schrodinger.glide module

This module provides Python wrappers to the Glide backend C++ library, as well as some helper functions to make use of the library more Pythonic.

class schrodinger.glide.AtomPhob

schrodinger::glide::AtomPhob

__init__(*args, **kwargs)

atom_id

atom_score

class schrodinger.glide.Config(glide_job=None)

Glide job configuration; holds the values of all the keywords from the Glide input file (.in), and default values for unspecified keywords.

This class has a generic get() method that works for all types, but only for official keywords. For unofficial keywords, use the type-specific methods inherited from the parent class (getInt, getDouble, getString, getBool, getIntArray, getDoubleArray, getStringArray, getBoolArray), which also take an optional default value as a second argument (use of the second argument is strongly encouraged unless you can be certain that the keyword will be present in the input config).

__init__(glide_job=None)

Parameters:

glide_job (Union[schrodinger.application.glide.glide.GlideJob, dict,str,None]) – SIF input filename, keyword dict, GlideJob object, or None, where None means use default settings for docking.

Raises:

ValueError – job uses unsupported features

get(keyword: str)

Return the value of an official keyword (i.e., one listed in mmim_keywords.yaml).

Parameters:

keyword – keyword name

Return type:

Union[int, float, str, bool, list]

Throw:

KeyError if keyword is unknown. Note that this is unlike dict.get!

getUpdated(additional_keywords: dict)

Return a new Config object with the keywords updated according to the input dictionary. Note that this method does not validate the input keywords for potential keyword conflicts or unsupported features.

Parameters:

additional_keywords (Dict[str, Union[int, float, str, bool, list]]) – dictionary of keyword-value pairs

Return type:

Config

getInt(*args)

getBool(*args)

getDouble(*args)

getString(*args)

getIntArray(*args)

getBoolArray(*args)

getDoubleArray(*args)

getStringArray(*args)

getType(keyword)

class schrodinger.glide.Conformer

schrodinger::glide::Conformer

__init__(*args, **kwargs)

adjustTorsion(self, idx, value) → Conformer

calcScore(self, calc)

getDiameterAtomIndices(self) → std::pair< int,int >

getEnergy(self) → double

getId(self) → int

getLigand(self) → Ligand

getRotamerAngles(self) → _TplDoubleListList

getRotamerStructures(self) → std::vector< schrodinger::Structure,std::allocator< schrodinger::Structure > >

getRotamers(self, std) → _TplRotamerGroupList

getRotamers(self, std_conf_xyz) → _TplRotamerGroupList

getScore(self) → double

getStandardOrientation(self) → schrodinger::Structure

getStandardOrientation(self, xyz) → None

getStructure(self) → schrodinger::Structure

getTemplate(self) → std::shared_ptr< schrodinger::glide::ConformerTemplate >

getTorsions(self) → std::vector< double,std::allocator< double > >

class schrodinger.glide.ConformerEnsemble

schrodinger::glide::ConformerEnsemble

__init__(*args, **kwargs)

getConformerStructures(self) → std::vector< schrodinger::Structure,std::allocator< schrodinger::Structure > >

getConformers(self) → _TplConformerList

getLigand(self) → std::shared_ptr< schrodinger::glide::Ligand const >

getRotamerStructures(self) → std::vector< schrodinger::Structure,std::allocator< schrodinger::Structure > >

getTemplateStructures(self) → std::vector< schrodinger::Structure,std::allocator< schrodinger::Structure > >

getTemplates(self) → _TplConformerTemplateList

static makeSingleConformer(lig, config) → std::shared_ptr< schrodinger::glide::ConformerEnsemble const >

static readEnsemble(filename, lig, config) → std::shared_ptr< schrodinger::glide::ConformerEnsemble const >

static runConfgen()

schrodinger::glide::ConformerEnsemble::runConfgen(lig, config) -> std::shared_ptr< schrodinger::glide::ConformerEnsemble const > runConfgen(lig, config, constraints) -> std::shared_ptr< schrodinger::glide::ConformerEnsemble const >

