#include "gmxpre.h"
#include "gromacs/selection/indexutil.h"
#include <cstdlib>
#include <cstring>
#include <algorithm>
#include <numeric>
#include <string>
#include <vector>
#include "gromacs/topology/block.h"
#include "gromacs/topology/index.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textwriter.h"

Include dependency graph for indexutil.cpp:

Description

Implements functions in indexutil.h.

Author: Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Classes
struct	gmx_ana_indexgrps_t
	Stores a set of index groups. More...

Functions
void	gmx_ana_indexgrps_init (gmx_ana_indexgrps_t *g, gmx_mtop_t top, const char *fnm)
	Reads index groups from a file or constructs them from topology. More...

void	gmx_ana_indexgrps_free (gmx_ana_indexgrps_t *g)
	Frees memory allocated for index groups. More...

bool	gmx_ana_indexgrps_extract (gmx_ana_index_t dest, std::string destName, gmx_ana_indexgrps_t *src, int n)
	Extracts a single index group. More...

bool	gmx_ana_indexgrps_find (gmx_ana_index_t dest, std::string destName, gmx_ana_indexgrps_t src, const char name)
	Finds and extracts a single index group by name. More...

void	gmx_ana_indexgrps_print (gmx::TextWriter writer, gmx_ana_indexgrps_t g, int maxn)
	Writes out a list of index groups. More...

void	gmx_ana_index_reserve (gmx_ana_index_t *g, int isize)
	Reserves memory to store an index group of size `isize`. More...

void	gmx_ana_index_squeeze (gmx_ana_index_t *g)
	Frees any memory not necessary to hold the current contents. More...

void	gmx_ana_index_clear (gmx_ana_index_t *g)
	Initializes an empty index group. More...

void	gmx_ana_index_set (gmx_ana_index_t g, int isize, int index, int nalloc)
	Constructs a `gmx_ana_index_t` from given values. More...

void	gmx_ana_index_init_simple (gmx_ana_index_t *g, int natoms)
	Creates a simple index group from the first to the `natoms'th` atom. More...

void	gmx_ana_index_deinit (gmx_ana_index_t *g)
	Frees memory allocated for an index group. More...

void	gmx_ana_index_copy (gmx_ana_index_t dest, gmx_ana_index_t src, bool bAlloc)
	Copies a `gmx_ana_index_t`. More...

void	gmx_ana_index_dump (gmx::TextWriter writer, gmx_ana_index_t g, int maxn)
	Writes out the contents of a index group. More...

int	gmx_ana_index_get_max_index (gmx_ana_index_t *g)
	Returns maximum atom index that appears in an index group. More...

bool	gmx_ana_index_check_sorted (gmx_ana_index_t *g)
	Checks whether an index group is sorted. More...

bool	gmx_ana_index_check_range (gmx_ana_index_t *g, int natoms)
	Checks whether an index group has atoms from a defined range. More...

void	gmx_ana_index_sort (gmx_ana_index_t *g)
	Sorts the indices within an index group. More...

void	gmx_ana_index_remove_duplicates (gmx_ana_index_t *g)
	Removes duplicates from a sorted index group. More...

bool	gmx_ana_index_equals (gmx_ana_index_t a, gmx_ana_index_t b)
	Checks whether two index groups are equal. More...

bool	gmx_ana_index_contains (gmx_ana_index_t a, gmx_ana_index_t b)
	Checks whether a sorted index group contains another sorted index group. More...

void	gmx_ana_index_intersection (gmx_ana_index_t dest, gmx_ana_index_t a, gmx_ana_index_t *b)
	Calculates the intersection between two sorted index groups. More...

void	gmx_ana_index_difference (gmx_ana_index_t dest, gmx_ana_index_t a, gmx_ana_index_t *b)
	Calculates the set difference between two sorted index groups. More...

int	gmx_ana_index_difference_size (gmx_ana_index_t a, gmx_ana_index_t b)
	Calculates the size of the difference between two sorted index groups. More...

