_calculate_mopac_desc(calcMopacDescList, mopac_input, mopac_tmp_file, st, nstructures, i)
Calculates the mopac descriptors for the given structure 'st'

_get_qikprop_cmd(options, structfile, qikprop_tmp_file)

_calculate_qikprop_desc(options, calcQikpropDescList, qikprop_cmd, qikprop_tmp_file, st, structfile, nstructures, i)
Calculates the qikprop descriptors for the given structure 'st'

_print_descriptors(options, calcTopoDescList, calcMopacDescList, calcQikpropDescList)

calculate_using_file(options, structfile)
Calculate molecular descriptors using structure file.

calculate_using_st(options, st)
Calculate molecular descriptors using given structure.

_do_cleanup()
Remove the temporary files created by mopac or qikprop

_get_maestro_type(value)

_export_to_mae(st, st_writer, do_topo, calcTopoDescList, descResults, skip_topo, do_mopac, calcMopacDescList, mopacResults, skip_mopac, do_qikprop, calcQikpropDescList, qikPropResults, skip_qikprop)
Exports calculated descriptors into Maestro format file

_export_to_csv(st, csv_writer, do_topo, calcTopoDescList, descResults, skip_topo, do_mopac, calcMopacDescList, mopacResults, skip_mopac, do_qikprop, calcQikpropDescList, qikPropResults, skip_qikprop)
Exports calculated descriptors into CSV format file

add_moldescriptors_options(parser, options=[TOPO,MOPAC,QIKPROP,OMAE,OCSV], group_options=True)
Adds common molecular descriptors options to a SingleDashOptionParser instance.

Variables

[hide private]

__doc__ = ...

nx = None
hash(x)

mopac_descriptors = False
hash(x)

debug = os.environ.has_key('SCHRODINGER_DESCRIPTOR_DEBUG')

verbose = False
hash(x)

VAN_DER_WAALS_VOLUME = {5: 17.875, 6: 22.449, 7: 15.599, 8: 11...

ELECTRONEGATIVITY = {5: 2.275, 6: 2.746, 7: 3.194, 8: 3.654, 9...

POLARIZABILITY = {5: 3.030, 6: 1.760, 7: 1.100, 8: 0.802, 9: 0...

COVALENT_RADIUS = {5: 0.83, 6: 0.68, 7: 0.68, 8: 0.68, 9: 0.64...

PEOE_INTERVAL = [-0.30,-0.25,-0.20,-0.15,-0.10,-0.05, 0, 0.05,...

ALOGP_INTERVAL = [-0.4,-0.20, 0, 0.10, 0.15, 0.20, 0.25, 0.30,...

MR_INTERVAL = [0.11, 0.26, 0.35, 0.39, 0.44, 0.485, 0.56,]

IS_CANVAS_LIC_CHECKED = False
hash(x)

CANVAS_LIC = None
hash(x)

descriptors = 'ZM1', 'First Zagreb', calculate_zagreb_m1, ('ZM...

valence_electrons = {}

cleanup_files = []

Function Details

[hide private]

calculate_zagreb_m1(st)

Decorators:

@trapError

calculate_zagreb_m1_valence_vertex_degree(st)

Decorators:

@trapError

calculate_zagreb_m2(st)

Decorators:

@trapError

calculate_zagreb_m2_valence_vertex_degree(st)

Decorators:

@trapError

calculate_polarity(st)

Decorators:

@trapError

calculate_simple_topological(st)

Decorators:

@trapError

calculate_harmonic_topological(st)

Decorators:

@trapError

calculate_geometric_topological(st)

Decorators:

@trapError

calculate_total_structure_connectivity(st)

Decorators:

@trapError

calculate_wiener(st)

Decorators:

@trapError

calculate_mean_wiener(st)

Decorators:

@trapError

calculate_radial_centric(st)

Decorators:

@trapError

calculate_xu(st)

Decorators:

@trapError

calculate_qindex(st)

Decorators:

@trapError

calculate_lprs(st)

Decorators:

@trapError

calculate_superpendentic(st)

Decorators:

@trapError

calculate_mean_square_distance_balaban(st)

Decorators:

@trapError

calculate_harary(st)

Decorators:

@trapError

calculate_smt(st)

Decorators:

@trapError

calculate_smt_valence_vertex_degree(st)

Decorators:

@trapError

calculate_pogliani(st)

Decorators:

@trapError

calculate_mean_distance_degree_deviation(st)

Decorators:

@trapError

calculate_ramification(st)

Decorators:

@trapError

calculate_gutman_molecular_topological(st)

Decorators:

@trapError

calculate_gutman_mti_valence_vertex_degrees(st)

Decorators:

@trapError

calculate_average_vertex_distance_degree(st)

Decorators:

@trapError

calculate_unipolarity(st)

Decorators:

@trapError

calculate_centralization(st)

Decorators:

@trapError

calculate_variation(st)

Decorators:

@trapError

_calculate_field_effect(st)

Decorators:

@trapError

calculate_mev(st)

Decorators:

@trapError

calculate_mepv(st)

Decorators:

@trapError

calculate_menv(st)

Decorators:

@trapError

calculate_eccentric_connectivity(st)

Decorators:

@trapError

calculate_eccentricity(st)

Decorators:

@trapError

calculate_average_eccentricity(st)

Decorators:

@trapError

calculate_eccentric(st)

Decorators:

@trapError

calculate_valence_connectivity_chi_0(st)

Decorators:

@trapError

calculate_valence_connectivity_chi_1(st)

Decorators:

@trapError

calculate_valence_connectivity_chi_2(st)

Decorators:

@trapError

calculate_valence_connectivity_chi_3(st)

Decorators:

@trapError

calculate_valence_connectivity_chi_4(st)

Decorators:

@trapError

calculate_valence_connectivity_chi_5(st)

Decorators:

@trapError

calculate_average_valence_connectivity_chi_0(st)

Decorators:

@trapError

calculate_average_valence_connectivity_chi_1(st)

Decorators:

@trapError

calculate_average_valence_connectivity_chi_2(st)

Decorators:

@trapError

calculate_average_valence_connectivity_chi_3(st)

Decorators:

@trapError

calculate_average_valence_connectivity_chi_4(st)

Decorators:

@trapError

calculate_average_valence_connectivity_chi_5(st)

Decorators:

@trapError

calculate_kier_benzene_likeliness(st)

Decorators:

@trapError

calculate_quasi_wiener(st)

Decorators:

@trapError

calculate_spanning_tree_number(st)

Decorators:

@trapError

calculate_first_mohar(st)

Decorators:

@trapError

calculate_second_mohar(st)

Decorators:

@trapError

_calculate_charge_term_matrix(st)

Decorators:

@trapError

calculate_topological_charge_index_order_n(st, distance)

Decorators:

@trapError

calculate_mean_topological_charge_index_order_n(st, distance)

Decorators:

@trapError

calculate_global_topological_charge(st)

Decorators:

@trapError

calculate_hyper_distance_path(st)

Decorators:

@trapError

calculate_reciprocal_hyper_distance_path(st)

Decorators:

@trapError

calculate_square_reciprocal_distance_sum(st)

Decorators:

@trapError

calculate_modified_randic_connectivity(st)

Decorators:

@trapError

calculate_kier_hall_electronegativity_index(st)

Decorators:

@trapError

_calculate_balaban_and_looping_centic(st)

Decorators:

@trapError

_calculate_sum_of_topological_distances(st)

Decorators:

@trapError

_get_scientific_matrix(st)

Decorators:

@trapError

calculate_wiener_z_matrix(st)

Decorators:

@trapError

calculate_wiener_electronegativity_matrix(st)

Decorators:

@trapError

calculate_wiener_mass_matrix(st)

Decorators:

@trapError

calculate_wiener_van_der_waals_matrix(st)

Decorators:

@trapError

calculate_wiener_polarizability_matrix(st)

Decorators:

@trapError

calculate_balaban_distance_connectivity(st)

Decorators:

@trapError

calculate_balaban_z_matrix(st)

Decorators:

@trapError

calculate_balaban_electronegativity_matrix(st)

Decorators:

@trapError

calculate_balaban_mass_matrix(st)

Decorators:

@trapError

calculate_balaban_van_der_waals_matrix(st)

Decorators:

@trapError

calculate_balaban_polarizability_matrix(st)

Decorators:

@trapError

calculate_topological_diameter(st)

Decorators:

@trapError

calculate_topological_radius(st)

Decorators:

@trapError

calculate_petitjean_shape(st)

Decorators:

@trapError

calculate_solvation_connectivity_indices_0(st)

Decorators:

@trapError

calculate_solvation_connectivity_indices_1(st)