static runConfgenFromTemplates(lig, templates, config, constraints) → std::shared_ptr< schrodinger::glide::ConformerEnsemble const >

class schrodinger.glide.ConformerTemplate

schrodinger::glide::ConformerTemplate

__init__(*args, **kwargs)

calculateForceFieldEnergy(self, torsions, grad=None) → double

calculateInternalEnergy(self, torsions, grad=None) → double

calculateTorsionEnergy(self, torsions, grad=None) → double

getCentralAtoms(self) → boost::dynamic_bitset< > const &

getCentralInteractingAtomIndices(self) → std::vector< int,std::allocator< int > >

getCoreRestraintIndex(self) → std::optional< int >

getCoreRotbondIndices(self) → std::vector< int,std::allocator< int > >

getEnergies(self) → _TplDoubleListList

getGroundStateEnergy(self) → double

getId(self) → int

getLigand(self) → std::shared_ptr< schrodinger::glide::Ligand const >

getMinima(self) → _TplMinimaList

getNumPeripheralRotbonds(self) → int

getRotamerGroupIndices(self) → std::vector< int,std::allocator< int > >

getRotatableBonds(self) → std::shared_ptr< schrodinger::glide::RotatableBonds const >

getStructure(self) → schrodinger::Structure

getXYZ(self) → std::vector< Eigen::Vector3d,std::allocator< Eigen::Vector3d > > const &

class schrodinger.glide.ConstraintWithAtom

schrodinger::glide::ConstraintWithAtom

__init__(*args, **kwargs)

atom_idx

constraint

class schrodinger.glide.CoreDefinition

schrodinger::glide::CoreDefinition

__init__(*args, **kwargs)

addProperties(self, st, pose)

getBestMatchAndRmsd(self, xyz) → std::pair< int,double >

getCoreAtoms(self) → std::vector< int,std::allocator< int > > const &

getCoreIndices(self) → std::vector< int,std::allocator< int > > const &

getCoreRestraintIndex(self, pose) → std::optional< int >

getCoreSmarts(self) → std::string

getMatches(self) → _TplIntListList

getNumCores(self) → int

getRefCoords(self) → std::vector< Eigen::Vector3d,std::allocator< Eigen::Vector3d > > const &

getTolerance(self) → double

hasMatch(self) → bool

measureRmsd(self, xyz) → double

measureRmsd(self, pose) → double

measureRmsd(self, pose) → double

measureRmsd(self, conf) → double

class schrodinger.glide.DataFiles

schrodinger::glide::DataFiles

__init__(*args, **kwargs)

getDirections(self, ndir) → std::vector< Eigen::Vector3d,std::allocator< Eigen::Vector3d > > const &

class schrodinger.glide.Docker

schrodinger::glide::Docker

__init__(*args, **kwargs)

dockConformerEnsemble(self, confs, ligandConstraintData) → std::shared_ptr< schrodinger::glide::RefinedPoseEnsemble >

roughDockConformerEnsemble(self, confs, ligand_constraint_data) → std::shared_ptr< schrodinger::glide::RoughPoseEnsemble >

schrodinger.glide.DockingLicense(config=None)

Context manager to check out a docking license, and checking it in on exit. :raise schrodinger.infra.licensing.LicenseCheckoutError: can’t check out

class schrodinger.glide.EnergyComponents

schrodinger::glide::EnergyComponents

__init__(*args, **kwargs)

coul

e_xvol

isValid(self) → bool

restraint

total(self) → double

vdw

class schrodinger.glide.EnergyOptions

schrodinger::glide::EnergyOptions

__init__(*args, **kwargs)

charge_correction

core_restraint_index

coul_weight

denscore_gaussian_resolution

denscore_radius

density_weight

dielco

hard

ligand_constraint_data

out_of_box_treatment

use_electron_density_forces

use_shape_constraints

use_smooth_scaling

vdw_weight

class schrodinger.glide.FullMinimizer

schrodinger::glide::FullMinimizer

__init__(*args, **kwargs)

minimize(self, pose) → MinimizerResult

class schrodinger.glide.GridArchive

schrodinger::glide::GridArchive

__init__(*args, **kwargs)

cloneWithNewCoords(self, new_coords, datafiles=schrodinger::glide::DataFiles()) → std::shared_ptr< schrodinger::glide::GridArchive const >