void	gmx_ana_index_partition (gmx_ana_index_t dest1, gmx_ana_index_t dest2, gmx_ana_index_t src, gmx_ana_index_t g)
	Calculates the intersection and the difference in one call. More...

void	gmx_ana_index_union (gmx_ana_index_t dest, gmx_ana_index_t a, gmx_ana_index_t *b)
	Calculates the union of two sorted index groups. More...

void	gmx_ana_index_union_unsorted (gmx_ana_index_t dest, gmx_ana_index_t a, gmx_ana_index_t *b)
	Calculates the union of two index groups, where the second group may not be sorted. More...

void	gmx_ana_index_merge (gmx_ana_index_t dest, gmx_ana_index_t a, gmx_ana_index_t *b)
	Merges two distinct sorted index groups. More...

static bool	next_group_index (int atomIndex, const gmx_mtop_t top, e_index_t type, int id)
	Helper for splitting a sequence of atom indices into groups. More...

void	gmx_ana_index_make_block (t_blocka t, const gmx_mtop_t top, gmx_ana_index_t *g, e_index_t type, bool bComplete)
	Partition a group based on topology information. More...

bool	gmx_ana_index_has_full_blocks (const gmx_ana_index_t g, const gmx::RangePartitioning b)
	Checks whether a group consists of full blocks. More...

bool	gmx_ana_index_has_full_ablocks (gmx_ana_index_t g, t_blocka b)
	Checks whether a group consists of full blocks. More...

static bool	is_at_residue_boundary (const gmx_mtop_t &top, int a, int *molb)
	Returns if an atom is at a residue boundary. More...

bool	gmx_ana_index_has_complete_elems (gmx_ana_index_t g, e_index_t type, const gmx_mtop_t top)
	Checks whether a group consists of full residues/molecules. More...

void	gmx_ana_indexmap_clear (gmx_ana_indexmap_t *m)
	Initializes an empty index group mapping. More...

void	gmx_ana_indexmap_reserve (gmx_ana_indexmap_t *m, int nr, int isize)
	Reserves memory for an index group mapping. More...

void	gmx_ana_indexmap_init (gmx_ana_indexmap_t m, gmx_ana_index_t g, const gmx_mtop_t *top, e_index_t type)
	Initializes an index group mapping. More...

int	gmx_ana_indexmap_init_orgid_group (gmx_ana_indexmap_t m, const gmx_mtop_t top, e_index_t type)
	Initializes `orgid` entries based on topology grouping. More...

void	gmx_ana_indexmap_set_static (gmx_ana_indexmap_t m, t_blocka b)
	Sets an index group mapping to be static. More...

void	gmx_ana_indexmap_copy (gmx_ana_indexmap_t dest, gmx_ana_indexmap_t src, bool bFirst)
	Makes a deep copy of an index group mapping. More...

static void	set_atoms (gmx_ana_indexmap_t m, int isize, int index)
	Helper function to set the source atoms in an index map. More...

void	gmx_ana_indexmap_update (gmx_ana_indexmap_t m, gmx_ana_index_t g, bool bMaskOnly)
	Updates an index group mapping. More...

void	gmx_ana_indexmap_deinit (gmx_ana_indexmap_t *m)
	Frees memory allocated for index group mapping. More...

Function Documentation

bool gmx_ana_index_check_range	(	gmx_ana_index_t *	g,
		int	natoms
	)

Checks whether an index group has atoms from a defined range.

Parameters

[in]	g	Index group to check.
[in]	natoms	Largest atom number allowed.

Returns: true if all atoms in the index group are in the range 0 to natoms (i.e., no atoms over natoms are referenced).

bool gmx_ana_index_check_sorted ( gmx_ana_index_t * g )

Checks whether an index group is sorted.

Parameters

[in] g Index group to check.

Returns: true if the index group is sorted and has no duplicates, false otherwise.

void gmx_ana_index_clear ( gmx_ana_index_t * g )

Initializes an empty index group.

