schrodinger.infra.canvas module

Canvas C++ wrappers

class schrodinger.infra.canvas.AtomData

::AtomData

__init__(*args, **kwargs)

cachedCoords

constrained

declareAromatic

fixed

hasCoords

hidden

ignored

owner

class schrodinger.infra.canvas.AtomicInvariant

::AtomicInvariant

__init__(*args, **kwargs)

getAtomicCharge(self) → char

getAtomicMass(self) → uchar

getAtomicNumber(self) → uchar

getBondsToNonHydrogen(self) → uchar

getTotalHydrogens(self) → uchar

getTotalValence(self) → uchar

class schrodinger.infra.canvas.BondData

::BondData

__init__(*args, **kwargs)

owner

schrodinger.infra.canvas.CHM_FORCE2D(mol, force2D, arg3) → bool

class schrodinger.infra.canvas.Chm2DCoordGen

::Chm2DCoordGen

__init__(*args, **kwargs)

static assignCoordsForHiddenAtoms(mol)

static assignCoordsForNullAtoms(mol)

static assignMissingCoords(mol)

static center(mol) → ChmPoint

static centerAndRescale(mol, desiredBondLength=1.3)

static checkForNAN(mol) → bool

static exportCoordinatesFromMinimizer(min, mol)

static flipHorizontal(mol)

static flipVertical(mol)

static generateAndApply(mol, arg2=H_Default, arg3=Default)

static generateCoordinates(mol, precision=SKETCHER_STANDARD_PRECISION)

static generateFromTemplateAndApply(mol, templateMol, molAtomNumbers, templateAtomNumbers, arg5=H_Default, arg6=Default, fixup=False, completelyByPassCoordgen=False, copyOverOriginalTemplateCoordinates=False)

static generateFromTemplateAndApply2(mol, templateMol, matches, arg4=H_Default, arg5=Default, fixup=False, completelyByPassCoordgen=False, copyOverOriginalTemplateCoordinates=False)

static getBounds(mol) → std::pair< ChmPoint,ChmPoint >

static getScale(mol) → float

static hasCorrectScale(mol, desiredBondLength=1.3, relativeTolerance=0.05) → bool

static initializeMinimizerFromMolecule(min, mol)

static isAvailable() → bool

static rotate(mol, degrees)

static rotateAbout(mol, degrees, center)

static sketcherBondStereoFromChmBond(chmBond, bond) → sketcherMinimizerBondStereoInfo

static sketcherChiralityFromChmChirality(info, atoms) → sketcherMinimizerAtomChiralityInfo

static translate(mol, offset)

static visibleAtomsAtOrigin(mol) → ChmBitset

schrodinger.infra.canvas.Chm2DCoordGen_assignCoordsForHiddenAtoms(mol)

schrodinger.infra.canvas.Chm2DCoordGen_assignCoordsForNullAtoms(mol)

schrodinger.infra.canvas.Chm2DCoordGen_assignMissingCoords(mol)

schrodinger.infra.canvas.Chm2DCoordGen_center(mol) → ChmPoint

schrodinger.infra.canvas.Chm2DCoordGen_centerAndRescale(mol, desiredBondLength=1.3)

schrodinger.infra.canvas.Chm2DCoordGen_checkForNAN(mol) → bool

schrodinger.infra.canvas.Chm2DCoordGen_exportCoordinatesFromMinimizer(min, mol)

schrodinger.infra.canvas.Chm2DCoordGen_flipHorizontal(mol)

schrodinger.infra.canvas.Chm2DCoordGen_flipVertical(mol)

schrodinger.infra.canvas.Chm2DCoordGen_generateAndApply(mol, arg2=H_Default, arg3=Default)

schrodinger.infra.canvas.Chm2DCoordGen_generateCoordinates(mol, precision=SKETCHER_STANDARD_PRECISION)

schrodinger.infra.canvas.Chm2DCoordGen_generateFromTemplateAndApply(mol, templateMol, molAtomNumbers, templateAtomNumbers, arg5=H_Default, arg6=Default, fixup=False, completelyByPassCoordgen=False, copyOverOriginalTemplateCoordinates=False)

schrodinger.infra.canvas.Chm2DCoordGen_generateFromTemplateAndApply2(mol, templateMol, matches, arg4=H_Default, arg5=Default, fixup=False, completelyByPassCoordgen=False, copyOverOriginalTemplateCoordinates=False)

schrodinger.infra.canvas.Chm2DCoordGen_getBounds(mol) → std::pair< ChmPoint,ChmPoint >

schrodinger.infra.canvas.Chm2DCoordGen_getScale(mol) → float

schrodinger.infra.canvas.Chm2DCoordGen_hasCorrectScale(mol, desiredBondLength=1.3, relativeTolerance=0.05) → bool

schrodinger.infra.canvas.Chm2DCoordGen_initializeMinimizerFromMolecule(min, mol)

schrodinger.infra.canvas.Chm2DCoordGen_isAvailable() → bool

schrodinger.infra.canvas.Chm2DCoordGen_rotate(mol, degrees)

schrodinger.infra.canvas.Chm2DCoordGen_rotateAbout(mol, degrees, center)

schrodinger.infra.canvas.Chm2DCoordGen_sketcherBondStereoFromChmBond(chmBond, bond) → sketcherMinimizerBondStereoInfo

schrodinger.infra.canvas.Chm2DCoordGen_sketcherChiralityFromChmChirality(info, atoms) → sketcherMinimizerAtomChiralityInfo

schrodinger.infra.canvas.Chm2DCoordGen_translate(mol, offset)

schrodinger.infra.canvas.Chm2DCoordGen_visibleAtomsAtOrigin(mol) → ChmBitset

class schrodinger.infra.canvas.ChmAssignments

::ChmIterator< int64 >

__init__(*args, **kwargs)

__len__()

Return len(self).

asVector(self) → std::vector< long long,std::allocator< long long > > const &

asVector(self) → std::vector< long long,std::allocator< long long > >

at(self, index) → long long &

at(self, index) → long long const

checked random access

chmtostring(self) → std::string

hasNext(self) → bool

hasPrev(self) → bool

isValid(self) → bool

next(self) → long long

prev(self) → long long

rewind(self)

size(self) → int

sort(self)

class schrodinger.infra.canvas.ChmAtom

::ChmAtom

__init__(*args, **kwargs)

canBeChiral(self) → bool

chmtostring(self) → std::string

clone(self) → ChmAtom

get an identical but independent copy of this, attached to no molecule

countNeighborsByAtomicNumber(self, filterBy) → int

firstNeighbor(self) → ChmAtom

flipChirality(self)

getAtomicNumber(self) → periodicTable::atomicNumber

getAttachedHydrogens(self) → ChmAtoms

getBond(self, index) → ChmBond

get bond by index

getBondCount(self, wantImplicitHydrogens=False) → int

get count of bonds

getBondTo(self, otherAtom) → ChmBond

getBondByAtom

getBonds(self, wantImplicitHydrogens=False) → ChmBonds

get iterator over this atom’s bonds

getChiralCenters(self) → ChmAtoms

getChiralDeterminant(self, atomOrdering, mappedAtomsCount, force3D) → double

getChiralDeterminant(self, permutation) → double

getChiralDeterminant(self) → double

getChiralityInfo(self) → ChmChiralityInfo

getChiralityType(self) → ChmChiralityType

getCoords(self) → ChmPoint

getElementalInfo(self) → ChmElement

getFormalCharge(self) → int

getHeavyBondCount(self) → int

getHeavyBonds(self) → ChmBonds

getHeavyNeighbors(self) → ChmAtoms

getHybridization(self) → ChmAtomHybridization

getHydrogenCount(self) → int

getImplicitHydrogenCount(self) → int

getImplicitNeighbors(self) → ChmAtoms

getInvariant(self) → AtomicInvariant

getIsotope(self, specified=None) → int

getLabel(self, oneBased=False) → std::string

getLonePairCount(self, considerConjugation=False) → int

getMDLParity(self) → int

getMol(self) → ChmMol

get owning Molecule (if any)

getMolIndex(self) → int

getMolSize(self) → int

getNeighbors(self, wantImplicitHydrogens=False, wantExplicitHydrogens=True) → ChmAtoms

getNeighborsByAtomicNumber(self, filterBy) → ChmAtoms

getNeighborsMasked(self, exclude) → ChmAtoms

getPartialCharge(self) → float

getRGroup(self) → int

getReactionAtomIndex(self) → int

getRingBondCount(self) → int

getRingSize(self) → int

getSmilesChirality(self) → ChmSmilesChirality

getSymbol(self) → std::string

getSymbolForSMARTS(self) → std::string

getTotalValence(self) → int

getUnpairedElectronCount(self) → uint

getUserData(self) → int

getVisibleHydrogenCount(self) → int

getX(self) → float

getY(self) → float

getZ(self) → float

has3DCoords(self) → bool

hasCoords(self) → bool

hasMetallicNeighbor(self) → bool

hasNeighborOfElementType(self, an) → bool

hasOnlyWedge(self) → bool

hasPolarNeighbor(self) → bool

hasRingNeighbor(self) → bool

hasSpecifiedIsotope(self, specified=None) → bool

hasWedge(self) → bool

isAcid(self) → bool

isAliphatic(self) → bool

isAromatic(self) → bool

isBondedTo(self, rhs) → bool

isCarbon(self) → bool

isCarbonyl(self) → bool

isChiral(self) → bool

isChiralAttachment(self) → bool

isConjugated(self) → bool

isConstrained(self) → bool

isDummy(self) → bool

isEZAttachment(self) → bool

isEZAttachmentToN(self) → bool

isEster(self) → bool

isFixed(self) → bool

isHalogen(self) → bool

isHeavy(self) → bool

isHetero(self) → bool

isHidden(self) → bool

isHydrogen(self, excludeIsotopicVariants=False) → bool

isIgnored(self) → bool

isImplicit(self) → bool

isInMol(self) → bool

check if owned by Molecule

isInRing(self) → bool

isMetal(self) → int

isNitrogen(self) → bool

isOxygen(self) → bool

isPhosphorous(self) → bool

isPolar(self) → bool

isPolarHydrogen(self) → bool

isPyroleN(self) → bool

isSP(self) → bool

isSP2(self) → bool

isSP3(self) → bool

isSulfur(self) → bool

isTerminal(self) → bool

isVisible(self) → bool

isWildcard(self) → bool

perceiveTetrahedralChirality(self)

setAtomicNumber(self, arg2)

setChiralityType(self, chirality)

setConstrained(self, on)

setCoords(self, point)

setFixed(self, on)

setFormalCharge(self, charge)

setHidden(self, on)

setHybridization(self, hyb)

setHydrogensHidden(self, on)

setIgnored(self, on)

setIsotope(self, val)

setPartialCharge(self, charge)

setRGroup(self, group)

setReactionAtomIndex(self, rxn)

setSmilesChirality(self, code)

setUnpairedElectronCount(self, unpaired) → uint

setUserData(self, data)

setVisibility(self, arg2) → bool

setXYZ(self, x, y, z)

testVisibility(self, arg2) → bool

validateChirality(self)

wedgeCount(self) → int

class schrodinger.infra.canvas.ChmAtomHybridizationTyper

::ChmAtomHybridizationTyper

__init__(*args, **kwargs)

type(self, mol, arg3=False) → ChmAssignments

class schrodinger.infra.canvas.ChmAtomIterator

::ChmIterator< ChmAtom >

__init__(*args, **kwargs)

__len__()

Return len(self).

asVector(self) → std::vector< ChmAtom,std::allocator< ChmAtom > > const &

asVector(self) → std::vector< ChmAtom,std::allocator< ChmAtom > >

at(self, index) → ChmAtom

at(self, index) → ChmAtom

checked random access

chmtostring(self) → std::string

hasNext(self) → bool

hasPrev(self) → bool

isValid(self) → bool

next(self) → ChmAtom

prev(self) → ChmAtom

rewind(self)

size(self) → int

sort(self)

class schrodinger.infra.canvas.ChmAtomOption

::ChmAtomOption

H_All = 8

H_AsIs = -1

H_Chiral = 4

H_Default = 1

H_ExplicitChiral = 5

H_ExplicitOnly = 1

H_ExplicitPolar = 3

H_ExplicitPolarAndChiral = 6

H_Never = 0

H_Polar = 2

__init__(*args, **kwargs)

class schrodinger.infra.canvas.ChmAtomTyper

::ChmAtomTyper

__init__(*args, **kwargs)

calculateScalar(self, mol, wantImplicitHydrogens=False, et=extendedTypeLast) → double

calculate a ChmValueAssignment for each atom in the molecule and then return their sum

calculateWeightedScalar(self, mol, smoothingWeights, wantImplicitHydrogens=False, et=extendedTypeLast) → double

calculate a ChmValueAssignment for each atom in the molecule and then return their sum, then smooth them according to coefficients supplied in the weights vector, then finally sum them

extendedType(self, mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

obtains all assignments, not just the last

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(self, mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

returns the mean of values for all types assigned to each atom in the given molecule

extendedValueTypeSum(self, mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

getAllPossibleAssignments(self) → ChmValueAssignmentIterator

makeGaussianWeights(self, maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(self, maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

used to create a weights vector for calculateScalar using 1/ (r^p) where r is the bond-length radius and p is the power

setRules(self, rulesString)

setRulesFile(self, rulesFile)

type(self, mol, wantImplicitHydrogens=False) → ChmAssignments

just return the types assigned to each atom in the given molecule

valueType(self, mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(self, mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmAtomTyperAlogP

::ChmAtomTyperAlogP

__init__(*args, **kwargs)

class schrodinger.infra.canvas.ChmAtomTyperEstate

::ChmAtomTyperEstate

__init__(*args, **kwargs)

calculateScalar(self, mol, wantImplicitHydrogens=False, et=extendedTypeLast) → double

getFallOffPower(self) → int

getMaxPath(self) → int

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

setParam(self, maxPath, fallOffPower)

class schrodinger.infra.canvas.ChmAtomTyperEstateBinned

::ChmAtomTyperEstateBinned

__init__(*args, **kwargs)

type(self, mol, wantImplicitHydrogens=False) → ChmAssignments

class schrodinger.infra.canvas.ChmAtomTyperMR

::ChmAtomTyperMR

__init__(*args, **kwargs)

class schrodinger.infra.canvas.ChmAtomTyperPSA

::ChmAtomTyperPSA

__init__(*args, **kwargs)

class schrodinger.infra.canvas.ChmAtomTyperPolarMiller

::ChmAtomTyperPolarMiller

__init__(*args, **kwargs)

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

class schrodinger.infra.canvas.ChmAtoms

::ChmAtoms

__init__(*args, **kwargs)

barycenterOf(self) → ChmPointT< float,true >

centerOf(self) → ChmPointT< float,true >

centerOf(self, include) → ChmPointT< float,true >

distanceTo(self, pt) → float

distanceTo(self, atom) → float

getMW(self) → double

toBitset(self) → ChmBitset

class schrodinger.infra.canvas.ChmAtomsAndBonds

::ChmAtomsAndBonds

__init__(*args, **kwargs)

atoms

bonds

class schrodinger.infra.canvas.ChmBitComparable32

::ChmBitComparable< uint >

__init__(*args, **kwargs)

__len__()

Return len(self).

count(self) → uint64

countCommonOff(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

countDifference(self, rhs) → uint64

distDixon(self, rhs, forceBinary=False) → double

distEuclidean(self, rhs, forceBinary=False) → double

distHamming(self, rhs, normalized=False, forceBinary=False, overrideSize=None) → double

normalization is for size

distPatternDifference(self, rhs, forceBinary=False, overrideSize=None) → double

distShape(self, rhs, forceBinary=False, overrideSize=None) → double

distSize(self, rhs, forceBinary=False, overrideSize=None) → double

distSoergel(self, rhs, forceBinary=False) → double

distSquaredEuclidean(self, rhs, forceBinary=False) → double

distTanimoto(self, rhs, forceBinary=False) → double

these are all dissimilarities

distVariance(self, rhs, forceBinary=False, overrideSize=None) → double

getType(self) → int

simBuser(self, rhs, forceBinary=False, overrideSize=None) → double

simCosine(self, rhs, forceBinary=False) → double

simDice(self, rhs, forceBinary=False) → double

simHamann(self, rhs, forceBinary=False, overrideSize=None) → double

simKulczynski(self, rhs, forceBinary=False) → double

simMatching(self, rhs, forceBinary=False, overrideSize=None) → double

simMcConnaughey(self, rhs, forceBinary=False) → double

simMinMax(self, rhs, forceBinary=False) → double

simModifiedTanimoto(self, rhs, forceBinary=False, overrideSize=None) → double

simPearson(self, rhs, forceBinary=False, overrideSize=None) → double

simPetke(self, rhs, forceBinary=False) → double

simRogersTanimoto(self, rhs, forceBinary=False, overrideSize=None) → double

simSimpson(self, rhs, forceBinary=False) → double

simTanimoto(self, rhs, forceBinary=False) → double

simTversky(self, rhs, alpha, beta, forceBinary=False) → double

simYule(self, rhs, forceBinary=False, overrideSize=None) → double

size(self) → uint64

class schrodinger.infra.canvas.ChmBitComparable64

::ChmBitComparable< uint64 >

__init__(*args, **kwargs)

__len__()

Return len(self).

