Package moldescriptors

Get number of chiral atoms in a structure. This will consider only "R" or "S" for chiral category as of now.

Return van der waals surface area of a molecule
vsa = sigma(vsa of each atom i)

    where

  vsa of each atom i = 4*pi*ri*ri - pi*ri*
                     sigma((rj*rj-(ri-dij)*(ri-dij))/dij)
                     for j running for each bond of atom i
        ri, rj -> van der waals radius of respective atoms
        dij    -> min(max(|ri-rj|,bij),ri+rj)
        bij    -> ideal bond length, bij = sij - oij
        sij    -> bond length of atom i and j calculated using
                  MMFF94
        oij    -> correction in bond length
                  ( 0 for single, 0.1 for aromatic, 0.2 for double,
                    0.3 for triple )

Initializes the structure:
 -> calculates adjacency matrix
 -> calculates distance matrix
 and other information

Calculate molecular descriptors using structure file. Based on the options passed it calculates Topological, Mopac or Qikprop descriptors and allows user to export descriptors into structure file and into CSV file.

Parameters:

• options (Object) - Containing values of all valid options.
• structfile (String) - Input structure file name.

  @rtype : None @return : None

Calculate molecular descriptors using given structure.
Based on the options passed it calculates Topological, Mopac or Qikprop
descriptors and returns the list of descriptors and their values.
Please note: In this function following options are not in use...
    options.list
    options.omae and
    options.ocsv

@type options: Object
@param options: Containing values of all valid options.

@type st: Structure object
@param st: Valid structure object

@rtype : List
@return : List of descriptors and their values.

Adds common molecular descriptors options to a SingleDashOptionParser
instance.

The options are specified as a list of module enums. Accepted values are
IN, TOPO, MOPAC, METHOD, NOGEOPT, QIKPROP, SLOW, LIST, OMAE, OCSV

@type parser: SingleDashOptionParser
@param parser:  Instance of SingleDashOptionParser.

@type options:  List
@param options:  List of module enums that indicate what options to
    add to the parser.

@type group_options:  Boolean
@param group_options:  If True then group the added options (via an
    optparse.OptionGroup) in the help message under the header 'Molecualr
    Descriptors Options'.

@rtype : None
@return : None

__doc__

Value:

""" A Python script that computes molecular indices for each input structure in the input file. The details of the descriptors implemented here is taken from 'Handbook of Molecular Descriptors by Mannhols, Kubinyi and Timmerman' . ...

VAN_DER_WAALS_VOLUME

Value:

{5: 17.875, 6: 22.449, 7: 15.599, 8: 11.494, 9: 9.203, 13: 36.511, 14: 31.976, 15: 26.522, ...

ELECTRONEGATIVITY

Value:

{5: 2.275, 6: 2.746, 7: 3.194, 8: 3.654, 9: 4.0, 13: 1.714, 14: 2.138, 15: 2.515, ...

POLARIZABILITY

Value:

{5: 3.03, 6: 1.76, 7: 1.1, 8: 0.802, 9: 0.557, 13: 6.8, 14: 5.38, 15: 3.63, ...

COVALENT_RADIUS

Value:

{5: 0.83, 6: 0.68, 7: 0.68, 8: 0.68, 9: 0.64, 13: 1.35, 14: 1.2, 15: 1.05, ...

PEOE_INTERVAL

Value:

[-0.3, -0.25, -0.2, -0.15, -0.1, -0.05, 0, 0.05, ...

descriptors

Value:

'ZM1', 'First Zagreb', calculate_zagreb_m1, ('ZM1V', 'First Zagreb ind ex by valence vertex degrees', calculate_zagreb_m1_valence_vertex_degr ee), ('ZM2', 'Second Zagreb', calculate_zagreb_m2), ('ZM2V', 'Second Z agreb index by valence vertex degrees', calculate_zagreb_m2_valence_ve rtex_degree), ('Pol', 'Polarity', calculate_polarity), ('NST', 'Narumi Simple Topological', calculate_simple_topological), ('NHT', 'Narumi H armonic Topological', calculate_harmonic_topological), ('NGT', 'Narumi Geometric Topological', calculate_geometric_topological), ('TSC', 'To ...