Public API

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class sire.io.parser.DCD

This class represents a DCD file reader.

The format is described here

https:www.ks.uiuc.eduResearchvmdpluginsmolfiledcdplugin.html

Author: Christopher Woods

assign((DCD)arg1, (DCD)other) → DCD :

C++ signature :

SireIO::DCD {lvalue} assign(SireIO::DCD {lvalue},SireIO::DCD)

clone((DCD)arg1) → DCD :

C++ signature :

SireIO::DCD clone(SireIO::DCD)

construct((DCD)arg1, (object)filename, (PropertyMap)map) → object :

Return this parser constructed from the passed filename

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::DCD {lvalue},QString,SireBase::PropertyMap)

construct( (DCD)arg1, (object)lines, (PropertyMap)map) -> object :

Return this parser constructed from the passed set of lines

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::DCD {lvalue},QStringList,SireBase::PropertyMap)

construct( (DCD)arg1, (System)system, (PropertyMap)map) -> object :

Return this parser constructed from the passed SireSystem::System

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::DCD {lvalue},SireSystem::System,SireBase::PropertyMap)

count((DCD)arg1) → int :

C++ signature :

int count(SireIO::DCD {lvalue})

disable_parallel()

disableParallel( (MoleculeParser)arg1) -> None :

Disable code to parse files in parallel - parsing will happen in serial

C++ signature :

void disableParallel(SireIO::MoleculeParser {lvalue})

enable_parallel()

enableParallel( (MoleculeParser)arg1) -> None :

Enable code to parse files in parallel

C++ signature :

void enableParallel(SireIO::MoleculeParser {lvalue})

error_report()

errorReport( (MoleculeParser)arg1) -> object :

Return the error report, if this parser is broken. If it isnt,

then an empty string is returned.

C++ signature :

QString errorReport(SireIO::MoleculeParser {lvalue})

format_description()

formatDescription( (DCD)arg1) -> object :

Return a description of the file format

C++ signature :

QString formatDescription(SireIO::DCD {lvalue})

format_name()

formatName( (DCD)arg1) -> object :

Return the format name that is used to identify this file format within Sire

C++ signature :

QString formatName(SireIO::DCD {lvalue})

format_suffix()

formatSuffix( (DCD)arg1) -> object :

Return the suffixes that DCD files will typically have

C++ signature :

QStringList formatSuffix(SireIO::DCD {lvalue})

get_frame()

getFrame( (DCD)arg1, (int)i) -> Frame :

C++ signature :

SireMol::Frame getFrame(SireIO::DCD {lvalue},int)

has_warnings()

hasWarnings( (MoleculeParser)arg1) -> bool :

Return whether there were any warnings when loading the file

using this parser

C++ signature :

bool hasWarnings(SireIO::MoleculeParser {lvalue})

is_binary_file()

isBinaryFile( (MoleculeParser)arg1) -> bool :

C++ signature :

bool isBinaryFile(SireIO::MoleculeParser {lvalue})

is_broken()

isBroken( (MoleculeParser)arg1) -> bool :

Return whether or not this parser is broken

C++ signature :

bool isBroken(SireIO::MoleculeParser {lvalue})

is_empty()

isEmpty( (MoleculeParser)arg1) -> bool :

C++ signature :

bool isEmpty(SireIO::MoleculeParser {lvalue})

is_frame()

isFrame( (DCD)arg1) -> bool :

C++ signature :

bool isFrame(SireIO::DCD {lvalue})

is_supplementary()

isSupplementary( (MoleculeParser)arg1) -> bool :

Return whether or not this parser is a supplementary parser

C++ signature :

bool isSupplementary(SireIO::MoleculeParser {lvalue})

is_text_file()

isTextFile( (DCD)arg1) -> bool :

This is not a text file

C++ signature :

bool isTextFile(SireIO::DCD {lvalue})

is_topology()

isTopology( (MoleculeParser)arg1) -> bool :

Return whether or not this parser is a topology parser

C++ signature :

bool isTopology(SireIO::MoleculeParser {lvalue})

num_atoms()

nAtoms( (DCD)arg1) -> int :

Return the number of atoms whose coordinates are contained in this restart file

C++ signature :

int nAtoms(SireIO::DCD {lvalue})

num_frames()

nFrames( (DCD)arg1) -> int :

C++ signature :

int nFrames(SireIO::DCD {lvalue})

static parse((object)filename) → DCD :

Parse from the passed file

C++ signature :