count(self) → uint64

countCommonOff(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

countDifference(self, rhs) → uint64

distDixon(self, rhs, forceBinary=False) → double

distEuclidean(self, rhs, forceBinary=False) → double

distHamming(self, rhs, normalized=False, forceBinary=False, overrideSize=None) → double

normalization is for size

distPatternDifference(self, rhs, forceBinary=False, overrideSize=None) → double

distShape(self, rhs, forceBinary=False, overrideSize=None) → double

distSize(self, rhs, forceBinary=False, overrideSize=None) → double

distSoergel(self, rhs, forceBinary=False) → double

distSquaredEuclidean(self, rhs, forceBinary=False) → double

distTanimoto(self, rhs, forceBinary=False) → double

these are all dissimilarities

distVariance(self, rhs, forceBinary=False, overrideSize=None) → double

getType(self) → int

simBuser(self, rhs, forceBinary=False, overrideSize=None) → double

simCosine(self, rhs, forceBinary=False) → double

simDice(self, rhs, forceBinary=False) → double

simHamann(self, rhs, forceBinary=False, overrideSize=None) → double

simKulczynski(self, rhs, forceBinary=False) → double

simMatching(self, rhs, forceBinary=False, overrideSize=None) → double

simMcConnaughey(self, rhs, forceBinary=False) → double

simMinMax(self, rhs, forceBinary=False) → double

simModifiedTanimoto(self, rhs, forceBinary=False, overrideSize=None) → double

simPearson(self, rhs, forceBinary=False, overrideSize=None) → double

simPetke(self, rhs, forceBinary=False) → double

simRogersTanimoto(self, rhs, forceBinary=False, overrideSize=None) → double

simSimpson(self, rhs, forceBinary=False) → double

simTanimoto(self, rhs, forceBinary=False) → double

simTversky(self, rhs, alpha, beta, forceBinary=False) → double

simYule(self, rhs, forceBinary=False, overrideSize=None) → double

size(self) → uint64

class schrodinger.infra.canvas.ChmBitset

::ChmBitset

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

__len__(self) → uint64

all(self) → bool

any(self) → bool

bit testing operations

blockReverse(self)

chmtostring(self) → std::string

clear(self)

clear(self, index) → None

compare(self, rhs) → int

contains(self, rhs) → bool

countCommonOff(self, rhs) → uint64

countCommonOff(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

Overload 1: ChmBitComparable

Overload 2: specializations

countDifference(self, rhs) → uint64

countDifference(self, rhs) → uint64

empty(self) → bool

Add consistent interface for EV 101799.

flip(self)

flip(self, index) → None

bit level operations

static fromBinary(onesAndZeros) → ChmBitset

static fromBlob(raw) → ChmBitset

get(self, index) → bool

getHash(self) → uint

getHash64(self) → uint64

getWord(self, index) → uint &

hasDifference(self, rhs) → bool

intersects(self, rhs) → bool

isContainedBy(self, rhs) → bool

isSubsetOf(self, rhs) → bool

Add consistent interface for EV 101799.

none(self) → bool

physicalSize(self) → size_t

reserve(self, blocks)

resize(self, logicalSize)

reverse(self)

set(self)

set(self, index) → None

set(self, index, on) → None

store(self, inputStream)

storeRaw(self, inputStream)

swap(self, rhs)

toBitString(self) → std::string

csv all data

toBlob(self) → std::string

toHexString(self) → std::string

toHexString(self, arg2) → None

hex string

toMmbs(self, base=1) → int

toString(self, oneBased=False, wantCounts=False) → std::string

other operations csv hits only

toVector(self, oneBased=False) → std::vector< uint,std::allocator< uint > >

class schrodinger.infra.canvas.ChmBitset64

::ChmBitset64

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

__len__(self) → uint64

all(self) → bool

any(self) → bool

bit testing operations

blockReverse(self)

chmtostring(self) → std::string

clear(self)

clear(self, index) → None

compare(self, rhs) → int

contains(self, rhs) → bool

countCommonOff(self, rhs) → uint64

countCommonOff(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

ChmBitComparable

countDifference(self, rhs) → uint64

countDifference(self, rhs) → uint64

flip(self)

flip(self, index) → None

bit level operations

static fromBinary(onesAndZeros) → ChmBitset64

static fromBlob(raw) → ChmBitset64

static fromHex(hexstring) → ChmBitset64

static fromHex(hexstring, len) → ChmBitset64

get(self, index) → bool

getHash(self) → uint

getHash64(self) → uint64

getWord(self, index) → uint64 &

hasDifference(self, rhs) → bool

intersects(self, rhs) → bool

isContainedBy(self, rhs) → bool

isSubsetOf(self, rhs) → bool

Add consistent interface for EV 101799.

none(self) → bool

physicalSize(self) → size_t

reserve(self, blocks)

resize(self, logicalSize)

reverse(self)

set(self)

set(self, index) → None

set(self, index, on) → None

store(self, outputStream)

storeRaw(self, outputStream)

swap(self, rhs)

toBitString(self) → std::string

csv all data

toBlob(self) → std::string

toHexString(self) → std::string

toHexString(self, arg2) → None

hex string

toString(self, oneBased=False, wantCounts=False) → std::string

other operations csv hits only

toVector(self, oneBased=False) → std::vector< uint64,std::allocator< uint64 > >

toVector(self, dest, oneBased=False) → None

schrodinger.infra.canvas.ChmBitset64_fromBinary(onesAndZeros) → ChmBitset64

schrodinger.infra.canvas.ChmBitset64_fromBlob(raw) → ChmBitset64

schrodinger.infra.canvas.ChmBitset64_fromHex(hexstring) → ChmBitset64

schrodinger.infra.canvas.ChmBitset64_fromHex(hexstring, len) → ChmBitset64

class schrodinger.infra.canvas.ChmBitsetIterator

::ChmIterator< ChmBitset >

__init__(*args, **kwargs)

__len__()

Return len(self).

asVector(self) → ChmBitsetVector

asVector(self) → ChmBitsetVector

at(self, index) → ChmBitset

at(self, index) → ChmBitset

checked random access

chmtostring(self) → std::string

hasNext(self) → bool

hasPrev(self) → bool

isValid(self) → bool

next(self) → ChmBitset

prev(self) → ChmBitset

rewind(self)

size(self) → int

sort(self)

class schrodinger.infra.canvas.ChmBitsetVector

std::vector< ChmBitset >

__init__(*args, **kwargs)

__len__()

Return len(self).

append(self, x)

assign(self, n, x)

back(self) → ChmBitset

begin(self) → std::vector< ChmBitset >::iterator

capacity(self) → std::vector< ChmBitset >::size_type

clear(self)

empty(self) → bool

end(self) → std::vector< ChmBitset >::iterator

erase(self, pos) → std::vector< ChmBitset >::iterator

erase(self, first, last) → std::vector< ChmBitset >::iterator

front(self) → ChmBitset

get_allocator(self) → std::vector< ChmBitset >::allocator_type

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

insert(self, pos, n, x) → None

iterator(self) → SwigPyIterator

pop(self) → ChmBitset

pop_back(self)

push_back(self, x)

rbegin(self) → std::vector< ChmBitset >::reverse_iterator

rend(self) → std::vector< ChmBitset >::reverse_iterator

reserve(self, n)

resize(self, new_size)

resize(self, new_size, x) → None

size(self) → std::vector< ChmBitset >::size_type

swap(self, v)

schrodinger.infra.canvas.ChmBitset_fromBinary(onesAndZeros) → ChmBitset

schrodinger.infra.canvas.ChmBitset_fromBlob(raw) → ChmBitset

class schrodinger.infra.canvas.ChmBond

::ChmBond

__init__(*args, **kwargs)

atom1(self) → ChmAtom

the first atom to add this bond

atom2(self) → ChmAtom

the second atom to add this bond

chmtostring(self) → std::string

clearBondDirectionHint(self)

directionDown = 6

directionNone = 0

directionUp = 1

flipBondDirectionHint(self)

getBondDirectionHint(self) → ChmBond::bondDirectionHint

getBondLength(self) → float

getCis(self, atomIndex1, atomIndex4)

getMaeOrder(self) → int

getMolIndex(self) → int

getMolSize(self) → int

getOrder(self) → ChmBondOrder

getRingSize(self) → int

returns 0 if exocyclic, otherwise size of smallest ring containing this bond

getStereo(self) → ChmBondStereo

getStereoDeterminant(self, externalOrder, f1, f2, f3, f4) → double

getSymbolForSMARTS(self) → std::string

getTrans(self, atomIndex1, atomIndex4)

getUserData(self) → int

hasBondDirectionHint(self) → bool

idealLength(self) → double

isAromatic(self) → bool

isChiral(self) → bool

isConjugated(self) → bool

isDouble(self) → bool

isDown(self) → bool

isHidden(self) → bool

isInRing(self) → bool

isRotatable(self) → bool

isSingle(self) → bool

isStereo(self) → bool

isTerminal(self) → bool

isTriple(self) → bool

isUp(self) → bool

isVisible(self) → bool

mate(self, reference) → ChmAtom

noHint = 15

otherAtom(self, reference) → ChmAtom

setBondDirectionHint(self, hint)

setCis(self, atomIndex1, atomIndex4)

setCis(self, atom1, atom4) → None

setOrder(self, arg2)

setRingSize(self, arg2)

setStereo(self, arg2)

setTrans(self, atomIndex1, atomIndex4)

setTrans(self, atom1, atom4) → None

setUserData(self, data)

validateStereo(self)

class schrodinger.infra.canvas.ChmBondIterator

::ChmIterator< ChmBond >

__init__(*args, **kwargs)

__len__()

Return len(self).

asVector(self) → std::vector< ChmBond,std::allocator< ChmBond > > const &

asVector(self) → std::vector< ChmBond,std::allocator< ChmBond > >

at(self, index) → ChmBond

at(self, index) → ChmBond

checked random access

chmtostring(self) → std::string

hasNext(self) → bool

hasPrev(self) → bool

isValid(self) → bool

next(self) → ChmBond

prev(self) → ChmBond

rewind(self)

size(self) → int

sort(self)

class schrodinger.infra.canvas.ChmBonds

::ChmBonds

__init__(*args, **kwargs)

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

toBitset(self) → ChmBitset

class schrodinger.infra.canvas.ChmCSVBinaryOut

::ChmCSVBinaryOut

__init__(*args, **kwargs)

static parseHeader(items, binPref='BIT') → ChmSparseBitset

static parseHeader64(items, binPref='BIT') → ChmSparseBitset64

schrodinger.infra.canvas.ChmCSVBinaryOut_parseHeader(items, binPref='BIT') → ChmSparseBitset

schrodinger.infra.canvas.ChmCSVBinaryOut_parseHeader64(items, binPref='BIT') → ChmSparseBitset64

class schrodinger.infra.canvas.ChmChiralityInfo

::ChmChiralityInfo

__init__(*args, **kwargs)

atom1

atom2

atomLookingFrom

centralAtom

direction

class schrodinger.infra.canvas.ChmClusterGrouper

::ChmClusterGrouper

__init__(*args, **kwargs)

group(self, source, info_file, out_file, numGroups, skipSingletons, collectDuplicates)

class schrodinger.infra.canvas.ChmColumnUIDFilter

::ChmColumnUIDFilter

__init__(*args, **kwargs)

static fromFile(filename) → ChmColumnUIDFilter

getAutoScaleInfo(self) → std::map< uint64,std::pair< double,double >,std::less< uint64 >,std::allocator< std::pair< uint64 const,std::pair< double,double > > > > const &

hasAutoScaleInfo(self) → bool

setAutoScaleInfo(self, info)

schrodinger.infra.canvas.ChmColumnUIDFilter_fromFile(filename) → ChmColumnUIDFilter

class schrodinger.infra.canvas.ChmCombinationOut32

::ChmCombinationOut32

__init__(*args, **kwargs)

addDefaultSources(self)

addSource(self, source)

this object takes ownership of source

clearAllSources(self)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

open(self, filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone)

class schrodinger.infra.canvas.ChmCombinationOut64

::ChmCombinationOut64

__init__(*args, **kwargs)

addDefaultSources(self)

addSource(self, source)

this object takes ownership of source

clearAllSources(self)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

open(self, filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone)

class schrodinger.infra.canvas.ChmCompressedBitset

::ChmCompressedBitset

no randomAccess!

__init__(*args, **kwargs)

bitwiseAnd(self, rhs, wantPopulationCount) → ChmCompressedBitset

bitwiseNot(self) → ChmCompressedBitset

bitwiseOr(self, rhs, wantPopulationCount) → ChmCompressedBitset

bitwiseXor(self, rhs, wantPopulationCount) → ChmCompressedBitset

chmtostring(self) → std::string

countCommonOff(self, rhs) → uint64

countCommonOff(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

Overload 1: ChmBitComparable

Overload 2: specializations

countDifference(self, rhs) → uint64

countDifference(self, rhs) → uint64

defaultLogicalSize = -1

static fromString(idstring) → ChmCompressedBitset

getCompressionRatio(self) → float

metadata

getCompressionWithHeader(self) → float

getHash(self) → uint

getHash64(self) → uint64

getStorage(self) → size_t

returns number of bytes required

getUncompressedStorage(self) → uint64

returns number of bytes require to store logicalSize bits

isWordAligned(self) → bool

redoCount(self) → uint

store(self, sdata)

store(self, outputStream, extra=True) → None

store(self, os) → None

swap(self, rhs)

toBitString(self) → std::string

csv all data

toBitset(self) → ChmBitset

toSet(self, hits)

toString(self) → std::string

toString(self, outputStream) → None

ioisaFill csv hits only

toVector(self) → std::vector< uint,std::allocator< uint > >

toVector(self, hits) → None

class schrodinger.infra.canvas.ChmCompressedBitset64

::ChmCompressedBitset64

__init__(*args, **kwargs)

bitwiseAnd(self, rhs, wantPopulationCount) → ChmCompressedBitset64

bitwiseNot(self) → ChmCompressedBitset64

bitwiseOr(self, rhs, wantPopulationCount) → ChmCompressedBitset64

bitwiseXor(self, rhs, wantPopulationCount) → ChmCompressedBitset64

chmtostring(self) → std::string

countCommonOff(self, rhs) → uint64

countCommonOff(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

Overload 1: BitComparable

Overload 2: specializationsbase

countDifference(self, rhs) → uint64

countDifference(self, rhs) → uint64

defaultLogicalSize = -66

static fromString(idstring) → ChmCompressedBitset64

getCompressionRatio(self) → float

metadata

getCompressionWithHeader(self) → float

getHash(self) → uint

getHash64(self) → uint64

getStorage(self) → uint64

return number of words require to store actual bits

getUncompressedStorage(self) → uint64

return number of words require to store logicalSize bits

isWordAligned(self) → bool

redoCount(self) → uint64

store(self, sdata)

store(self, outputStream, extra=True) → None

store(self, os) → None

swap(self, rhs)

toBitString(self) → std::string

csv all data

toSet(self, hits)

toString(self) → std::string

toString(self, outputStream) → None

io csv hits only

toVector(self) → std::vector< uint64,std::allocator< uint64 > >

toVector(self, hits) → None

schrodinger.infra.canvas.ChmCompressedBitset64_fromString(idstring) → ChmCompressedBitset64

class schrodinger.infra.canvas.ChmCompressedBitsetIterator

::ChmCompressedBitsetIterator

__init__(*args, **kwargs)

hasNext(self) → bool

next(self) → uint

rewind(self)

class schrodinger.infra.canvas.ChmCompressedBitsetIterator64

::ChmCompressedBitsetIterator64

iterator through on bits

__init__(*args, **kwargs)

hasNext(self) → bool

next(self) → uint64

rewind(self)

class schrodinger.infra.canvas.ChmCompressedBitsetWordIterator

::ChmCompressedBitsetWordIterator

__init__(*args, **kwargs)

finishWord(self)

getRepeatLength(self) → uint

hasNext(self) → bool

isFill(self) → bool

isOneFill(self) → bool

isZeroFill(self) → bool

next(self) → uint

rewind(self)

skip(self, n)

class schrodinger.infra.canvas.ChmCompressedBitsetWordIterator64

::ChmCompressedBitsetWordIterator64

iterator through on bits

__init__(*args, **kwargs)

finishWord(self)

getRepeatLength(self) → uint64

hasNext(self) → bool

isFill(self) → bool

isOneFill(self) → bool

isZeroFill(self) → bool

next(self) → uint64

rewind(self)

skip(self, n)

schrodinger.infra.canvas.ChmCompressedBitset_fromString(idstring) → ChmCompressedBitset

class schrodinger.infra.canvas.ChmCoordGenOption

::ChmCoordGenOption

Default = 1

NoScaling = 0

Physical = 1

Rendering = 2

__init__(*args, **kwargs)

class schrodinger.infra.canvas.ChmCustomMetric

::ChmCustomMetric

__init__(*args, **kwargs)

calculateMetric(self, arg2, arg3, arg4, arg5) → double

isSimilarity(self) → bool

class schrodinger.infra.canvas.ChmCustomOut32

::ChmCustomOut32

__init__(*args, **kwargs)

write(self, bs, id)

write(self, bs, id, extraData) → None

class schrodinger.infra.canvas.ChmCustomOut64

::ChmCustomOut64

__init__(*args, **kwargs)

write(self, bs, id)

write(self, bs, id, extraData) → None

class schrodinger.infra.canvas.ChmDelimitedPatterns

::ChmDelimitedPatterns

__init__(*args, **kwargs)

close(self)

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

static getDelimiter(filename) → char

static getDelimiterAndQualifier(filename) → std::pair< char,char >

getFilename(self) → std::string const &

getHeaderLine(self) → std::string

getIncludedColIndexes(self) → std::vector< size_t,std::allocator< size_t > >

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

getIncludedCols(self) → int

getIndex(self, field) → int

getIndexWithinSelection(self, field) → int

returns the index within the selected fields. 0-start returns -1 if not exist.