Parameters

[out] g Output structure.

Any contents of g are discarded without freeing.

bool gmx_ana_index_contains	(	gmx_ana_index_t *	a,
		gmx_ana_index_t *	b
	)

Checks whether a sorted index group contains another sorted index group.

Parameters

[in]	a	Index group to check against.
[in]	b	Index group to check.

Returns: true if b is contained in a, false otherwise.

If the elements are not in the same order in both groups, the function fails. However, the groups do not need to be sorted.

void gmx_ana_index_copy	(	gmx_ana_index_t *	dest,
		gmx_ana_index_t *	src,
		bool	bAlloc
	)

Copies a gmx_ana_index_t.

Parameters

[out]	dest	Destination index group.
[in]	src	Source index group.
[in]	bAlloc	If true, memory is allocated at `dest`; otherwise, it is assumed that enough memory has been allocated for index.

void gmx_ana_index_deinit ( gmx_ana_index_t * g )

Frees memory allocated for an index group.

Parameters

[in] g Index group structure.

The pointer g is not freed.

void gmx_ana_index_difference	(	gmx_ana_index_t *	dest,
		gmx_ana_index_t *	a,
		gmx_ana_index_t *	b
	)

Calculates the set difference between two sorted index groups.

Parameters

[out]	dest	Output index group (the difference `a` - `b`).
[in]	a	First index group.
[in]	b	Second index group.

dest can equal a, but not b.

int gmx_ana_index_difference_size	(	gmx_ana_index_t *	a,
		gmx_ana_index_t *	b
	)

Calculates the size of the difference between two sorted index groups.

Parameters

[in]	a	First index group.
[in]	b	Second index group.

Returns: Size of the difference a - b.

void gmx_ana_index_dump	(	gmx::TextWriter *	writer,
		gmx_ana_index_t *	g,
		int	maxn
	)

Writes out the contents of a index group.

Parameters

[in]	writer	Writer to use for output.
[in]	g	Index group to print.
[in]	maxn	Maximum number of indices to print (-1 = print all).

bool gmx_ana_index_equals	(	gmx_ana_index_t *	a,
		gmx_ana_index_t *	b
	)

Checks whether two index groups are equal.

Parameters

[in]	a	Index group to check.
[in]	b	Index group to check.

Returns: true if a and b are equal, false otherwise.

int gmx_ana_index_get_max_index ( gmx_ana_index_t * g )

Returns maximum atom index that appears in an index group.

Parameters

[in] g Index group to query.

Returns: Largest atom index that appears in g, or zero if g is empty.

bool gmx_ana_index_has_complete_elems	(	gmx_ana_index_t *	g,
		e_index_t	type,
		const gmx_mtop_t *	top
	)

Checks whether a group consists of full residues/molecules.

Parameters

[in]	g	Index group to check.
[in]	type	Block data to check against.
[in]	top	Topology data.

Returns: true if g consists of one or more complete elements of type type, false otherwise.

g is assumed to be sorted, otherwise may return false negatives.

If type is INDEX_ATOM, the return value is always true. If type is INDEX_UNKNOWN or INDEX_ALL, the return value is always false.

bool gmx_ana_index_has_full_ablocks	(	gmx_ana_index_t *	g,
		t_blocka *	b
	)

Checks whether a group consists of full blocks.

Parameters

[in]	g	Index group to check.
[in]	b	Block data to check against.

Returns: true if g consists of one or more complete blocks from b, false otherwise.

The atoms in g and b->a are assumed to be in the same order.

bool gmx_ana_index_has_full_blocks	(	const gmx_ana_index_t *	g,
		const gmx::RangePartitioning *	b
	)

Checks whether a group consists of full blocks.

Parameters

[in]	g	Index group to check.
[in]	b	Block data to check against.

Returns: true if g consists of one or more complete blocks from b, false otherwise.

