Package Chem :: Package Pharm2D :: Module Utils

Module Utils

utility functionality for the 2D pharmacophores code

See Docs/Chem/Pharm2D.triangles.jpg for an illustration of the way
pharmacophores are broken into triangles and labelled.

See Docs/Chem/Pharm2D.signatures.jpg for an illustration of bit
numbering

Functions

[hide private]

GetTriangles(nPts)
returns a tuple with the distance indices for...

source code

_fact(x)

source code

BinsTriangleInequality(d1, d2, d3)
checks the triangle inequality for combinations of distance bins.

source code

ScaffoldPasses(combo, bins=None)
checks the scaffold passed in to see if all...

source code

NumCombinations(nItems, nSlots)
returns the number of ways to fit nItems into nSlots We assume that (x,y) and (y,x) are equivalent, and (x,x) is allowed.

source code

CountUpTo(nItems, nSlots, vs, idx=0, startAt=0)
Figures out where a given combination of indices would...

source code

GetIndexCombinations(nItems, nSlots, slot=0, lastItemVal=0)
Generates all combinations of nItems in nSlots without including...

source code

GetAllCombinations(choices, noDups=1, which=0)
Does the combinatorial explosion of the possible combinations of the elements of _choices_.

source code

UniquifyCombinations(combos)
uniquifies the combinations in the argument...

source code

GetPossibleScaffolds(nPts, bins)
gets all realizable scaffolds (passing the triangle inequality) with the...

source code

Variables

[hide private]

nPointDistDict = {2: ((0, 1)), 3: ((0, 1), (0, 2), (1, 2)), 4:...

nDistPointDict = {1: 2, 3: 3, 5: 4, 7: 5, 9: 6, 11: 7, 13: 8, ...

_trianglesInPharmacophore = {}

_numCombDict = {}

_verbose = 0

_countCache = {}

_indexCombinations = {}

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]

GetTriangles(nPts)

source code

returns a tuple with the distance indices for
triangles composing an nPts-pharmacophore

BinsTriangleInequality(d1, d2, d3)

source code

checks the triangle inequality for combinations
of distance bins.

the general triangle inequality is:
   d1 + d2 >= d3
the conservative binned form of this is:
   d1(upper) + d2(upper) >= d3(lower)

ScaffoldPasses(combo, bins=None)

source code

checks the scaffold passed in to see if all
contributing triangles can satisfy the triangle inequality

the scaffold itself (encoded in combo) is a list of binned distances

NumCombinations(nItems, nSlots)

source code

returns the number of ways to fit nItems into nSlots

We assume that (x,y) and (y,x) are equivalent, and
(x,x) is allowed.

General formula is, for N items and S slots:
  res = (N+S-1)! / ( (N-1)! * S! )

CountUpTo(nItems, nSlots, vs, idx=0, startAt=0)

source code

Figures out where a given combination of indices would
 occur in the combinatorial explosion generated by _GetIndexCombinations_

 **Arguments**

   - nItems: the number of items to distribute

   - nSlots: the number of slots in which to distribute them

   - vs: a sequence containing the values to find

   - idx: used in the recursion

   - startAt: used in the recursion
  
**Returns**

   an integer

GetIndexCombinations(nItems, nSlots, slot=0, lastItemVal=0)

source code

Generates all combinations of nItems in nSlots without including
  duplicates

**Arguments**

  - nItems: the number of items to distribute

  - nSlots: the number of slots in which to distribute them

  - slot: used in recursion

  - lastItemVal: used in recursion

**Returns**

  a list of lists

GetAllCombinations(choices, noDups=1, which=0)

source code

Does the combinatorial explosion of the possible combinations
of the elements of _choices_.

**Arguments**

  - choices: sequence of sequences with the elements to be enumerated

  - noDups: (optional) if this is nonZero, duplicates will not be included
    in the values returned

  - noDups: (optional) if this is nonzero, results with duplicates,
    e.g. (1,1,0), will not be generated

  - which: used in recursion

**Returns**
  
  a list of lists

UniquifyCombinations(combos)

source code

uniquifies the combinations in the argument

**Arguments**:

  - combos: a sequence of sequences

**Returns**

  - a list of tuples containing the unique combos

**Notes**

  - the order of the indices of the individual combos in the
    results list is modified (they are sorted)

GetPossibleScaffolds(nPts, bins)

source code

gets all realizable scaffolds (passing the triangle inequality) with the
given number of points and returns them as a list of tuples

Variables Details

[hide private]

nPointDistDict

Value:

{2: ((0, 1)),
 3: ((0, 1), (0, 2), (1, 2)),
 4: ((0, 1), (0, 2), (0, 3), (1, 2), (2, 3)),
 5: ((0, 1), (0, 2), (0, 3), (0, 4), (1, 2), (2, 3), (3, 4)),
 6: ((0, 1),
     (0, 2),
     (0, 3),
     (0, 4),
...

nDistPointDict

Value:

{1: 2, 3: 3, 5: 4, 7: 5, 9: 6, 11: 7, 13: 8, 15: 9, 17: 10}