getLastLine(self) → std::string

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

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

getObservationIncludedIndex(self) → size_t

getObservationIndex(self) → size_t

getObservationName(self) → std::string

getTotalCols(self) → int

getValuesOfColumn(self, index, values)

hasHeader(self) → bool

isBinaryColumn(self, index, onBits) → bool

setObservationName(self, name)

skip(self)

schrodinger.infra.canvas.ChmDelimitedPatterns_getDelimiter(filename) → char

schrodinger.infra.canvas.ChmDelimitedPatterns_getDelimiterAndQualifier(filename) → std::pair< char,char >

class schrodinger.infra.canvas.ChmDendriticOut32

::ChmDendriticOut32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

getMaxPath(self) → int

getMaxSpan(self) → int

getMinPath(self) → int

setMaxPath(self, maxPath_)

setMaxSpan(self, maxSpan_)

setMinPath(self, minPath_)

class schrodinger.infra.canvas.ChmDendriticOut64

::ChmDendriticOut64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

getMaxPath(self) → int

getMaxSpan(self) → int

getMinPath(self) → int

setMaxPath(self, maxPath_)

setMaxSpan(self, maxSpan_)

setMinPath(self, minPath_)

class schrodinger.infra.canvas.ChmDenseFPOut

::ChmDenseFPOut

__init__(*args, **kwargs)

close(self)

getCurrentRowCount(self) → uint

open(self, filename, logicalSize, params)

write(self, bs)

write(self, bs, id) → None

class schrodinger.infra.canvas.ChmDescriptorInfo

::ChmDescriptorInfo

__init__(*args, **kwargs)

getDriver(self) → std::string

getRole(self) → std::string

m_longname

m_role

m_shortname

m_source

roleFP = 3

roleUnknown = 0

roleX = 2

roleY = 1

class schrodinger.infra.canvas.ChmDescriptorMarshaler

::ChmDescriptorMarshaler

__init__(*args, **kwargs)

getCanvasDescriptorsSwitch(self) → std::string

marshal(self, testMode=False) → std::string

writeCfgFile(self, file) → bool

class schrodinger.infra.canvas.ChmDescriptorSourceMapper

::ChmDescriptorSourceMapper

__init__(*args, **kwargs)

canvasFPGen = 3

canvasMolDescriptors = 1

static getInfo(name) → ChmDescriptorInfo

static getInfoAll(names) → std::vector< ChmDescriptorInfo,std::allocator< ChmDescriptorInfo > >

mopac = 5

qikprop = 4

static sourceToString(arg1) → std::string

sourceUnknown = 0

topo = 2

schrodinger.infra.canvas.ChmDescriptorSourceMapper_getInfo(name) → ChmDescriptorInfo

schrodinger.infra.canvas.ChmDescriptorSourceMapper_getInfoAll(names) → std::vector< ChmDescriptorInfo,std::allocator< ChmDescriptorInfo > >

schrodinger.infra.canvas.ChmDescriptorSourceMapper_sourceToString(arg1) → std::string

class schrodinger.infra.canvas.ChmEstateDescriptors

::ChmEstateDescriptors

__init__(*args, **kwargs)

getAllEstates(self) → std::map< std::string,double,std::less< std::string >,std::allocator< std::pair< std::string const,double > > >

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

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

getAverage(self, mol, maxPath, fallOffPower, wantImpH=False) → std::map< std::string,double,std::less< std::string >,std::allocator< std::pair< std::string const,double > > >

returns a map of all keys, value is the sum of each type in mol.

getKeyBool(self, mol, wantImplicitH=False) → std::map< std::string,bool,std::less< std::string >,std::allocator< std::pair< std::string const,bool > > >

returns a map of all 85 MolConnZ keys, value is 1(present) or 0(absent)

getKeyCount(self, mol, wantImpH=False) → std::map< std::string,uint,std::less< std::string >,std::allocator< std::pair< std::string const,uint > > >

returns a map of all 85 keys, value is the counts of each

getSum(self, mol, maxPath, fallOffPower, wantImpH=False) → std::map< std::string,double,std::less< std::string >,std::allocator< std::pair< std::string const,double > > >

returns a map of all keys, value is the sum of each type in mol.

class schrodinger.infra.canvas.ChmEstateKey

::ChmEstateKey

__init__(*args, **kwargs)

refNum

style

value

exception schrodinger.infra.canvas.ChmException

class schrodinger.infra.canvas.ChmFPCombiner

::ChmFPCombiner

__init__(*args, **kwargs)

addFile(self, fileName)

clearFiles(self)

combine(self, outputFileName, compress=False, cat=False)

files must have same set of ids in the same order files need NOT have same set of ids in the same order this is more resource intensive than combineInOrder

combineInOrder(self, outputFileName, endToEnd=False, compress=False)

files must have same set of ids in the same order

deleteFiles(self)

isUnfiltered(self) → bool

class schrodinger.infra.canvas.ChmFPCombiner64

::ChmFPCombiner64

__init__(*args, **kwargs)

addFile(self, fileName)

clearFiles(self)

combine(self, outputFileName, compress=False, cat=False)

files must have same set of ids in the same order files need NOT have same set of ids in the same order this is more resource intensive than combineInOrder

combineInOrder(self, outputFileName, endToEnd=False, compress=False)

files must have same set of ids in the same order,

deleteFiles(self)

isUnfiltered(self) → bool

class schrodinger.infra.canvas.ChmFPIn32

::ChmFPIn< ChmSparseBitset >

__init__(*args, **kwargs)

copyTo(self, dest)

decoder(self) → ChmFPDecode const &

filter(self, minFreq, maxFreq, maxBits, reduceBits)

note, this filtering is done in place. If you wish to retain the original then use the next function, copyTo, then filter it.

getCounts(self) → std::vector< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,ChmFPIn< ChmSparseBitset >::POS_TYPE >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,ChmFPIn< ChmSparseBitset >::POS_TYPE > > > const &

getCovariance(self, covar, means)

getCovarianceofTranspose(self, covar, means)

getDisplayTypeInfo(self) → std::string

getExtraColumnNames(self) → std::vector< std::string,std::allocator< std::string > > const &

getFilename(self) → std::string

getFrequencyHash(self) → uint64

getInvariantBits(self) → ChmSparseBitset

getMapping(self, key) → ChmFPIn< ChmSparseBitset >::KEY_TYPE

getMatrix(self, unionData)

getOnBits(self) → ChmSparseBitset

getPos(self) → ChmFPIn< ChmSparseBitset >::OFFSET_TYPE

getPositionsByBitCount(self, posCount)

getRequired(self) → ChmSparseBitset

getRowCount(self) → ChmFPIn< ChmSparseBitset >::COUNT_TYPE

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

getScaledCovariance(self, covar, means, scalingFactors, tolerance)

getScaledCovarianceofTranspose(self, covar, means, scalingFactors, tolerance)

getTypeInfo(self) → std::string

getTypeInfoEx(self) → ChmFPTypeInfo

getUnionCount(self) → ChmFPIn< ChmSparseBitset >::COUNT_TYPE

getValues(self) → std::vector< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,double >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,double > > > const &

getVariances(self) → std::vector< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,double >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,double > > >

hasNext(self) → bool

static isCorrectPrecision(filename) → bool

next(self) → ChmSparseBitset

nextExtra(self) → ChmSparseBitset

nextReduced(self) → ChmBitset

nextReducedExtra(self) → ChmBitset

nextReducedValues(self) → std::vector< float,std::allocator< float > >

nextReducedValuesExtra(self) → std::vector< float,std::allocator< float > >

rewind(self)

setPos(self, pos)

shannonEntropy(self) → double

schrodinger.infra.canvas.ChmFPIn32_isCorrectPrecision(filename) → bool

class schrodinger.infra.canvas.ChmFPIn64

::ChmFPIn< ChmSparseBitset64 >

__init__(*args, **kwargs)

copyTo(self, dest)

decoder(self) → ChmFPDecode const &

filter(self, minFreq, maxFreq, maxBits, reduceBits)

note, this filtering is done in place. If you wish to retain the original then use the next function, copyTo, then filter it.

getCounts(self) → std::vector< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,ChmFPIn< ChmSparseBitset64 >::POS_TYPE >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,ChmFPIn< ChmSparseBitset64 >::POS_TYPE > > > const &

getCovariance(self, covar, means)

getCovarianceofTranspose(self, covar, means)

getDisplayTypeInfo(self) → std::string

getExtraColumnNames(self) → std::vector< std::string,std::allocator< std::string > > const &

getFilename(self) → std::string

getFrequencyHash(self) → uint64

getInvariantBits(self) → ChmSparseBitset64

getMapping(self, key) → ChmFPIn< ChmSparseBitset64 >::KEY_TYPE

getMatrix(self, unionData)

getOnBits(self) → ChmSparseBitset64

getPos(self) → ChmFPIn< ChmSparseBitset64 >::OFFSET_TYPE

getPositionsByBitCount(self, posCount)

getRequired(self) → ChmSparseBitset64

getRowCount(self) → ChmFPIn< ChmSparseBitset64 >::COUNT_TYPE

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

getScaledCovariance(self, covar, means, scalingFactors, tolerance)

getScaledCovarianceofTranspose(self, covar, means, scalingFactors, tolerance)

getTypeInfo(self) → std::string

getTypeInfoEx(self) → ChmFPTypeInfo

getUnionCount(self) → ChmFPIn< ChmSparseBitset64 >::COUNT_TYPE

getValues(self) → std::vector< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,double >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,double > > > const &

getVariances(self) → std::vector< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,double >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,double > > >

hasNext(self) → bool

static isCorrectPrecision(filename) → bool

next(self) → ChmSparseBitset64

nextExtra(self) → ChmSparseBitset64

nextReduced(self) → ChmBitset

nextReducedExtra(self) → ChmBitset

nextReducedValues(self) → std::vector< float,std::allocator< float > >

nextReducedValuesExtra(self) → std::vector< float,std::allocator< float > >

rewind(self)

setPos(self, pos)

shannonEntropy(self) → double

schrodinger.infra.canvas.ChmFPIn64_isCorrectPrecision(filename) → bool

class schrodinger.infra.canvas.ChmFPMap32

::ChmFPMap< ChmSparseBitset >

__init__(*args, **kwargs)

chmtostring(self) → std::string

customize(self)

filter(self, requiredAtoms, requiredCnt=1) → ChmSparseBitset

getAtomsMaskForCode(self, hashCode) → ChmBitsetVector

getBondsMaskForCode(self, hashCode) → ChmBitsetVector

returns set of bitsets representing atoms that comprise the given

getCode(self, index) → ChmFPMap< ChmSparseBitset >::key_type

getCodeCount(self) → uint

getCodeForAtom(self, atomIndex) → ChmFPMap< ChmSparseBitset >::key_type

getItem(self, index) → ChmFPMapItem32

getItemCount(self) → uint

getItemsForAtom(self, atomIndex) → std::vector< ChmFPMapItem< ChmFPMap< ChmSparseBitset >::key_type >,std::allocator< ChmFPMapItem< ChmFPMap< ChmSparseBitset >::key_type > > >

getOnBits(self) → ChmSparseBitset

getOnBitsCopy(self) → ChmSparseBitset

getOnBitsCount(self) → uint

getUniqueItems(self, uniqueItems)

hasCode(self, hashCode) → bool

m_atomCount

m_atomTypingStyle

m_bondCount

m_isSubStructural

m_onBits

m_scaleType

m_sortedItems

makeUniqueCode(self) → uint64

removeByAtomMask(self, atoms) → ChmFPMap32

note this is const- RETURNS the filtered set

store(self, arg2)

class schrodinger.infra.canvas.ChmFPMap64

::ChmFPMap< ChmSparseBitset64 >

__init__(*args, **kwargs)

chmtostring(self) → std::string

customize(self)

filter(self, requiredAtoms, requiredCnt=1) → ChmSparseBitset64

getAtomsMaskForCode(self, hashCode) → ChmBitsetVector

getBondsMaskForCode(self, hashCode) → ChmBitsetVector

returns set of bitsets representing atoms that comprise the given

getCode(self, index) → ChmFPMap< ChmSparseBitset64 >::key_type

getCodeCount(self) → uint

getCodeForAtom(self, atomIndex) → ChmFPMap< ChmSparseBitset64 >::key_type

getItem(self, index) → ChmFPMapItem64

getItemCount(self) → uint

getItemsForAtom(self, atomIndex) → std::vector< ChmFPMapItem< ChmFPMap< ChmSparseBitset64 >::key_type >,std::allocator< ChmFPMapItem< ChmFPMap< ChmSparseBitset64 >::key_type > > >

getOnBits(self) → ChmSparseBitset64

getOnBitsCopy(self) → ChmSparseBitset64

getOnBitsCount(self) → uint

getUniqueItems(self, uniqueItems)

hasCode(self, hashCode) → bool

m_atomCount

m_atomTypingStyle

m_bondCount

m_isSubStructural

m_onBits

m_scaleType

m_sortedItems

makeUniqueCode(self) → uint64

removeByAtomMask(self, atoms) → ChmFPMap64

note this is const- RETURNS the filtered set

store(self, arg2)

class schrodinger.infra.canvas.ChmFPMapItem32

::ChmFPMapItem< uint >

__init__(*args, **kwargs)

addItem(self, atoms, bonds, _atomIndices)

chmtostring(self) → std::string

getAtomAndBondCount(self) → uint

getAtomCount(self) → uint

getBondCount(self) → uint

getItemCount(self) → uint

getMatchCount(self) → uint

m_atomCount

m_atomIndices

m_atomSize

m_atomsThatMatch

m_bondCount

m_bondSize

m_bondsThatMatch

m_hashCode

store(self, os)

class schrodinger.infra.canvas.ChmFPMapItem64

::ChmFPMapItem< uint64 >

__init__(*args, **kwargs)

addItem(self, atoms, bonds, _atomIndices)

chmtostring(self) → std::string

getAtomAndBondCount(self) → uint

getAtomCount(self) → uint

getBondCount(self) → uint

getItemCount(self) → uint

getMatchCount(self) → uint

m_atomCount

m_atomIndices

m_atomSize

m_atomsThatMatch

m_bondCount

m_bondSize

m_bondsThatMatch

m_hashCode

store(self, os)

class schrodinger.infra.canvas.ChmFPOut32

::ChmFPOut32

__init__(*args, **kwargs)

addZeros(self, toAdd)

close(self)

close(self, minFreq, maxFreq, maxBits) → None

close(self, minFreq, maxFreq, maxBits, reduceBits) → None

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

getCurrentRowCount(self) → uint

getFilename(self) → std::string

getTypeInfo(self) → std::string

m_scaleType

needsDM(self) → bool

needsStereo(self) → bool

open(self, filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

write(self, mol, excludeAtomMask=None)

write(self, mol, extraData, excludeAtomMask=None) → None

write(self, mol, id, excludeAtomMask=None) → None

write(self, mol, id, extraData, excludeAtomMask=None) → None

Overload 1: uses molecule name

Overload 2: uses molecule name but allows extra fields

Overload 3: uses molecule name but allows extra fields

Overload 4: overrides molecule name

Overload 5: overrides molecule name

Overload 6: overrides molecule name and allows extra fields

Overload 7: overrides molecule name and allows extra fields

writeNameAndProps(self, mol, id, extraData)

Python-friendly version for writing name and properties.

class schrodinger.infra.canvas.ChmFPOut64

::ChmFPOut64

__init__(*args, **kwargs)

addZeros(self, toAdd)

close(self)

close(self, minFreq, maxFreq, maxBits) → None

close(self, minFreq, maxFreq, maxBits, reduceBits) → None

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

getCurrentRowCount(self) → uint

getFilename(self) → std::string

getTypeInfo(self) → std::string

m_scaleType

needsDM(self) → bool

needsStereo(self) → bool

open(self, filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

write(self, mol, excludeAtomMask=None)

write(self, mol, extraData, excludeAtomMask=None) → None

write(self, mol, id, excludeAtomMask=None) → None

write(self, mol, id, extraData, excludeAtomMask=None) → None

Overload 1: uses molecule name

Overload 2: uses molecule name but allows extra fields to override molecule name

Overload 3: uses molecule name but allows extra fields to override molecule name

Overload 4: overrides molecule name and allows extra fields

Overload 5: overrides molecule name and allows extra fields

writeNameAndProps(self, mol, id, extraData)

Python-friendly version for writing name and properties.

class schrodinger.infra.canvas.ChmFPSplitter

::ChmFPSplitter

__init__(*args, **kwargs)

getInputFileName(self) → std::string

Returns the name of the input fingerprint file.

getMaxFpFilesOpen(self) → uint

Returns the maximum number of output fingerprint files that may be open at any time.

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

Returns the names of the fingerprint files created. These are of the form <base_out>_1.fp, <base_out>_2.fp, etc.

getPrecision(self) → int

Returns the fingerprint precision: 32 or 64.

getRowCount(self) → uint

Returns the number of rows in the input fingerprint file.

class schrodinger.infra.canvas.ChmFPTypeInfo

::ChmFPTypeInfo

__init__(*args, **kwargs)

static areCompatible(fp1, fp2) → bool

static fromFile(fpInfoFile) → ChmFPTypeInfo

getBool(self, key) → bool

getDalkeHeader(self) → std::string

getDisplayInfo(self) → std::string

getDisplayInfoEx(self) → std::string

getFloat(self, key) → float

getInt(self, key) → int

getMaxBits(self) → uint64

getMaxFreq(self) → float

getMinFreq(self) → float

getProp(self, key, missingOk=False) → std::string

getProps(self) → std::map< std::string,std::string,std::less< std::string >,std::allocator< std::pair< std::string const,std::string > > > const &

getRightShift(self) → uint

getScaleType(self) → FingerprintScaleType

getUID(self) → int64

hasProp(self, key) → bool

hasValues(self) → bool

is32Bit(self) → bool

is64Bit(self) → bool

isCompatible(self, rhs) → bool

isConsistentWith(self, rhs, ignoreFiltering, ignoreScale) → bool

isCustom(self) → bool

isCustomType(self) → bool

isFiltered(self) → bool

isFilteredOrReduced(self) → bool

isReduced(self) → bool

isSupersetOf(self, rhs) → bool

isValid(self) → bool

makeTableName(self) → std::string

makeXORTableName(self) → std::string

testProp(self, key, value) → bool

toFPOut(self) → ChmFPOut32

toFPOut64(self) → ChmFPOut64

toString(self) → std::string

schrodinger.infra.canvas.ChmFPTypeInfo_areCompatible(fp1, fp2) → bool

schrodinger.infra.canvas.ChmFPTypeInfo_fromFile(fpInfoFile) → ChmFPTypeInfo

class schrodinger.infra.canvas.ChmFPWrapper

::ChmFPWrapper

__init__(*args, **kwargs)

class schrodinger.infra.canvas.ChmFingerprints

::ChmFingerprints

__init__(*args, **kwargs)

static getRGACodes(mol) → ChmSparseBitset

choices for atom typing ascending ordered from most general to most specific 1 least specific through 10 most specific other typing schemes can be used by either 1. subclassing ChmAtomAndBondTyperBase 2. manually providing a vector of types for the atoms and bonds and feeding them to a template functions below

schrodinger.infra.canvas.ChmFingerprints_getRGACodes(mol) → ChmSparseBitset

choices for atom typing ascending ordered from most general to most specific 1 least specific through 10 most specific other typing schemes can be used by either 1. subclassing ChmAtomAndBondTyperBase 2. manually providing a vector of types for the atoms and bonds and feeding them to a template functions below

class schrodinger.infra.canvas.ChmGasteigerCharge

::ChmGasteigerCharge

__init__(*args, **kwargs)

calcGasteigerCharges(self, arg2, maxIter=7, delta=0.001) → bool

Calculate partial charge up to maxIter(ations) or all the charge shifts < delta. Return false if unsuccessful.

getAtomTypes(self) → std::vector< int64,std::allocator< int64 > >

return atom types for each atom.

getCharges(self, includeImplicitH=True) → std::vector< double,std::allocator< double > >

return final partial charge of each atom.

getStepAtomicCharge(self, atom, iter) → double

return partial charge after a certain iteration

getStepAtomicEneg(self, atom, iter) → double

return electronegativity after a certain iteration.

getTotalIteration(self) → size_t

return total number of iterations.

class schrodinger.infra.canvas.ChmHbond

::ChmHbond

__init__(*args, **kwargs)

assignAcceptors(self, mol)

assignDonors(self, mol)

includes implicit H.

isAcceptor(self, atomIndex) → bool

isDonor(self, atomIndex) → bool

isUsingDefaultAcceptorFile(self) → bool

isUsingDefaultDonorFile(self) → bool

overrideAcceptorFile(self, acceptorFile)

overrideDonorFile(self, donorFile)

printHBADef(self)

printHBDDef(self)

class schrodinger.infra.canvas.ChmHierarchicalClustering

::ChmHierarchicalClustering

CompleteLinkage = 2

FlexibleBetaLinkage = 8

GroupAverageLinkage = 3

SchrodingerLinkage = 9

SingleLinkage = 1

UnweightedCentroidLinkage = 4

UseEither = 0

UseLower = 4

UseMaxAB = 2

UseMinAB = 1

UseUpper = 3

WardsMinimumVarianceLinkage = 6

WeightedAverageLinkage = 5

WeightedCentroidLinkage = 7

__init__(*args, **kwargs)

cluster(self, source, dendrogram_filename, intermediate_info_filename, statistics_filename, arg6, collectDuplicates) → double

cluster(self, source, dendrogram_filename, grouping_detail_filename, threshold, arg6, collectDuplicates) → double

class schrodinger.infra.canvas.ChmKPLSParser

::ChmKPLSParser

__init__(*args, **kwargs)

getAUC(self, numFactor) → std::string

getCISDAll(self, numFactor) → std::vector< std::string,std::allocator< std::string > >

getCISDs(self, numFactor) → std::vector< std::string,std::allocator< std::string > >

getConfidenceIntervals(self, numFactor) → std::vector< std::string,std::allocator< std::string > >

getFPTypeInfo(self) → std::string

getMaxFactor(self) → size_t

getMinFactor(self) → size_t

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

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

Returns a vector of 3 integers: #. of observations (molecules) in training set, test set and total.

