schrodinger.infra.fast3d module¶

Fast3D wrappers

class schrodinger.infra.fast3d.Canonicalizer¶

__init__(*args, **kwargs)¶

canonicalize(self, ct) → std::string¶

canonicalizePositions(self, ct)¶

class schrodinger.infra.fast3d.Engine¶

FROZEN_ATOMS_PROPERTY_NAME = 's_f3d_frozen_atoms'¶

SCHRODINGER_CONFGENX_CSP_MODE = 'SCHRODINGER_CONFGENX_CSP_MODE'¶

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)¶

acceptableHeavyAtomsOverlap¶

appendRepository(self, path)¶

autoIncreaseThreshold(self, arg2)¶
autoIncreaseThreshold(self) → unsigned int

static dataDir() → std::string¶

static defaultCustomRepository() → std::string¶

static defaultRepositories() → stringvector¶

disableDuplicatesElimination(self)¶

disallowCisAmides(self, arg2)¶
disallowCisAmides(self) → bool

invertNitrogens(self, arg2)¶
invertNitrogens(self) → bool

static isFragmentLibraryFile(arg1) → bool¶

partition(self, ct) → PyObject *¶

run(self, ct)¶

setDesiredNumberOfConformers(self, arg2)¶

stereo(self, arg2)¶
stereo(self) → int

schrodinger.infra.fast3d.Engine_FROZEN_ATOMS_PROPERTY_NAME_get()¶

schrodinger.infra.fast3d.Engine_SCHRODINGER_CONFGENX_CSP_MODE_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(arg1) → bool¶

class schrodinger.infra.fast3d.Generalizer¶

__init__(*args, **kwargs)¶

appendRule(self, smarts, atomicNumber, numHydrogensToAdd)¶

generalize(self, arg2) → boost::shared_ptr< RDKit::RWMol >¶

class schrodinger.infra.fast3d.LigPrep3Volumizer¶

__init__(*args, **kwargs)¶

class schrodinger.infra.fast3d.SingleConformerEngine¶

__init__(*args, **kwargs)¶

run(self, ct)¶
run(self, ct, oneBasedFrozenAtomIndices) → None

stereo(self, mode)¶
stereo(self) → int

class schrodinger.infra.fast3d.Volumizer¶

__init__(*args, **kwargs)¶

static defaultConfig() → std::string¶

dielectricConstant(self, arg2)¶

ffldVersion(self, arg2)¶

static newForMaestro() → Volumizer¶

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

skipCM1A(self, arg2)¶

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

schrodinger.infra.fast3d.Volumizer_newForMaestro() → Volumizer¶

exception schrodinger.infra.fast3d.f3d_Exception¶

class schrodinger.infra.fast3d.intvector¶

std::vector< int >

__init__(*args, **kwargs)¶

__len__()¶: Return len(self).

append(self, x)¶

assign(self, n, x)¶

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

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

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

clear(self)¶

empty(self) → bool¶

end(self) → std::vector< int >::iterator¶

erase(self, pos) → std::vector< int >::iterator¶
erase(self, first, last) → std::vector< int >::iterator

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

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

insert(self, pos, x) → std::vector< int >::iterator¶
insert(self, pos, n, x) → None

iterator(self) → SwigPyIterator¶

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

pop_back(self)¶

push_back(self, x)¶

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

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

reserve(self, n)¶

resize(self, new_size)¶
resize(self, new_size, x) → None

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

swap(self, v)¶

class schrodinger.infra.fast3d.stringvector¶

std::vector< std::string >

__init__(*args, **kwargs)¶

__len__()¶: Return len(self).

append(self, x)¶

assign(self, n, x)¶

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

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

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

clear(self)¶

empty(self) → bool¶

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

erase(self, pos) → std::vector< std::string >::iterator¶
erase(self, first, last) → std::vector< std::string >::iterator

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

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

insert(self, pos, x) → std::vector< std::string >::iterator¶
insert(self, pos, n, x) → None

iterator(self) → SwigPyIterator¶

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

pop_back(self)¶

push_back(self, x)¶

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

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

reserve(self, n)¶

resize(self, new_size)¶
resize(self, new_size, x) → None

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

swap(self, v)¶

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

schrodinger.infra.fast3d.uniquesmiles(ct) → std::string¶