loos::Amber Class Reference

Class for reading in AMBER parmtop/coord files... More...

#include <amber.hpp>

Inheritance diagram for loos::Amber:

Collaboration diagram for loos::Amber:

Public Member Functions
	Amber (const std::string &fname)
	Read in a parmtop file.
	Amber (std::istream &ifs)
virtual Amber *	clone (void) const
	Clones an object for polymorphism...
Amber	copy (void) const
	Deep copy.
void	read (std::istream &ifs)
	Parse the parmtop file.
std::string	title () const
	Return the title.
Public Member Functions inherited from loos::AtomicGroup
	AtomicGroup (const int n)
	Creates a new AtomicGroup with n un-initialized atoms.
	AtomicGroup (const AtomicGroup &g)
	Copy constructor (atoms and box shared)
AtomicGroup	copy (void) const
	Creates a deep copy of this group.
uint	length (void) const
uint	size (void) const
bool	empty (void) const
pAtom	getAtom (const int i) const
	Get the ith atom from this group.
pAtom &	operator[] (const int i)
	Same as getAtom(i)
const pAtom &	operator[] (const int i) const
AtomicGroup &	append (pAtom pa)
	Append the atom onto the group.
AtomicGroup &	append (std::vector< pAtom > pas)
	Append a vector of atoms.
AtomicGroup &	append (const AtomicGroup &grp)
	Append an entire AtomicGroup onto this one (concatenation)
AtomicGroup &	remove (pAtom pa)
	Delete a single atom.
AtomicGroup &	remove (std::vector< pAtom > pas)
	Deletes a set of atoms.
AtomicGroup &	remove (const AtomicGroup &grp)
	Deletes all atoms in the passed grp that are also in the current group.
AtomicGroup &	operator+= (const AtomicGroup &rhs)
AtomicGroup &	operator+= (const pAtom &rhs)
AtomicGroup	operator+ (const AtomicGroup &rhs)
AtomicGroup	operator+ (const pAtom &rhs)
bool	operator== (AtomicGroup &rhs)
	Equality test for two groups.
bool	operator!= (AtomicGroup &rhs)
	Inequality test for two groups.
bool	operator== (const AtomicGroup &rhs) const
	Equality test for const groups.
bool	operator!= (const AtomicGroup &rhs) const
	Inequality test for two groups.
AtomicGroup	subset (const int offset, const int len=0)
	subset() and excise() args are patterned after perl's substr...
AtomicGroup	excise (const int offset, const int len=0)
	excise returns the excised atoms as a group...
template<class EqualsOp >
bool	contains (const pAtom &p, const EqualsOp &op) const
	Determines if a pAtom is contained in this group using the EqualsOp atom-equality policy.
bool	contains (const pAtom &p) const
	Determines if a pAtom is contained in this group using the AtomEquals policy (ie the default comparison policy)
template<class EqualsOp >
bool	contains (const AtomicGroup &g, const EqualsOp &op) const
	Determines if the passed group is a subset of the current group using the EqualsOp atom-equality policy.
bool	contains (const AtomicGroup &g) const
	Determines if a group is a subset of the current group using the default AtomEquals policy.
template<class EqualsOp >
bool	containsAny (const AtomicGroup &g, const EqualsOp &op) const
	Determines if a group contains any atom.
bool	containsAny (const AtomicGroup &g) const
	Determines if a group contains any atom using the default AtomEquals policy.
template<class EqualsOp >
AtomicGroup	intersect (const AtomicGroup &g, const EqualsOp &op)
	Computes the intersection of two groups using the EqualsOp atom-equality policy.
AtomicGroup	intersect (const AtomicGroup &g)
	Intersection of two groups.
template<class EqualsOp >
AtomicGroup	merge (const AtomicGroup &g, const EqualsOp &op)
	Union of two groups using the specified atom-equality policy.
AtomicGroup	merge (const AtomicGroup &g)
	Union of two groups using the default AtomEquals atom-equality policy.
AtomicGroup	select (const AtomSelector &sel) const
	Return a group consisting of atoms for which sel predicate returns true...
std::vector< AtomicGroup >	splitByUniqueSegid (void) const
	Returns a vector of AtomicGroups split from the current group based on segid.
std::vector< AtomicGroup >	splitByMolecule (void) const
	Returns a vector of AtomicGroups split based on bond connectivity.
std::vector< AtomicGroup >	splitByMolecule (const std::string &selection) const
std::vector< AtomicGroup >	splitByResidue (void) const
	Returns a vector of AtomicGroups, each comprising a single residue.
std::map< std::string, AtomicGroup >	splitByName (void) const
	Returns a vector of AtomicGroups, each containing atoms with the same name.
AtomicGroup	centrifyByMolecule () const
	Replace a group with the center of masses of contained molecules.
AtomicGroup	centrifyByResidue () const
	Replace a group with the cente of masses of contained residues (see centrifyByMolecule())
pAtom	findById (const int id) const
	Find a contained atom by its atomid.
AtomicGroup	groupFromID (const std::vector< int > &id_list) const
	Create a new group from a vector of atomids.
AtomicGroup	groupFromID (const std::pair< int, int > &id_pair) const
	Create a new group from a pair of atomids.
AtomicGroup	getResidue (pAtom res)
std::string	asString () const
void	renumber (const int start=1, const int stride=1)
	Renumber the atomid's of the contained atoms...
int	minId (void) const
int	maxId (void) const
int	minResid (void) const
int	maxResid (void) const
int	numberOfResidues (void) const
int	numberOfSegids (void) const
bool	allHaveProperty (const Atom::bits &property) const
	True if all atoms in the group have the passed property(ies)
bool	anyHaveProperty (const Atom::bits &property) const
	True if any atom in the group have the passed property(ies)
bool	hasBonds (void) const
	Does any atom in the group have bond information???
bool	hasCoords (void) const
	Do all the atoms in the group have coordinates?
void	clearBonds (void)
	Remove any bonding information present in contained atoms.
void	pruneBonds ()
	Attempt to prune connectivity (only retain bonds to atoms within this AtomicGroup)
void	resetAtomIndices ()
	Reset the atom indices (used for interfacing with trajectories)
uint	deduceAtomicNumberFromMass (const double tol=0.1)
	Deduce atomic number from mass (if present), returning number of atoms assigned.
double	deduceMassFromAtomicNumber ()
	Deduce mass from atomic number (if present), returning the number of atoms assigned.
bool	sorted (void) const
	Is the array of atoms already sorted???
