topology.utils

topology.utils

Functions

Name	Description
get_is_reactive_predicate_f	Returns whether a moleculetype name is configured to be recognized as reactive.
get_is_reactive_predicate_from_config_f	Returns whether a moleculetype name is configured to be recognized as reactive.
get_moleculetype_atomics	Get content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.
get_moleculetype_header	Get content of the header of a moleculetype from a topology dict.
get_protein_section	Get content of a section in the first moleculetype (protein) from a topology dict.
get_reactive_section	Get content of a section in the Reactive moleculetype from a topology dict.
get_residue_by_bonding	Get the residue of an atom by its bonding.
get_residue_fragments	Splits a residue into fragments after a bond has been broken.
get_top_section	Get content of a section from a topology dict.
is_not_solvent_or_ion	Returns whether a moleculetype name is not solvent or ion.
set_reactive_section	Set content of a section in the first moleculetype (protein) from a topology dict.
set_top_section	Set content of a section from a topology dict.

topology.utils.get_is_reactive_predicate_f(include, exclude)

Returns whether a moleculetype name is configured to be recognized as reactive.

topology.utils.get_is_reactive_predicate_from_config_f(cfg)

Returns whether a moleculetype name is configured to be recognized as reactive.

topology.utils.get_moleculetype_atomics(top, moleculetype)

Get content of subsections (atoms/bonds/angles etc.) of a moleculetype from a topology dict.

Resolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.

topology.utils.get_moleculetype_header(top, moleculetype)

Get content of the header of a moleculetype from a topology dict.

Resolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.

topology.utils.get_protein_section(top, name)

Get content of a section in the first moleculetype (protein) from a topology dict.

topology.utils.get_reactive_section(top, name)

Get content of a section in the Reactive moleculetype from a topology dict.

topology.utils.get_residue_by_bonding(atom, atoms)

Get the residue of an atom by its bonding.

Avoids traversing the whole topology.

Name	Type	Description	Default
atom	Atom	Atom of the residue	required
atoms	dict[str, Atom]	All atoms of a topology	required

Name	Type	Description
	Atoms of the residue

topology.utils.get_residue_fragments(
    top
    residue
    start1
    start2
    iterations=20
)

Splits a residue into fragments after a bond has been broken.

Name	Type	Description	Default
top	Topology	Topology	required
residue	list[Atom]	All atoms of current residue. Ok, when it contains more atoms as long as those are not connected to broken bond.	required
start1	Atom	First atom with broken bond	required
start2	Atom	Second atom with broken bond	required
iterations	int	Max number of bonds from start atoms to be included when building fragmets, by default 20	`20`

Name	Type	Description
	Two fragments, or one fragment and empty set in case the	residue did not change its size.

topology.utils.get_top_section(top, name, moleculetype=None)

Get content of a section from a topology dict.

Resolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.

topology.utils.is_not_solvent_or_ion(name)

Returns whether a moleculetype name is not solvent or ion.

topology.utils.set_reactive_section(top, name, value)

Set content of a section in the first moleculetype (protein) from a topology dict.

topology.utils.set_top_section(top, name, value, moleculetype=None)

Set content of a section from a topology dict.

Resolves any #ifdef statements by check in the top[‘define’] dict and chooses the ‘content’ or ‘else_content’ depending on the result.