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

getPredAll(self, numFactor) → std::vector< std::string,std::allocator< std::string > >

getQsqr(self, numFactor) → std::string

getRsqr(self, numFactor) → std::string

getSD(self, numFactor) → std::string

getSigma(self) → double

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

getTestSetPred(self, numFactor) → std::vector< std::string,std::allocator< std::string > >

getTestSetRMSE(self, numFactor) → std::string

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

getTrainingSetPred(self, numFactor) → std::vector< std::string,std::allocator< std::string > >

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

getYvar(self) → std::string

haveConfidenceInterval(self) → bool

haveTestSet(self) → bool

haveTrainingSet(self) → bool

writePredictions(self, filename, namefield='name', delim='\t', extraParameter=-1)

class schrodinger.infra.canvas.ChmLicenseAutoQsar

::ChmLicenseAutoQsar

__init__(*args, **kwargs)

getType(self) → canvasLicenseType

static isValid() → bool

schrodinger.infra.canvas.ChmLicenseAutoQsar_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseElements

::ChmLicenseElements

__init__(*args, **kwargs)

getType(self) → canvasLicenseType

static isValid() → bool

class schrodinger.infra.canvas.ChmLicenseElementsOrFull

::ChmLicenseElementsOrFull

__init__(*args, **kwargs)

isValid(self) → bool

schrodinger.infra.canvas.ChmLicenseElements_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseFull

::ChmLicenseFull

__init__(*args, **kwargs)

getType(self) → canvasLicenseType

static isValid() → bool

class schrodinger.infra.canvas.ChmLicenseFullOrMain

::ChmLicenseFullOrMain

__init__(*args, **kwargs)

isValid(self) → bool

schrodinger.infra.canvas.ChmLicenseFull_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseMain

::ChmLicenseMain

__init__(*args, **kwargs)

getType(self) → canvasLicenseType

static isValid() → bool

reset(self)

schrodinger.infra.canvas.ChmLicenseMain_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseMatSci

::ChmLicenseMatSci

__init__(*args, **kwargs)

getType(self) → canvasLicenseType

static isValid() → bool

schrodinger.infra.canvas.ChmLicenseMatSci_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseShared

::ChmLicenseShared

__init__(*args, **kwargs)

getType(self) → canvasLicenseType

static isValid() → bool

schrodinger.infra.canvas.ChmLicenseShared_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseXCluster

::ChmLicenseXCluster

__init__(*args, **kwargs)

getType(self) → canvasLicenseType

static isValid() → bool

schrodinger.infra.canvas.ChmLicenseXCluster_isValid() → bool

class schrodinger.infra.canvas.ChmLinearOut32

::ChmLinearOut32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

getHalfStep(self) → bool

getMaxPath(self) → int

getMaxRingPath(self) → int

getMinPath(self) → int

setHalfStep(self, halfstep)

setMaxPath(self, maxPath_)

setMaxRingPath(self, maxRingPath_)

setMinPath(self, minPath_)

class schrodinger.infra.canvas.ChmLinearOut64

::ChmLinearOut64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

getHalfStep(self) → bool

getMaxPath(self) → int

getMaxRingPath(self) → int

getMinPath(self) → int

setHalfStep(self, halfstep)

setMaxPath(self, maxPath_)

setMaxRingPath(self, maxRingPath_)

setMinPath(self, minPath_)

class schrodinger.infra.canvas.ChmMCSRecord

::ChmMCSRecord

DetailBitset = 1

DetailMapping = 2

DetailNone = 0

__init__(*args, **kwargs)

abCount

atomCount

atoms

bondCount

bonds

code

containmentGroup

fepNoRingBreak = 1

fepNone = 0

fepRingBreak = 2

findInvalidAtomsAndBonds(self, mol) → std::pair< ChmBitset,ChmBitset >

fixInvalidAtomsAndBonds(self, mol, atomPositionsToRemove, bondPositionsToRemove)

m_score

mapAtoms

mapBonds

markMappedAtomsAndBonds(self, mol)

mcsSmarts

molCount

molID

molSMILES

page

policy

printCSVHeader(self, os, outputDelim)

printCSVProperties(self, os, mol, outputDelim, oneBased, wantUniqueSMILES)

printPWHeader(self, os, outputDelim)

score(self) → double

setAsMaeProperties(self, ctHandle, molTitle, colorInt)

setAsSDProperties(self, mol)

weight(self) → double

wscore(self) → double

class schrodinger.infra.canvas.ChmMaccsOut32

::ChmMaccsOut32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

class schrodinger.infra.canvas.ChmMaccsOut64

::ChmMaccsOut64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

class schrodinger.infra.canvas.ChmMatch

::ChmMatch

__init__(*args, **kwargs)

getMatchedAtoms(self) → ChmAtoms

getMatchedAtomsInfo(self) → SwigChmAtomIntPairVector

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

class schrodinger.infra.canvas.ChmMatchEx

::ChmMatchEx

__init__(*args, **kwargs)

getMatchedAtomIndices(self, base=0) → std::vector< int,std::allocator< int > >

getMatchedAtoms(self) → ChmAtoms

getMatchedAtomsInfo(self) → SwigChmAtomIntPairVector

getMatchedBondIndices(self, base=0) → std::vector< int,std::allocator< int > >

getMatchedBonds(self) → ChmBonds

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

class schrodinger.infra.canvas.ChmMatchExIterator

::ChmIterator< ChmMatchEx >

__init__(*args, **kwargs)

__len__()

Return len(self).

asVector(self) → std::vector< ChmMatchEx,std::allocator< ChmMatchEx > > const &

asVector(self) → std::vector< ChmMatchEx,std::allocator< ChmMatchEx > >

at(self, index) → ChmMatchEx

at(self, index) → ChmMatchEx

checked random access

chmtostring(self) → std::string

hasNext(self) → bool

hasPrev(self) → bool

isValid(self) → bool

next(self) → ChmMatchEx

prev(self) → ChmMatchEx

rewind(self)

size(self) → int

sort(self)

class schrodinger.infra.canvas.ChmMatchIterator

::ChmIterator< ChmMatch >

__init__(*args, **kwargs)

__len__()

Return len(self).

asVector(self) → std::vector< ChmMatch,std::allocator< ChmMatch > > const &

asVector(self) → std::vector< ChmMatch,std::allocator< ChmMatch > >

at(self, index) → ChmMatch

at(self, index) → ChmMatch

checked random access

chmtostring(self) → std::string

hasNext(self) → bool

hasPrev(self) → bool

isValid(self) → bool

next(self) → ChmMatch

prev(self) → ChmMatch

rewind(self)

size(self) → int

sort(self)

class schrodinger.infra.canvas.ChmMatcherData

::ChmMatcherData

__init__(*args, **kwargs)

allowRelative

hydrogensInterchangeable

ignoreImplicitHydrogens

limit

mol

query

rigorousValidationOfSource

unique

class schrodinger.infra.canvas.ChmMatches

::ChmMatches

__init__(*args, **kwargs)

filter(self, atoms) → ChmMatches

class schrodinger.infra.canvas.ChmMatchesEx

::ChmMatchesEx

__init__(*args, **kwargs)

filter(self, atoms) → ChmMatchesEx

class schrodinger.infra.canvas.ChmMatrixUnsignedInt

::ChmMatrix< uint >

__init__(*args, **kwargs)

autoScale(self, tolerance=1.0e-24)

base(self) → unsigned int const *

center(self)

chmtostring(self) → std::string

clear(self)

cols(self) → uint

doubleCenter(self)

fastItem(self, i, j) → unsigned int &

non virtual!!

fastReadItem(self, i, j) → unsigned int const &

non virtual!!

fill(self, value)

getColumnMeans(self, means)

getColumnMeansAndDeviations(self, means, stdDeviations)

getCovariance(self, covariance)

getCovariance(self, rhs, covariance) → None

getCovariance(self, covariance, means) → None

getCovariance(self, covariance, means, scalingFactors, tolerance=1.0e-24) → None

getDM(self, distanceMatrix, lambda1=2, lambda2=0.5)

get pairwise distances- generalized minkowski metric , default to euclidean

dij = pow( pow(sum(dx), lamba1 ), lamdba2 )

getLaplacian(self, laplacian)

getLaplacian(self, laplacian) → None

getMahalanobisDM(self, distanceMatrix, lambda1=2, lambda2=0.5) → int

getRMSD(self, rmsd)

getRMSD(self, rhs, rmsd) → None

getScaledCovariance(self, covariance, tolerance=1.0e-24)

getScaledCovariance(self, rhs, covariance, tolerance=1.0e-24) → None

getScaledMahalanobisDM(self, distanceMatrix, lambda1=2, lambda2=0.5, tolerance=1.0e-24) → int

invert(self)

isSquare(self) → bool

item(self, i, j) → unsigned int &

pivot(self, piv) → ChmMatrixUnsignedInt

pivot(self, piv, fromIndex, toIndex) → ChmMatrixUnsignedInt

readItem(self, i, j) → unsigned int const &

resize(self, dim)

resize(self, rows, cols) → None

rows(self) → uint

swap(self, rhs)

transpose(self) → ChmMatrixUnsignedInt

type(self) → bool

class schrodinger.infra.canvas.ChmMinimalRPParser

::ChmMinimalRPParser

__init__(*args, **kwargs)

m_xvarNames

m_yvarNames

writePredictions(self, filename, namefield='name', delim='\t', extraParameter=-1)

class schrodinger.infra.canvas.ChmMmctAdaptor

::ChmMmctAdaptor

NoStereo = 0

StereoFromAnnotation = 3

StereoFromAnnotationAndGeometry = 5

StereoFromAnnotationAndGeometry_Safe = 6

StereoFromAnnotation_Safe = 4

StereoFromGeometry = 1

StereoFromGeometry_Safe = 2

__init__(*args, **kwargs)

static applyBondOrdersAndCharges(source, dest)

static calculateSASA(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, excludeH=True, divideByTotalAtomSurfaceArea=False, usePBC=False) → double

static calculateSASA(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False, usePBC=False) → double

static calculateSASA(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False, usePBC=False) → double

static calculateSASAByAtom(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, excludeH=True, divideByTotalAtomSurfaceArea=False, usePBC=False) → std::vector< double,std::allocator< double > >

static calculateSASAByAtom(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False, usePBC=False) → std::vector< double,std::allocator< double > >

static calculateSASAByAtom(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False, usePBC=False) → std::vector< double,std::allocator< double > >

static calculateVolume(ctHandle, gridAngstroms=1.0, excludeH=True) → double

static collectMaeProperties(maefile, props, wantMMStereo, pf)

create(self, a_ctHandle, a_mol, stereo=NoStereo, hydrogenTreatment=H_ExplicitOnly, wantProperties=True, wantMMStereoProps=False, readAtomBondProperties=True, allowRadicals=False)

create(self, a_ctHandle, stereo=NoStereo, hydrogenTreatment=H_ExplicitOnly, wantProperties=True, wantMMStereoProps=False, readAtomBondProperties=True, allowRadicals=False) → ChmMol

create(self, a_mol, wantProperties=True, hydrogenTreatment=H_AsWritten) → MM_Index

Overload 1: This is the main function used to create ChmMol object for a given Ct

Overload 2: overload of above that returns the molecule instead

Overload 3: overload of above that returns the molecule instead

Overload 4: overload of above that returns the molecule instead

Overload 5: overload of above that returns the molecule instead

Overload 6: overload of above that returns the molecule instead

Overload 7: overload of above that returns the molecule instead

Overload 8: overload of above that returns the molecule instead

Overload 9: This is the main function used to create ct from ChmMol,

Overload 10: This is the main function used to create ct from ChmMol,

Overload 11: This is the main function used to create ct from ChmMol,

static estimateRecordCount(maefile, scanDepth, isExact) → uint64

This function opens the input maestro file and estimates the total record count

getAcyclicBonds(self, a_ctHandle) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

getAromaticityInfo(self, a_ctHandle) → std::vector< bool,std::allocator< bool > >

returns vector of size (numAtoms> with boolean isAromatic;

static getComponents(source, mappings) → std::vector< ChmMMIndex,std::allocator< ChmMMIndex > >

static getComponents(source) → std::vector< ChmMMIndex,std::allocator< ChmMMIndex > >

getRingBonds(self, a_ctHandle) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

getTitle(self, maestring) → std::string

kekulize(self, target) → bool

load(self, maesource, rf, mols, positions, offset, blockSize, stereo, hydrogenTreatment, wantProperties, wantMMStereoProps, readPartial, fieldAsName, textOnly, decode, wantMolData) → bool

readProperties(self, a_ctHandle, properties, wantMMStereoProps, decode)

readProperties(self, maestring, properties, wantMMStereoProps, stripOutProp, decode) → bool

Overload 1: just reads the properties from a ct handle

Overload 2: just reads the properties from a a string

static safeDelete(ctHandle, warn=False)

delete Ct handle.

simpleLoad(self, maefile, decode=False, wantEmpty=True) → std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoadWithFilter(self, maefile, logicalRowFilter, decode=False, wantEmpty=True) → std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoadWithFilterRegEx(self, maefile, filter, regularExpressionToMatch, decode=False, wantEmpty=True) → std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoadWithFilterRegExs(self, maefile, filter, regularExpressionsToMatch, decode=False, wantEmpty=True) → std::vector< ChmMol,std::allocator< ChmMol > >

schrodinger.infra.canvas.ChmMmctAdaptor_applyBondOrdersAndCharges(source, dest)

schrodinger.infra.canvas.ChmMmctAdaptor_calculateSASA(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, excludeH=True, divideByTotalAtomSurfaceArea=False, usePBC=False) → double

schrodinger.infra.canvas.ChmMmctAdaptor_calculateSASA(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False, usePBC=False) → double

schrodinger.infra.canvas.ChmMmctAdaptor_calculateSASA(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False, usePBC=False) → double

schrodinger.infra.canvas.ChmMmctAdaptor_calculateSASAByAtom(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, excludeH=True, divideByTotalAtomSurfaceArea=False, usePBC=False) → std::vector< double,std::allocator< double > >

schrodinger.infra.canvas.ChmMmctAdaptor_calculateSASAByAtom(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False, usePBC=False) → std::vector< double,std::allocator< double > >

schrodinger.infra.canvas.ChmMmctAdaptor_calculateSASAByAtom(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False, usePBC=False) → std::vector< double,std::allocator< double > >

schrodinger.infra.canvas.ChmMmctAdaptor_calculateVolume(ctHandle, gridAngstroms=1.0, excludeH=True) → double

schrodinger.infra.canvas.ChmMmctAdaptor_collectMaeProperties(maefile, props, wantMMStereo, pf)

schrodinger.infra.canvas.ChmMmctAdaptor_estimateRecordCount(maefile, scanDepth, isExact) → uint64

This function opens the input maestro file and estimates the total record count

schrodinger.infra.canvas.ChmMmctAdaptor_getComponents(source, mappings) → std::vector< ChmMMIndex,std::allocator< ChmMMIndex > >

schrodinger.infra.canvas.ChmMmctAdaptor_getComponents(source) → std::vector< ChmMMIndex,std::allocator< ChmMMIndex > >

schrodinger.infra.canvas.ChmMmctAdaptor_safeDelete(ctHandle, warn=False)

delete Ct handle.

