Module Spyder :: Class HaddockGuruInterface

Class HaddockGuruInterface

          object --+        
                   |        
HaddockEasyInterface --+    
                       |    
  HaddockExpertInterface --+
                           |
                          HaddockGuruInterface

Spyder-generated class

module haddock

file /home/sjoerd/data/Spyder-devel/haddock/haddock.spy

Description

Web form for the HADDOCK server Guru Interface

Wiki

http://www.spyderware.nl/wiki/classes/HaddockGuruInterface

Validate block

>>>            
if par_nonbonded != None: assert par_nonbonded in ("PROLSQ", "PARMALLH6", "PARALLHDG", "OPLSX")
if dielec != None: assert dielec in ("cdie", "rdie")
assert w_vdw == None or len(w_vdw) == 3
assert w_elec == None or len(w_elec) == 3
assert w_dist == None or len(w_dist) == 3
assert w_sani == None or len(w_sani) == 3
assert w_dani == None or len(w_dani) == 3
assert w_vean == None or len(w_vean) == 3
assert w_cdih == None or len(w_cdih) == 3
assert w_sym == None or len(w_sym) == 3
assert w_bsa == None or len(w_bsa) == 3
assert w_deint == None or len(w_deint) == 3
assert w_desolv == None or len(w_desolv) == 3
if firstwater != None: assert firstwater in ("yes", "no")
if solvate_method != None: assert solvate_method in ("db", "restraints", "pnt")
assert ncssegments == None or len(ncssegments) <= 5    
assert c2segments == None or len(c2segments) <= 10
assert c3segments == None or len(c3segments) <= 5
assert c4segments == None or len(c4segments) == 0
assert c5segments == None or len(c5segments) <= 1
assert auto_passive_radius >= 0 and auto_passive_radius <= 1000               
>>>

Form block

>>>            
OPTION par_nonbonded "PROLSQ", "PARMALLH6", "PARALLHDG", "OPLSX"
OPTION dielec "cdie", "rdie"
LENGTH w_vdw 3
LENGTH w_elec 3
LENGTH w_dist 3
LENGTH w_sani 3
LENGTH w_dani 3
LENGTH w_vean 3
LENGTH w_cdih 3
LENGTH w_sym 3
LENGTH w_bsa 3
LENGTH w_deint 3
LENGTH w_desolv 3
OPTION firstwater "yes", "no"
OPTION solvate_method "db", "restraints", "pnt"               
>>>

Converters

Can be converted to:

HaddockExpertInterface
- CAST
HaddockEasyInterface
- CAST
HaddockRunParameters
- view converter (#1)
HaddockPredictionInterface
- CAST

Can be converted from:

Instance Methods

[hide private]

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __init__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Instance Variables

[hide private]

*String username

*String password

Bool xplortodiana = False

SymmetrySpecification ncs = dict(on= False, constant= 1)

*LabeledRangePairArray ncssegments

SymmetrySpecification symmetry = dict(on= False, constant= 10)

*LabeledRangePairArray c2segments

*LabeledRangeTripleArray c3segments

*LabeledRangeQuadrupleArray c4segments

*LabeledRangeQuintupleArray c5segments

*LabeledRangeTripleArray s3segments

ExtStageConstants unamb = 0, 2, (10, 10, 50, 50)

ExtStageConstants amb = 0, 2, (10, 10, 50, 50)

ExtStageConstants hbond = 1, 2, (10, 10, 50, 50)

StageConstants dihedrals = 5, 5, 50, 200

Bool air_scaling = False

Integer tot_unamb = 25

Integer tot_amb = 0

StageConstants mrswi = 0.5, 0.5, 0.5, 0.5

StageConstants rswi = 0.5, 0.5, 0.5, 0.5

StageConstants masy = -1,-1,-0.1,-0.1

StageConstants asy = 1, 1, 0.1, 0.1

KarplusConstants c1 = False, 6.98,-1.38, 1.72,-60, (0, 0.2, 1, 1)

KarplusConstants c2 = False, 6.98,-1.38, 1.72,-120, (0, 0.2, 1, 1)

KarplusConstants c3 = False, 6.98,-1.38, 1.72,-120, (0, 0.2, 1, 1)

KarplusConstants c4 = False, 6.98,-1.38, 1.72,-120, (0, 0.2, 1, 1)

KarplusConstants c5 = False, 6.98,-1.38, 1.72,-120, (0, 0.2, 1, 1)

RDCInterface rdc1 = "NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), ...

RDCInterface rdc2 = "NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), ...

RDCInterface rdc3 = "NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), ...

RDCInterface rdc4 = "NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), ...

RDCInterface rdc5 = "NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), ...

DANIInterface dan1 = "NO", (0, 2, (1, 5, 10, 10)), 9.771, 1.557, 0.455, 599....

DANIInterface dan2 = "NO", (0, 1, (1, 5, 10, 10)), 9.84,-1.35, 0.308, 599.91...

DANIInterface dan3 = "NO", (1, 1, (1, 5, 10, 10)), 9.84,-1.35, 0.308, 599.91...

DANIInterface dan4 = "NO", (0, 2, (1, 5, 10, 10)), 9.84,-1.35, 0.308, 599.91...

