Documentation
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Index ¶
- func RMSDTraj(mol chem.Atomer, ref *v3.Matrix, traj chem.ConcTraj, indexes []int, o *Options) ([]float64, int, error)
- type ConcTrajCloser
- type LOVOReturn
- type MolIDandChain
- type Options
- func (O *Options) AtomNames(names ...[]string) []string
- func (O *Options) Begin(n ...int) int
- func (O *Options) Chains(chains ...[]string) []string
- func (O *Options) Cpus(n ...int) int
- func (O *Options) LessThanRMSD(rmsd ...float64) float64
- func (O *Options) MinimumN(n ...int) int
- func (O *Options) Skip(n ...int) int
- func (O *Options) TrajName(name ...string) string
Constants ¶
This section is empty.
Variables ¶
This section is empty.
Functions ¶
func RMSDTraj ¶
func RMSDTraj(mol chem.Atomer, ref *v3.Matrix, traj chem.ConcTraj, indexes []int, o *Options) ([]float64, int, error)
RMSDTraj returns the RMSD for all atoms in a structure, averaged over the trajectory traj. Frames are read in sets of cpus at the time: The read starts at the set begin/cpus and we skip a set every skip/cpu (the numbers are, of course, rounded). The RMSDs and the total number of frames read are returned, together with an error or nil.
Types ¶
type ConcTrajCloser ¶
ConcTraje is an interface for a trajectory that can be read concurrently.
type LOVOReturn ¶
type LOVOReturn struct {
N int
FramesRead int //how many frames where actually read from the trajectory
Natoms []int //IDs of the N most rigid atoms
Nmols []*MolIDandChain //IDs for the N most rigid residues/molecules
RMSD []float64 //the RMSD for all residues, not only the N most rigid.
Iterations int //The iterations that were needed for convergency.
}
LOVOReturn contains the information returned by LOVOnMostRigid
func LOVO ¶
LOVO returns slices with the indexes of the n atoms and residues most rigid from mol, along the traj trajectory, considering only atoms with names in atomnames (normally, PDB names are used) and belonging to one of the chains in chains (only the first slice given in chains will be considered, if nothing is given, atoms from any chain will be considred. If you use this function in your research, please cite the references for the LOVO alignment method: 10.1371/journal.pone.0119264. 10.1186/1471-2105-8-306 If you use this function in a to-consumer program, please print a message asking to cite the references when the function is used.
func (*LOVOReturn) GMX ¶
func (L *LOVOReturn) GMX(chain ...string) string
Return the LOVO-selected residues in a format that can be pasted into the Gromacs gmx make_ndx tool to build a selection. The selection will incluede the residues from the chain given, and the chain ID, if given, or all residues matching, if not. The atomname (normally CA in atomistic simulations or BB in Martini ones is not added, mostly out of laziness and because it's easy to simply append " & a CA" or " & a BB" at the end of the string.
func (*LOVOReturn) Len ¶
func (L *LOVOReturn) Len() int
func (*LOVOReturn) Less ¶
func (L *LOVOReturn) Less(i, j int) bool
Implements Sort to sort by residue
func (*LOVOReturn) PyMOLSel ¶
func (L *LOVOReturn) PyMOLSel() string
PyMOLSel returns a string of text to create a PyMOL selection with the L.N most rigid residues from a LOVO calculation.
func (*LOVOReturn) String ¶
func (L *LOVOReturn) String() string
String returns a string representation of the LOVOReturn object.
func (*LOVOReturn) Swap ¶
func (L *LOVOReturn) Swap(i, j int)
type MolIDandChain ¶
type MolIDandChain struct {
// contains filtered or unexported fields
}
func (*MolIDandChain) Chain ¶
func (M *MolIDandChain) Chain() string
func (*MolIDandChain) MolID ¶
func (M *MolIDandChain) MolID() int
func (*MolIDandChain) String ¶
func (M *MolIDandChain) String() string
type Options ¶
type Options struct {
// contains filtered or unexported fields
}
Options contains various options for the LOVOnMostRigid and RMSDTraj functions
func DefaultCGOptions ¶
func DefaultCGOptions() *Options
DefaultCGOptions returns reasonable options for Martini trajectories.
func DefaultOptions ¶
func DefaultOptions() *Options
DefaultOptions return reasonable options for atomistic trajectories. It prepares a superposition of alpha carbons (CA) with all logical CPUs, trying to use for the superposition all CAs with RMSD lower than 1.0 A.
func (*Options) AtomNames ¶
Returns the atom names consiered or the alignment and sets them to new values, if those are given.
func (*Options) Begin ¶
Returns the value of the first frame of the sequence to use, and sets it to a new value, if given.
func (*Options) Chains ¶
Returns the atom names consiered or the alignment and sets them to new values, if those are given.
func (*Options) Cpus ¶
Returns the number of gorutines to be used, and sets it to a new value, if given.
func (*Options) LessThanRMSD ¶
Returns the minimum RMSD for an atom to be consiered as part of the alignment, and sets it to a new value, if given. if this flag is set to 0 or less, the regular LOVO convergency criterion is used.
func (*Options) MinimumN ¶
Returns the smallest acceptable number of atoms to be returned by the alinment procedure. Only used if the LessThanRMSD is active. and sets it to a new value, if given.
Source Files