mol_edit.cpp File Reference

Library routines used for atomic coordinates. More...

#include "rwmolecule.h"
#include "rwatomprop.h"
#include "rwresprop.h"
#include "mol_transform.h"
#include "mol_select.h"
#include "mol_edit.h"
#include "mol_util.h"
#include "seq_util.h"
#include "linked_list.h"
#include "Matrix3.h"
#include "random_numbers.h"
#include "utilities.h"

Functions
long	molgroup_set_atom_types_to_elements (Bmolgroup *molgroup)
	Sets atom types to element names. More...
int	molgroup_remove_hydrogens (Bmolgroup *molgroup)
	Removes all hydrogens from a molecular system. More...
bool	bond_find (Bmolgroup *molgroup, Batom *atom1, Batom *atom2)
int	molgroup_add_disulfides (Bmolgroup *molgroup, double distance)
	Adds disulfide bonds when sulfur atoms are close to each other. More...
Bmolgroup **	molgroup_split_into_slices (Bmolgroup *molgroup, double slice_thickness, int &nslices)
	Splits a set of coordinates into slices with a given thickness. More...
int	molgroup_insert (Bmolgroup *molgroup, Bmolgroup *molinsert, double distance)
	Inserts one set of molecules into another. More...
int	molgroup_randomize (Bmolgroup *molgroup, double random_max)
	Applies random displacements to coordinates. More...
int	molgroup_randomize_B (Bmolgroup *molgroup, double B)
	Applies random displacements to coordinates. More...
int	molgroup_random_displace_number (Bmolgroup *molgroup, long number, double stdev)
	Applies random displacements to a selected number of coordinates. More...
int	molgroup_remove_overlapping_atoms (Bmolgroup *molgroup, double mindist)
	Removes overlapping atoms. More...
int	molgroup_bond_pseudo_atoms (Bmolgroup *molgroup, int atoms_per_bond, int wrap)
	Places pseudo-atoms on bonds. More...
char *	grid_from_molgroup (Bmolgroup *molgroup, Vector3< double > min, double sampling, Vector3< int > size)
char *	grid_from_molecule (Bmolecule *mol, Vector3< double > min, double sampling, Vector3< int > size)
int	molgroup_prune_molecules (Bmolgroup *molgroup)
	Deletes overlapping molecules. More...
long	molgroup_delete_deselected_molecules (Bmolgroup *molgroup)
	Deletes deselected molecules. More...
long	molgroup_prune_overlapping_atoms (Bmolgroup *molgroup, double mindist)
	Prunes overlapping atoms based on a distance criterion. More...
long	molgroup_delete_deselected_atoms (Bmolgroup *molgroup)
	Deletes deselected atoms. More...
int	molgroup_untangle_molecules (Bmolgroup *molgroup, double sampling, double lambda)
	Moves overlapping molecules away from each other. More...
int	molgroup_untangle_groups (Bmolgroup *molgroup, double sampling, double lambda)
	Moves overlapping molecules away from each other. More...

Variables
int	verbose

Detailed Description

Library routines used for atomic coordinates.

Author

Bernard Heymann

Date

Created: 19980214

Modified: 20211029

Function Documentation

bond_find()

bool bond_find	(	Bmolgroup *	molgroup,
		Batom *	atom1,
		Batom *	atom2
	)

grid_from_molecule()

char * grid_from_molecule	(	Bmolecule *	mol,
		Vector3< double >	min,
		double	sampling,
		Vector3< int >	size
	)

grid_from_molgroup()

char * grid_from_molgroup	(	Bmolgroup *	molgroup,
		Vector3< double >	min,
		double	sampling,
		Vector3< int >	size
	)

molgroup_add_disulfides()

int molgroup_add_disulfides	(	Bmolgroup *	molgroup,
		double	distance
	)

Adds disulfide bonds when sulfur atoms are close to each other.

Parameters

*molgroup	molecule group structure.
distance	maximum separation between sulfur atoms.

Returns

int number of disulfide bonds added.

molgroup_bond_pseudo_atoms()

int molgroup_bond_pseudo_atoms	(	Bmolgroup *	molgroup,
		int	atoms_per_bond,
		int	wrap
	)

Places pseudo-atoms on bonds.

Parameters

*molgroup	the molecule group.
atoms_per_bond	number of pseudo-atoms per bond.
wrap	wrap around periodic boundaries if !=0.

Returns

Bbond* new bond list.

The requested number of new atoms are placed to coincide with each bond.

molgroup_delete_deselected_atoms()

long molgroup_delete_deselected_atoms

(

Bmolgroup *

molgroup

)

Deletes deselected atoms.

Parameters

*molgroup

molecule group structure to be modified.