getInfo(self) → std::string

getNumDirections(self) → size_t

getReceptor(self) → Receptor

getStructure(self) → schrodinger::Structure

getWaterStructure(self) → schrodinger::Structure

hasConstraints(self) → bool

hasXvolGrids(self) → bool

isEqual(self, archive, tolerance=1e-6) → bool

static readArchive(gridfile) → std::shared_ptr< schrodinger::glide::GridArchive const >

static runGridgen(recep, config, datafiles=schrodinger::glide::DataFiles()) → std::shared_ptr< schrodinger::glide::GridArchive const >

write(self, gridpath) → std::vector< std::string,std::allocator< std::string > >

writeMembers(self, basepath) → std::vector< std::string,std::allocator< std::string > >

writeZip(self, gridpath) → std::string

schrodinger.glide.GridgenLicense()

Context manager to check in a docking license, and checking it in on exit. :raise schrodinger.infra.licensing.LicenseCheckoutError: can’t check out

class schrodinger.glide.GroupPhobscorePacking

schrodinger::glide::GroupPhobscorePacking

__init__(*args, **kwargs)

atoms_phob

group_score

residue_nums

class schrodinger.glide.HBond

schrodinger::glide::HBond

__init__(*args, **kwargs)

angle

donor_atom

geometry_score

getLigDonorOrAcceptor(self) → PoseAtom

getRecepDonorOrAcceptor(self) → ReceptorAtom

lig_atom

recep_atom

type

weighed_score

class schrodinger.glide.HBondData

schrodinger::glide::HBondData

__init__(*args, **kwargs)

ligand_atom

receptor_atom

score

class schrodinger.glide.HBondType

NEUTRAL_NEUTRAL = 0

NEUTRAL_CHARGED = 1

CHARGED_CHARGED = 2

class schrodinger.glide.HBonds

schrodinger::glide::HBonds

__init__(*args, **kwargs)

charged_charged

hbonds

neutral_charged

neutral_neutral

class schrodinger.glide.Hybridization

FreeAtom = 0

sp1 = 1

sp2 = 2

sp3 = 3

exception schrodinger.glide.InputError

An input file or configuration setting is invalid and the job cannot proceed.

class schrodinger.glide.IntermolecularAtomPair

schrodinger::glide::IntermolecularAtomPair

__init__(*args, **kwargs)

ligand_atom

receptor_atom

class schrodinger.glide.JobConstraintData

schrodinger::glide::JobConstraintData

__init__(*args, **kwargs)

getConfig(self) → Config

getCoreAtoms(self) → std::vector< int,std::allocator< int > > const &

getIonicRadii(self) → std::vector< double,std::allocator< double > > const &

getReferenceLigand(self) → std::optional< schrodinger::Structure >

getShapeReferenceLigand(self) → std::optional< schrodinger::Structure >

setReferenceLigand(self, st)

setShapeReferenceLigand(self, st)

class schrodinger.glide.LicenseManager

schrodinger::glide::LicenseManager

__init__(*args, **kwargs)

checkInLicenses(self)

checkOutDocking(self, config=schrodinger::glide::Config(), auto_retry=True)

checkOutGridgen(self)

hasDocking(self) → bool

hasFitden(self) → bool

hasGridgen(self) → bool

static instance()

schrodinger::glide::LicenseManager::instance() -> std::shared_ptr< schrodinger::glide::LicenseManager >

class schrodinger.glide.Ligand

schrodinger::glide::Ligand

__init__(*args, **kwargs)

static fromSmiles(smiles, config=schrodinger::glide::Config(), datafiles=schrodinger::glide::DataFiles()) → std::shared_ptr< schrodinger::glide::Ligand const >