Decorators:

@trapError

calculate_solvation_connectivity_indices_2(st)

Decorators:

@trapError

calculate_solvation_connectivity_indices_3(st)

Decorators:

@trapError

calculate_solvation_connectivity_indices_4(st)

Decorators:

@trapError

calculate_solvation_connectivity_indices_5(st)

Decorators:

@trapError

calculate_reciprocal_distance_randic(st)

Decorators:

@trapError

calculate_reciprocal_distance_square_randic(st)

Decorators:

@trapError

calculate_connectivity_chi_0(st)

Decorators:

@trapError

calculate_randic_connectivity(st)

Decorators:

@trapError

calculate_connectivity_chi_2(st)

Decorators:

@trapError

calculate_connectivity_chi_3(st)

Decorators:

@trapError

calculate_connectivity_chi_4(st)

Decorators:

@trapError

calculate_connectivity_chi_5(st)

Decorators:

@trapError

calculate_average_connectivity_chi_0(st)

Decorators:

@trapError

calculate_average_connectivity_chi_1(st)

Decorators:

@trapError

calculate_average_connectivity_chi_2(st)

Decorators:

@trapError

calculate_average_connectivity_chi_3(st)

Decorators:

@trapError

calculate_average_connectivity_chi_4(st)

Decorators:

@trapError

calculate_average_connectivity_chi_5(st)

Decorators:

@trapError

calculate_kier_alpha_modified_shape_1(st)

Decorators:

@trapError

calculate_kier_alpha_modified_shape_2(st)

Decorators:

@trapError

calculate_kier_alpha_modified_shape_3(st)

Decorators:

@trapError

calculate_kier_flexbility(st)

Decorators:

@trapError

calculate_path_walk_2(st)

Decorators:

@trapError

calculate_path_walk_3(st)

Decorators:

@trapError

calculate_path_walk_4(st)

Decorators:

@trapError

calculate_path_walk_5(st)

Decorators:

@trapError

calculate_e_state(st)

Decorators:

@trapError

calculate_chiral_count(st)

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

Decorators:

@trapError

calculate_ringcount(st, n)

Decorators:

@trapError

calculate_ringcount3(st)

Decorators:

@trapError

calculate_ringcount4(st)

Decorators:

@trapError

calculate_ringcount5(st)

Decorators:

@trapError

calculate_ringcount6(st)

Decorators:

@trapError

calculate_ringcount7(st)

Decorators:

@trapError

calculate_ringcount8(st)

Decorators:

@trapError

calculate_ringcount9(st)

Decorators:

@trapError

calculate_ringcount10(st)

Decorators:

@trapError

calculate_ringcount11(st)

Decorators:

@trapError

calculate_ringcount12(st)

Decorators:

@trapError

calculate_ringcount13(st)

Decorators:

@trapError

calculate_ringcount14(st)

Decorators:

@trapError

calculate_ringcount15(st)

Decorators:

@trapError

calculate_ringcount16(st)

Decorators:

@trapError

calculate_ringcount17(st)

Decorators:

@trapError

calculate_ringcount18(st)

Decorators:

@trapError

calculate_ringcount19(st)

Decorators:

@trapError

calculate_ringcount20(st)

Decorators:

@trapError

calculate_atomcount(st)

Decorators:

@trapError

calculate_bondcount(st)

Decorators:

@trapError

calculate_atom_rings_count(st)

Decorators:

@trapError

calculate_bond_rings_count(st)

Decorators:

@trapError

calculate_cyclomatic(st)

Decorators:

@trapError

calculate_num_ring_systems(st)

Decorators:

@trapError

calculate_normalized_num_ring_systems(st)

Decorators:

@trapError

calculate_total_ring_size(st)

Decorators:

@trapError

calculate_ring_perimeter(st)

Decorators:

@trapError

calculate_ring_bridge(st)

Decorators:

@trapError

calculate_molecule_cyclized_degree(st)

Decorators:

@trapError

calculate_ring_fusion_density(st)

Decorators:

@trapError

calculate_ring_complexity_index(st)

Decorators:

@trapError

calculate_ring_fusion_degree(st)

Decorators:

@trapError

calculate_van_der_waals_surface_area(st)


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 )

Decorators:

@trapError

_calculate_peoe(st, n)

Return atomic contribution based on Gasteiger charges. This is useful to capture direct electrostatic interactions.