DANIInterface dan5 = "NO", (0, 2, (1, 5, 10, 10)), 9.84,-1.35, 0.308, 599.91...

String par_nonbonded = "OPLSX"

Bool dihedflag = True

Bool elecflag_0 = True

Bool elecflag_1 = True

String dielec = "cdie"

Float inter_rigid = 1

ScalingConstants scaling_init = 0.001, 0.001, 0.05

ScalingConstants scaling_fin = 0.001, 1, 1

FloatArray w_vdw = 0.01, 1, 1

FloatArray w_elec = 1, 1, 0.2

FloatArray w_dist = 0.01, 0.1, 0.1

FloatArray w_sani = 0.1, 0.1, 0.1

FloatArray w_dani = 0.01, 0.1, 0.1

FloatArray w_vean = 0.1, 0.1, 0.1

FloatArray w_cdih = 0, 0, 0

FloatArray w_sym = 0.1, 0.1, 0.1

FloatArray w_bsa = -0.01,-0.01, 0

FloatArray w_deint = 0, 0, 0

FloatArray w_desolv = 1, 1, 1

Integer skip_struc = 0

Bool crossdock = True

Bool ensemble_multiply = False

Bool randorien = True

Bool rigidmini = True

Bool rigidtrans = True

Integer iniseed = 917

Integer tadhigh_t = 2000

Integer tadinit1_t = 2000

Integer tadfinal1_t = 500

Integer tadinit2_t = 1000

Integer tadfinal2_t = 50

Integer tadinit3_t = 500

Integer tadfinal3_t = 50

Float timestep = 0.002

Integer tadfactor = 8

Integer initiosteps = 500

Integer cool1_steps = 500

Integer cool2_steps = 1000

Integer cool3_steps = 1000

String firstwater = "yes"

Integer waterheatsteps = 100

Integer watersteps = 1250

Integer watercoolsteps = 500

Bool calcdesolv = False

String solvate_method = "db"

Float water_restraint_initial = 5

Float water_restraint_cutoff = 5

Float water_restraint_scale = 25

Float water_tokeep = 0.25

Float water_randfrac = 0

Float water_surfcutoff = 8

Bool water_analysis = False

Bool transwater = True

Integer waterensemble = 1

Integer anastruc_1 = 200

Float dist_hb = 2.5

Float dist_nb = 3.9

Bool keepwater = False

Delete (password)

Delete (username)

Inherited from HaddockExpertInterface

Delete (form)

Delete (p1)

Delete (p2)

Delete (validate)

Float auto_passive_radius = 6.5

Float clust_rmsd = 7.5

Integer clust_size = 4

Bool cmrest = False

Bool create_narestraints = True

Bool delenph = True

*File dihedralfile

Float epsilon = 10

*File hbondfile

Float kcont = 1

Float ksurf = 1

Float ncvpart = 2

Bool noecv = True

Integer ntrials = 5

HaddockPartnerInterface p1

HaddockPartnerInterface p2

Bool ranair = False

Bool rotate180_0 = True

Bool rotate180_1 = False

Bool smoothing = False

String solvent = "water"

Integer structures_0 = 1000

Integer structures_1 = 200

Bool surfrest = False

*File tblfile

*File unambigtblfile

Bool waterdock = False

Integer waterrefine = 200

Inherited from HaddockEasyInterface

*String runname

Properties

[hide private]

Inherited from object: __class__

Instance Variable Details

[hide private]

rdc1

Type:: RDCInterface

Value:

"NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), (10, 40, 40, 40
), (0.25, 2.5, 10, 10), (2.5, 10, 10, 10)

rdc2

Type:: RDCInterface

Value:

"NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), (10, 40, 40, 40
), (0.25, 2.5, 10, 10), (2.5, 10, 10, 10)

rdc3

Type:: RDCInterface

Value:

"NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), (10, 40, 40, 40
), (0.25, 2.5, 10, 10), (2.5, 10, 10, 10)

rdc4

Type:: RDCInterface

Value:

"NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), (10, 40, 40, 40
), (0.25, 2.5, 10, 10), (2.5, 10, 10, 10)

rdc5

Type:: RDCInterface

Value:

"NO", 0.4, 8, (0, 2, (0.1, 1, 1, 1)), (1, 10, 40, 40), (10, 40, 40, 40
), (0.25, 2.5, 10, 10), (2.5, 10, 10, 10)

dan1

Type:: DANIInterface

Value:

"NO", (0, 2, (1, 5, 10, 10)), 9.771, 1.557, 0.455, 599.91, 60.82

dan2

Type:: DANIInterface

Value:

"NO", (0, 1, (1, 5, 10, 10)), 9.84,-1.35, 0.308, 599.91, 60.82

dan3

Type:: DANIInterface

Value:

"NO", (1, 1, (1, 5, 10, 10)), 9.84,-1.35, 0.308, 599.91, 60.82

dan4

Type:: DANIInterface

Value:

"NO", (0, 2, (1, 5, 10, 10)), 9.84,-1.35, 0.308, 599.91, 60.82

dan5

Type:: DANIInterface

Value:

"NO", (0, 2, (1, 5, 10, 10)), 9.84,-1.35, 0.308, 599.91, 60.82