static fromStructure()

schrodinger::glide::Ligand::fromStructure(st, config=schrodinger::glide::Config(), datafiles=schrodinger::glide::DataFiles()) -> std::shared_ptr< schrodinger::glide::Ligand const >

getNumCoreRotbonds(self) → int

getNumRotbondsBetween(self, atom1, atom2) → int

getRotatableBonds(self) → _TplRotBondList

class schrodinger.glide.LigandAtom

schrodinger::glide::LigandAtom

__init__(*args, **kwargs)

getRing(self) → Ring

getRingSystemIndex(self) → int

getSigmaScaled(self) → double

class schrodinger.glide.LigandConstraintData

schrodinger::glide::LigandConstraintData

__init__(*args, **kwargs)

addProperties(self, st, pose, score_info)

canRestrainCore(self) → bool

canSnapCore(self) → bool

getConfig(self) → Config

getCoreDefinition(self) → std::shared_ptr< schrodinger::glide::CoreDefinition const >

getIonicRadii(self) → std::vector< double,std::allocator< double > > const &

getJobConstraintData(self) → std::shared_ptr< schrodinger::glide::JobConstraintData const >

getLigand(self) → std::shared_ptr< schrodinger::glide::Ligand const >

getTorsionalConstraints(self) → std::shared_ptr< schrodinger::glide::TorsionalRestraintCalculator const >

hasCore(self) → bool

hasLigandDensity(self) → bool

hasReceptorBasedConstraints(self) → bool

hasReceptorBasedFiltersAndRestraints(self) → bool

hasReferenceShape(self) → bool

hasShapeConstraints(self) → bool

hasTorsionalConstraints(self) → bool

satisfiesReceptorBasedConstraints(self, pose) → bool

class schrodinger.glide.LoggerConfig

schrodinger::glide::LoggerConfig

__init__(*args, **kwargs)

configure(self, config_str)

disableCapture(self)

enableCapture(self)

static getCurrentConfig() → LoggerConfig

getMessages(self) → std::string

setDefaultMain(self, level)

setDefaultNonRecursive(self, name, level)

setDefaultRecursive(self, name, level)

setMain(self, level)

setNonRecursive(self, name, level)

setRecursive(self, name, level)

schrodinger.glide.LoggerContext(levels: Optional[Dict[str, int]] = None, capture: Optional[bool] = None, main_level: Optional[int] = None, default_main_level: Optional[int] = None) → ContextManager

Context manager to set default logging levels and capturing for a given scope. Returns the new LoggerConfig, which can be used for further configuration or to fetch the captured messages.

Parameters:

• levels – dict of {name: level} to set the logging level for specific loggers. If a name has a “+” suffix, the setting will be recursive (apply to the logger’s children).

• capture – If True, enable capture; if False, disable capture; if None, keep the current capture setting.

• main_level – change the main logging level, with applies to functions that are not covered by any of the keys in levels.

• default_main_level – change the default for the main level, but only if the global default level is not already set, for example by the SCHRODINGER_GLIDE_LOG environment variable or by an enclosing LoggerContext.

Yield:

LoggerConfig

class schrodinger.glide.LoggerManager

schrodinger::glide::LoggerManager

__init__(*args, **kwargs)

getConfig(self) → LoggerConfig

static instance() → std::shared_ptr< schrodinger::glide::LoggerManager >

restoreConfig(self)

