The Molecular Entity

This document describes the EntityHandle and the related classes.

The Handle Classes

Entity, residue, atom and bond handles can store arbitrary generic properties.

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

Entity Handle

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.

properties

All the generic properties are available.

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_atoms

Center of atoms, that is the average atom position of the entity. Use center_of_mass for the the mass-weighted center of the entity. Also available as GetCenterOfAtoms().

Type:

Vec3

center_of_mass

Center of mass of the entity. Also available as GetCenterOfMass()

Type:

Vec3

geometric_center

Mid-point of the axis aligned bounding box of the entity. Also available as GetGeometricCenter()

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

valid

Validity of handle.

Type:

bool

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.

GetMass()

See mass

GetCenterOfAtoms()

See center_of_atoms

GetCenterOfMass()

See center_of_mass

GetGeometricCenter()

See geometric_center

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)

IsValid()

See valid

Chain Handle

class ChainHandle

A chain of one or more residues. Chains are always part of an entity (see note on memory management).

properties

All the generic properties are available.

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

center_of_atoms

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

Type:

Vec3

center_of_mass

Center of mass. Also available as GetCenterOfMass().

Type:

Vec3

geometric_center

Mid-point of the axis aligned bounding box of the chain. Also available as GetGeometricCenter()

Type:

Vec3

description

Details about the chain. Not categorised, just text.

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
is_oligosaccharide

Indicates if the chain is an oligosaccharide, a branched, non-linear entity of multiple sugars. Also available as IsOligosaccharide().

Type:

bool

is_polymer

Indicates if a chain is a polymer. True for polypeptides, polynucleotides, polysaccharides, oligosaccharides and branched chains. Also available as IsPolymer().

Type:

bool

is_polynucleotide

Indicates if a chain is a nucleic acid. Also available as IsPolynucleotide().

Type:

bool

is_polypeptide

Indicates if a chain is a protein. Also available as IsPolypeptide().

Type:

bool

is_polysaccharide

Indicates if a chain is a polysaccharide. Also available as IsPolysaccharide().

Type:

bool

mass

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

Type:

float

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

residue_count

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

Type:

int

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)

type

Describes the type of the chain.

Type:

ChainType.

hash_code

A unique identifier for this chain. Note that a deep copy of an entity (see EntityHandle.Copy()) will have chains with differing identifiers. Shallow copies of the entity preserve the identifier. Also available as GetHashCode().

Type:

int

valid

Validity of handle.

Type:

bool

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

GetResidueCount()

See residue_count

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

IsOligosaccharide()

See is_oligosaccharide

IsPolymer()

See is_polymer

IsPolynucleotide()

See is_polynucleotide

IsPolypeptide()

See is_polypeptide

IsPolysaccharide()

See is_polysaccharide

GetDescription()

See description

GetHashCode()

See hash_code

Return type:

int

IsValid()

See valid

Residue Handle

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, and of an entity (see note on memory management).

properties

All the generic properties are available.

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. Also available as GetName().

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

Type:

str

qualified_name

The qualified name consists of a residue identifier and chain name. For a glycine with residue number 2 of chain A, the qualified name is “A.GLY2”. Also available as GetQualifiedName().

Type:

str

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)

atom_count

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

Type:

int

bond_count

Number of bonds. Read-only. See GetBondCount().

Type:

int

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_atoms

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

Type:

Vec3

center_of_mass

Center of mass. Also available as GetCenterOfMass()

Type:

Vec3

geometric_center

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

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()

omega_torsion

The OMEGA 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 OMEGA torsion is an invalid handle.

Read-only. Also available as GetOmegaTorsion()

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. When loading MMCIF structures, this property is set based on seqres information and differs from PDB structures. Also available as IsLigand(), SetIsLigand().

Type:

bool

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.

Type:

bool

peptide_linking

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

Type:

bool

nucleotide_linking

Whether residue can form nucleotide 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.

central_atom

Central atom used for rendering traces. For peptides, this is usually the CA atom. For nucleotides, this is usually the P atom.

Type:

AtomHandle

central_normal

Normal computed for central_atom. Only defined for peptides and nucleotides if all required atoms available. Otherwise, the (1,0,0) vector is returned.

Type:

Vec3

hash_code

A unique identifier for this residue. Note that a deep copy of an entity (see EntityHandle.Copy()) will have residues with differing identifiers. Shallow copies of the entity preserve the identifier. Also available as GetHashCode().

Type:

int

valid

Validity of handle.

Type:

bool

next

Residue after this one in the same chain. Invalid handle returned if there is no next residue. Residues are ordered as in ChainHandle.residues independently on whether they are connected or not (see InSequence() to check for connected residues).

Type:

ResidueHandle

prev

Residue before this one in the same chain. Otherwise same behaviour as next.

