Chem.Features.FeatDirUtilsRD

Package Chem :: Package Features :: Module FeatDirUtilsRD |
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# Module FeatDirUtilsRD

source code

Functions | [hide private]
cross(v1, v2) | source code
findNeighbors(atomId, adjMat) Find the IDs of the neighboring atom IDs... | source code
_findAvgVec(conf, center, nbrs) | source code
GetAromaticFeatVects(conf, featAtoms, featLoc, scale=1.5) Compute the direction vector for an aromatic feature... | source code
ArbAxisRotation(theta, ax, pt) | source code
GetAcceptor2FeatVects(conf, featAtoms, scale=1.5) Get the direction vectors for Acceptor of type 2 This is the acceptor with two adjacent heavy atoms. | source code
_GetTetrahedralFeatVect(conf, aid, scale) | source code
GetDonor3FeatVects(conf, featAtoms, scale=1.5) Get the direction vectors for Donor of type 3 This is a donor with three heavy atoms as neighbors. | source code
GetAcceptor3FeatVects(conf, featAtoms, scale=1.5) Get the direction vectors for Donor of type 3 This is a donor with three heavy atoms as neighbors. | source code
_findHydAtoms(nbrs, atomNames) | source code
_checkPlanarity(conf, cpt, nbrs, tol=0.001) | source code
GetDonor2FeatVects(conf, featAtoms, scale=1.5) Get the direction vectors for Donor of type 2 This is a donor with two heavy atoms as neighbors. | source code
GetDonor1FeatVects(conf, featAtoms, scale=1.5) Get the direction vectors for Donor of type 1 This is a donor with one heavy atom. | source code
GetAcceptor1FeatVects(conf, featAtoms, scale=1.5) Get the direction vectors for Acceptor of type 1 This is a acceptor with one heavy atom neighbor. | source code

Variables | [hide private]
| Complex0 = ``'``F``'``
| Complex16 = ``'``F``'``
| Complex32 = ``'``F``'``
| Complex64 = ``'``D``'``
| Complex8 = ``'``F``'``
| Float0 = ``'``f``'``
| Float16 = ``'``f``'``
| Float32 = ``'``f``'``
| Float64 = ``'``d``'``
| Float8 = ``'``f``'``
| Int0 = ``'``1``'``
| Int16 = ``'``s``'``
| Int32 = ``'``i``'``
| Int8 = ``'``1``'``
| absolute = `<ufunc 'absolute'>`
| add = `<ufunc 'add'>`
| arccos = `<ufunc 'arccos'>`
| arccosh = `<ufunc 'arccosh'>`
| arcsin = `<ufunc 'arcsin'>`
| arcsinh = `<ufunc 'arcsinh'>`
| arctan = `<ufunc 'arctan'>`
| arctan2 = `<ufunc 'arctan2'>`
| arctanh = `<ufunc 'arctanh'>`
| bitwise_and = `<ufunc 'bitwise_and'>`
| bitwise_or = `<ufunc 'bitwise_or'>`
| bitwise_xor = `<ufunc 'bitwise_xor'>`
| ceil = `<ufunc 'ceil'>`
| conjugate = `<ufunc 'conjugate'>`
| cos = `<ufunc 'cos'>`
| cosh = `<ufunc 'cosh'>`
| divide = `<ufunc 'divide'>`
| divide_safe = `<ufunc 'divide_safe'>`
| e = `2.71828182846`
| equal = `<ufunc 'equal'>`
| exp = `<ufunc 'exp'>`
| fabs = `<ufunc 'fabs'>`
| floor = `<ufunc 'floor'>`
| floor_divide = `<ufunc 'floor_divide'>`
| fmod = `<ufunc 'fmod'>`
| greater = `<ufunc 'greater'>`
| greater_equal = `<ufunc 'greater_equal'>`
| hypot = `<ufunc 'hypot'>`
| invert = `<ufunc 'invert'>`
| left_shift = `<ufunc 'left_shift'>`
| less = `<ufunc 'less'>`
| less_equal = `<ufunc 'less_equal'>`
| log = `<ufunc 'log'>`
| log10 = `<ufunc 'log10'>`
| logical_and = `<ufunc 'logical_and'>`
| logical_not = `<ufunc 'logical_not'>`
| logical_or = `<ufunc 'logical_or'>`
| logical_xor = `<ufunc 'logical_xor'>`
| maximum = `<ufunc 'maximum'>`
| minimum = `<ufunc 'minimum'>`
| multiply = `<ufunc 'multiply'>`
| negative = `<ufunc 'negative'>`
| not_equal = `<ufunc 'not_equal'>`
| pi = `3.14159265359`
| power = `<ufunc 'power'>`
| remainder = `<ufunc 'remainder'>`
| right_shift = `<ufunc 'right_shift'>`
| sin = `<ufunc 'sin'>`
| sinh = `<ufunc 'sinh'>`
| sqrt = `<ufunc 'sqrt'>`
| subtract = `<ufunc 'subtract'>`
| tan = `<ufunc 'tan'>`
| tanh = `<ufunc 'tanh'>`
| true_divide = `<ufunc 'true_divide'>`

