Package schrodinger :: Package application :: Package bioluminate :: Package patch_utils :: Module patch_finder

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Module patch_finder

Classes

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Patch
Data about a single patch.

ResData
Data about a single residue.

ResidueDictionary
A dictionary that stores data about residues in a single structure.

ProteinProperties
Calculates protein properties for display on the Properties tab

PreAnalyzer
Perform patch finding calculations that only need to be done once per structure.

PatchFinder
Find surface patches using the output of PreAnalyzer.

PatchFinderRunner
An object used to run the PatchFinder analysis in a separate thread.

Functions

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_smooth_grid_vals(vpos, apos, aval, wfcn=u'ele', rcutoff=10.0, verbose=True)
wrapper function to call smooth_grid_values in msurfext -> ensures that all parameters are set properly.

_set_vertex_colors(vtxvals, clrscheme=((255, 255, 255), (0, 0, 0)), clrvals=(0.0, 1.0))
return for each vertex point a corresponding vertex color based on the smoothed vertex values.

float

triangle_area(coords)
Calculate the area of a triangle defined by three vertices

tuple

launch_pre_analysis(struc, asl)
Launch a pre-analysis job under job control.

Variables

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REGION_LABELS = [u'HFR1', u'HFR2', u'HFR3', u'HFR4', u'H1', u'...

SURF_NAME = u'Protein Patches'

CLOGP_PROP = u'r_psp_ClogP'

CLOGP_ITERS = 30

PARTIAL_CHARGE_PROP = u'r_m_charge1'

PARTIAL_CHARGE_ITERS = 30

ZYGG_ADD = 4.25

_pre_analyze_path = '/scr/buildbot/savedbuilds/NB/2016-4/build...

PRE_ANALYZE_PATH = u'/scr/buildbot/savedbuilds/NB/2016-4/build...

MIN_RES_CONTRIBUTION = {<PatchType.positive: ('Positive', 'pos...

DFLTCLRS = ((255, 255, 255), (0, 0, 0))

DFLTVALS = (0.0, 1.0)

__package__ = 'schrodinger.application.bioluminate.patch_utils'

Function Details

[hide private]

_smooth_grid_vals(vpos, apos, aval, wfcn=`u'ele'`, rcutoff=10.0, verbose=True)


wrapper function to call smooth_grid_values in msurfext -> ensures that all
parameters are set properly.
Input:
    @param vpos: input vertex coordinates (x,y,z for each entry is expected)
    @type  vpos: list/tuple
    @param apos: input atom positions (x,y,z format)
    @type  apos: list/tuple
    @param aval: atom-specific values (e.g. charges, hydrophobicity)
    @type  aval: list/tuple

Option:
    @param wfcn: specify the type of smoothing - ('ele' for partial charge
                 smoothing, 'lipo' for lipophilic data smoothing)
    @type  wfcn: string
    @param rcutoff: distance radius - specify, how far out the atom value
                    should be "felt". Change only, if you know what you
                    are doing.
    @type  rcutoff: float
    @param verbose: verbosity flag

@rtype:  list
@return: list of length vpos with smoothed values

_set_vertex_colors(vtxvals, clrscheme=`((`255`,` 255`,` 255`),` `(`0`,` 0`,` 0`))`, clrvals=`(`0.0`,` 1.0`)`)


return for each vertex point a corresponding vertex color based on the
smoothed vertex values.
Input:
    @param vtxvals: smoothed vertex values
    @type  vtxvals: list/tuple

    Option:
        @param clrcheme: list/tuple of reference colors (RGB for each entry)
        @param clrvals:  list/tuple of reference values

triangle_area(coords)

Calculate the area of a triangle defined by three vertices

Parameters:

coords (list) - A list of (x, y, z) coordinates for each vertex of the triangle, where each coordinate is a numpy array.

Returns: float

The area of the specified triangle

Note: The formula used here is taken from http://mathworld.wolfram.com/TriangleArea.html

launch_pre_analysis(struc, asl)

Launch a pre-analysis job under job control. This method will return as soon as the job has been launched.

Parameters:

struc (schrodinger.structure.Structure) - The structure to analyze
asl (str) - An ASL describing atoms of struc to analyze

Returns: tuple

A tuple of:

A job object for the running job (schrodinger.job.jobcontrol.Job)
The basename for the job output (str)
The job directory (str)
The job log file (str)

Variables Details

[hide private]

REGION_LABELS

Value:

[u'HFR1',
 u'HFR2',
 u'HFR3',
 u'HFR4',
 u'H1',
 u'H2',
 u'H3',
 u'CH1',
...

_pre_analyze_path

Value:

'/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6/lib/Linux-
x86_64/lib/python2.7/site-packages/schrodinger/application/bioluminate
/patch_utils'

PRE_ANALYZE_PATH

Value:

u'/scr/buildbot/savedbuilds/NB/2016-4/build-126/mmshare-v3.6/lib/Linux
-x86_64/lib/python2.7/site-packages/schrodinger/application/bioluminat
e/patch_utils/pre_analyze.py'

MIN_RES_CONTRIBUTION

Value:

{<PatchType.positive: ('Positive', 'pos', 'eV')>: 5.0,
 <PatchType.negative: ('Negative', 'neg', 'eV')>: 5.0,
 <PatchType.hydrophobic: ('Hydrophobic', 'hyd', 'sLogP')>: 2.5}

Module patch_finder

_smooth_grid_vals(vpos, apos, aval, wfcn=u'ele', rcutoff=10.0, verbose=True)

_set_vertex_colors(vtxvals, clrscheme=((255, 255, 255), (0, 0, 0)), clrvals=(0.0, 1.0))

triangle_area(coords)

launch_pre_analysis(struc, asl)

REGION_LABELS

_pre_analyze_path

PRE_ANALYZE_PATH

MIN_RES_CONTRIBUTION

_smooth_grid_vals(vpos, apos, aval, wfcn=`u'ele'`, rcutoff=10.0, verbose=True)

_set_vertex_colors(vtxvals, clrscheme=`((`255`,` 255`,` 255`),` `(`0`,` 0`,` 0`))`, clrvals=`(`0.0`,` 1.0`)`)