Package AutoDockTools :: Package Utilities24 :: Module compute_rms_between_methods

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Module compute_rms_between_methods

source code

Functions

[hide private]

dist(coords1, coords2)
return distance between two atoms, a and b.

usage()
Print helpful, accurate usage statement to stdout.

Variables

[hide private]

refdirectory = None

directory = None

rms_tolerance = 1.5

verbose = None

outputfilename = "summary_rms_results"

ref_dlg_list = glob.glob(refdirectory+ '/*.dlg')

ref_d = Docking()

coords = ref_d.ligMol.allAtoms.coords [:]

ref_LE_coords = ref_d.ligMol.allAtoms.coords [:]

ref_largest = ref_d.clusterer.clustering_dict [rms_tolerance] [0]

ref_LC_coords = ref_d.ligMol.allAtoms.coords [:]

dlg_list = glob.glob(directory+ '/*.dlg')

d = Docking()

clust0 = d.clusterer.clustering_dict [rms_tolerance] [0]

c = clust0 [0]

LE_coords = d.ligMol.allAtoms.coords [:]

rms_LE_LE = c.getRMSD(ref_LE_coords)

dist_LE_LE = dist(ref_LE_coords, LE_coords)

rms_LE_LC = c.getRMSD(ref_LC_coords)

dist_LE_LC = dist(ref_LC_coords, LE_coords)

largest = d.clusterer.clustering_dict [rms_tolerance] [0]

conf_LC = largest [0]

LC_coords = d.ligMol.allAtoms.coords [:]

rms_LC_LE = conf_LC.getRMSD(ref_LE_coords)

dist_LC_LE = dist(LC_coords, ref_LE_coords)

rms_LC_LC = conf_LC.getRMSD(ref_LC_coords)

dist_LC_LC = dist(LC_coords, ref_LC_coords)

first = not os.path.exists(outputfilename)

fptr = open(outputfilename, 'a')

ostr = "% 10s,% 10.4f,% 10.4f,% 10.4f,% 10.4f,% 10.4f,% 10....

Function Details

[hide private]

dist(coords1, coords2)

source code

return distance between two atoms, a and b.

usage()

source code

Print helpful, accurate usage statement to stdout.

Variables Details

[hide private]

refdirectory

None

Value:

None

rms_tolerance

None

Value:

1.5

verbose

None

Value:

None

outputfilename

None

Value:

"summary_rms_results"

ref_dlg_list

None

Value:

glob.glob(refdirectory+ '/*.dlg')

ref_d

None

Value:

Docking()

coords

None

Value:

ref_d.ligMol.allAtoms.coords [:]

ref_LE_coords

None

Value:

ref_d.ligMol.allAtoms.coords [:]

ref_largest

None

Value:

ref_d.clusterer.clustering_dict [rms_tolerance] [0]

ref_LC_coords

None

Value:

ref_d.ligMol.allAtoms.coords [:]

dlg_list

None

Value:

glob.glob(directory+ '/*.dlg')

d

None

Value:

Docking()

clust0

None

Value:

d.clusterer.clustering_dict [rms_tolerance] [0]

c

None

Value:

clust0 [0]

LE_coords

None

Value:

d.ligMol.allAtoms.coords [:]

rms_LE_LE

None

Value:

c.getRMSD(ref_LE_coords)

dist_LE_LE

None

Value:

dist(ref_LE_coords, LE_coords)

rms_LE_LC

None

Value:

c.getRMSD(ref_LC_coords)

dist_LE_LC

None

Value:

dist(ref_LC_coords, LE_coords)

largest

None

Value:

d.clusterer.clustering_dict [rms_tolerance] [0]

conf_LC

None

Value:

largest [0]

LC_coords

None

Value:

d.ligMol.allAtoms.coords [:]

rms_LC_LE

None

Value:

conf_LC.getRMSD(ref_LE_coords)

dist_LC_LE

None

Value:

dist(LC_coords, ref_LE_coords)

rms_LC_LC

None

Value:

conf_LC.getRMSD(ref_LC_coords)

dist_LC_LC

None

Value:

dist(LC_coords, ref_LC_coords)

first

None

Value:

not os.path.exists(outputfilename)

fptr

None

Value:

open(outputfilename, 'a')

ostr

None

Value:

"% 10s,% 10.4f,% 10.4f,% 10.4f,% 10.4f,% 10.4f,% 10.4f,% 10.4f,% 10.4f
,\n" %(d.ligMol.name, rms_LE_LE, dist_LE_LE, rms_LE_LC, dist_LE_LC, rm
s_LC_LC, dist_LC_LC, rms_LC_LE, dist_LC_LE)