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

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_protein_section(top, name, value)

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

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.