NMA Model Editing

This module defines functions for editing normal mode data.

extendModel(model, nodes, atoms, norm=False)[source]

Extend a coarse grained model built for nodes to atoms. model may be ANM, GNM, PCA, or NMA instance. This function will take part of the normal modes for each node (i.e. Cα atoms) and extend it to all other atoms in the same residue. For each atom in nodes argument atoms argument must contain a corresponding residue. If norm is True, extended modes are normalized.

extendMode(mode, nodes, atoms, norm=False)[source]

Extend a coarse grained normal mode built for nodes to atoms. This function will take part of the normal modes for each node (i.e. Cα atoms) and extend it to all other atoms in the same residue. For each atom in nodes argument atoms argument must contain a corresponding residue. Extended mode is multiplied by the square root of variance of the mode. If norm is True, extended mode is normalized.

extendVector(vector, nodes, atoms)[source]

Extend a coarse grained vector for nodes to atoms. This function will take part of the normal modes for each node (i.e. Cα atoms) and extend it to all other atoms in the same residue. For each atom in nodes, atoms argument must contain a corresponding residue.

sliceMode(mode, atoms, select)[source]

Returns part of the mode for atoms matching select. This works slightly different from sliceVector(). Mode array (eigenvector) is multiplied by square-root of the variance along the mode. If mode is from an elastic network model, variance is defined as the inverse of the eigenvalue. Note that returned Vector instance is not normalized.

Parameters:
  • mode (Mode) – mode instance to be sliced
  • atoms (Atomic) – atoms for which mode describes a deformation, motion, etc.
  • select (Selection, str) – an atom selection or a selection string
Returns:

(Vector, Selection)
sliceModel(model, atoms, select)[source]

Returns a part of the model (modes calculated) for atoms matching select. Note that normal modes are sliced instead the connectivity matrix. Sliced normal modes (eigenvectors) are not normalized.

Parameters:
  • mode (NMA) – NMA model instance to be sliced
  • atoms (Atomic) – atoms for which the model was built
  • select (Selection, str) – an atom selection or a selection string
Returns:

(NMA, Selection)
sliceModelByMask(model, mask)[source]

Returns a part of the model indicated by mask. Note that normal modes (eigenvectors) are not normalized.

Parameters:
  • mode (NMA) – NMA model instance to be sliced
  • mask (list, ndarray) – an Integer array or a Boolean array where "True" indicates the parts being selected
Returns:

NMA
sliceVector(vector, atoms, select)[source]

Returns part of the vector for atoms matching select. Note that returned Vector instance is not normalized.

Parameters:
  • vector (VectorBase) – vector instance to be sliced
  • atoms (Atomic) – atoms for which vector describes a deformation, motion, etc.
  • select (Selection, str) – an atom selection or a selection string
Returns:

(Vector, Selection)
reduceModel(model, atoms, select)[source]

Returns reduced NMA model. Reduces a NMA model to a subset of atoms matching select. This function behaves differently depending on the type of the model argument. For ANM and GNM or other NMA models, force constant matrix for system of interest (specified by the select) is derived from the force constant matrix for the model by assuming that for any given displacement of the system of interest, other atoms move along in such a way as to minimize the potential energy. This is based on the formulation in [KH00]. For PCA models, this function simply takes the sub-covariance matrix for selection.

[KH00]Hinsen K, Petrescu A-J, Dellerue S, Bellissent-Funel M-C, Kneller GR. Harmonicity in slow protein dynamics. Chem Phys 2000 261:25-37.
Parameters:
  • model (ANM, GNM, or PCA) – dynamics model
  • atoms (Atomic) – atoms that were used to build the model
  • select (Selection, str) – an atom selection or a selection string
Returns:

(NMA, Selection)
reduceModelByMask(model, mask)[source]

Returns NMA model reduced based on mask.

Parameters:
  • model (ANM, GNM, or PCA) – dynamics model
  • mask (list, ndarray) – an Integer array or a Boolean array where "True" indicates the parts being selected
Returns:

NMA
trimModel(model, atoms, select)[source]

Returns a part of the model for atoms matching select. This method removes columns and rows in the connectivity matrix and fix the diagonal sums. Normal modes need to be calculated again after the trim.

Parameters:
  • mode (NMA) – NMA model instance to be sliced
  • atoms (Atomic) – atoms for which the model was built
  • select (Selection, str) – an atom selection or a selection string
Returns:

(NMA, Selection)
trimModelByMask(model, mask)[source]

Returns a part of the model indicated by mask. This method removes columns and rows in the connectivity matrix indicated by mask and fix the diagonal sums. Normal modes need to be calculated again after the trim.

Parameters:
  • mode (NMA) – NMA model instance to be sliced
  • mask (list, ndarray) – an Integer array or a Boolean array where "True" indicates the parts being selected
Returns:

NMA