Decorators:

@trapError

calculate_peoe1(st)

Decorators:

@trapError

calculate_peoe2(st)

Decorators:

@trapError

calculate_peoe3(st)

Decorators:

@trapError

calculate_peoe4(st)

Decorators:

@trapError

calculate_peoe5(st)

Decorators:

@trapError

calculate_peoe6(st)

Decorators:

@trapError

calculate_peoe7(st)

Decorators:

@trapError

calculate_peoe8(st)

Decorators:

@trapError

calculate_peoe9(st)

Decorators:

@trapError

calculate_peoe10(st)

Decorators:

@trapError

calculate_peoe11(st)

Decorators:

@trapError

calculate_peoe12(st)

Decorators:

@trapError

calculate_peoe13(st)

Decorators:

@trapError

calculate_peoe14(st)

Decorators:

@trapError

_calculate_alogp(st, n)

Return atomic contributions based on Alpgp values. This is useful to capture hydrophobic and hydrophillic effect.

Decorators:

@trapError

calculate_alogp1(st)

Decorators:

@trapError

calculate_alogp2(st)

Decorators:

@trapError

calculate_alogp3(st)

Decorators:

@trapError

calculate_alogp4(st)

Decorators:

@trapError

calculate_alogp5(st)

Decorators:

@trapError

calculate_alogp6(st)

Decorators:

@trapError

calculate_alogp7(st)

Decorators:

@trapError

calculate_alogp8(st)

Decorators:

@trapError

calculate_alogp9(st)

Decorators:

@trapError

calculate_alogp10(st)

Decorators:

@trapError

_calculate_mr(st, n)

Return atomic contribution based on MR values. This will help to capture polarizability.

Decorators:

@trapError

calculate_mr1(st)

Decorators:

@trapError

calculate_mr2(st)

Decorators:

@trapError

calculate_mr3(st)

Decorators:

@trapError

calculate_mr4(st)

Decorators:

@trapError

calculate_mr5(st)

Decorators:

@trapError

calculate_mr6(st)

Decorators:

@trapError

calculate_mr7(st)

Decorators:

@trapError

calculate_mr8(st)

Decorators:

@trapError

init(st)


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

_get_mopac_results(mopac_output, mopacCodes)

Decorators:

@trapError

calculate_using_file(options, structfile)

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_using_st(options, st)


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.

add_moldescriptors_options(parser, options=[TOPO,MOPAC,QIKPROP,OMAE,OCSV], group_options=True)


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

Variables Details

[hide private]

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, 16: 24.429, 17: 23.228, 26: 41.052, 27: 35.041, 2
8: 17.157, 29: 11.494, 30: 38.351, 35: 31.059, 50: 45.830, 53: 38.792,
}

ELECTRONEGATIVITY

Value:

{5: 2.275, 6: 2.746, 7: 3.194, 8: 3.654, 9: 4.000, 13: 1.714, 14: 2.13
8, 15: 2.515, 16: 2.957, 17: 3.475, 26: 2.000, 27: 2.000, 28: 2.000, 2
9: 2.033, 30: 2.223, 35: 3.219, 50: 2.298, 53: 2.778, 34: 2.55,}

POLARIZABILITY

Value:

{5: 3.030, 6: 1.760, 7: 1.100, 8: 0.802, 9: 0.557, 13: 6.800, 14: 5.38
0, 15: 3.630, 16: 2.900, 17: 2.180, 26: 8.400, 27: 7.500, 28: 6.800, 2
9: 6.100, 30: 7.100, 35: 3.050, 50: 7.700, 53: 5.350,}

COVALENT_RADIUS

Value:

{5: 0.83, 6: 0.68, 7: 0.68, 8: 0.68, 9: 0.64, 13: 1.350, 14: 1.200, 15
: 1.050, 16: 1.020, 17: 0.990, 26: 1.340, 27: 1.330, 28: 1.500, 29: 1.
520, 30: 1.450, 35: 1.210, 50: 1.460, 53: 1.400, 34: 1.22,}

PEOE_INTERVAL

Value:

[-0.30,-0.25,-0.20,-0.15,-0.10,-0.05, 0, 0.05, 0.10, 0.15, 0.20, 0.25,
 0.30,]

ALOGP_INTERVAL

Value:

[-0.4,-0.20, 0, 0.10, 0.15, 0.20, 0.25, 0.30, 0.4,]

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
...