Module Spyder :: Class HaddockMultiRunParameters

Class HaddockMultiRunParameters

          object --+                
                   |                
HaddockEasyInterface --+            
                       |            
  HaddockExpertInterface --+        
                           |        
        HaddockGuruInterface --+    
                               |    
            HaddockRunParameters --+
                                   |
                                  HaddockMultiRunParameters

Spyder-generated class

module haddock

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

Wiki

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

Validate block

>>>            
if p == None or len(p) == 0: raise HaddockValidationError("Please specify at least one partner molecule")               
>>>

Converters

Can be converted to:

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]

*HaddockPartnerParametersArray p

Delete (p1)

Delete (p2)

Inherited from HaddockRunParameters

HaddockPartnerInterface p1

HaddockPartnerInterface p2

Delete (dan1)

Delete (dan2)

Delete (dan3)

Delete (dan4)

Delete (dan5)

Delete (dihedralfile)

Delete (hbondfile)

Delete (rdc1)

Delete (rdc2)

Delete (rdc3)

Delete (rdc4)

Delete (rdc5)

Delete (tblfile)

Delete (unambigtblfile)

Delete (validate)

DANIInterface dan1

DANIInterface dan2

DANIInterface dan3

DANIInterface dan4

DANIInterface dan5

*String dihedraldata

*String hbonddata

RDCInterface rdc1

RDCInterface rdc2

RDCInterface rdc3

RDCInterface rdc4

RDCInterface rdc5

*String tbldata

*String unambigtbldata

Inherited from HaddockGuruInterface

Delete (password)

Delete (username)

Bool air_scaling = False

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

Integer anastruc_1 = 200

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)

*LabeledRangePairArray c2segments

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

*LabeledRangeTripleArray c3segments

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

*LabeledRangeQuadrupleArray c4segments

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

*LabeledRangeQuintupleArray c5segments

Bool calcdesolv = False

Integer cool1_steps = 500

Integer cool2_steps = 1000

Integer cool3_steps = 1000

Bool crossdock = True

String dielec = "cdie"

Bool dihedflag = True

StageConstants dihedrals = 5, 5, 50, 200

Float dist_hb = 2.5

Float dist_nb = 3.9

Bool elecflag_0 = True

Bool elecflag_1 = True

Bool ensemble_multiply = False

String firstwater = "yes"

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

Integer iniseed = 917

Integer initiosteps = 500

Float inter_rigid = 1

Bool keepwater = False

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

StageConstants mrswi = 0.5, 0.5, 0.5, 0.5

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

*LabeledRangePairArray ncssegments

String par_nonbonded = "OPLSX"

*String password

Bool randorien = True

Bool rigidmini = True

Bool rigidtrans = True

StageConstants rswi = 0.5, 0.5, 0.5, 0.5

*LabeledRangeTripleArray s3segments

ScalingConstants scaling_fin = 0.001, 1, 1

ScalingConstants scaling_init = 0.001, 0.001, 0.05

Integer skip_struc = 0

String solvate_method = "db"

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

Integer tadfactor = 8

Integer tadfinal1_t = 500

Integer tadfinal2_t = 50

Integer tadfinal3_t = 50

Integer tadhigh_t = 2000

Integer tadinit1_t = 2000

Integer tadinit2_t = 1000

Integer tadinit3_t = 500

Float timestep = 0.002

Integer tot_amb = 0

Integer tot_unamb = 25

Bool transwater = True

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

*String username

FloatArray w_bsa = -0.01,-0.01, 0

FloatArray w_cdih = 0, 0, 0

FloatArray w_dani = 0.01, 0.1, 0.1

FloatArray w_deint = 0, 0, 0

FloatArray w_desolv = 1, 1, 1

FloatArray w_dist = 0.01, 0.1, 0.1

FloatArray w_elec = 1, 1, 0.2

FloatArray w_sani = 0.1, 0.1, 0.1

FloatArray w_sym = 0.1, 0.1, 0.1

FloatArray w_vdw = 0.01, 1, 1

FloatArray w_vean = 0.1, 0.1, 0.1

Bool water_analysis = False

Float water_randfrac = 0

Float water_restraint_cutoff = 5

Float water_restraint_initial = 5

Float water_restraint_scale = 25

Float water_surfcutoff = 8

Float water_tokeep = 0.25

Integer watercoolsteps = 500

Integer waterensemble = 1

Integer waterheatsteps = 100

Integer watersteps = 1250

Bool xplortodiana = False

Inherited from HaddockExpertInterface

Delete (form)

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

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__