Class for reading a subset of the TinkerXYZ format. More...
#include <tinkerxyz.hpp>
Inheritance diagram for loos::TinkerXYZ:
Collaboration diagram for loos::TinkerXYZ:
Public Member Functions | |
| TinkerXYZ (const std::string &fname) | |
| TinkerXYZ (std::istream &ifs) | |
| virtual TinkerXYZ * | clone (void) const |
| Clones an object for polymorphism (see AtomicGroup::clone() for more info) | |
| TinkerXYZ | copy (void) const |
| Creates a deep copy (see AtomicGroup::copy() for more info) | |
| void | read (std::istream &is) |
 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 a subset of the TinkerXYZ format.
Notes:
The tinker ARC trajectory file format is just concatenated XYZ, so this code should be shared.
Member Function Documentation
◆ clone()
|
virtual |
Clones an object for polymorphism (see AtomicGroup::clone() for more info)
Reimplemented from loos::AtomicGroup.
The documentation for this class was generated from the following files:
- src/tinkerxyz.hpp
- src/tinkerxyz.cpp