The atoms in g are assumed to be sorted.

void gmx_ana_index_init_simple	(	gmx_ana_index_t *	g,
		int	natoms
	)

Creates a simple index group from the first to the natoms'th atom.

Parameters

[out]	g	Output structure.
[in]	natoms	Number of atoms.

void gmx_ana_index_intersection	(	gmx_ana_index_t *	dest,
		gmx_ana_index_t *	a,
		gmx_ana_index_t *	b
	)

Calculates the intersection between two sorted index groups.

Parameters

[out]	dest	Output index group (the intersection of `a` and `b`).
[in]	a	First index group.
[in]	b	Second index group.

dest can be the same as a or b.

void gmx_ana_index_make_block	(	t_blocka *	t,
		const gmx_mtop_t *	top,
		gmx_ana_index_t *	g,
		e_index_t	type,
		bool	bComplete
	)

Partition a group based on topology information.

Parameters

[in,out]	t	Output block.
[in]	top	Topology structure (only used if `type` is INDEX_RES or INDEX_MOL, can be NULL otherwise).
[in]	g	Index group (can be NULL if `type` is INDEX_UNKNOWN).
[in]	type	Type of partitioning to make.
[in]	bComplete	If true, the index group is expanded to include any residue/molecule (depending on `type`) that is partially contained in the group. If `type` is not INDEX_RES or INDEX_MOL, this has no effect.

m should have been initialized somehow (calloc() is enough). g should be sorted.

void gmx_ana_index_merge	(	gmx_ana_index_t *	dest,
		gmx_ana_index_t *	a,
		gmx_ana_index_t *	b
	)

Merges two distinct sorted index groups.

Parameters

[out]	dest	Output index group (the union of `a` and `b`).
[in]	a	First index group.
[in]	b	Second index group.

a and b should not have common items. dest can equal a or b.

See Also: gmx_ana_index_union()

void gmx_ana_index_partition	(	gmx_ana_index_t *	dest1,
		gmx_ana_index_t *	dest2,
		gmx_ana_index_t *	src,
		gmx_ana_index_t *	g
	)

Calculates the intersection and the difference in one call.

Parameters

[out]	dest1	Output group 1 (will equal `g`).
[out]	dest2	Output group 2 (will equal `src` - `g`).
[in]	src	Group to be partitioned.
[in]	g	One partition.

Precondition: g is a subset of src and both sets are sorted; dest1 has allocated storage to store src

Postcondition: dest1 == g; dest2 == src - g

No storage should be allocated for dest2; after the call, dest2->index points to the memory allocated for dest1 (to a part that is not used by dest1).

The calculation can be performed in-place by setting dest1 equal to src.

void gmx_ana_index_remove_duplicates ( gmx_ana_index_t * g )

Removes duplicates from a sorted index group.

Parameters

[in,out] g Index group to be processed.

void gmx_ana_index_reserve	(	gmx_ana_index_t *	g,
		int	isize
	)

Reserves memory to store an index group of size isize.

Parameters

[in,out]	g	Index group structure.
[in]	isize	Maximum number of atoms to reserve space for.

void gmx_ana_index_set	(	gmx_ana_index_t *	g,
		int	isize,
		int *	index,
		int	nalloc
	)

Constructs a gmx_ana_index_t from given values.

Parameters

[out]	g	Output structure.
[in]	isize	Number of atoms in the new group.
[in]	index	Array of `isize` atoms (can be NULL if `isize` is 0).
[in]	nalloc	Number of elements allocated for `index` (if 0, `index` is not freed in gmx_ana_index_deinit())

No copy if index is made.

void gmx_ana_index_sort ( gmx_ana_index_t * g )

Sorts the indices within an index group.

Parameters

[in,out] g Index group to be sorted.

void gmx_ana_index_squeeze ( gmx_ana_index_t * g )

Frees any memory not necessary to hold the current contents.

Parameters

[in,out] g Index group structure.

Resizes the memory allocated for holding the indices such that the current contents fit.

void gmx_ana_index_union	(	gmx_ana_index_t *	dest,
		gmx_ana_index_t *	a,
		gmx_ana_index_t *	b
	)

Calculates the union of two sorted index groups.