saveConfig(self) → LoggerConfig

class schrodinger.glide.MinimizerResult

schrodinger::glide::MinimizerResult

__init__(*args, **kwargs)

energy

num_evals

status

class schrodinger.glide.MinimizerStatus

OK = 0

OutOfBox = 1

Exception = 2

class schrodinger.glide.Minimum

schrodinger::glide::Minimum

__init__(*args, **kwargs)

angle

energy

class schrodinger.glide.OutOfBoxTreatment

strict = 0

restrain = 1

class schrodinger.glide.PhobscoreData

schrodinger::glide::PhobscoreData

__init__(*args, **kwargs)

groups

phobscore

class schrodinger.glide.Placement

schrodinger::glide::Placement

__init__(*args, **kwargs)

ijk

phi

psi

theta

xyz

class schrodinger.glide.Pose

schrodinger::glide::Pose

__init__(*args, **kwargs)

computeScore(self, archive, config, datafiles=schrodinger::glide::DataFiles()) → std::shared_ptr< schrodinger::glide::ScoreInfo >

getAtom(self, index) → PoseAtom

getAtom(self, index) → PoseAtom

getAtomicNumber(self, atom_index) → int

getAtoms(self, _from, to) → schrodinger::glide::GlideAtomRange< schrodinger::glide::Pose,schrodinger::glide::PoseAtom >

getAtoms(self) → schrodinger::glide::GlideAtomRange< schrodinger::glide::Pose,schrodinger::glide::PoseAtom >

getAtoms(self, _from, to) → schrodinger::glide::GlideAtomRange< schrodinger::glide::Pose const,schrodinger::glide::PoseAtom const >

getAtoms(self) → schrodinger::glide::GlideAtomRange< schrodinger::glide::Pose const,schrodinger::glide::PoseAtom const >

getConformer(self) → std::shared_ptr< schrodinger::glide::Conformer const >

getInternalEnergy(self) → double

getLigand(self) → Ligand

getNumAtoms(self) → unsigned int

getRefinedPose(self) → RefinedPose

getScoredStructure(self, archive, config, constraints=schrodinger::glide::LigandConstraintData(), datafiles=schrodinger::glide::DataFiles()) → schrodinger::Structure

getStructure(self) → schrodinger::Structure

getXyzRef(self) → std::vector< Eigen::Vector3d,std::allocator< Eigen::Vector3d > > const &

getXyzRef(self) → std::vector< Eigen::Vector3d,std::allocator< Eigen::Vector3d > >

class schrodinger.glide.PoseAtom

schrodinger::glide::PoseAtom

__init__(*args, **kwargs)

getNeighbors(self) → _TplPoseAtomList

getPose(self) → Pose

getXyzRef(self) → Eigen::Vector3d const &

getXyzRef(self) → Eigen::Vector3d

isSpecialHydroxyl(self) → bool

class schrodinger.glide.Ptype

DSC_PHOBHYD = 0

DSC_PHOBHVY = 1

DSC_DONOR = 2

DSC_ACCEP = 3

DSC_POLAR = 4

DSC_METAL = 5

DSC_MAX_BASE = 5

DSC_HALO_DONOR = 12

DSC_HALO_ACCEP = 13

DSC_DEFAULT = 0

class schrodinger.glide.Receptor

schrodinger::glide::Receptor

__init__(*args, **kwargs)

countMetalsInBox(self, archive) → int

static fromStructure()

schrodinger::glide::Receptor::fromStructure(st, config, datafiles=schrodinger::glide::DataFiles()) -> std::shared_ptr< schrodinger::glide::Receptor const >

getDistanceCell(self, distance) → schrodinger::DistanceCell const &

isEqual(self, recep, tolerance) → bool

class schrodinger.glide.ReceptorAtom

schrodinger::glide::ReceptorAtom

__init__(*args, **kwargs)

getHBondEquivalentAtoms(self) → _TplReceptorAtomList

getIndexResOrder(self) → int

getLongSaltBridge(self) → int

getMungedPdbName(self) → std::string

getMungedResidueName(self) → resname_t

getPDBAtomName(self) → std::string

getResidueNum(self) → int

getShortSaltBridge(self) → int

isMovable(self) → bool

class schrodinger.glide.RefinedPose

schrodinger::glide::RefinedPose

__init__(*args, **kwargs)

center_xyz

conf

constraint_tuple

emodel

euler_angles

static fromConformer(conf) → RefinedPose

static fromRoughPose(rough_pose) → RefinedPose

getInternalEnergy(self) → double

getLigand(self) → Ligand

getStructure(self) → schrodinger::Structure

minimized_energy

minimum_ensemble_energy

posenum

rot_bonds_torsions

score

class schrodinger.glide.RefinedPoseEnsemble

schrodinger::glide::RefinedPoseEnsemble

__init__(*args, **kwargs)

assignPosenums(self)