Type:

ResidueHandle

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

HasAltAtoms()

Returns whether the residue has any alternative atom groups

Return type:

bool

HasAltAtomGroup(group_name)

Returns whether the residue has a certain alternative atom group

Parameters:

group_name (str) – Group of interest

Return type:

bool

GetAltAtomGroupNames()

Returns names of all alternative atom groups in residue

Return type:

list of str

GetCurrentAltGroupName()

Returns the currently active alternative atom group, empty str if residue has no alternative atom groups

Return type:

str

SwitchAtomPos(group_name)

Switches the atoms in residue to the specified alternative atom group

Parameters:

group_name (str) – Group of interest

Return type:

bool

Returns:

Whether the switch was successful (e.g. False if no such group exists)

GetName()

See name

GetQualifiedName()

See qualified_name

GetNumber()

See number

GetOneLetterCode()

See one_letter_code

GetAtomList()

See atoms

GetAtomCount()

See atom_count

GetBondCount()

See bond_count

GetBounds()

See bounds

GetMass()

See mass

GetCenterOfAtoms()

See center_of_atoms

GetCenterOfMass()

See center_of_mass

GetGeometricCenter()

See geometric_center

GetChain()

See chain

GetPhiTorsion()

See phi_torsion

GetPsiTorsion()

See psi_torsion

GetOmegaTorsion()

See omega_torsion

GetChemClass()

See chem_class

GetChemType()

See chem_type

GetSecStructure()

See sec_structure

IsLigand()

See is_ligand

IsProtein()

See is_protein

IsPeptideLinking()

See peptide_linking

IsNucleotideLinking()

See nucleotide_linking

GetIndex()

See index

GetCentralAtom()
SetCentralAtom()

See central_atom

GetCentralNormal()

See central_normal

GetHashCode()

See hash_code

Return type:

int

IsValid()

See valid

SetIsLigand()

Set the IsLigand() flag explicitly.

Parameters:

ligand (bool) – Whether this residue is a ligand or not

SetIsProtein()

Set the IsProtein() flag explicitly.

Parameters:

protein (bool) – Whether this residue is a protein or not

GetNext()

See next

GetPrev()

See next

Atom Handle

class AtomHandle

Represents an atom in a molecular structure. Atoms are always part of a residue and of an entity (see note on memory management)

properties

All the generic properties are available.

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 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. By convention in Openstructure, this is the chemical symbol in uppercase, but this is not strictly enforced and may be a non- existing element or 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. Also available as GetHashCode().

Type:

int

valid

Validity of handle.

Type:

bool

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 (list of BondHandle)

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

Bond Handle

class BondHandle

Represents a chemical bond between two atoms (first and second).

properties

All the generic properties are available.

first
second

Atoms involved in the bond. No assumptions about the order should be made. With the internal coordinate system enabled, first and second may even be swapped when rebuilding the internal connectivity tree. Also available as GetFirst() and GetSecond().

Type:

AtomHandle

pos

Midpoint between the two atoms (transformed coordinates). Also available as GetPos().

Type:

Vec3

length

Length of the bond. Also available as GetLength().

Type:

float

bond_order

The bond order. Possible values:

  • 1 - single bond

  • 2 - double bond

  • 3 - triple bond

  • 4 - aromatic bond

Also available as GetBondOrder().

Type:

int

hash_code

A unique identifier for this bond handle. Also available as GetHashCode().

Type:

int

valid

Validity of handle. Also available as IsValid().

Type:

bool

GetFirst()

See first

GetSecond()

See second

GetPos()

See pos

GetLength()

See length

GetBondOrder()

See bond_order

GetOther(other_atom)

Get the other atom. Returns the one of the two atoms that does not match the given one.

Parameters:

other_atom (AtomHandle) – The other atom

Return type:

AtomHandle

SetBondOrder(order)

Set the bond order. See GetBondOrder().

Parameters:

order (int) – The bond order

See bond_order

IsValid()

See valid

GetHashCode()

See hash_code

The View Classes

Entity, residue and atom views can store arbitrary generic properties.

Entity View

class EntityView

An entity view represents a structural subset of an EntityHandle and contains ChainViews, ResidueViews, AtomViews and BondHandles. For an introduction, see Introduction to the mol Module.

properties

All the generic properties are available.

handle

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

Type:

EntityHandle

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

See EntityHandle.bounds

mass

See EntityHandle.mass

center_of_atoms

See EntityHandle.center_of_atoms

center_of_mass

See EntityHandle.center_of_mass

geometric_center

See EntityHandle.geometric_center

valid

Validity of view.

Type:

bool

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 get the chain with residues and atoms, go like:

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

Note that the view above still lacks bonds which can be added with the AddAllInclusiveBonds() method.

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 ViewAddFlag.

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)

Deprecated. Use ViewForHandle() instead.

Parameters:

residue (ResidueHandle) – Residue handle

Returns:

The residue view pointing the handle, or an invalid handle if the residue is not part of the view

Return type:

ResidueView

FindResidue(chain_name, res_num)

Find residue by chain name and residue number.

Parameters:
  • chain_name (str) – Chain identifier, e.g. “A”

  • res_num (ResNum) – residue number

Returns:

The residue if present in the view, an invalid ResidueView otherwise

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

Returns:

The atom if present in the view, an invalid AtomView otherwise

Return type:

AtomView

ViewForHandle(handle)

Find chain view, residue view or atom view of pointing to the given handle.