Parameters

[out]	dest	Output index group (the union of `a` and `b`).
[in]	a	First index group.
[in]	b	Second index group.

a and b can have common items. dest can equal a or b.

See Also: gmx_ana_index_merge()

void gmx_ana_index_union_unsorted	(	gmx_ana_index_t *	dest,
		gmx_ana_index_t *	a,
		gmx_ana_index_t *	b
	)

Calculates the union of two index groups, where the second group may not be sorted.

Parameters

[out]	dest	Output index group (the union of `a` and `b`).
[in]	a	First index group (must be sorted).
[in]	b	Second index group.

a and b can have common items. dest can equal a or b.

bool gmx_ana_indexgrps_extract	(	gmx_ana_index_t *	dest,
		std::string *	destName,
		gmx_ana_indexgrps_t *	src,
		int	n
	)

Extracts a single index group.

Parameters

[out]	dest	Output structure.
[out]	destName	Receives the name of the group if found.
[in]	src	Input index groups.
[in]	n	Number of the group to extract.

Returns: true if n is a valid group in src, false otherwise.

bool gmx_ana_indexgrps_find	(	gmx_ana_index_t *	dest,
		std::string *	destName,
		gmx_ana_indexgrps_t *	src,
		const char *	name
	)

Finds and extracts a single index group by name.

Parameters

[out]	dest	Output structure.
[out]	destName	Receives the name of the group if found.
[in]	src	Input index groups.
[in]	name	Name (or part of the name) of the group to extract.

Returns: true if name is a valid group in src, false otherwise.

Uses the Gromacs routine find_group() to find the actual group; the comparison is case-insensitive.

void gmx_ana_indexgrps_free ( gmx_ana_indexgrps_t * g )

Frees memory allocated for index groups.

Parameters

[in] g Index groups structure.

The pointer g is invalid after the call.

void gmx_ana_indexgrps_init	(	gmx_ana_indexgrps_t **	g,
		gmx_mtop_t *	top,
		const char *	fnm
	)

Reads index groups from a file or constructs them from topology.

Parameters

[out]	g	Index group structure.
[in]	top	Topology structure.
[in]	fnm	File name for the index file. Memory is automatically allocated.

One or both of top or fnm can be NULL. If top is NULL, an index file is required and the groups are read from the file (uses Gromacs routine init_index()). If fnm is NULL, default groups are constructed based on the topology (uses Gromacs routine analyse()). If both are null, the index group structure is initialized empty.

void gmx_ana_indexgrps_print	(	gmx::TextWriter *	writer,
		gmx_ana_indexgrps_t *	g,
		int	maxn
	)

Writes out a list of index groups.

Parameters

[in]	writer	Writer to use for output.
[in]	g	Index groups to print.
[in]	maxn	Maximum number of indices to print (-1 = print all, 0 = print only names).

void gmx_ana_indexmap_clear ( gmx_ana_indexmap_t * m )

Initializes an empty index group mapping.

Parameters

[out] m Output structure.

Any contents of m are discarded without freeing.

void gmx_ana_indexmap_copy	(	gmx_ana_indexmap_t *	dest,
		gmx_ana_indexmap_t *	src,
		bool	bFirst
	)

Makes a deep copy of an index group mapping.

Parameters

[in,out]	dest	Destination data structure.
[in]	src	Source mapping.
[in]	bFirst	If true, memory is allocated for `dest` and a full copy is made; otherwise, only variable parts are copied, and no memory is allocated.

dest should have been initialized somehow (calloc() is enough).

void gmx_ana_indexmap_deinit ( gmx_ana_indexmap_t * m )

Frees memory allocated for index group mapping.

Parameters

[in,out] m Mapping structure to free.