calculateSelfDensity(self, archive, jcd)

clusterSelection(self, archive, ligand_constraint_data)

computeEmodels(self, archive, config, datafiles, constraints=schrodinger::glide::LigandConstraintData())

copyAndCalculateSelfDensity(self, archive, jcd) → RefinedPoseEnsemble

copyAndClusterSelection(self, archive, ligand_constraint_data) → RefinedPoseEnsemble

copyAndComputeEmodels(self, archive, config, datafiles, constraints=schrodinger::glide::LigandConstraintData()) → RefinedPoseEnsemble

copyAndCreateConstraintCopies(self, maxref, ligand_constraint_data) → RefinedPoseEnsemble

copyAndFilterByCoreRmsd(self, core) → RefinedPoseEnsemble

copyAndMinimizePoses(self, archive, config, ligand_constraint_data) → RefinedPoseEnsemble

copyAndResampleConformers(self, archive, config, ligand_constraint_data, datafiles) → RefinedPoseEnsemble

copyAndTruncate(self, new_size) → RefinedPoseEnsemble

createConstraintCopies(self, maxref, ligand_constraint_data)

filterByCoreRmsd(self, core)

static fromConformerEnsemble(confs) → RefinedPoseEnsemble

getMinEnergy(self) → double

getPoses(self) → _TplRefinedPoseList

getRefinedStructures(self) → std::vector< schrodinger::Structure,std::allocator< schrodinger::Structure > >

minimizePoses(self, archive, config, ligand_constraint_data)

resampleConformers(self, archive, config, ligand_constraint_data, datafiles)

truncate(self, new_size)

class schrodinger.glide.Ring

schrodinger::glide::Ring

__init__(*args, **kwargs)

atoms

is_terminal

class schrodinger.glide.RotType

CORE = 0

PERIPHERAL = 1

class schrodinger.glide.RotamerGroup

schrodinger::glide::RotamerGroup

__init__(*args, **kwargs)

getCoords(self) → std::vector< std::vector< Eigen::Vector3d,std::allocator< Eigen::Vector3d > >,std::allocator< std::vector< Eigen::Vector3d,std::allocator< Eigen::Vector3d > > > >

num_rotamers

rotbond

class schrodinger.glide.RotatableBond

schrodinger::glide::RotatableBond

__init__(*args, **kwargs)

atom1

atom2

moving_atoms

num_moving_rotbonds

type

class schrodinger.glide.Rotation

schrodinger::glide::Rotation

__init__(*args, **kwargs)

phi

psi

theta

class schrodinger.glide.RoughPose

schrodinger::glide::RoughPose

__init__(*args, **kwargs)

conformer

getStructure(self) → schrodinger::Structure

interacting_greedy_score

placement

refinePose(self, archive, lig, ligand_constraint_data) → RefinedPose

score

class schrodinger.glide.RoughPoseEnsemble

schrodinger::glide::RoughPoseEnsemble

__init__(*args, **kwargs)

getPoses(self) → _TplRoughPoseList

getRoughStructures(self) → std::vector< schrodinger::Structure,std::allocator< schrodinger::Structure > >

