§ Molecule() [1/2]
| magnes::Molecule::Molecule |
( |
| ) |
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§ Molecule() [2/2]
| magnes::Molecule::Molecule |
( |
const Molecule & |
mol | ) |
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§ At()
| Molecule magnes::Molecule::At |
( |
size_t |
frame | ) |
const |
return frame i as a complete new molecule
§ Atoms() [1/2]
| const std::vector<Atom>& magnes::Molecule::Atoms |
( |
| ) |
const |
- Returns
- a const stl vector of atoms in this molecule
§ Atoms() [2/2]
| std::vector<Atom>& magnes::Molecule::Atoms |
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| ) |
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- Returns
- a const stl vector of atoms in this molecule
§ Bonds() [1/2]
| const std::vector<Bond>& magnes::Molecule::Bonds |
( |
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const |
- Returns
- a const stl vector of bonds in this molecule
§ Bonds() [2/2]
| std::vector<Bond>& magnes::Molecule::Bonds |
( |
| ) |
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- Returns
- a const stl vector of bonds in this molecule
§ CalculateWeight()
| double magnes::Molecule::CalculateWeight |
( |
| ) |
const |
Calculate Molecular Weight
§ CheckConformersSanity()
| bool magnes::Molecule::CheckConformersSanity |
( |
| ) |
const |
§ CurrentFrame() [1/2]
| const Frame& magnes::Molecule::CurrentFrame |
( |
| ) |
const |
- Returns
- a const reference to the current conformer
§ CurrentFrame() [2/2]
| Frame& magnes::Molecule::CurrentFrame |
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- Returns
- a reference to the current conformer
§ CurrentFrameIndex()
| size_t magnes::Molecule::CurrentFrameIndex |
( |
| ) |
const |
return the index of the current conformer
§ EckartTransform()
| std::vector< std::vector< double > > magnes::Molecule::EckartTransform |
( |
size_t |
reframe, |
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const std::vector< size_t > & |
atoms |
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) |
| |
superimpose all frames to reference frame f, minimizing the displacements for atoms,using mass weighted coordinate and Kersley algorithms
§ Elements()
| std::list<int> magnes::Molecule::Elements |
( |
| ) |
const |
return a ordered list with the different element atomic numbers present in the molecule
§ ElementSymbols()
| std::list<std::string> magnes::Molecule::ElementSymbols |
( |
| ) |
const |
return a ordered list with the different element atomic numbers present in the molecule
§ EssentialRings()
| std::vector< std::vector<size_t> > magnes::Molecule::EssentialRings |
( |
size_t |
size = 0 | ) |
const |
Get the essential rings of size size
§ FileName()
| const std::string& magnes::Molecule::FileName |
( |
| ) |
const |
return the filename of the molecule
§ FindAtomByName()
| std::vector<int> magnes::Molecule::FindAtomByName |
( |
const std::string & |
name | ) |
const |
§ Frames() [1/2]
| const std::vector<Frame>& magnes::Molecule::Frames |
( |
| ) |
const |
- Returns
- a const stl vector with all conformers
§ Frames() [2/2]
| std::vector<Frame>& magnes::Molecule::Frames |
( |
| ) |
|
- Returns
- a stl vector with all conformers
§ Hybridization()
Get Hybridization type for atom i
§ IndexFromPDB()
| size_t magnes::Molecule::IndexFromPDB |
( |
const std::string & |
pdbname, |
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const std::string & |
resname, |
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const std::string & |
resindex |
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) |
| const |
return the index of the atom from its pdb name
§ IsRingTied()
| bool magnes::Molecule::IsRingTied |
( |
const std::vector< size_t > & |
ring | ) |
const |
return true if ring is a tied ring
§ MoveToCentroid()
| void magnes::Molecule::MoveToCentroid |
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| ) |
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move molecule to the centroid
§ NBonds()
| size_t magnes::Molecule::NBonds |
( |
size_t |
i, |
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|
size_t |
j |
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) |
| const |
- Returns
- the number of bonds between atoms i and j
§ Neighbours()
| std::vector<size_t> magnes::Molecule::Neighbours |
( |
size_t |
i | ) |
const |
- Returns
- a vector with the indexes of the atoms connected to atom i
§ operator=()
§ Populations() [1/2]
| const std::vector<double>& magnes::Molecule::Populations |
( |
| ) |
const |
§ Populations() [2/2]
| std::vector<double>& magnes::Molecule::Populations |
( |
| ) |
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§ ReparentFrames()
| void magnes::Molecule::ReparentFrames |
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| ) |
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reparent all frames in the molecule
§ Residues() [1/2]
| const std::vector<PDBResidue*>& magnes::Molecule::Residues |
( |
| ) |
const |
return a list of PDB residues
§ Residues() [2/2]
| std::vector<PDBResidue*>& magnes::Molecule::Residues |
( |
| ) |
|
return a list of PDB residues
§ Rings()
| std::vector< std::vector<size_t> > magnes::Molecule::Rings |
( |
size_t |
size = 0 | ) |
const |
Get the rings of size size
§ SetBonds()
| void magnes::Molecule::SetBonds |
( |
bool |
eachframe = false | ) |
|
automatically setup bonds based on atomic distances
§ SetCurrentFrame()
| void magnes::Molecule::SetCurrentFrame |
( |
size_t |
i | ) |
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set the active conformer to i
§ SetFileName()
| void magnes::Molecule::SetFileName |
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const std::string & |
filename | ) |
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set the filename for the molecule
§ ShortestPath()
| std::vector<size_t> magnes::Molecule::ShortestPath |
( |
size_t |
i, |
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size_t |
j |
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) |
| const |
return the shortest path between atoms of indexes i and j
§ SuperImpose()
| std::vector< std::vector<double> > magnes::Molecule::SuperImpose |
( |
size_t |
reframe, |
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const std::vector< size_t > & |
atoms, |
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bool |
massweighted = false |
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) |
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superimpose all frames to reference frame f, minimizing the displacements for atoms, returns a list with the rmsd for the atomlist using Kearsley quaternion algorithm Kearsley, S. K. Acta Crystallographica 1989, A45, 208–210. doi: 10.1107/S0108767388010128
§ SuperImposeMackay()
| std::vector< std::vector<double> > magnes::Molecule::SuperImposeMackay |
( |
size_t |
reframe, |
|
|
const std::vector< size_t > & |
atoms |
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) |
| |
superimpose all frames to reference frame f, minimizing the displacements for atoms, returns a list with squared distnces for the atomlist using Mackay quaternion SVD algorithm Mackay, A. L. QActa Crystallographica 1984, A40, 165–166. The default implementation seems to have problems when theta/2=45
§ Weight()
| double magnes::Molecule::Weight |
( |
| ) |
const |
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inline |
The documentation for this class was generated from the following file:
- /Users/armando/worksrc/magnes-code/trunk/magnes/core/molecule.h
