chfl_residue type¶

type chfl_residue¶

A chfl_residue is a group of atoms belonging to the same logical unit. They can be small molecules, amino-acids in a protein, monomers in polymers, etc.

Type fields:

% init [subroutine] :: chfl_residue%init() % copy [subroutine] :: chfl_residue%copy() % name [function] :: chfl_residue%name() % id [function] :: chfl_residue%id() % atoms_count [function] :: chfl_residue%atoms_count() % add_atom [subroutine] :: chfl_residue%add_atom() % contains [function] :: chfl_residue%contains() % atoms [subroutine] :: chfl_residue%atoms() % set [subroutine] :: chfl_residue%set() % get [function] :: chfl_residue%get() % properties_count [function] :: chfl_residue%properties_count() % list_properties [subroutine] :: chfl_residue%list_properties() % free [subroutine] :: chfl_residue%free()

subroutine chfl_residue%init(name[, id, status])¶

Initialize the residue with a new residue with the given name and optional residue id. This subroutine allocate memory which must be released with chfl_residue%free().

Parameters:	name [character(len=*)] :: residue name
Options:	id [integer] :: residue id status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine chfl_residue%copy(residue[, status])¶

Initialize this residue with a copy of residue. This subroutine allocate memory which must be released with chfl_residue%free().

Parameters:	residue [type(chfl_residue)] :: residue to copy
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

function chfl_residue%name([status])¶

Get the name of the residue. If the name is longer than CHFL_STRING_LENGTH, it will be truncated.

Return:	character (len=CHFL_STRING_LENGTH)
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

function chfl_residue%id([status])¶

Get the residue id. If the residue do not have an id, status is set to CHFL_GENERIC_ERROR, and no value is returned.

Return:	integer
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

function chfl_residue%atoms_count([status])¶

Get the number of atoms in the residue.

Return:	integer
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine chfl_residue%add_atom(index[, status])¶

Add the atom at the given index in the residue.

Parameters:	index [integer] :: index of the atom to add
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

function chfl_residue%contains(index[, status])¶

Check if the atom at the given index is in the residue.

Return:	logical
Parameters:	index [integer] :: index of the atom
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine chfl_residue%atoms(data[, status])¶

Get the list of atoms in the topology in the pre-allocated array data of size chfl_residue%atoms_count().

Parameters:	data [integer,dimension(:)] :: array to be filled with the indexes of atoms in the residue
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine chfl_residue%set(name, property[, status])¶

Add a new property with the given name to this residue.

If a property with the same name already exists, this function override the existing property with the new one.

property can either be a chfl_property, or any value that can be stored in a chfl_property: logical, real, string, or vector3d.

Parameters:	name [character(len=*)] :: property name property [type(chfl_property)] :: the new property
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

function chfl_residue%get(name[, status])¶

Get a copy of the property with the given name in this residue. If no property exist with this name, status will be set to CHFL_PROPERTY_ERROR.

The associated memory must be released by calling chfl_property%free().

Return:	type (chfl_property)
Parameters:	name [character(len=*)] :: property name
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

function chfl_residue%properties_count([status])¶

Get the number of properties in this residue.

Return:	integer
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine chfl_residue%list_properties(names[, status])¶

Fill the pre-allocated array names with the names of the properties in this residue. The array must have room for chfl_residue%properties_count() values of type character(len=CHFL_STRING_LENGTH).

Return:	integer
Parameters:	names (:) [character(len=CHFL_STRING_LENGTH)] :: list of properties names
Options:	status [integer(chfl_status)] :: status code of the operation. If it is not CHFL_SUCCESS, use chfl_last_error() to learn more about the error.

subroutine chfl_residue%free()¶

Destroy a residue, and free the associated memory