Returns

long number of atoms deleted.

molgroup_delete_deselected_molecules()

long molgroup_delete_deselected_molecules

(

Bmolgroup *

molgroup

)

Deletes deselected molecules.

Parameters

*molgroup

molecule group structure to be modified.

Returns

long number of molecules deleted.

molgroup_insert()

int molgroup_insert	(	Bmolgroup *	molgroup,
		Bmolgroup *	molinsert,
		double	distance
	)

Inserts one set of molecules into another.

Molecules overlapping in the receiving molecule group are deleted.
The footprint of the molecules being inserted is calculated on a grid
and all atoms within this footprint is tested for deletion.
Note: The molecule list is transferred from the insertion group to 
    the main group and the insertion group is deallocated.

Parameters

*molgroup	molecule group structure to be modified.
*molinsert	molecule group structure to insert. (deallocated)
distance	cutoff distance to remove atoms.

Returns

int 0.

molgroup_prune_molecules()

int molgroup_prune_molecules

(

Bmolgroup *

molgroup

)

Deletes overlapping molecules.

Parameters

*molgroup

the molecule group.

Returns

int 0.

molgroup_prune_overlapping_atoms()

long molgroup_prune_overlapping_atoms	(	Bmolgroup *	molgroup,
		double	mindist
	)

Prunes overlapping atoms based on a distance criterion.

The first atom in any pair of overlapping atoms is kept.

Parameters

*molgroup	molecule group structure to be modified.
mindist	distance criterion.

Returns

long number of remaining atoms.

molgroup_random_displace_number()

int molgroup_random_displace_number	(	Bmolgroup *	molgroup,
		long	number,
		double	stdev
	)

Applies random displacements to a selected number of coordinates.

Parameters

*molgroup	molecule group structure to be modified.
number	number of coordinates to displace.
stdev	standard devaition of displacement.

Returns

int 0.

molgroup_randomize()

int molgroup_randomize	(	Bmolgroup *	molgroup,
		double	random_max
	)

Applies random displacements to coordinates.

Parameters

*molgroup	molecule group structure to be modified.
random_max	maximum displacement.

Returns

int 0.

molgroup_randomize_B()

int molgroup_randomize_B	(	Bmolgroup *	molgroup,
		double	B
	)

Applies random displacements to coordinates.

Parameters

*molgroup	molecule group structure to be modified.
B	B factor.

Returns

int 0.

molgroup_remove_hydrogens()

int molgroup_remove_hydrogens

(

Bmolgroup *

molgroup

)

Removes all hydrogens from a molecular system.

Parameters

*molgroup

molecule group structure.

Returns

int number of hydrogens removed.

molgroup_remove_overlapping_atoms()

int molgroup_remove_overlapping_atoms	(	Bmolgroup *	molgroup,
		double	mindist
	)

Removes overlapping atoms.

Parameters

*molgroup	molecule group.
mindist	minimum distance allowed between atoms.

Returns

int number of atoms removed, <0 on error.

The input molecule group is checked for any atom pairs closer than
a minimum allowed distance. The second atom of an overlapping pair
is removed. This is intended to clean up after symmetry operations
that generate overlapping pseudo-atoms lying on symmetry axes.

molgroup_set_atom_types_to_elements()

long molgroup_set_atom_types_to_elements

(

Bmolgroup *

molgroup

)

Sets atom types to element names.

Parameters

*molgroup

molecule group structure.

Returns

long number of atoms.

molgroup_split_into_slices()

Bmolgroup ** molgroup_split_into_slices	(	Bmolgroup *	molgroup,
		double	slice_thickness,
		int &	nslices
	)

Splits a set of coordinates into slices with a given thickness.

Parameters

*molgroup	molecule group structure.
slice_thickness	slice thickness (in angstrom).
&nslices	pointer to the number of slices generated

Returns

Bmolgroup** set of molecule groups.

molgroup_untangle_groups()

int molgroup_untangle_groups	(	Bmolgroup *	molgroup,
		double	sampling,
		double	lambda
	)

Moves overlapping molecules away from each other.

The overlap of molecules are assessed by projecting atom positions
onto a grid. Overlapping molecules are then moved away from each other
along a vector through their centers-of-mass.

Parameters

*molgroup	the molecule group.
sampling	grid sampling (angstrom).
lambda	damping factor.

Returns

int 0.

molgroup_untangle_molecules()

int molgroup_untangle_molecules	(	Bmolgroup *	molgroup,
		double	sampling,
		double	lambda
	)

Moves overlapping molecules away from each other.

The overlap of molecules are assessed by projecting atom positions
onto a grid. Overlapping molecules are then moved away from each other
along a vector through their centers-of-mass.

Parameters

*molgroup	the molecule group.
sampling	grid sampling (angstrom).
lambda	damping factor.

Returns

int 0.

Variable Documentation

verbose

int verbose

extern