void	sort (void)
	Sort based on atomid.
bool	isPeriodic (void) const
	Test whether or not periodic boundary conditions are set.
GCoord	periodicBox (void) const
	Fetch the periodic boundary conditions.
void	periodicBox (const GCoord &c)
	Set the periodic boundary conditions.
void	periodicBox (const greal x, const greal y, const greal z)
	Set the periodic boundary conditions.
const greal	ocf (uint offset)
	compute OCF for all atom-pairs in AG of distance offset from one another
loos::SharedPeriodicBox	sharedPeriodicBox () const
	Provide access to the underlying shared periodic box...
void	removePeriodicBox ()
	Remove periodicity.
void	reimage ()
void	reimageByAtom ()
	Reimage atoms individually into the primary cell.
void	mergeImage (pAtom &p)
	Takes a group that's split across a periodic boundary and reimages it so it's all together.
void	mergeImage ()
	Takes a group that's split across a periodic boundary and reimages it so it's all together, using the first atom in the AtomicGroup as the reference.
AtomicGroup	within (const double dist, AtomicGroup &grp) const
	Find atoms in the current group that are within dist angstroms of any atom in grp.
AtomicGroup	within (const double dist, AtomicGroup &grp, const GCoord &box) const
	Find atoms in grp that are within dist angstroms of atoms in the current group, considering periodicity.
bool	contactWith (const double dist, const AtomicGroup &grp, const uint min=1) const
	Returns true if any atom of current group is within dist angstroms of grp.
bool	contactWith (const double dist, const AtomicGroup &grp, const GCoord &box, const uint min=1) const
	Returns true if any atom of current group is within dist angstroms of grp.
std::vector< std::pair< int, int > >	getBondsIDs () const
	return a list of atom ID pairs that correspond to all unique bonds.
std::vector< AtomicGroup >	getBondsAGs () const
	return a list of atom index pairs corresponding to all unique bonds.
void	findBonds (const double dist, const GCoord &box)
	Distance-based search for bonds.
void	findBonds (const double dist)
void	findBonds (const GCoord &box)
void	findBonds ()
template<class T >
T	apply (T func)
	Apply a functor or a function to each atom in the group.
iterator	begin (void)
iterator	end (void)
const_iterator	begin (void) const
const_iterator	end (void) const
std::vector< GCoord >	boundingBox (void) const
	Bounding box for the group...
GCoord	centerAtOrigin (void)
	Translates the group so that the centroid is at the origin.
GCoord	centroid (void) const
	Centroid of atoms (ignores mass, operates in group coordinates)
greal	radius (const bool use_atom_as_reference=false) const
	Maximum radius from centroid of all atoms (not gyration)
GCoord	centerOfMass (void) const
	Center of mass of the group (in group coordinates)
GCoord	centerOfElectrons (void) const
	Analogous to center of mass.
GCoord	dipoleMoment (void) const
	Dipole moment, relative to group's centroid.
greal	totalCharge (void) const
greal	totalMass (void) const
greal	radiusOfGyration (void) const
greal	sphericalVariance (const pAtom) const
	Spherical variance of group with respect to target atom.
greal	sphericalVariance (const GCoord) const
greal	stacking (const AtomicGroup &, const GCoord &box, const double threshold) const
	Estimate stacking, as between two nucleobases.
greal	rmsd (const AtomicGroup &)
	Compute the RMSD between two groups.
greal	kineticEnergy ()
	Compute kinetic energy of group.
std::vector< GCoord >	getTransformedCoords (const XForm &) const
	Returns a vector of coordinates transformed by the passed XForm.
std::vector< GCoord >	differenceVectors (const AtomicGroup &other)
	Compute difference vectors between two AtomicGroups.
void	translate (const GCoord &v)
	Translate an atomic group by vector v.
void	rotate (const GCoord &axis, const greal angle_in_degrees)
	Rotate group's coordinates (right-handed, about centroid)
void	applyTransform (const XForm &)
	Apply the given transform to the group's coordinates...
void	copyCoordinatesWithIndex (const std::vector< GCoord > &coords)
	Copy coordinates from a vector of GCoords using the atom index as an index into the vector.
void	copyVelocitiesWithIndex (const std::vector< GCoord > &velocities)
	Copy velocities from a vector of GCoords using the atom index as an index into the vector.
void	copyCoordinatesFrom (const AtomicGroup &g, const uint offset=0, const uint length=0)
	Copy coordinates from g into current group.
std::vector< uint >	atomOrderMapFrom (const AtomicGroup &g)
	Map the order of atoms in AtomicGroup g into the current group.
void	copyMappedCoordinatesFrom (const AtomicGroup &g, const std::vector< uint > &order)
	Given a mapping of atom order, copy the coordinates into the current group.
void	copyMappedCoordinatesFrom (const AtomicGroup &g)
	Copy the coordinates from the group mapping the atom order.
void	perturbCoords (const greal)
	Each atom is moved in a random direction by a vector of the passed size.
std::vector< GCoord >	principalAxes (void) const
	Compute the principal axes of a group.
double	principalAxesOrder (void) const
	Computes order parameter based on principalAxes.
std::vector< GCoord >	momentsOfInertia (void) const
	Computes the moments of inertia for a group.
GMatrix	superposition (const AtomicGroup &)
	Calculates the transformation matrix for superposition of groups.
GMatrix	alignOnto (const AtomicGroup &)
	Superimposes the current group onto the passed group.
void	orientAlong (const GCoord &)
	Orient the principal axis of this group along the supplied vector.
void	setCoords (double *seq, int m, int n)
void	getCoords (double **outseq, int *m, int *n)
std::vector< double >	coordsAsVector () const
double	packingScore (const AtomicGroup &other, const GCoord &box, bool norm) const
double	logisticContact (const AtomicGroup &group, double radius, int sigma, const GCoord &box) const
double	logisticContact2D (const AtomicGroup &group, double radius, int sigma, const GCoord &box) const
double	hardContact (const AtomicGroup &group, double radius, const GCoord &box) const
double	hardContact2D (const AtomicGroup &group, double radius, const GCoord &box) const
std::vector< double >	scattering (const double qmin, const double max, const uint numValues, loos::FormFactorSet &formFactors)