Parameters:

handle – handle to search for

Returns:

The view pointing the handle, or an invalid handle if the handle is not part of the view

Return type:

(Chain|Residue|Atom)View

ExtendViewToResidues()

Extend current view to include all atoms of each residue where at least one atom is selected currently.

Returns:

The extended view

Return type:

EntityView

ExtendViewToSurrounding(handle)

Extend current view to include all atoms that are within the sum of their van-der-Waals radius + gap.

This includes all atoms within: at1.GetRadius() + at2.GetRadius() + gap.

Parameters:

gap (float) – the gap between atoms

Returns:

The extended view

Return type:

EntityView

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

Dump()

Returns a string containing a human-readable summary of the entity view.

Return type:

str

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

Return type:

int

GetBondList()

See bonds

Return type:

BondHandleList (list of BondHandle)

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

IsValid()

See valid

Chain View

class ChainView

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

properties

All the generic properties are available.

handle

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

Type:

ChainHandle

hash_code

A unique identifier for this chain view. Note, that this is not the same as for the chain handle (see ChainHandle.hash_code). Also available as GetHashCode().

Type:

int

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

Note that the value of in_sequence is independent from the value of ChainHandle.in_sequence.

Type:

bool

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_atoms

See ChainHandle.center_of_atoms

center_of_mass

See ChainHandle.center_of_mass

geometric_center

See ChainHandle.geometric_center

valid

Validity of view.

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 ViewAddFlag.

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.

ViewForHandle(handle)

Find residue view or atom view of pointing to the given handle.

Parameters:

handle – handle to search for

Returns:

The view pointing the handle, or an invalid handle if the handle is not part of the view

Return type:

(Residue|Atom)View

GetCenterOfAtoms()

See center_of_atoms

GetCenterOfMass()

See center_of_mass

GetEntity()

The parent entity.

GetGeometricCenter()

See geometric_center

GetHandle()

See handle

GetHashCode()

See hash_code

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

Residue View

class ResidueView

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

properties

All the generic properties are available.

handle

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

Type:

ResidueHandle

hash_code

A unique identifier for this residue view. Note, that this is not the same as for the residue handle (see ResidueHandle.hash_code). Also available as GetHashCode().

Type:

int

name
qualified_name
number
one_letter_code
bounds
mass
center_of_atoms
center_of_mass
geometric_center
phi_torsion
psi_torsion
omega_torsion
chem_class
chem_type
sec_structure
is_ligand
is_protein
peptide_linking
nucleotide_linking
central_atom
central_normal
valid
next
prev

See the respective attributes in ResidueHandle.

atoms

Get list of all atoms of this residue included in the view. 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 included in the view. Read-only. See GetAtomCount().

Type:

int

chain

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

Type:

ChainView

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

ViewForHandle(handle)

Find atom view of pointing to the given handle.

Parameters:

handle – handle to search for

Returns:

The view pointing the handle, or an invalid handle if the handle is not part of the view

Return type:

AtomView

GetHandle()

See handle

GetHashCode()

See hash_code

GetName()
GetQualifiedName()
GetNumber()
GetOneLetterCode()
GetBounds()
GetMass()
GetCenterOfAtoms()
GetCenterOfMass()
GetGeometricCenter()
GetPhiTorsion()
GetPsiTorsion()
GetOmegaTorsion()
GetChemClass()
GetChemType()
GetSecStructure()
IsLigand()
SetIsLigand()
IsProtein()
IsPeptideLinking()
IsNucleotideLinking()
GetCentralAtom()
SetCentralAtom()
GetCentralNormal()
IsValid()
GetNext()
GetPrev()

See the respective methods in ResidueHandle.

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

IsAtomIncluded(atom_handle)

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

Parameters:

atom_handle (AtomHandle) –

Return type:

bool

AddAtom(atom_handle[, flags])

Add atom to the view.

Parameters:
Return type:

AtomView

GetAtomList()

See atoms

GetAtomCount()

See atom_count

GetIndex()

See index

Select(query, flags=0)

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

Parameters:
Return type:

EntityView

Atom View

class AtomView

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

properties

All the generic properties are available.

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). Also available as GetHashCode().

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. Openstructure supports a range of (-8388608 to 8388607) for the numeric part. However, the PDB format only supports a range of (-999, 9999). This becomes relevant when a structure is saved in PDB format where an IOException is raised if the PDB range is not respected.

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_BRANCHED, CHAINTYPE_OLIGOSACCHARIDE, 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

ViewAddFlag

class ViewAddFlag

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

Flags can be ORed to combine them.

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’

The constants are defined directly within the mol module. Python can implicitly convert characters to objects of this type. Note however that only the first character of a str object is considered!

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. Note however that only the first character of a str object is considered!

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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Contents

Documentation is available for the following OpenStructure versions:

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This documentation is still under heavy development!
If something is missing or if you need the C++ API description in doxygen style, check our old documentation for further information.