class schrodinger.infra.canvas.ChmMmctSmilesGenerator

::ChmMmctSmilesGenerator

__init__(*args, **kwargs)

canonicalize(self, smiles) → std::string

getHashCode(self, a_ctHandle, arg3=StereoFromAnnotationAndGeometry) → uint

getHashCode64(self, a_ctHandle, arg3=StereoFromAnnotationAndGeometry) → uint64

getSMARTS(self, a_ctHandle, arg3=H_Default, arg4=X_Default, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, wantCharge=True) → std::string

getSmiles(self, a_ctHandle, arg3=StereoFromAnnotationAndGeometry, wildCardHeavyAtoms=False) → std::string

generate smiles strings for a given ct

getSmilesAndMap(self, a_ctHandle, arg3=StereoFromAnnotationAndGeometry) → std::string

mapping holds one-based ct atom numbers position 0 in the smiles corresponds to the atom whose one-based index is stored at position 0 in the mapping

getSubsetSMARTS(self, a_ctHandle, atomInclusionMask, markRings=False, arg5=H_Default, arg6=X_Default, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, wantCharge=True) → std::string

getTautomerCode(self, a_ctHandle, arg3=StereoFromAnnotationAndGeometry) → uint

getTautomerCode64(self, a_ctHandle, arg3=StereoFromAnnotationAndGeometry) → uint64

getUniqueSmiles(self, a_ctHandle, arg3=StereoFromAnnotationAndGeometry, wildCardHeavyAtoms=False) → std::string

getUniqueSmilesAndMap(self, a_ctHandle, arg3=StereoFromAnnotationAndGeometry) → std::string

mapping holds one-based ct atom numbers position 0 in the smiles corresponds to the atom whose one-based index is stored at position 0 in the mapping

neutralize(self, smiles) → std::string

neutralize2(self, smiles) → std::string

setCharge(self, a_val)

charge on/off (default on)

setChiral(self, a_val)

set options functions chirality on/off (default on)

setForceAllBondOrders(self, a_val)

write implicit bond orders (-,:) (default off)

setForceHydrogens(self, a_val)

hydrogens as explicit atoms on/off (default off)

validateSmilesString(self, smiles) → bool

validateSmilesString(self, smiles, errorString) → bool

class schrodinger.infra.canvas.ChmModelParser

::ChmModelParser

__init__(*args, **kwargs)

clear(self)

static getResultsParser(file) → ChmModelParser

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

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

read(self, arg2, arg3)

writePredictions(self, filename, namefield='name', delim='\t', extraParameter=-1)

schrodinger.infra.canvas.ChmModelParser_getResultsParser(file) → ChmModelParser

class schrodinger.infra.canvas.ChmModelReporter

::ChmModelReporter

__init__(*args, **kwargs)

appendErr(self, str)

appendLog(self, str)

appendWarning(self, str)

getStatus(self) → ChmModelStatus

m_maxFactor

m_method

m_qsqr

m_rcorr

m_regB

m_regBSE

m_regF

m_regP

m_regSD

m_regStability

m_regVarNames

m_regrsqr

m_regrsqrCv

m_rmsErr_test

m_rmsErr_train

m_testList

m_trainList

m_yobsBinTestBayes

m_yobsBinTrainBayes

m_yobsLabelTestBayes

m_yobsLabelTrainBayes

m_yobsTest

m_yobsTestNnet

m_yobsTestOK

m_yobsTestOKNnet

m_yobsTrain

m_yobsTrainNnet

m_ypredBinTestBayes

m_ypredBinTrainBayes

m_ypredLabelTestBayes

m_ypredLabelTrainBayes

m_ypredTestNnetVec

m_ypredTestVec

m_ypredTrainNnetVec

m_ypredTrainVec

printErr(self, os)

printLog(self, os)

printWarning(self, os)

setStatus(self, s)

success(self) → bool

static translateCode(st) → std::string

schrodinger.infra.canvas.ChmModelReporter_translateCode(st) → std::string

class schrodinger.infra.canvas.ChmModelTypeInfo

::ChmModelTypeInfo

__init__(*args, **kwargs)

getChmDescriptorInfo(self) → std::vector< ChmDescriptorInfo,std::allocator< ChmDescriptorInfo > >

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

getModelType(self) → ChmModelTypeInfo::modelType

getSource(self) → std::string

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

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

modelBayes = 11

modelKPLS = 14

modelMLR = 16

modelMultiKPLS = 15

modelNnet = 13

modelPCAReg = 17

modelPLS = 18

modelRP = 12

modelUnknown = 0

show(self, testMode=False) → std::string

class schrodinger.infra.canvas.ChmMol

::ChmMol

__init__(*args, **kwargs)

addAtom(self, arg2)

addBond(self, a1, a2, order=Single) → ChmBond

addDoubleBond(self, a1, a2, cisTrans=BondNotApplicable)

addMoleculeRaw(self, arg2, arg3)

addSingleBond(self, a1, a2)

addTripleBond(self, a1, a2)

addZeroOrderBond(self, a1, a2)

areBonded(self, atomIndex1, atomIndex2) → bool

checkCoords(self)

checkStereo(self)

chiralCenters(self, includeUndefined=False) → int

chmtostring(self) → std::string

cisTransBonds(self) → int

clear(self)

clearAtomProperty(self, atom, key)

clearConfs(self)

clearCoords(self)

clearProperties(self)

clone(self, randomizeNumbering=False, atomsToDiscard=None, raw=False) → ChmMol

cloneProperties(self, mol)

deleteProperty(self, key)

destroyAtom(self, arg2, packIndices=True)

destroyAtom(self, index, packIndices=True) → None

removes and frees given atom and its bonds

destroyBond(self, bond)

destroyBond(self, index) → None

removes and frees given bond

static fromMAE(maeString) → ChmMol

static fromMDL(arg1, autoName=False, validateCisTrans=False, perceiveHybridization=True, rigorousAromaticity=True) → ChmMol

static fromSMILES()

genCoords(self)

getAtom(self, arg2) → ChmAtom

getAtomCount(self, wantImplicitHydrogens=False) → int

getAtoms(self, wantImplicitHydrogens=False) → ChmAtoms

getAtomsByMask(self, mask) → ChmAtoms

getBond(self, arg2) → ChmBond

getBond(self, a1, a2) → ChmBond

getBondCount(self, wantImplicitHydrogens=False) → int

getBondMaskForAtomMask(self, atomMask) → ChmBitset

getBonds(self, wantImplicitHydrogens=False) → ChmBonds

getBondsForAtomMask(self, atomMask) → ChmBonds

getComponentCount(self) → uint

getConformation(self, arg2) → ChmConformation

getConformationCount(self) → int

getConnectionTable(self, wantImplicitHydrogens=False) → ChmSymmetricMatrixUnsignedInt

getConnectionTableWithBondOrders(self, wantImplicitHydrogens=False, wantMaeOrder=False) → ChmSymmetricMatrixUnsignedInt

getCoordinates(self, coords)

getDistanceMatrix(self, wantImplicitHydrogens=False, storeInfiniteDistancesAsZero=True, throwExceptionIfMultipleFragments=False) → ChmSymmetricMatrixUnsignedInt

getDistanceMatrix3D(self, wantImplicitHydrogens=False, wantRoot=True) → ChmSymmetricMatrix< float >

getFirstImplicitHydrogenIndex(self) → int

getHash(self) → uint

getHash64(self) → uint64

getHeavyAtomCount(self) → int

getHeavyAtoms(self) → ChmAtoms

getHeavyBondCount(self) → int

getHeavyBonds(self) → ChmBonds

getMW(self) → double

getName(self) → std::string

getNetCharge(self) → int

getProperties(self) → PROPDATA

getPropertiesBegin(self) → CHMMOLPROPINFO::const_iterator

getPropertiesEnd(self) → CHMMOLPROPINFO::const_iterator

getPropertiesFor(self, atom) → std::vector< PROPPAIR,std::allocator< PROPPAIR > >

getPropertiesFor(self, bond) → std::vector< PROPPAIR,std::allocator< PROPPAIR > >

getProperty(self, arg2) → std::string

getPropertyCount(self) → size_t

getPropertyForAtom(self, arg2, arg3) → std::string

getPropertyForBond(self, arg2, arg3) → std::string

getRingCount(self, deterministic=False) → int

getRotatableBonds(self) → ChmBonds

getSMARTS(self, arg2=H_Default, arg3=X_Default, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False, wantCharge=True) → std::string

getSMARTS(self, atomMask, bondMask, markRings=False, arg5=H_Default, arg6=X_Default, wantStereo=False, wantMapping=False, overrideAtomLabels=None, overrideBondLabels=None, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False, wantCharge=True) → std::string

getSMARTS(self, atomMask, markRings=False, arg4=H_Default, arg5=X_Default, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False, wantCharge=True) → std::string

getSMARTS(self, atomInfo, bondInfo, arg4=H_Default, arg5=X_Default, wantStereo=True, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False, wantCharge=True) → std::string

getTautomerCode(self, considerEZStereo=True, considerRSStereo=True) → uint

getTautomerCode64(self, considerEZStereo=True, considerRSStereo=True) → uint64

getUserData(self) → uint

getZeroOrderBonds(self) → std::vector< CHMZOBITEM,std::allocator< CHMZOBITEM > >

has2DCoords(self, duplicateOK=False, implicitToo=True) → bool

has3DCoords(self, duplicateOK=False, implicitToo=True) → bool

hasAllHydrogens(self) → bool

hasBondDirectionHint(self) → bool

hasCoords(self) → bool

hasDistinctCoords(self, arg2=H_ExplicitOnly) → bool

hasImplicitHydrogens(self) → bool

hasIsotope(self) → bool

hasProperty(self, arg2) → bool

isEmpty(self) → bool

isKekulized(self) → bool

kekulize(self)

makeWildcard(self)

markHydrogens(self, arg2) → int

markProchiral(self, onlyTerminal=False)

Add unnatural isotopes to atoms that can be geometrically but not topologically distinguished - for example two topologically identical atoms on one end of a double bond where the atoms on the other end are different. :type onlyTerminal: boolean, in, optional :param onlyTerminal: skips such processing unless the atoms are

terminal as is required by MCS perception, for example

needsBondDirectionHint(self) → bool

neutralize(self)

packIndices(self) → bool

returns true if atom indices have changed packing preserves relative ordering but removes gaps in atom indices

perceiveHybridization(self)

perceiveHydrogens(self, wantRadicals=False)

check for missing implicit hydrogens and add them if required

perceiveRings(self, rigorousAromaticity=False, force=False)

placeHydrogens(self)

removeAtom(self, atom, packIndices=True)

atom remains usable but is no longer in molecule destroys bonds involving this atom

removeAtomByIndex(self, index, packIndices=True)

removeAtoms(self, atoms, packIndices=True)

removeFormalCharges(self)

removeHydrogens(self, hydrogenTreatment)

removeHydrogens(self) → None

remove all hydrogens

removeImplicitHydrogens(self)

remove only implicit hydrogens

removeNonPolarHydrogens(self)

setAbsoluteChiralityFlag(self, on)

setAtomProperty(self, atom, key, value)

setBondProperty(self, bond, key, value)

setCoordinates(self, newCoords)

setMaeProperty(self, key, value)

setMaeProperty(self, key, value) → None

setMaeProperty(self, key, value, precision=DEFAULT_PROP_PRECISION) → None

setMaeProperty(self, key, value) → None

setName(self, arg2)

setProperty()

setUserData(self, data)

store(self, os, wantCoordinates=True, overrideName=None)

subset(self, desiredAtoms, breakAliphaticRings=True, breakAromaticRings=False) → ChmMol

toCanonicalSMILES(self, wantAllH=False, test=False) → std::string

toChmQuery(self, allH=False, wantX=False) → ChmQuery

toChmQuery(self, atomInfo, bondInfo) → ChmQuery

toGenericSMARTS(self, wantBondOrder=False, wantCharge=False, wantAromaticity=False, genericAtomToo=False, wantStereo=False, wantAllHydrogens=False, wantAllClosureBonds=False) → std::string

toMAE(self, wantProperties, addH) → std::string

toMDL(self, arg2=H_Default, withprops=True, withCoords=True, overrideName=None, v3format=0, wantDollarSigns=True, echoMaeType=False, check=False) → std::string

toMDL(self, os, arg3=H_Default, withprops=True, withCoords=True, overrideName=None, v3format=0, wantDollarSigns=True, echoMaeType=False, check=False) → None

toSMILES(self, wantKekulized=False, wantAllH=False, wantStereo=True, wantCharge=True, test=False, forceOrder=False, rigorousAromaticity=True) → std::string

toString(self) → std::string

toUniqueSMILES(self, wantAllH=False, test=False) → std::string

translateAlleneStereo(self, atomChain, MorP)

translateCisTransStereo(self, atomChain, CisTrans, permissive=0)

translateTetrahedralStereo(self, central, priorities, RorS, permissive=0)

Sets smiles chirality of central ChmAtom based on an R or S chirality :type central: ChmAtom :param central: central chiral atom :type priorities: std::vector< ChmAtom,std::allocator< ChmAtom > > :param priorities: vector of atoms in CIP priority order :type RorS: int :param RorS: R or S chirality

undefinedChiralCenters(self) → int

unmarkProchiral(self)

removes any unnatural isotopes that may have been added by markProchiral()

validateCisTrans(self)

schrodinger.infra.canvas.ChmMol_fromMAE(maeString) → ChmMol

schrodinger.infra.canvas.ChmMol_fromMDL(arg1, autoName=False, validateCisTrans=False, perceiveHybridization=True, rigorousAromaticity=True) → ChmMol

schrodinger.infra.canvas.ChmMol_fromSMILES()

class schrodinger.infra.canvas.ChmMolprint2D32

::ChmMolprint2D32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

class schrodinger.infra.canvas.ChmMolprint2D64

::ChmMolprint2D64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

class schrodinger.infra.canvas.ChmMultiYDelimitedPatterns

::ChmMultiYDelimitedPatterns

__init__(*args, **kwargs)

close(self)

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

getDelimiter(self) → char

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

getIncludedColIndexes(self) → std::vector< size_t,std::allocator< size_t > >

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

getIncludedCols(self) → size_t

getIncludedXvarNames(self, indexes) → std::vector< std::string,std::allocator< std::string > >

getLastLine(self) → std::string

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

getObservationIncludedIndexes(self) → std::vector< size_t,std::allocator< size_t > >

getObservationIndexes(self) → std::vector< size_t,std::allocator< size_t > >

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

getTotalCols(self) → size_t

getValuesOfColumn(self, index, values)

hasHeader(self) → bool

setObservationNames(self, names)

skip(self)

class schrodinger.infra.canvas.ChmObjChmAtomImpl

::ChmObj< ChmAtomImpl >

__init__(*args, **kwargs)

chmtostring(self) → std::string

debug(self) → std::string

getUID(self) → size_t

isValid(self) → bool

class schrodinger.infra.canvas.ChmObjChmAtomTyperImpl

::ChmObj< ChmAtomTyperImpl >

__init__(*args, **kwargs)

chmtostring(self) → std::string

debug(self) → std::string

getUID(self) → size_t

isValid(self) → bool

class schrodinger.infra.canvas.ChmObjChmMatcherImpl

::ChmObj< ChmSmartsMatcherImpl >

__init__(*args, **kwargs)

chmtostring(self) → std::string

debug(self) → std::string

getUID(self) → size_t

isValid(self) → bool

class schrodinger.infra.canvas.ChmObjChmQueryImpl

::ChmObj< ChmQueryImpl >

__init__(*args, **kwargs)

chmtostring(self) → std::string

debug(self) → std::string

getUID(self) → size_t

isValid(self) → bool

class schrodinger.infra.canvas.ChmPLSParser

::ChmPLSParser

__init__(*args, **kwargs)

getLoading(self, var, pcIndex) → std::string

Return the loading of a var on the <pcIndex>th factor (1-start)

getMaxFactor(self) → size_t

getMinFactor(self) → size_t

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

Returns a vector of 3 integers: #. of observations (molecules) in training set, test set and total.

getNumOfXvarsWithLoading(self) → size_t

getPearsonR(self, numFactor) → std::string

getQsqr(self, numFactor) → std::string

getRegF(self, numFactor) → std::string

getRegP(self, numFactor) → std::string

getRsqr(self, numFactor) → std::string

getRsqrCv(self, numFactor) → std::string

getSD(self, numFactor) → std::string

getStability(self, numFactor) → std::string

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

getTestSetPred(self, numFactor) → std::vector< std::string,std::allocator< std::string > >

getTestSetRMSE(self, numFactor) → std::string

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

getTrainingSetPred(self, numFactor) → std::vector< std::string,std::allocator< std::string > >

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

getYvar(self) → std::string

hasLoading(self, var) → bool

haveTestSet(self) → bool

haveTrainingSet(self) → bool

writePredictions(self, filename, namefield='name', delim='\t', extraParameter=-1)

class schrodinger.infra.canvas.ChmPairwiseFPIn

::ChmPairwiseFPIn

__init__(*args, **kwargs)

cols(self) → size_t

getColumn(self, column, columnData, castAsDistances=False)

getColumn(self, column, columnData, castAsDistances=False) → None

getColumnName(self, index) → std::string

getColumnNames(self) → std::vector< std::string,std::allocator< std::string > > const &

getData(self, castAsDistances=False) → std::vector< std::vector< float,std::allocator< float > >,std::allocator< std::vector< float,std::allocator< float > > > >

getData(self, data, castAsDistances=False) → None

getData(self, data, rowIDs, castAsDistances=False) → None

getData(self, data, castAsDistances=False) → None

getData(self, data, rowIDs, castAsDistances=False) → None

getData(self, data, castAsDistances=False) → None

getData(self, data, rowIDs, castAsDistances=False) → None

getRow(self, index, castAsDistances=False) → std::vector< float,std::allocator< float > >

getRow(self, index, row, castAsDistances=False) → bool

getRow(self, index, row, name, castAsDistances=False) → bool

getRowName(self, index) → std::string

isDistanceMatrix(self) → bool

isSimilarityMatrix(self) → bool

isSquare(self) → bool

isSymmetric(self) → bool

isValid(self) → bool

rows(self) → size_t

sortFilter(self, outputFileName, mode, topR=0, topC=0, outputFormat=0)

class schrodinger.infra.canvas.ChmPairwiseFPOut

::ChmPairwiseFPOut

hides whether input is 32 or 64 bits

__init__(*args, **kwargs)

formatBinary = 0

formatCSV = 1

formatLong = 3

formatWide = 2

getFlattening(self) → double

getHumanReadable(self) → bool

getLowerBound(self) → double

getMaximumViolations(self) → int

getMetric(self) → ChmMetricStyle

getOutputType(self) → ChmPairwiseFPOut::outputType

getUpperBound(self) → double

hasLowerBound(self) → bool

hasUpperBound(self) → bool

process(self, fpFileName, readBlockSize=1000)

process(self, fpFileName, start, end, readBlockSize=1000) → None

process(self, fpFileName1, fpFileName2, readBlockSize=1000) → None

process(self, fpFileName1, start1, end1, fpFileName2, start2, end2, readBlockSize=1000) → None

process(self, fpFileName1, start1, end1, fpFileName2, readBlockSize=1000) → None

process(self, fpFileName1, fpFileName2, start2, end2, readBlockSize=1000) → None

Overload 1: for all pairs between files

Overload 2: fpFileName1 will appear as rows and fpFileName2 will appear as columns