Static Public Member Functions
static pAtomicGroup	create (const std::string &fname)

Additional Inherited Members
Public Types inherited from loos::AtomicGroup
typedef std::vector< pAtom >::iterator	iterator
typedef std::vector< pAtom >::const_iterator	const_iterator
typedef pAtom	value_type
Static Public Attributes inherited from loos::AtomicGroup
static const double	superposition_zero_singular_value = 1e-10
Protected Member Functions inherited from loos::AtomicGroup
void	setGroupConnectivity ()
Protected Attributes inherited from loos::AtomicGroup
std::vector< pAtom >	atoms
loos::SharedPeriodicBox	box

Detailed Description

Class for reading in AMBER parmtop/coord files...

This class is largely geared towards reading parmtop files. It only parses a subset of the spec and follows more the format as defined from example files and VMD than from the Amber website.

Atomic numbers will be deduced from the masses. No error is generated if an atomic mass is unknown to LOOS. In order to verify that all atoms have an assigned mass, use the following,

bool ok = amber.allHaveProperty(Atom::anumbit);

Member Function Documentation

clone()

virtual Amber * loos::Amber::clone ( void ) const

inlinevirtual

Clones an object for polymorphism...

Reimplemented from loos::AtomicGroup.

---

The documentation for this class was generated from the following files:

• src/amber.hpp
• src/amber.cpp