see EntityHandle.Copy()) will have atoms with differing identifiers. Shallow copies of the entity preserve the identifier. Atom views on a handle have different identifiers, but the atom view handles (see AtomView.handle) have the same identifier.

Type:int
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()

See hash_code

Return type:int
GetIndex()

See index

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.

Type:ChainViewList (list of ChainView)
chain_count

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

Type:int
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:ResidueViewList (list of ResidueView)
residue_count

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

Type:int
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:AtomViewList (list of AtomView)
atom_count

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

Type:int
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
GetName()
Returns:GetName() of entity handle.
Return type:str
SetName(name)
Parameters:name (str) – Passed to SetName() of handle.
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:
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:
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:
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:
Return type:

float

FindWithin(pos, radius)

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

Parameters:
  • pos (Vec3) – Center of sphere
  • radius (float) – The radius of the sphere
Returns:

AtomHandleList (list of AtomHandle)

FindChain(chain_name)

Find chain by name.

Parameters:chain_name (str) – Chain identifier, e.g. “A”
Returns:The chain if present in the view, an invalid ChainView otherwise
Return type: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: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:

AtomView

Select(query, flags=0)

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

Parameters:
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
GetCenterOfAtoms()

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

Return type:Vec3
GetBondCount()

Get number of bonds :rtype: int

GetBondList()

See bonds

Return type:BondHandleList
GetHandle()

See handle

Return type:EntityHandle
GetGeometricEnd()
Return type:Vec3
GetChainList()

See chains

GetChainCount()

See chain_count

GetResidueList()

See residues

GetResidueCount()

See residue_count

GetAtomList()

See atoms

GetAtomCount()

See atom_count

class ChainView

A view representation of a ChainHandle. Mostly, the same functionality is provided as for the handle.

name

The chain name. The name uniquely identifies the chain in the entity. In most cases, the chain name is one character. This is a 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:ResidueViewList (list of ResidueView)
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:AtomViewList (list of AtomView)
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
geometric_center

Mid-point of the axis aligned bounding box of the entity.

Type:Vec3
valid

Validity of handle.

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.

Parameters:
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:
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()

The parent 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

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=0)

Perform query on chain view. See EntityHandle.Select().

Parameters:
Return type:

EntityView

class ResidueView

A view representation of a ResidueHandle. Mostly, the same functionality is provided as for the handle.

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
atoms

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

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

Type:AtomHandleList (list of AtomHandle)
index

Residue index (starting at 0) within chain view.

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:
Return type:

AtomView

GetCenterOfAtoms()

See center_of_atoms

GetAtomList()

See atoms

Select(query, flags=0)

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

Parameters:
Return type:

EntityView

class AtomView

A view representation of an AtomHandle. Mostly, the same functionality is provided as for the handle.

handle

The underlying AtomHandle of the atom view. Also available as GetHandle().

Type:AtomHandle
hash_code

A unique identifier for this atom view. Note, that this is not the same as for the atom handle (see AtomHandle.hash_code).

Type:int
GetHandle()

See handle

GetHashCode()

See hash_code

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:
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:
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:

Residue Numbering

class ResNum(num, ins_code='0')

Number for a residue. The residue number has a numeric part and an (optional) insertion-code. You can work with this object as if it was an integer and comparison will look first at the numeric part and then the insertion-code. All access to existing objects is read-only.

Parameters:
  • num (int) – Numeric part of residue number.
  • ins_code (str) – Alpha-numeric part of residue number (optional insertion code). Only first character kept.
num

Numeric part of residue number.

Type:int
ins_code

Alpha-numeric part of residue number (insertion code). Single character.

Type:str
GetNum()
Returns:num
GetInsCode()
Returns:ins_code

ChainType

A ChainType fills the ChainHandle.type attribute. Different types are described in the ChainType enum. The type is set with an editor in EditorBase.SetChainType(). Further convenience functions are described here.

class ChainType

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_MACROLIDE, CHAINTYPE_CYCLIC_PSEUDO_PEPTIDE, CHAINTYPE_POLY_PEPTIDE_DN_RN, CHAINTYPE_N_CHAINTYPES

Where CHAINTYPE_N_CHAINTYPES holds the number of different types available.

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

class ViewAddFlags

Defines 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

SecStructure

class SecStructure(type)

Defines a secondary structure type following the types defined by DSSP.

Parameters:type (SecStructure.Type / str) – Type to be set for this object.
IsHelical()
Returns:True, if the set type is any type of helix (i.e. ALPHA_HELIX, PI_HELIX or THREE_TEN_HELIX)
IsExtended()
Returns:True, if the set type is any type of beta sheet (i.e. EXTENDED, BETA_BRIDGE)
IsCoil()
Returns:True, if the set type is any type of coil (i.e. TURN, BEND or COIL)
__str__()
Returns:The character corresponding to the set type (see SecStructure.Type)
class SecStructure.Type

Enumerates all popssible secondary structure types distinguished by DSSP. Their values with the corresponding character code are listed here:

  • 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:

  • 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.

Parameters:chem_class (str) – Chemical class to set.
IsPeptideLinking()
Returns:True, if set class is PEPTIDE_LINKING, D_PEPTIDE_LINKING or L_PEPTIDE_LINKING
IsNucleotideLinking()
Returns: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:

  • 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.

Parameters:chem_type (str) – Chemical type to set.
IsIon()
Returns:True, if set type is IONS or WATERCOORDIONS
IsNucleotide()
Returns:True, if set type is NUCLEOTIDES
IsSaccharide()
Returns:True, if set type is SACCHARIDES
IsAminoAcid()
Returns:True, if set type is AMINOACIDS
IsCoenzyme()
Returns:True, if set type is COENZYMES
IsDrug()
Returns:True, if set type is DRUGS
IsNonCanonical()
Returns:True, if set type is NONCANONICALMOLS
IsWater()
Returns:True, if set type is WATERS
IsKnown()
Returns:True, if set type is not UNKNOWN

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