Overload 3: fpFileName1 will appear as rows and fpFileName2 will appear as columns

setCustomMetric(self, metric)

setFlattening(self, value=25)

default is no flattening- range typically 0 to 100

setHumanReadable(self, on)

setLowerBound(self, value)

setMaximumViolations(self, value)

setMetric(self, style)

setOutputType(self, on)

setTverskyMetric(self, alpha, beta)

setUpperBound(self, value)

class schrodinger.infra.canvas.ChmPairwiseFPOut32

::ChmPairwiseFPOut32

__init__(*args, **kwargs)

getFlattening(self) → double

getHumanReadable(self) → bool

getLowerBound(self) → double

getMaximumViolations(self) → int

getMetric(self) → ChmMetricStyle

getOutputType(self) → ChmPairwiseFPOut::outputType

getUpperBound(self) → double

hasLowerBound(self) → bool

hasUpperBound(self) → bool

process(self, fpFileName, readBlockSize=1000)

process(self, fpFileName, start, end, readBlockSize=1000) → None

process(self, fpFileName1, fpFileName2, readBlockSize=1000) → None

process(self, fpFileName1, start1, end1, fpFileName2, start2, end2, readBlockSize=1000) → None

Overload 1: for all pairs between files

Overload 2: fpFileName1 will appear as rows and fpFileName2 will appear as columns

Overload 3: fpFileName1 will appear as rows and fpFileName2 will appear as columns

setCustomMetric(self, metric)

setFlattening(self, value=25)

setHumanReadable(self, on)

setLowerBound(self, value)

setMaximumViolations(self, value)

setMetric(self, style)

setOutputType(self, on)

setUpperBound(self, value)

class schrodinger.infra.canvas.ChmPairwiseFPOut64

::ChmPairwiseFPOut64

__init__(*args, **kwargs)

getFlattening(self) → double

getHumanReadable(self) → bool

getLowerBound(self) → double

getMaximumViolations(self) → int

getMetric(self) → ChmMetricStyle

getOutputType(self) → ChmPairwiseFPOut::outputType

getUpperBound(self) → double

hasLowerBound(self) → bool

hasUpperBound(self) → bool

process(self, fpFileName, readBlockSize=1000)

process(self, fpFileName, start, end, readBlockSize=1000) → None

process(self, fpFileName1, fpFileName2, readBlockSize=1000) → None

process(self, fpFileName1, start1, end1, fpFileName2, start2, end2, readBlockSize=1000) → None

Overload 1: for all pairs between files

Overload 2: fpFileName1 will appear as rows and fpFileName2 will appear as columns

Overload 3: fpFileName1 will appear as rows and fpFileName2 will appear as columns

setCustomMetric(self, metric)

setFlattening(self, value=25)

setHumanReadable(self, on)

setLowerBound(self, value)

setMaximumViolations(self, value)

setMetric(self, style)

setOutputType(self, on)

setUpperBound(self, value)

class schrodinger.infra.canvas.ChmPairwiseOut32

::ChmPairwiseOut32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generate(self, distanceMatrix) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

generateMap(self, distanceMatrix) → ChmFPMap32

set3D(self, on)

use atom xyz instead of topological distances

setBinWidth(self, width)

define width of bin size

setFuzzyDistance(self, fuzzy)

if distance is within this distance of a boundary, assign it to both bins

setMaxDistance(self, max)

ignore distances above this mark

setMinDistance(self, min)

ignore distances below this mark

class schrodinger.infra.canvas.ChmPairwiseOut64

::ChmPairwiseOut64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generate(self, distanceMatrix) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

generateMap(self, distanceMatrix) → ChmFPMap64

set3D(self, on)

use atom xyz instead of topological distances

setBinWidth(self, width)

define width of bin size

setFuzzyDistance(self, fuzzy)

if distance is within this distance of a boundary, assign it to both bins

setMaxDistance(self, max)

ignore distances above this mark

setMinDistance(self, min)

ignore distances below this mark

class schrodinger.infra.canvas.ChmPathTools

::ChmPathTools

__init__(*args, **kwargs)

static classifyAtoms(mol, atomClasses)

static computeLaplacian(mol) → ChmSymmetricMatrix< int >

static computeLaplacian(connectionTable, degrees) → ChmSymmetricMatrix< int >

static computePathsUpToLength(mol, length) → ChmSymmetricMatrixUnsignedInt

static computeShortestPaths(connectionTable, zeroOutDisconnected=True, throwExceptionIfDisconnnected=True) → ChmSymmetricMatrixUnsignedInt

static deriveMapping(source, sourcemcs, reference, referencemcs, mapatoms, mapbonds, rmsd, flipY) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

static deriveMapping(source, reference, alignBy, rmsd, flipY) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

static fuseRings(n)

when n is 0 (a legal but uncommon usage), all rings atoms are combined even if they are non-adjacent

static getComponentCount(mol) → uint

static getComponents(mol) → std::vector< ChmMol,std::allocator< ChmMol > >

static getComponents(mol, mappings) → std::vector< ChmMol,std::allocator< ChmMol > >

static getComponentsMappings(mol) → std::vector< std::vector< uint,std::allocator< uint > >,std::allocator< std::vector< uint,std::allocator< uint > > > >

static getCoreAtoms(mol, desiredHeavyAtomCount=20, binWidth=0.5) → ChmBitset

static getDistancesToCentroid(data, distancesToCentroid)

static getFeaturePaths(mol, atomsFeature1, atomsFeature2)

static getSSSR(mol, deterministic=False)

returns atom Numbers of acyclics and SSSRs in mol deterministic flag will return additional rings sets in excess of the frerejacques number that are degenerate for example cubane will produce 5 SSSR rings with deterministic=false. Half of the atoms will be part of 3 rings and the other half part of two. How this is partitioned depends on the original atom numbering. By supplying deterministic=true, 6 non-degenerate SSSR rings are returned with each atom belonging to 3 of them.

static getSSSRAndAcyclicAtoms(mol, deterministic=False)

static getShortestPathsBetweenAtoms(mol, startAtomIndex, endAtomIndex)

static getShortestPathsBetweenAtomsWithSideChains(mol, startAtomIndex, endAtomIndex)

static getSymmetryGroups(mol, groups, wantEZStereo=True, wantRSStereo=True, wantHydrogens=False, depth=10, atomTyping=7)

static getmmsymLikeGroup(mol, atomTyping) → std::vector< int,std::allocator< int > >

static isConnected(mol) → bool

static scoreConnections(mol, atom, ignoreAtoms, wantRingLogic) → std::vector< connectInfo,std::allocator< connectInfo > >

static scoreConnections(mol, bond, ignoreAtoms) → std::vector< connectInfo,std::allocator< connectInfo > >

static strip(mol) → ChmMol

static stripToScaffold(mol) → ChmMol

schrodinger.infra.canvas.ChmPathTools_classifyAtoms(mol, atomClasses)

schrodinger.infra.canvas.ChmPathTools_computeLaplacian(mol) → ChmSymmetricMatrix< int >

schrodinger.infra.canvas.ChmPathTools_computeLaplacian(connectionTable, degrees) → ChmSymmetricMatrix< int >

schrodinger.infra.canvas.ChmPathTools_computePathsUpToLength(mol, length) → ChmSymmetricMatrixUnsignedInt

schrodinger.infra.canvas.ChmPathTools_computeShortestPaths(connectionTable, zeroOutDisconnected=True, throwExceptionIfDisconnnected=True) → ChmSymmetricMatrixUnsignedInt

schrodinger.infra.canvas.ChmPathTools_deriveMapping(source, sourcemcs, reference, referencemcs, mapatoms, mapbonds, rmsd, flipY) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

schrodinger.infra.canvas.ChmPathTools_deriveMapping(source, reference, alignBy, rmsd, flipY) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

schrodinger.infra.canvas.ChmPathTools_fuseRings(n)

when n is 0 (a legal but uncommon usage), all rings atoms are combined even if they are non-adjacent

schrodinger.infra.canvas.ChmPathTools_getComponentCount(mol) → uint

schrodinger.infra.canvas.ChmPathTools_getComponents(mol) → std::vector< ChmMol,std::allocator< ChmMol > >

schrodinger.infra.canvas.ChmPathTools_getComponents(mol, mappings) → std::vector< ChmMol,std::allocator< ChmMol > >

schrodinger.infra.canvas.ChmPathTools_getComponentsMappings(mol) → std::vector< std::vector< uint,std::allocator< uint > >,std::allocator< std::vector< uint,std::allocator< uint > > > >

schrodinger.infra.canvas.ChmPathTools_getCoreAtoms(mol, desiredHeavyAtomCount=20, binWidth=0.5) → ChmBitset

schrodinger.infra.canvas.ChmPathTools_getDistancesToCentroid(data, distancesToCentroid)

schrodinger.infra.canvas.ChmPathTools_getFeaturePaths(mol, atomsFeature1, atomsFeature2)

schrodinger.infra.canvas.ChmPathTools_getSSSR(mol, deterministic=False)

returns atom Numbers of acyclics and SSSRs in mol deterministic flag will return additional rings sets in excess of the frerejacques number that are degenerate for example cubane will produce 5 SSSR rings with deterministic=false. Half of the atoms will be part of 3 rings and the other half part of two. How this is partitioned depends on the original atom numbering. By supplying deterministic=true, 6 non-degenerate SSSR rings are returned with each atom belonging to 3 of them.

schrodinger.infra.canvas.ChmPathTools_getSSSRAndAcyclicAtoms(mol, deterministic=False)

schrodinger.infra.canvas.ChmPathTools_getShortestPathsBetweenAtoms(mol, startAtomIndex, endAtomIndex)

schrodinger.infra.canvas.ChmPathTools_getShortestPathsBetweenAtomsWithSideChains(mol, startAtomIndex, endAtomIndex)

schrodinger.infra.canvas.ChmPathTools_getSymmetryGroups(mol, groups, wantEZStereo=True, wantRSStereo=True, wantHydrogens=False, depth=10, atomTyping=7)

schrodinger.infra.canvas.ChmPathTools_getmmsymLikeGroup(mol, atomTyping) → std::vector< int,std::allocator< int > >

schrodinger.infra.canvas.ChmPathTools_isConnected(mol) → bool

schrodinger.infra.canvas.ChmPathTools_scoreConnections(mol, atom, ignoreAtoms, wantRingLogic) → std::vector< connectInfo,std::allocator< connectInfo > >

schrodinger.infra.canvas.ChmPathTools_scoreConnections(mol, bond, ignoreAtoms) → std::vector< connectInfo,std::allocator< connectInfo > >

schrodinger.infra.canvas.ChmPathTools_strip(mol) → ChmMol

schrodinger.infra.canvas.ChmPathTools_stripToScaffold(mol) → ChmMol

class schrodinger.infra.canvas.ChmPattern

::ChmPattern

__init__(*args, **kwargs)

__len__()

Return len(self).

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

chmtostring(self) → std::string

empty(self) → bool

getDouble(self, index) → double

getID(self) → std::string

getString(self, index, wasQuoted=None) → std::string

size(self) → uint

class schrodinger.infra.canvas.ChmPatterns

::ChmPatterns

__init__(*args, **kwargs)

getBitMask(self) → ChmBitset

getColMask(self) → ChmBitset

getColumnName(self, index) → std::string

getRowMask(self) → ChmBitset

hasNext(self) → bool

isNumericalCol(self, index) → bool

nextPattern(self) → ChmPattern

numericalCols(self) → size_t

rewind(self)

setBitMask(self, mask)

setColMask(self, mask)

setRowMask(self, mask)

skip(self, numberOfRows=1)

class schrodinger.infra.canvas.ChmProfiler

::ChmProfiler

__init__(*args, **kwargs)

compute(self, smiles, id)

compute(self, smiles, id, prop_pairs) → None

Overload 1: Computes a fingerprint and properties for the provided SMILES. Writes the fingerprint, id, SMILES and properties to the fingerprint file if a file name was supplied in the constructor. Use getFingerprintRef(), getFingerprintCopy() and getPropertyPairs() to retrieve the computed data.

Overload 2: Overloaded version that uses external properties rather than computed properties. May be used whether or not a fingerprint file is attached to the object. Property values may be integer, real or string, but they must be cast as strings.

getFingerprintCopy(self) → ChmSparseBitset

Returns an independent copy of the most recently computed fingerprint. This method should be used if the returned fingerprint must survive subsequent calls to compute().

getFingerprintRef(self) → ChmSparseBitset

Returns a reference to the most recently computed fingerprint. This method is preferred when invoking from Python, as it vastly reduces the memory built up from repeated calls through the Swig wrappers. However, the returned fingerprint will be overwritten by the next call to compute().

getPropertyPairs(self) → ChmProfilerPropPairs const &

Returns a reference to the most recently computed/provided properties. Computed properties follow the same order as PROFILER_PROPERTIES.

getRequestedProperties(self) → std::vector< std::string,std::allocator< std::string > > const &

Returns the names of the properties requested in the constructor, following the same order as PROFILER_PROPERTIES.

static get_num_aromatic_rings(mol) → int

Computes and returns the number of aromatic rings.

static get_num_rotatable_bonds(mol) → int

Computes and returns the number of rotatable bonds using logic borrowed from the Python function analyze.get_num_rotatable_bonds().

schrodinger.infra.canvas.ChmProfiler_get_num_aromatic_rings(mol) → int

Computes and returns the number of aromatic rings.

schrodinger.infra.canvas.ChmProfiler_get_num_rotatable_bonds(mol) → int

Computes and returns the number of rotatable bonds using logic borrowed from the Python function analyze.get_num_rotatable_bonds().

class schrodinger.infra.canvas.ChmQuartetOut32

::ChmQuartetOut32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generate(self, distanceMatrix) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

generateMap(self, distanceMatrix) → ChmFPMap32

set3D(self, on)

use atom xyz instead of topological distances

setBinWidth(self, width)

define width of bin size

setFuzzyDistance(self, fuzzy)

if distance is within this distance of a boundary, assign it to both bins

setMaxDistance(self, max)

ignore distances above this mark

setMinDistance(self, min)

ignore distances below this mark

class schrodinger.infra.canvas.ChmQuartetOut64

::ChmQuartetOut64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generate(self, distanceMatrix) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

generateMap(self, distanceMatrix) → ChmFPMap64

set3D(self, on)

use atom xyz instead of topological distances

setBinWidth(self, width)

define width of bin size

setFuzzyDistance(self, fuzzy)

if distance is within this distance of a boundary, assign it to both bins

setMaxDistance(self, max)

ignore distances above this mark

setMinDistance(self, min)

ignore distances below this mark

class schrodinger.infra.canvas.ChmQuery

::ChmQuery

MDL = 3

SMARTS = 2

SMILES = 1

UNKNOWN = 0

__init__(*args, **kwargs)

clear(self)

clone(self) → ChmQuery

static fromMDL(molData, v3, wantX) → ChmQuery

static fromMDLFile(source, v3, wantX) → ChmQuery

static fromMDLFile(fileName, v3, wantX) → ChmQuery

static fromSMARTS(smarts) → ChmQuery

static fromStream(inputstream) → ChmQuery

getABInfo(self, arg2, arg3, hydrogenOk) → ChmMol

getAtomCount(self) → int

getBondCount(self) → int

getFragmentCount(self) → int

getSearchKey(self) → ChmSearchKey

getSource(self) → std::string const &

getSourceType(self) → ChmQuery::sourceType

involvesAromaticity(self) → bool

involvesCisTrans(self) → bool

involvesHybridization(self) → bool

isIndexable(self) → bool

mapToSource(self, pos) → int

store(self, os)

toSMARTS(self) → std::string

static validateSMARTS(smarts) → std::pair< bool,std::string >

class schrodinger.infra.canvas.ChmQueryMatcher

::ChmQueryMatcher

__init__(*args, **kwargs)

clear(self)

clone(self) → ChmQueryMatcher

getAllowRelativeStereoMatches(self) → bool

getHydrogensInterchangeable(self) → bool

getImplicitHydrogensIgnored(self) → bool

getMatchCountLimit(self) → int

getUniqueFilter(self) → bool

hasExactMatch(self, query, mol) → bool

hasMatch(self, query, mol) → bool

hasMatchStartingWith(self, query, mol, startingAtom) → bool

hideMatched(self, query, mol)

hideNonMatched(self, query, mol)

match(self, query, mol) → ChmMatches

get match information in terms of ChmAtoms

matchCount(self, query, mol) → int

matchEx(self, query, mol) → ChmMatchesEx

gets match in terms of ChmAtoms and ChmBonds

matchMask(self, query, mol) → ChmBitsetIterator

get match information in terms of ChmBitsets which in turn represent zero-based atom indices.