SireIO::DCD parse(QString)

set_use_parallel()

setUseParallel( (MoleculeParser)arg1, (bool)on) -> None :

Set whether or not to parse files in parallel or serial

C++ signature :

void setUseParallel(SireIO::MoleculeParser {lvalue},bool)

size((DCD)arg1) → int :

C++ signature :

int size(SireIO::DCD {lvalue})

supported_formats()

supportedFormats() -> object :

This returns a human readable set of lines describing the formats supported by MoleculeParser. Each line is formatted as extension : description where extension is the unique extension of the file used by MoleculeParser, and description is a description of the file format

C++ signature :

QString supportedFormats()

to_string()

toString( (DCD)arg1) -> object :

C++ signature :

QString toString(SireIO::DCD {lvalue})

to_system()

toSystem( (MoleculeParser)arg1, (PropertyMap)map) -> System :

Return the System that is constructed from the data in this parser

C++ signature :

SireSystem::System toSystem(SireIO::MoleculeParser {lvalue},SireBase::PropertyMap)

toSystem( (MoleculeParser)arg1, (MoleculeParser)other, (PropertyMap)map) -> System :

Return the System that is constructed from the data in the two passed parsers (i.e. representing a topology and a coordinate file)

C++ signature :

SireSystem::System toSystem(SireIO::MoleculeParser {lvalue},SireIO::MoleculeParser,SireBase::PropertyMap)

toSystem( (MoleculeParser)arg1, (object)others, (PropertyMap)map) -> System :

Return the System that is constructed from the information in the passed parsers. This will parse the information in order, meaning that data contained in earlier parsers may be overwritten by data from later parsers

C++ signature :

SireSystem::System toSystem(SireIO::MoleculeParser {lvalue},QList<SireBase::PropPtr<SireIO::MoleculeParser>>,SireBase::PropertyMap)

toSystem( (MoleculeParser)arg1) -> System :

Return the System that is constructed from the data in this parser

C++ signature :

SireSystem::System toSystem(SireIO::MoleculeParser {lvalue})

toSystem( (MoleculeParser)arg1, (MoleculeParser)other) -> System :

Return the System that is constructed from the data in the two passed parsers (i.e. representing a topology and a coordinate file)

C++ signature :

SireSystem::System toSystem(SireIO::MoleculeParser {lvalue},SireIO::MoleculeParser)

toSystem( (MoleculeParser)arg1, (object)others) -> System :

Return the System that is constructed from the information in the passed parsers. This will parse the information in order, meaning that data contained in earlier parsers may be overwritten by data from later parsers

C++ signature :

SireSystem::System toSystem(SireIO::MoleculeParser {lvalue},QList<SireBase::PropPtr<SireIO::MoleculeParser>>)

typename()

typeName() -> str :

C++ signature :

char const* typeName()

uses_parallel()

usesParallel( (MoleculeParser)arg1 [, (int)n=-1]) -> bool :

Return whether or not this parser runs in parallel - this will depend

on whether parallel was enabled for parsing, we have more than one thread available, and the number of items (n) makes it worth parsing in parallel. Pass in n<=0 if you dont want to check the last condition.

C++ signature :

bool usesParallel(SireIO::MoleculeParser {lvalue} [,int=-1])

what((DCD)arg1) → str :

C++ signature :

char const* what(SireIO::DCD {lvalue})

write_to_file()

writeToFile( (DCD)arg1, (object)filename) -> object :

Write this binary file filename

C++ signature :

QStringList writeToFile(SireIO::DCD {lvalue},QString)

sire.io.parser.G87

alias of Gro87

sire.io.parser.GTOP

alias of GroTop

sire.io.parser.MOL2

alias of Mol2

sire.io.parser.PDB

alias of PDB2

class sire.io.parser.PDBx

This class holds a parser for reading and writing PDBxmmcif files

assign((PDBx)arg1, (PDBx)other) → PDBx :

C++ signature :

SireIO::PDBx {lvalue} assign(SireIO::PDBx {lvalue},SireIO::PDBx)

clone((PDBx)arg1) → PDBx :

C++ signature :

SireIO::PDBx clone(SireIO::PDBx)

construct((PDBx)arg1, (object)filename, (PropertyMap)map) → object :

Return the parser that has been constructed by reading in the passed

file using the passed properties

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::PDBx {lvalue},QString,SireBase::PropertyMap)

construct( (PDBx)arg1, (object)lines, (PropertyMap)map) -> object :

Return the parser that has been constructed by reading in the passed text lines using the passed properties