All the memory allocated for the mapping structure is freed, and the pointers set to NULL. The pointer m is not freed.

void gmx_ana_indexmap_init	(	gmx_ana_indexmap_t *	m,
		gmx_ana_index_t *	g,
		const gmx_mtop_t *	top,
		e_index_t	type
	)

Initializes an index group mapping.

Parameters

[in,out]	m	Mapping structure to initialize.
[in]	g	Index group to map (can be NULL if `type` is INDEX_UNKNOWN).
[in]	top	Topology structure (can be NULL if `type` is not INDEX_RES or INDEX_MOL).
[in]	type	Type of mapping to construct.

Initializes a new index group mapping. The index group provided to gmx_ana_indexmap_update() should always be a subset of the g given here.

m should have been initialized somehow (calloc() is enough).

int gmx_ana_indexmap_init_orgid_group	(	gmx_ana_indexmap_t *	m,
		const gmx_mtop_t *	top,
		e_index_t	type
	)

Initializes orgid entries based on topology grouping.

Parameters

[in,out]	m	Mapping structure to use/initialize.
[in]	top	Topology structure (can be NULL if not required for `type`).
[in]	type	Type of groups to use.

Returns: The number of groups of type type that were present in m.

Exceptions

InconsistentInputError if the blocks in m do not have a unique group (e.g., contain atoms from multiple residues with type == INDEX_RES).

By default, the gmx_ana_indexmap_t::orgid fields are initialized to atom/residue/molecule indices from the topology (see documentation for the struct for more details). This function can be used to set the field to a zero-based group index instead. The first block will always get orgid[0] = 0, and all following blocks that belong to the same residue/molecule (type) will get the same index. Each time a block does not belong to the same group, it will get the next available number. If type == INDEX_ATOM, the orgid field is initialized as 0, 1, ..., independent of whether the blocks are single atoms or not.

Strong exception safety guarantee.

void gmx_ana_indexmap_reserve	(	gmx_ana_indexmap_t *	m,
		int	nr,
		int	isize
	)

Reserves memory for an index group mapping.

Parameters

[in,out]	m	Mapping structure.
[in]	nr	Maximum number of blocks to reserve space for.
[in]	isize	Maximum number of atoms to reserve space for.

void gmx_ana_indexmap_set_static	(	gmx_ana_indexmap_t *	m,
		t_blocka *	b
	)

Sets an index group mapping to be static.

Parameters

[in,out]	m	Mapping structure to initialize.
[in]	b	Block information to use for data.

Frees some memory that is not necessary for static index group mappings. Internal pointers are set to point to data in b; it is the responsibility of the caller to ensure that the block information matches the contents of the mapping. After this function has been called, the index group provided to gmx_ana_indexmap_update() should always be the same as g given here.

This function breaks modularity of the index group mapping interface in an ugly way, but allows reducing memory usage of static selections by a significant amount.

void gmx_ana_indexmap_update	(	gmx_ana_indexmap_t *	m,
		gmx_ana_index_t *	g,
		bool	bMaskOnly
	)

Updates an index group mapping.

Parameters

[in,out]	m	Mapping structure.
[in]	g	Current index group.
[in]	bMaskOnly	true if the unused blocks should be masked with -1 instead of removing them.

Updates the index group mapping with the new index group g.

See Also: gmx_ana_indexmap_t

static bool is_at_residue_boundary	(	const gmx_mtop_t &	top,
		int	a,
		int *	molb
	)

static

Returns if an atom is at a residue boundary.

Parameters

[in]	top	Topology data.
[in]	a	Atom index to check, should be -1 <= `a` < top->natoms.
[in,out]	molb	The molecule block of atom a

Returns: true if atoms a and a + 1 are in different residues, false otherwise.

static void set_atoms	(	gmx_ana_indexmap_t *	m,
		int	isize,
		int *	index
	)

static

Helper function to set the source atoms in an index map.

Parameters

[in,out]	m	Mapping structure.
[in]	isize	Number of atoms in the `index` array.
[in]	index	List of atoms.

Description

Classes

Functions

Function Documentation