matchMaskSubset(self, query, mol, subset) → ChmBitsetIterator

get match information in terms of ChmBitsets which in turn represent zero-based atom indices. will ignore matches having any atoms outside of subset

matchMasks(self, query, mol) → ChmAtomAndBondMasks

matchSubset(self, query, mol, subset) → ChmMatches

will ignore matches having any atoms outside of subset

matchTo(self, query, mol, startingAtom) → ChmMatches

matchToEx(self, query, mol, startingAtom) → ChmMatchesEx

matchToMask(self, query, mol, startingAtom) → ChmBitsetIterator

setAllowRelativeStereoMatches(self, on)

these flags are for relative stereochemistry support

setHydrogensInterchangeable(self, on)

setImplicitHydrogensIgnored(self, on)

setMatchCountLimit(self, limit)

limits the number of total matches returned for any query defaults to CHM_DEFAULT_QLIMIT, minimum is 1

setUniqueFilter(self, on)

schrodinger.infra.canvas.ChmQuery_fromMDL(molData, v3, wantX) → ChmQuery

schrodinger.infra.canvas.ChmQuery_fromMDLFile(source, v3, wantX) → ChmQuery

schrodinger.infra.canvas.ChmQuery_fromMDLFile(fileName, v3, wantX) → ChmQuery

schrodinger.infra.canvas.ChmQuery_fromSMARTS(smarts) → ChmQuery

schrodinger.infra.canvas.ChmQuery_fromStream(inputstream) → ChmQuery

schrodinger.infra.canvas.ChmQuery_validateSMARTS(smarts) → std::pair< bool,std::string >

class schrodinger.infra.canvas.ChmRadialOut32

::ChmRadialOut32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

getConsiderHydrogens(self) → bool

getConsiderStereoEZ(self) → bool

getConsiderStereoRS(self) → bool

getIterations(self) → int

getMinSize(self) → uint

setConsiderHydrogens(self, on)

setConsiderStereoEZ(self, on)

setConsiderStereoRS(self, on)

setIterations(self, iterations_)

setMinSize(self, minSize_)

class schrodinger.infra.canvas.ChmRadialOut64

::ChmRadialOut64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

getConsiderHydrogens(self) → bool

getConsiderStereoEZ(self) → bool

getConsiderStereoRS(self) → bool

getIterations(self) → int

getMinSize(self) → uint

setConsiderHydrogens(self, on)

setConsiderStereoEZ(self, on)

setConsiderStereoRS(self, on)

setIterations(self, iterations_)

setMinSize(self, minSize_)

class schrodinger.infra.canvas.ChmRandom

::ChmRandom

__init__(*args, **kwargs)

static fromSeed(seed) → ChmRandom

nextBitset(self, length, density) → ChmBitset

nextBitset(self, length, onBits) → ChmBitset

nextDouble(self) → double

nextGaussian(self, mean=0.0, stddev=1.0) → double

nextGaussianFast(self, mean=0.0, stddev=1.0) → double

nextInt(self) → uint

nextInt(self, n) → uint

nextInt64(self) → uint64

nextInt64(self, n) → uint64

nextPartition(self, length, numberOfBins, sortEachBin, memberships, binBase=0)

nextSelectWithReplacementSet(self, size, subset)

nextString(self, len) → std::string

nextSubset(self, length, density, subset)

nextSubset(self, length, numberToChoose, subset) → None

schrodinger.infra.canvas.ChmRandom_fromSeed(seed) → ChmRandom

class schrodinger.infra.canvas.ChmRangeFilter

::ChmRangeFilter

__init__(*args, **kwargs)

chmtostring(self) → std::string

count(self) → uint

excludeNext(self) → bool

static fromSubFormat(os) → ChmRangeFilter

getLast(self) → uint

getOpposite(self) → ChmRangeFilter

getOrder(self) → std::vector< uint,std::allocator< uint > > const &

includeNext(self) → bool

isDefault(self) → bool

isEOF(self) → bool

isEverything(self) → bool

isIndefinite(self) → bool

isSorted(self) → bool

static makeFilter(oneBasedLogicalItemsToInclude) → ChmRangeFilter

rewind(self)

resets to beginning

store(self, os)

toBitset(self, logicalSize) → ChmBitset

toBitsetExclude(self, logicalSize) → ChmBitset

toSubFormat(self, inputstream)

toVector(self, itemList, toEnd)

schrodinger.infra.canvas.ChmRangeFilter_fromSubFormat(os) → ChmRangeFilter

schrodinger.infra.canvas.ChmRangeFilter_makeFilter(oneBasedLogicalItemsToInclude) → ChmRangeFilter

class schrodinger.infra.canvas.ChmRangeUIDFilter

::ChmRangeUIDFilter

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

chmtostring(self) → std::string

contains(self, rhs) → bool

containsKey(self, key) → bool

count(self) → uint64

static fromBlob(raw) → ChmRangeUIDFilter

static fromFile(filename) → ChmRangeUIDFilter

getFirstItem(self) → uint64

getHash(self) → uint

getOrder(self) → std::vector< uint64,std::allocator< uint64 > > const *

hasNext(self) → bool

isEOF(self) → bool

isSorted(self) → bool

logicalSize(self) → uint64

next(self) → int64

rewind(self)

store(self, os)

toBlob(self) → std::string

toCSV(self, os)

toFile(self, filename)

toSQL(self, os)

toSet(self, uids)

toUIDS(self)

schrodinger.infra.canvas.ChmRangeUIDFilter_fromBlob(raw) → ChmRangeUIDFilter

schrodinger.infra.canvas.ChmRangeUIDFilter_fromFile(filename) → ChmRangeUIDFilter

class schrodinger.infra.canvas.ChmRowUIDFilter

::ChmRowUIDFilter

__init__(*args, **kwargs)

static fromFile(filename) → ChmRowUIDFilter

schrodinger.infra.canvas.ChmRowUIDFilter_fromFile(filename) → ChmRowUIDFilter

class schrodinger.infra.canvas.ChmSDReader

::ChmSDReader

__init__(*args, **kwargs)

static estimateRecordCount(filename, scanDepth=1000, isExact=None) → uint64

getError(self) → std::string

getLastRecordInfo(self)

getNameField(self) → std::string const &

getUnionOfDataFields(self, selectStr='1:', isUniform=False, removeNameField=False) → std::vector< std::string,std::allocator< std::string > >

hasError(self) → bool

hasNext(self) → bool

isV3000(self) → bool

next(self) → ChmMol

reset(self)

setNameField(self, nameField)

class schrodinger.infra.canvas.ChmSDReaderImpl

::ChmObj< ChmSDReaderImpl >

__init__(*args, **kwargs)

chmtostring(self) → std::string

debug(self) → std::string

getUID(self) → size_t

isValid(self) → bool

schrodinger.infra.canvas.ChmSDReader_estimateRecordCount(filename, scanDepth=1000, isExact=None) → uint64

class schrodinger.infra.canvas.ChmSMARTSOut32

::ChmSMARTSOut32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

class schrodinger.infra.canvas.ChmSMARTSOut64

::ChmSMARTSOut64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

class schrodinger.infra.canvas.ChmScaffold

::ChmScaffold

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

contains(self, scaffold, countExact=False, embed=False) → bool

contains(self, scaffold, subScaffolds, countExact=False, embed=False) → bool

Overload 1: Returns true if the supplied scaffold is a subscaffold of the current scaffold. If countExact is true, an exact match will be counted. If embed is true, this function will return true only if the supplied scaffold is not a true subscaffold, but yields an embedded match, which means one or more of its ring systems or linkers only partially match the corresponding ring systems or linkers of the current scaffold. For example, imidazole is an embedded subscaffold of benzimidazole.

Overload 2: Version that can be used to speedup repetitive calls by eliminating the need to regenerate subscaffolds of the current scaffold. It is assumed that subScaffolds was obtained by a call to the getSubScaffolds function of the current object.

Overload 3: Version that can be used to speedup repetitive calls by eliminating the need to regenerate subscaffolds of the current scaffold. It is assumed that subScaffolds was obtained by a call to the getSubScaffolds function of the current object.

Overload 4: Version that can be used to speedup repetitive calls by eliminating the need to regenerate subscaffolds of the current scaffold. It is assumed that subScaffolds was obtained by a call to the getSubScaffolds function of the current object.

containsFuzzy(self, scaffold, level=0, countExact=False, embed=False) → bool

containsFuzzy(self, scaffold, subScaffolds, level=0, countExact=False, embed=False) → bool

Overload 1: Returns true if the supplied scaffold is a fuzzy subscaffold of the current scaffold. See getFuzzyScaffold for details about fuzzy matching.

Overload 2: Version that can be used to speedup repetitive calls by eliminating the need to regenerate subscaffolds of the current scaffold.

Overload 3: Version that can be used to speedup repetitive calls by eliminating the need to regenerate subscaffolds of the current scaffold.

Overload 4: Version that can be used to speedup repetitive calls by eliminating the need to regenerate subscaffolds of the current scaffold.

Overload 5: Version that can be used to speedup repetitive calls by eliminating the need to regenerate subscaffolds of the current scaffold.

getAtomCount(self, wantHydrogens=False) → int

Returns the number of atoms in the scaffold. If wantHydrogens is false, only the heavy atom count will be returned. If wantHydrogens is true, the count of heavy atoms + all hydrogens will be returned.

getFuzzyScaffold(self, level=0) → std::string

Returns a fuzzy representation of the scaffold. By default, this is a SMARTS with the same framework as the scaffold, but with all heavy atoms replaced by “[!#1]” and all bonds replaced by “~”.

Note that any explict charges in the scaffold are removed.

level - Fuzziness level:

0 - As above. 1 - Distinguish aromatic and non-aromatic atoms. For example,

c1ncccc1COC2CC=CCC2 –> a1~a~a~a~a~a1~A~A~A2~A~A~A~A~A2

2 - Distinguish all types of bonds. For example,

c1ncccc1COC2CC=CCC2 –> a1aaaaa1AAA2AA=AAA2

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

Returns all linkers connected to ring system i, including exolinker atoms that are not stripped off. Exolinker atoms are inserted just after the linker atom to which they are connected. Each returned vector will contain an atom list that follows one of 4 conventions:

ri,…,rj rj,…,ri ri,…,nj ni,…,nj

Where ri is an atom in ring system i, rj is an atom in another ring system, and nj and nj are linker nodes where 3 or more linkers intersect.

i runs from 0 to getRingSystemCount() - 1, and atom numbering corresponds to the ChmMol returned by getScaffoldMol().

getLinkerCount(self) → int

getLinkerCount(self, i) → int

Overload 1: Returns the total number of linkers.

Overload 2: Returns the number of linkers connected to ring system i. i runs from 0 to getRingSystemCount() - 1.

getMW(self) → double

Returns scaffold MW.

getRingPath(self, i, j) → std::vector< int,std::allocator< int > >

Returns the atoms in the shortest exocyclic path that connects ring systems i and j. The first and last elements of the returned vector are members of the two ring systems, and the other elements are linker atoms that join the ring systems. If i and j are not connected by a linker, the returned vector will be empty. i and j run from 0 to getRingSystemCount() - 1.

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

Returns the atoms in the ith ring system, including exocyclic atoms that are not stripped off. i runs from 0 to getRingSystemCount() - 1, and ring systems are sorted from high to low by the number of atoms. The atom numbering corresponds to the ChmMol returned by getScaffoldMol().

getRingSystemCount(self) → int

Returns the number of ring systems in the scaffold.

getRingSystemSize(self, i) → int

Returns the number of atoms in the ith ring system, including exocyclic atoms that are not stripped off. i runs from 0 to getRingSystemCount() - 1, and sizes are sorted from high to low.

getScaffoldMol(self) → ChmMol

Returns a non-stereochemical ChmMol that represents the scaffold. The atom numbering in the ChmMol is consistent with the atom numbers returned by the functions getLinkerAtoms and getRingSystemAtoms.

getScaffoldSMARTS(self) → std::string

Returns a non-stereochemical SMARTS that represents the scaffold. This differs from getScaffoldSMILES in that implicit hydrogens on nitrogens will be replaced with the “X” primitive:

[nH] –> [nX3] [nH+] –> [nX3+] [NH2+]= –> [NX3+]= (one double bond, no single bonds) [NH+]= –> [NX3+]= (one double bond, one single bond) [NH+] –> [NX4+] (no double bonds) [NH2+] –> [NX4+] (no double bonds)

getScaffoldSMILES(self) → std::string

Returns a non-stereochemical canonical SMILES that represents the scaffold.

getSubScaffolds(self) → std::vector< ChmScaffold,std::allocator< ChmScaffold > >

Returns all subscaffolds, sorted by decreasing size according to the less-than operator.

class schrodinger.infra.canvas.ChmScaffoldFinder

::ChmScaffoldFinder

ChmScaffoldFinder.hpp - Header file for the ChmScaffoldFinder class.

Author - Steve Dixon

ChmScaffoldFinder identifies the scaffolds in a set of structures. A scaffold is comprised of one or more ring systems and the linkers that join them. The largest scaffold in a structure is obtained by removing all terminal atoms and side chains, with the exception of exocyclic and and exolinker double bonds, such as >C=O. Larger scaffolds are split into smaller scaffolds by removing linkers between ring systems, not by splitting ring systems.

__init__(*args, **kwargs)

exportScaffolds(self, outFile, base=0)

exportScaffolds(self, outStream, base=0) → None

Overload 1: Exports scaffold information to a CSV file with the following format:

SMILES,ID,Source,Super,Sub <SMILES0>,<ID0>,<Source0>,<Super0>,<Sub0> <SMILES1>,<ID1>,<Source1>,<Super1>,<Sub1>

Where,

<SMILESN> = canononical SMILES for the Nth scaffold <IDN> = Integer ID for the Nth scaffold <SourceN> = Quoted, space-delimited list of source input structure numbers <SuperN> = Quoted, space-delimited list of superscaffold IDs <SubN> = Quoted, space-delimited list of subscaffold IDs

Embedded relationships are designated by the presence of the letter ‘e’ at the end of each applicable integer in the Source, Super and Sub columns.

The value base will be added to each integer value in the columns ID, Source, Super, Sub. Thus if base = 1, all numbering will start at 1.

Overload 2: Exports scaffold information in CSV format to an open ostream.

Overload 3: Exports scaffold information in CSV format to an open ostream.

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

Returns exocyclic SMARTS patterns.

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

Returns exolinker SMARTS patterns.

getScaffold(self, i) → ChmScaffold

Returns the ith scaffold. i runs from 0 to getScaffoldCount() - 1.

getScaffoldCount(self) → int

Returns the total number of scaffolds found.

getScaffoldSources(self, i, embed=False) → std::vector< int,std::allocator< int > >

Returns the indices (starting at 0) of the input structures that contain the ith scaffold. If embed is true, only structures which yield an embedded match will be returned. An embedded match means that the scaffold backbone is contained within the structure, but that backbone is part of a larger scaffold whose ring systems and/or linkers are only partially matched by the ring systems and/or linkers of scaffold i. For example, imidazole would yield an embedded match to benzimidazole. By definition, a scaffold cannot yield both a full match and an embedded match to a given structure. If a a full match is possible, embedded matches are ignored. i runs from 0 to getScaffoldCount() - 1.

getScaffoldSourcesCount(self, i, embed=False) → int

Returns the number of input structures that contain the specified scaffold.

getScaffolds(self) → std::vector< ChmScaffold,std::allocator< ChmScaffold > >

Returns all scaffolds found.

getSubScaffolds(self, i, embed=False) → std::vector< int,std::allocator< int > >

Returns subscaffolds of the ith scaffold. Each element of the returned vector can be supplied to getScaffold. If embed is true, only embedded subscaffolds will be returned. i runs from 0 to getScaffoldCount() - 1.

getSubScaffoldsCount(self, i, embed=False) → int

Returns the number of subscaffolds contained in the ith scaffold.

getSuperScaffolds(self, i, embed=False) → std::vector< int,std::allocator< int > >

Returns superscaffolds of the ith scaffold. Each element of the returned vector can be supplied to getScaffold. If embed is true, only scaffolds in which the ith scaffold is embedded will be returned. i runs from 0 to getScaffoldCount() - 1.

getSuperScaffoldsCount(self, i, embed=False) → int

Returns the number of superscaffolds of the ith scaffold.

saveObject(self, outFile)

saveObject(self, outStream) → None

Overload 1: Saves the object contents to a file as zlib-compressed data.

Overload 2: Saves the object contents to an open ostream in uncompressed format.

class schrodinger.infra.canvas.ChmScaffoldMatcher

::ChmScaffoldMatcher

ChmScaffoldMatcher.hpp - Header file for the ChmScaffoldMatcher class.

Author - Steve Dixon

Given a set of scaffolds and a single structure, ChmScaffoldMatcher determines which scaffolds are contained in that structure.

__init__(*args, **kwargs)

getFuzzyMatches(self, mol, level=0, embed=False) → std::vector< int,std::allocator< int > >

getFuzzyMatches(self, smiles, level=0, embed=False) → std::vector< int,std::allocator< int > >

Overload 1: Returns the IDs of scaffolds that yield a fuzzy match to the supplied structure. By default, a fuzzy match is obtained by representing each scaffold as a SMARTS with the same framework as the scaffold, but with all atoms replaced by ‘*’ and all bonds replaced by ‘~’. For example,

c1ncccc1COC2CC=CCC2 –> *1~*~*~*~*~*1~*~*~*2~*~*~*~*~*2

Note that any explict charges in the scaffold are removed.

level controls how generic the matching should be: 0 - As above. 1 - Distinguish aromatic and non-aromatic atoms. For example,

c1ncccc1COC2CC=CCC2 –> a1aaaaa1~A~A~A2~A~A~A~A~A2

2 - Distinguish all types of bonds. For example,

c1ncccc1COC2CC=CCC2 –> a1aaaaa1AAA2AA=AAA2

Overload 2: Returns the IDs of scaffolds that yield a fuzzy match to a structure created from the supplied SMILES.

Overload 3: Returns the IDs of scaffolds that yield a fuzzy match to a structure created from the supplied SMILES.

Overload 4: Returns the IDs of scaffolds that yield a fuzzy match to a structure created from the supplied SMILES.

getMatches(self, mol, embed=False) → std::vector< int,std::allocator< int > >

getMatches(self, smiles, embed=False) → std::vector< int,std::allocator< int > >

Overload 1: Returns the IDs of the scaffolds contained within the supplied structure. If embed is true, only embedded matches will be retuned.

Overload 2: Returns the IDs of the scaffolds contained within a structure created from the supplied SMILES.

