schrodinger.infra.fast3d module

Fast3D wrappers

class schrodinger.infra.fast3d.Canonicalizer

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

canonicalize(ct) → std::string

canonicalizePositions(ct)

next()

returns the next ‘this’ object

class schrodinger.infra.fast3d.Engine

FROZEN_ATOMS_PROPERTY_NAME = 's_f3d_frozen_atoms'

SCHRODINGER_CONFGENX_FEPGPGPU_MODE = 'SCHRODINGER_CONFGENX_FEPGPGPU_MODE'

SCHRODINGER_CONFGENX_IFDMD_MODE = 'SCHRODINGER_CONFGENX_IFDMD_MODE'

SCHRODINGER_CONFGENX_PHASE_MODE = 'SCHRODINGER_CONFGENX_PHASE_MODE'

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

acceptableHeavyAtomsOverlap

append()

appends another ‘this’ object

appendRepository(path)

autoIncreaseThreshold(arg2)

autoIncreaseThreshold() -> unsigned int

static dataDir() → std::string

static defaultCustomRepository() → std::string

static defaultRepositories() → stringvector

disableDuplicatesElimination()

disallowCisAmides(arg2)

disallowCisAmides() -> bool

invertNitrogens(arg2)

invertNitrogens() -> bool

static isFragmentLibraryFile(arg1) → bool

next()

returns the next ‘this’ object

partition(ct) → PyObject *

run(ct)

setDesiredNumberOfConformers(arg2)

stereo(arg2)

stereo() -> int

schrodinger.infra.fast3d.Engine_FROZEN_ATOMS_PROPERTY_NAME_get()

schrodinger.infra.fast3d.Engine_SCHRODINGER_CONFGENX_FEPGPGPU_MODE_get()

schrodinger.infra.fast3d.Engine_SCHRODINGER_CONFGENX_IFDMD_MODE_get()

schrodinger.infra.fast3d.Engine_SCHRODINGER_CONFGENX_PHASE_MODE_get()

schrodinger.infra.fast3d.Engine_dataDir() → std::string

schrodinger.infra.fast3d.Engine_defaultCustomRepository() → std::string

schrodinger.infra.fast3d.Engine_defaultRepositories() → stringvector

schrodinger.infra.fast3d.Engine_isFragmentLibraryFile(arg2) → bool

class schrodinger.infra.fast3d.Generalizer

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

appendRule(smarts, atomicNumber, numHydrogensToAdd)

generalize(arg2) → ChmMol

next()

returns the next ‘this’ object

class schrodinger.infra.fast3d.LigPrep3Volumizer

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

static defaultConfig() → std::string

dielectricConstant(arg2)

ffldVersion(arg2)

static newForMaestro() → Volumizer

next()

returns the next ‘this’ object

run(ct, addHydrogens=False, runStereoizer=False)

run(ct, addHydrogens=False) run(ct)

skipCM1A(arg2)

class schrodinger.infra.fast3d.SingleConformerEngine

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

run(ct)

run(ct, oneBasedFrozenAtomIndices)

stereo(mode)

stereo() -> int

class schrodinger.infra.fast3d.Volumizer

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

static defaultConfig() → std::string

dielectricConstant(arg2)

ffldVersion(arg2)

static newForMaestro() → Volumizer

next()

returns the next ‘this’ object

run(ct, addHydrogens=False, runStereoizer=False)

run(ct, addHydrogens=False) run(ct)

skipCM1A(arg2)

schrodinger.infra.fast3d.Volumizer_defaultConfig() → std::string

schrodinger.infra.fast3d.Volumizer_newForMaestro() → Volumizer

exception schrodinger.infra.fast3d.f3d_Exception

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.infra.fast3d.intvector

std::vector< int >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append(x)

assign(n, x)

back() → std::vector< int >::value_type const &

begin() → std::vector< int >::iterator

capacity() → std::vector< int >::size_type

clear()

empty() → bool

end() → std::vector< int >::iterator

erase(pos) → std::vector< int >::iterator

erase(first, last) -> std::vector< int >::iterator

front() → std::vector< int >::value_type const &

get_allocator() → std::vector< int >::allocator_type

insert(pos, x) → std::vector< int >::iterator

insert(pos, n, x)

iterator() → SwigPyIterator

next()

returns the next ‘this’ object

pop() → std::vector< int >::value_type

pop_back()

push_back(x)

rbegin() → std::vector< int >::reverse_iterator

rend() → std::vector< int >::reverse_iterator

reserve(n)

resize(new_size)

resize(new_size, x)

size() → std::vector< int >::size_type

swap(v)

class schrodinger.infra.fast3d.stringvector

std::vector< std::string >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append(x)

assign(n, x)

back() → std::vector< std::string >::value_type const &

begin() → std::vector< std::string >::iterator

capacity() → std::vector< std::string >::size_type

clear()

empty() → bool

end() → std::vector< std::string >::iterator

erase(pos) → std::vector< std::string >::iterator

erase(first, last) -> std::vector< std::string >::iterator

front() → std::vector< std::string >::value_type const &

get_allocator() → std::vector< std::string >::allocator_type

insert(pos, x) → std::vector< std::string >::iterator

insert(pos, n, x)

iterator() → SwigPyIterator

next()

returns the next ‘this’ object

pop() → std::vector< std::string >::value_type

pop_back()

push_back(x)

rbegin() → std::vector< std::string >::reverse_iterator

rend() → std::vector< std::string >::reverse_iterator

reserve(n)

resize(new_size)

resize(new_size, x)

size() → std::vector< std::string >::size_type

swap(v)

schrodinger.infra.fast3d.surfnet(protein_data, ligand_data, min_radius=1.0, max_radius=4.0) → PyObject

surfnet(protein_data, ligand_data, min_radius=1.0) -> PyObject surfnet(protein_data, ligand_data) -> PyObject *

schrodinger.infra.fast3d.weakref_proxy()

proxy(object[, callback]) – create a proxy object that weakly references ‘object’. ‘callback’, if given, is called with a reference to the proxy when ‘object’ is about to be finalized.