Package AutoDockTools :: Package Utilities24 :: Module prepare_ligand

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Module prepare_ligand

source code

Functions

[hide private]

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

Variables

[hide private]

ligand_filename = None

verbose = None

add_bonds = False

repairs = ""

charges_to_add = 'gasteiger'

preserve_charge_types = ''

cleanup = "nphs_lps"

allowed_bonds = ""

root = 'auto'

outputfilename = None

check_for_fragments = False

bonds_to_inactivate = ""

inactivate_all_torsions = False

mode = 'automatic'

dict = None

mols = Read(ligand_filename)

mol = mols [0]

ctr = 1

preserved = {}

preserved_types = preserve_charge_types.split(',')

LPO = LigandPreparation(mol, mode, repairs, charges_to_add...

Function Details

[hide private]

usage()

source code

Print helpful, accurate usage statement to stdout.

Variables Details

[hide private]

ligand_filename

None

Value:

None

verbose

None

Value:

None

add_bonds

None

Value:

False

repairs

None

Value:

""

charges_to_add

None

Value:

'gasteiger'

preserve_charge_types

None

Value:

''

cleanup

None

Value:

"nphs_lps"

allowed_bonds

None

Value:

""

root

None

Value:

'auto'

outputfilename

None

Value:

None

check_for_fragments

None

Value:

False

bonds_to_inactivate

None

Value:

""

inactivate_all_torsions

None

Value:

False

mode

None

Value:

'automatic'

dict

None

Value:

None

mols

None

Value:

Read(ligand_filename)

mol

None

Value:

mols [0]

ctr

None

Value:

preserved

None

Value:

{}

preserved_types

None

Value:

preserve_charge_types.split(',')

LPO

None

Value:

LigandPreparation(mol, mode, repairs, charges_to_add, cleanup, allowed
_bonds, root, outputfilename= outputfilename, dict= dict, check_for_fr
agments= check_for_fragments, bonds_to_inactivate= bonds_to_inactivate
, inactivate_all_torsions= inactivate_all_torsions)