Overload 3: Returns the IDs of the scaffolds contained within a structure created from the supplied SMILES.

class schrodinger.infra.canvas.ChmSearchKey

::ChmSearchKeyT< 8 >

__init__(*args, **kwargs)

__len__()

Return len(self).

bits(self) → uint

bytes(self) → uint

chmtostring(self) → std::string

clear(self)

count(self) → uint

dbTestIdentity(self, target) → int

dbTestSubstructure(self, target) → int

dbTestSuperstructure(self, target) → int

static fromBinary(arg1) → ChmSearchKey

static fromHex(data) → ChmSearchKey

hash(self) → uint

hash64(self) → uint64

isEmpty(self) → bool

isFull(self) → bool

set(self)

size(self) → uint

testIdentity(self, query) → int

testSubstructure(self, query) → int

testSuperstructure(self, query) → int

toBinary(self) → std::vector< uint64,std::allocator< uint64 > >

toBitset(self) → ChmBitset

toHex(self) → std::string

toSqlite(self) → std::string

toSqlite(self, os) → None

schrodinger.infra.canvas.ChmSearchKey_fromBinary(arg1) → ChmSearchKey

schrodinger.infra.canvas.ChmSearchKey_fromHex(data) → ChmSearchKey

class schrodinger.infra.canvas.ChmSmiles

::ChmSmiles

__init__(*args, **kwargs)

setSmiles(self, smiles)

class schrodinger.infra.canvas.ChmSmilesFileReader

::ChmSmilesFileReader

__init__(*args, **kwargs)

getError(self) → std::string

getFailureCount(self) → size_t

getLastName(self) → std::string

getLastRecordInfo(self, name, moldata)

getLastSMILES(self) → std::string

getSuccessCount(self) → size_t

hasError(self) → bool

hasNextMol(self) → bool

nextMol(self) → ChmMol

skip(self)

class schrodinger.infra.canvas.ChmSmilesGenerator

::ChmSmilesGenerator

__init__(*args, **kwargs)

clone(self) → ChmSmilesGenerator

getSmiles(self, mol, test=False, forceOrder=False, rigorousAromaticy=True) → std::string

getSmiles(self, mol, mapping, test=False, forceOrder=False, rigorousAromaticy=True) → std::string

getSmilesAndMap(self, mol, test=False, forceOrder=False, rigorousAromaticy=True) → std::string

wantAllBondOrders(self, on)

wantAllBondOrders(self) → bool

wantAllClosureBonds(self, on)

wantAllClosureBonds(self) → bool

wantAllHydrogens(self, newval)

wantAllHydrogens(self) → bool

wantAromaticity(self) → bool

wantAromaticity(self, newval) → None

wantAtomicNumber(self) → bool

wantAtomicNumber(self, newval) → None

wantBondOrder(self) → bool

wantBondOrder(self, newval) → None

wantCharge(self) → bool

wantCharge(self, newval) → None

wantKekulized(self) → bool

wantKekulized(self, newval) → None

wantMapping(self) → bool

wantMapping(self, newval) → None

wantStereo(self) → bool

wantStereo(self, newval) → None

class schrodinger.infra.canvas.ChmSparseBitset

::ChmSparseBitset

handles values from 0 to 4294967295

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

__len__(self) → uint64

accumulate(self, total)

accumulate(self, total) → None

chmtostring(self) → std::string

contains(self, rhs) → bool

contains(self, key) → bool

contract(self)

countCommonOff(self, rhs) → uint64

countCommonOff(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

Overload 1: ChmBitComparable interfacepair of tests

Overload 2: specialization of this interface

countDifference(self, rhs) → uint64

countDifference(self, rhs) → uint64

static createModal(toCombine) → ChmSparseBitset

density(self) → double

digest(self, arg2)

empty(self) → bool

expand(self, forceBinary=False)

foldXOR(self, dest, scale=7)

foldXOR(self, scale=7) → ChmBitset

static fromBlob(raw) → ChmSparseBitset

static fromString(idstring, logicalSize=static_cast< uint64 >(4294967296ULL)) → ChmSparseBitset

getHash(self) → int

getHash64(self) → int64

getMaxXY(self, rhs) → double

getMaxXY(self, rhs) → double

getMinXY(self, rhs) → double

getMinXY(self, rhs) → double

getScaleType(self) → FingerprintScaleType

getSumX(self) → double

getValue(self, pos) → float

getValues(self) → std::vector< float,std::allocator< float > > const &

getX2(self) → double

getXY(self, rhs) → double

getXY(self, rhs) → double

hasDifference(self, rhs) → bool

hasValues(self, strict) → bool

hasValues(self) → bool

intersects(self, rhs) → bool

isSubsetOf(self, rhs) → bool

move(self, offset)

pack(self)

positionOf(self, key) → int

reduceToBitset(self, size) → ChmBitset

rescale(self, scale)

setCompressedSource(self, cs)

setScaleType(self, type)

setValues(self, values, swap=False)

store(self, sdata)

store(self, os) → None

swap(self, rhs)

toBitset(self) → ChmBitset

toBlob(self) → std::string

toVector(self) → std::vector< ChmSparseBitset::key_type,std::allocator< ChmSparseBitset::key_type > >

Provide an interface consistent with ChmBitset; EV 101803.

class schrodinger.infra.canvas.ChmSparseBitset64

::ChmSparseBitset64

handles values from 0 .. 18446744073709551615

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

__len__(self) → uint64

chmtostring(self) → std::string

contains(self, rhs) → bool

contains(self, key) → bool

contract(self)

countCommonOff(self, rhs) → uint64

countCommonOff(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

countCommonOn(self, rhs) → uint64

Overload 1: ChmBitComparable interface

Overload 2: specialization of this interface

countDifference(self, rhs) → uint64

countDifference(self, rhs) → uint64

static createModal(toCombine) → ChmSparseBitset64

density(self) → double

digest(self, arg2)

empty(self) → bool

expand(self, forceBinary=False)

foldXOR(self, dest, scale=7)

foldXOR(self, scale=7) → ChmBitset

static fromBlob(raw) → ChmSparseBitset64

static fromString(idstring, logicalSize=static_cast< uint64 >(0ULL)) → ChmSparseBitset64

getHash(self) → int

getHash64(self) → int64

getMaxXY(self, rhs) → double

getMaxXY(self, rhs) → double

getMinXY(self, rhs) → double

getMinXY(self, rhs) → double

getScaleType(self) → FingerprintScaleType

getSumX(self) → double

getValue(self, pos) → float

getValues(self) → std::vector< float,std::allocator< float > > const &

getX2(self) → double

getXY(self, rhs) → double

getXY(self, rhs) → double

hasDifference(self, rhs) → bool

hasValues(self, strict) → bool

hasValues(self) → bool

intersects(self, rhs) → bool

isSubsetOf(self, rhs) → bool

move(self, offset)

pack(self)

positionOf(self, key) → int

reduceToBitset(self, size) → ChmBitset

reduceToBitset64(self, size) → ChmBitset64

rescale(self, scale)

setCompressedSource(self, cs)

setScaleType(self, type)

setValues(self, values, swap=False)

store(self, sdata)

store(self, os) → None

swap(self, rhs)

CHMFROMRAW(ChmSparseBitset64)

toBitset(self) → ChmBitset

toBitset64(self) → ChmBitset64

toBlob(self) → std::string

toVector(self) → std::vector< ChmSparseBitset64::key_type,std::allocator< ChmSparseBitset64::key_type > > const

schrodinger.infra.canvas.ChmSparseBitset64_createModal(toCombine) → ChmSparseBitset64

schrodinger.infra.canvas.ChmSparseBitset64_fromBlob(raw) → ChmSparseBitset64

schrodinger.infra.canvas.ChmSparseBitset64_fromString(idstring, logicalSize=static_cast< uint64 >(0ULL)) → ChmSparseBitset64

schrodinger.infra.canvas.ChmSparseBitset_createModal(toCombine) → ChmSparseBitset

schrodinger.infra.canvas.ChmSparseBitset_fromBlob(raw) → ChmSparseBitset

schrodinger.infra.canvas.ChmSparseBitset_fromString(idstring, logicalSize=static_cast< uint64 >(4294967296ULL)) → ChmSparseBitset

class schrodinger.infra.canvas.ChmSymmetricMatrixUnsignedInt

::ChmSymmetricMatrix< uint >

__init__(*args, **kwargs)

fastItem(self, i, j) → unsigned int &

non virtual!!

fastReadItem(self, i, j) → unsigned int const &

non virtual!!

getItem(self, i, j) → unsigned int

transpose(self) → ChmSymmetricMatrixUnsignedInt

class schrodinger.infra.canvas.ChmTautomericAtomTyper

::ChmTautomericAtomTyper

__init__(*args, **kwargs)

setup(self, considerCharge, considerIsotope)

type(self, mol, arg3=False) → ChmAssignments

class schrodinger.infra.canvas.ChmTopologicalTorsionOut32

::ChmTopologicalTorsionOut32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

class schrodinger.infra.canvas.ChmTopologicalTorsionOut64

::ChmTopologicalTorsionOut64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

class schrodinger.infra.canvas.ChmTripletOut32

::ChmTripletOut32

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset

generate(self, distanceMatrix) → ChmSparseBitset

generateMap(self, mol, distanceMatrix=None) → ChmFPMap32

generateMap(self, distanceMatrix) → ChmFPMap32

set3D(self, on)

use atom xyz instead of topological distances

setBinWidth(self, width)

define width of bin size

setFuzzyDistance(self, fuzzy)

if distance is within this distance of a boundary, assign it to both bins

setMaxDistance(self, max)

ignore distances above this mark

setMinDistance(self, min)

ignore distances below this mark

class schrodinger.infra.canvas.ChmTripletOut64

::ChmTripletOut64

__init__(*args, **kwargs)

generate(self, mol, distanceMatrix=None) → ChmSparseBitset64

generate(self, distanceMatrix) → ChmSparseBitset64

generateMap(self, mol, distanceMatrix=None) → ChmFPMap64

generateMap(self, distanceMatrix) → ChmFPMap64

set3D(self, on)

use atom xyz instead of topological distances

setBinWidth(self, width)

define width of bin size

setFuzzyDistance(self, fuzzy)

if distance is within this distance of a boundary, assign it to both bins

setMaxDistance(self, max)

ignore distances above this mark

setMinDistance(self, min)

ignore distances below this mark

class schrodinger.infra.canvas.ChmUniqueSmilesGenerator

::ChmUniqueSmilesGenerator

__init__(*args, **kwargs)

clone(self) → ChmUniqueSmilesGenerator

getHash(self, mol) → uint

getHash(self, uniqueSmiles) → uint

getHash64(self, mol) → uint64

getHash64(self, uniqueSmiles) → uint64

getSmiles(self, mol, test=False) → std::string

getSmilesAndMap(self, mol, test=False) → std::string

wantAllBondOrders(self, on)

wantAllBondOrders(self) → bool

wantAllClosureBonds(self, on)

wantAllClosureBonds(self) → bool

wantAllHydrogens(self, newval)

wantAllHydrogens(self) → bool

wantCharge(self, on)

wantCharge(self) → bool

wantStereo(self) → bool

wantStereo(self, newval) → None

class schrodinger.infra.canvas.ChmValueAssignment

::ChmValueAssignment

__init__(*args, **kwargs)

chmtostring(self) → std::string

getKey(self) → int64

getName(self) → std::string const &

getValue(self) → double

class schrodinger.infra.canvas.ChmValueAssignmentIterator

::ChmIterator< ChmValueAssignment >

__init__(*args, **kwargs)

__len__()

Return len(self).

asVector(self) → std::vector< ChmValueAssignment,std::allocator< ChmValueAssignment > > const &

asVector(self) → std::vector< ChmValueAssignment,std::allocator< ChmValueAssignment > >

at(self, index) → ChmValueAssignment

at(self, index) → ChmValueAssignment

checked random access

chmtostring(self) → std::string

hasNext(self) → bool

hasPrev(self) → bool

isValid(self) → bool

next(self) → ChmValueAssignment

prev(self) → ChmValueAssignment

rewind(self)

size(self) → int

sort(self)

exception schrodinger.infra.canvas.CtAssertion

exception schrodinger.infra.canvas.CtException

exception schrodinger.infra.canvas.CtMsgException

exception schrodinger.infra.canvas.CtRdrException

schrodinger.infra.canvas.GetEigenVectorAndValues(matrix, eigenVector, eigenValues, dimensions, rank)

class schrodinger.infra.canvas.MCSsettings

::MCSsettings

Hold all settings for MCS jobs. Also includes throwIfDurationTooLong(), which throws an exception if the calculation has gone on too long.

MCSStop

__init__(*args, **kwargs)

allH

allowDisconnect

atomTyping

collectAfterBond

configuration_problem

deleteInput

elementsToken

exclusive

forceDetail

fromCanvasGUI

getElapsedTime(self) → double

static isFEPAtomtype(x) → bool

static isFEPAtomtype() → bool

isPW

maxCount

minCount

minPathLength

noDetail

nobreakaring

nobreakring

ordinal

outputDelim

outputRequiresCoords

pathLength

prochiral

ringPathLength

scaleXYZ

showAllMatches

shuffleAtomOrder

silent

sortName

throwIfDurationTooLong(self)

timeout

uniqueSMILES

v3SDF

wantH

wantRingCodes

wantX

class schrodinger.infra.canvas.SortChmMCSRecordByScore

::SortChmMCSRecordByScore

__init__(*args, **kwargs)

class schrodinger.infra.canvas.SortChmMCSRecordByScoreAndWeight

::SortChmMCSRecordByScoreAndWeight

__init__(*args, **kwargs)

class schrodinger.infra.canvas.SortChmMCSRecordByWeight

::SortChmMCSRecordByWeight

__init__(*args, **kwargs)

class schrodinger.infra.canvas.XYZ

::XYZ

__init__(*args, **kwargs)

isDefined(self) → bool

x

y

z

schrodinger.infra.canvas.bit_reverse(x) → uint

schrodinger.infra.canvas.checkCanvasElementsLicense(lic1, lic2, elemPass, driver, host, want_exit=True)

schrodinger.infra.canvas.checkLicense(licenseMask, className=None) → int

schrodinger.infra.canvas.chmacos(x) → double

schrodinger.infra.canvas.chmcos(radians) → double

schrodinger.infra.canvas.chmendl(os) → std::ostream &

schrodinger.infra.canvas.chmround(val) → double

schrodinger.infra.canvas.chmsin(radians) → double

schrodinger.infra.canvas.cleanup(molUI)

schrodinger.infra.canvas.cleanup(inner) → None

class schrodinger.infra.canvas.connectInfo

::connectInfo

__init__(*args, **kwargs)

getConnectionOrder(self) → int

m_centralAtom

m_firstAtom

m_restOfAtoms

toString(self) → std::string

schrodinger.infra.canvas.considersOffBits(value) → bool

schrodinger.infra.canvas.createElementsToken() → std::string

schrodinger.infra.canvas.doAnd(x, y, wantPopulationCount) → ChmCompressedBitset

schrodinger.infra.canvas.doAnd(x, y, wantPopulationCount) → ChmCompressedBitset64

schrodinger.infra.canvas.doOr(x, y, wantPopulationCount) → ChmCompressedBitset

schrodinger.infra.canvas.doOr(x, y, wantPopulationCount) → ChmCompressedBitset64

schrodinger.infra.canvas.doXor(x, y, wantPopulationCount) → ChmCompressedBitset

schrodinger.infra.canvas.doXor(x, y, wantPopulationCount) → ChmCompressedBitset64

schrodinger.infra.canvas.getAutoscaleFactor(variance, varianceCutoff) → double

schrodinger.infra.canvas.getFPInfo(filename) → ChmFPTypeInfo

schrodinger.infra.canvas.getFPPrecision(filename) → int

schrodinger.infra.canvas.getMapping(item, outputDelim, onebased) → std::string

schrodinger.infra.canvas.getMetricString(value) → std::string

schrodinger.infra.canvas.getMetricStyle(value) → ChmMetricStyle

schrodinger.infra.canvas.getNumberOfUniqueValues(filename) → uint64

schrodinger.infra.canvas.getSize(overrideSize, logicalSize) → CANVAS_MAXFPLEN_TYPE

schrodinger.infra.canvas.isMetricADistance(value) → bool

schrodinger.infra.canvas.isMetricASimilarity(value) → bool

schrodinger.infra.canvas.isValidSMARTS(smarts) → bool

schrodinger.infra.canvas.makeMask(index) → uint

schrodinger.infra.canvas.makeMaskLL(index) → uint64

schrodinger.infra.canvas.mol2grid(mol, atomProps, dest, sigma)

schrodinger.infra.canvas.nChooseK(bs) → uint64

schrodinger.infra.canvas.openPWM(filename, rowflag, colflag, checkSquare=False, checkDiag=False, checkSingular=False) → ChmPairwiseFPIn

class schrodinger.infra.canvas.optionMDL

::optionMDL

H_All = 3

H_AsWritten = 1

H_Chiral = 4

H_Default = 0

H_Never = 0

H_Polar = 2

H_Visible = 5

__init__(*args, **kwargs)

static translate(val) → ChmAtomOption::H

schrodinger.infra.canvas.optionMDL_translate(val) → ChmAtomOption::H

class schrodinger.infra.canvas.optionSMARTS

::optionSMARTS

H_Always = 1

H_Default = 0

H_Never = -1

H_SMILES_behavior = 0

X_Always = 2

X_AromaticNitrogensOnly = 1

X_Default = 1

X_No = 0

__init__(*args, **kwargs)

schrodinger.infra.canvas.printoutMCS(molecules, mcsItems, outputFile, toMae, toSD, toCSV, colorCode, useMolIndex, v3SDF, onebased, wantUniqueSMILES)

schrodinger.infra.canvas.printoutMCSFromCts(molecules, records, outputFile, colorCode, useMolIndex)

schrodinger.infra.canvas.printoutPWMCS(molecules, rec1, rec2, output, onebasedCSV, wantUniqueSMILES)

schrodinger.infra.canvas.runAllPairwiseMCS(molecules, settings) → std::vector< ChmPairwiseMCSRecord,std::allocator< ChmPairwiseMCSRecord > >

same as above but over all pairs of inputs

schrodinger.infra.canvas.runMCS(molecules, settings, allow_any_atom_type=False) → std::vector< ChmMCSRecord,std::allocator< ChmMCSRecord > >

Limited runMCS csv interface, to be exposed to Python Not all options are exposed

schrodinger.infra.canvas.runPairwiseMCS(molecules, settings, whichPairs) → std::vector< ChmPairwiseMCSRecord,std::allocator< ChmPairwiseMCSRecord > >

same as above but only over the pairs identified in ‘whichPairs’

schrodinger.infra.canvas.transpose(src, dest)

schrodinger.infra.canvas.transpose(src, dest) → None