class schrodinger.glide.ScoreDescriptors

schrodinger::glide::ScoreDescriptors

__init__(*args, **kwargs)

chemscore_clash

electrostatic_reward

energy_components

hbonds

hscore

intrahb_count

lipo_lipo

lipo_nonlipo

mass_reward

mass_weighted_rot_bond

metal

phobic_attractive

phobscore_data

pi_cation

polar_philic

polarscore

site_descs

special_charged_lig_atoms

special_hbond_pairs_data

special_hbonds_data

strain_energy

torsion_penalties

torsion_penalty

class schrodinger.glide.ScoreInfo

schrodinger::glide::ScoreInfo

__init__(*args, **kwargs)

descriptors

error_msg

gscore

internal_energy

terms

viz_data

class schrodinger.glide.ScoreTerms

schrodinger::glide::ScoreTerms

__init__(*args, **kwargs)

ecoul

electrostatic_reward

evdw

hbond_charged_charged

hscore

intrahb_reward

lipo

mass_reward

mass_weighted_rot_bond

metal

phobscore

pi_cation

polar_philic

polarscore

special_hbond

special_hbond_pair

strain_energy

torsion_penalty

class schrodinger.glide.SiteGridDescriptors

schrodinger::glide::SiteGridDescriptors

__init__(*args, **kwargs)

donor_attractive

donor_repulsive

phobic_attractive

polar_philic

polar_phobic

polarscore

exception schrodinger.glide.SkipLigand(reason, message)

Exception class for errors that mean that we cannot proceed with the current ligand, but are otherwise nonfatal. The expectation is that they will be caught and handled by the main ligand loop.

Variables:

• message – specific error message

• reason – general reason for skipping the ligand, as one of the members of the SkipReason enum (e.g., SkipReason.CONFGEN)

__init__(reason, message)

reason: SkipReason

message: str

toJSON()

classmethod fromJSON(json_str: str) → SkipLigand

class schrodinger.glide.SkipReason

ATOMIC_NUMBER = 0

ATOM_OVERLAP = 1

BAD_ATOM = 2

CONFGEN = 3

EMPTY_MCS = 4

FORCE_FIELD = 5

LIGAND_DATA = 6

LIGAND_SIZE = 7

MINIMIZATION = 8

NO_ATOMS = 9

NO_GOOD_POSES = 10

NO_MATCH = 11

NO_POSES_STORED = 12

PHASE_DB = 13

PULL = 14

REFINE = 15

ROTBONDS = 16

ROUGH_SCORE = 17

EXCEPTION = 18

class schrodinger.glide.SpecialHBondPairData

schrodinger::glide::SpecialHBondPairData

__init__(*args, **kwargs)

all_charged

score

special_pair

class schrodinger.glide.SpecialHBondPairsData

schrodinger::glide::SpecialHBondPairsData

__init__(*args, **kwargs)

special_hbond_pairs_data

total_score

class schrodinger.glide.SpecialHBondsData

schrodinger::glide::SpecialHBondsData

__init__(*args, **kwargs)

special_hbonds_data

total_score

class schrodinger.glide.StrainCorrectionOptions

schrodinger::glide::StrainCorrectionOptions

__init__(*args, **kwargs)

coul_weight

dielco

class schrodinger.glide.TorsionAndPlacementMinimizer

schrodinger::glide::TorsionAndPlacementMinimizer

__init__(*args, **kwargs)

minimize(self, refined_pose, maxeval, energy_options, rigid) → MinimizerResult

minimize(self, refined_pose) → MinimizerResult

class schrodinger.glide.TorsionPenalty

schrodinger::glide::TorsionPenalty

__init__(*args, **kwargs)

atom1

atom2

name

value

class schrodinger.glide.VisualizationData

schrodinger::glide::VisualizationData

__init__(*args, **kwargs)

charged_ligand_atom_score

hbonds_data

phobscore_data

special_charged_lig_atoms

special_hbond_pairs_data

special_hbonds_data

class schrodinger.glide.WaterMap

schrodinger::glide::WaterMap

__init__(*args, **kwargs)

getCoords(self, index) → Eigen::Vector3d const &

getDg(self, index) → double

getSize(self) → size_t

getWmapWater(self, index) → WmapWater

class schrodinger.glide.WmapWater

schrodinger::glide::WmapWater

__init__(*args, **kwargs)

getCoords(self) → Eigen::Vector3d const &

getDg(self) → double

schrodinger.glide.clear_glide_props(st)