Function Details | [hide private]

### findNeighbors(atomId, adjMat) | source code
    Find the IDs of the neighboring atom IDs

    ARGUMENTS:
    atomId - atom of interest
    adjMat - adjacency matrix for the compound

### GetAromaticFeatVects(conf, featAtoms, featLoc, scale=1.5) | source code
    Compute the direction vector for an aromatic feature

    ARGUMENTS:
       conf - a conformer
       featAtoms - list of atom IDs that make up the feature
       featLoc - location of the aromatic feature specified as point3d
       scale - the size of the direction vector

### GetAcceptor2FeatVects(conf, featAtoms, scale=1.5) | source code
    Get the direction vectors for Acceptor of type 2

    This is the acceptor with two adjacent heavy atoms. We will special case a few things here.
    If the acceptor atom is an oxygen we will assume a sp3 hybridization
    the acceptor directions (two of them)
    reflect that configurations. Otherwise the direction vector in plane with the neighboring
    heavy atoms

    ARGUMENTS:
        featAtoms - list of atoms that are part of the feature
        scale - length of the direction vector

### GetDonor3FeatVects(conf, featAtoms, scale=1.5) | source code
    Get the direction vectors for Donor of type 3

    This is a donor with three heavy atoms as neighbors. We will assume
    a tetrahedral arrangement of these neighbors. So the direction we are seeking
    is the last fourth arm of the sp3 arrangment

    ARGUMENTS:
      featAtoms - list of atoms that are part of the feature
      scale - length of the direction vector

### GetAcceptor3FeatVects(conf, featAtoms, scale=1.5) | source code
    Get the direction vectors for Donor of type 3

    This is a donor with three heavy atoms as neighbors. We will assume
    a tetrahedral arrangement of these neighbors. So the direction we are seeking
    is the last fourth arm of the sp3 arrangment

    ARGUMENTS:
      featAtoms - list of atoms that are part of the feature
      scale - length of the direction vector

### GetDonor2FeatVects(conf, featAtoms, scale=1.5) | source code
    Get the direction vectors for Donor of type 2

    This is a donor with two heavy atoms as neighbors. The atom may are may not have
    hydrogen on it. Here are the situations with the neighbors that will be considered here
      1. two heavy atoms and two hydrogens: we will assume a sp3 arrangement here
      2. two heavy atoms and one hydrogen: this can either be sp2 or sp3
      3. two heavy atoms and no hydrogens

    ARGUMENTS:
      featAtoms - list of atoms that are part of the feature
      scale - length of the direction vector

### GetDonor1FeatVects(conf, featAtoms, scale=1.5) | source code
    Get the direction vectors for Donor of type 1

    This is a donor with one heavy atom. It is not clear where we should we should be putting the
    direction vector for this. It should probably be a cone. In this case we will just use the
    direction vector from the donor atom to the heavy atom

    ARGUMENTS:

      featAtoms - list of atoms that are part of the feature
      scale - length of the direction vector

### GetAcceptor1FeatVects(conf, featAtoms, scale=1.5) | source code
    Get the direction vectors for Acceptor of type 1

    This is a acceptor with one heavy atom neighbor. There are two possibilities we will
    consider here
    1. The bond to the heavy atom is a single bond e.g. CO
       In this case we don't know the exact direction and we just use the inversion of this bond direction
       and mark this direction as a 'cone'
    2. The bond to the heavy atom is a double bond e.g. C=O
       In this case the we have two possible direction except in some special cases e.g. SO2
       where again we will use bond direction

    ARGUMENTS:
      featAtoms - list of atoms that are part of the feature
      scale - length of the direction vector