schrodinger.glide.clear_global_state_file()

schrodinger.glide.clear_group_properties(st)

schrodinger.glide.compute_strain_energy(pose, config) → double

schrodinger.glide.count_intramolecular_hbonds(pose) → int

schrodinger.glide.create_constraint_supporting_info(constraints) → schrodinger::glide::ConstraintSupportingInfo

schrodinger.glide.create_directories(directory_path)

schrodinger.glide.files_are_equal(stream_1, stream_2, skip=0) → bool

schrodinger.glide.find_data_file(basename, cwd='') → std::string

schrodinger.glide.find_test_file(basename) → std::string

schrodinger.glide.generate_templates(lig, starting_st, config) → _TplConformerTemplateList

schrodinger.glide.generate_templates(lig, starting_st, config, constraints) → _TplConformerTemplateList

schrodinger.glide.generate_templates(lig, structures, config, constraints) → _TplConformerTemplateList

schrodinger.glide.get_core_idcs(reflig, core_atoms) → std::pair< std::vector< int,std::allocator< int > >,int >

schrodinger.glide.get_core_smarts_idcs(reflig, smarts, core_atoms) → std::vector< int,std::allocator< int > >

schrodinger.glide.get_corrected_energy(pose, archive, config) → EnergyComponents

schrodinger.glide.get_energy_charge_correction(pose, recep, evdw_raw, dielco=DEFAULT_DIELCO) → EnergyComponents

schrodinger.glide.get_energy_for_strain_corrections(pose, options, calc) → std::pair< double,std::vector< Eigen::Vector3d,std::allocator< Eigen::Vector3d > > >

schrodinger.glide.get_hbonds(pose, recep) → HBonds

schrodinger.glide.get_intermolecular_energy_and_forces(pose, archive, options={}) → std::pair< schrodinger::glide::EnergyComponents,std::vector< Eigen::Vector3d,std::allocator< Eigen::Vector3d > > >

schrodinger.glide.get_intermolecular_energy_and_forces(pose, archive, options, total_forces) → EnergyComponents

schrodinger.glide.get_intramolecular_energy(pose, dielco=DEFAULT_DIELCO) → double

schrodinger.glide.get_rotated_rotamers(euler, rotamer_groups) → _TplRotamerGroupList

schrodinger.glide.get_total_energy(pose, archive, options={}) → double

schrodinger.glide.get_uncorrected_energy(pose, archive, config) → EnergyComponents

schrodinger.glide.get_unsupported_features(glide_job)

Check if the job is using any keyword not supported by Skate. (Developer keywords are ignored.)

Returns:

list of unsupported keyword names used by the job

Return type:

List(str)

schrodinger.glide.glide_ws_license_exists() → bool

schrodinger.glide.has_bad_contacts_for_sampling(pose, config) → bool

schrodinger.glide.has_bad_contacts_for_scoring(pose, config) → bool

schrodinger.glide.has_bad_contacts_for_scoring_relaxed(pose, config) → bool

schrodinger.glide.install_signal_handler()

schrodinger.glide.log(level, message)

schrodinger.glide.maybe_uncompress(file_name, file_stream) → std::unique_ptr< std::istream >

schrodinger.glide.minimize_xyz(pose, archive, maxeval, energy_options) → MinimizerResult

schrodinger.glide.read_and_combine_lines(stream, num_lines) → std::string

schrodinger.glide.refine_rough_poses(rough_poses, confs, archive, ligand_constraint_data) → std::shared_ptr< schrodinger::glide::RefinedPoseEnsemble >

schrodinger.glide.require_docking_license()

schrodinger.glide.require_fitden_license()

schrodinger.glide.require_gridgen_license()

schrodinger.glide.set_global_lignum(new_lignum)

schrodinger.glide.set_global_state_file(filename)

schrodinger.glide.skip_lines(stream, n)

schrodinger.glide.validate_smarts_and_core_atoms(reflig, smarts, core_atoms)