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::PDBx {lvalue},QStringList,SireBase::PropertyMap)

construct( (PDBx)arg1, (System)system, (PropertyMap)map) -> object :

Return the parser that has been constructed by extract all necessary data from the passed SireSystem::System using the specified properties

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::PDBx {lvalue},SireSystem::System,SireBase::PropertyMap)

format_description()

formatDescription( (PDBx)arg1) -> object :

Return a description of the file format

C++ signature :

QString formatDescription(SireIO::PDBx {lvalue})

format_name()

formatName( (PDBx)arg1) -> object :

Return the format name that is used to identify this file format within Sire

C++ signature :

QString formatName(SireIO::PDBx {lvalue})

format_suffix()

formatSuffix( (PDBx)arg1) -> object :

Return the suffixes that these files are normally associated with

C++ signature :

QStringList formatSuffix(SireIO::PDBx {lvalue})

get_frame()

getFrame( (PDBx)arg1, (int)i) -> Frame :

C++ signature :

SireMol::Frame getFrame(SireIO::PDBx {lvalue},int)

is_frame()

isFrame( (PDBx)arg1) -> bool :

C++ signature :

bool isFrame(SireIO::PDBx {lvalue})

is_topology()

isTopology( (PDBx)arg1) -> bool :

C++ signature :

bool isTopology(SireIO::PDBx {lvalue})

num_atoms()

nAtoms( (PDBx)arg1) -> int :

Return the total number of atoms in all molecules.

C++ signature :

int nAtoms(SireIO::PDBx {lvalue})

num_frames()

nFrames( (PDBx)arg1) -> int :

C++ signature :

int nFrames(SireIO::PDBx {lvalue})

to_lines()

toLines( (PDBx)arg1) -> object :

Convert the the parsed data to a collection of PDBx record lines.

C++ signature :

QVector<QString> toLines(SireIO::PDBx {lvalue})

to_string()

toString( (PDBx)arg1) -> object :

Return a string representation of this parser

C++ signature :

QString toString(SireIO::PDBx {lvalue})

typename()

typeName() -> str :

Return the C++ name for this class

C++ signature :

char const* typeName()

what((PDBx)arg1) → str :

Return the C++ name for this class

C++ signature :

char const* what(SireIO::PDBx {lvalue})

sire.io.parser.PRM

alias of AmberPrm

sire.io.parser.PSF

alias of CharmmPSF

sire.io.parser.RST

alias of AmberRst

sire.io.parser.RST7

alias of AmberRst7

class sire.io.parser.SDF

This class holds a parser for reading and writing Structure Data File (SDF) molecular file formats

Author: Christopher Woods

assign((SDF)arg1, (SDF)other) → SDF :

C++ signature :

SireIO::SDF {lvalue} assign(SireIO::SDF {lvalue},SireIO::SDF)

clone((SDF)arg1) → SDF :

C++ signature :

SireIO::SDF clone(SireIO::SDF)

construct((SDF)arg1, (object)filename, (PropertyMap)map) → object :

Return the parser that has been constructed by reading in the passed

file using the passed properties

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::SDF {lvalue},QString,SireBase::PropertyMap)

construct( (SDF)arg1, (object)lines, (PropertyMap)map) -> object :

Return the parser that has been constructed by reading in the passed text lines using the passed properties

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::SDF {lvalue},QStringList,SireBase::PropertyMap)

construct( (SDF)arg1, (System)system, (PropertyMap)map) -> object :

Return the parser that has been constructed by extract all necessary data from the passed SireSystem::System using the specified properties

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::SDF {lvalue},SireSystem::System,SireBase::PropertyMap)

format_description()

formatDescription( (SDF)arg1) -> object :

Return a description of the file format

C++ signature :

QString formatDescription(SireIO::SDF {lvalue})

format_name()

formatName( (SDF)arg1) -> object :

Return the format name that is used to identify this file format within Sire

C++ signature :

QString formatName(SireIO::SDF {lvalue})

format_suffix()

formatSuffix( (SDF)arg1) -> object :

Return the suffixes that these files are normally associated with

C++ signature :

QStringList formatSuffix(SireIO::SDF {lvalue})

get_frame()

getFrame( (SDF)arg1, (int)i) -> Frame :

C++ signature :

SireMol::Frame getFrame(SireIO::SDF {lvalue},int)

is_frame()

isFrame( (SDF)arg1) -> bool :

C++ signature :

bool isFrame(SireIO::SDF {lvalue})

is_topology()

isTopology( (SDF)arg1) -> bool :

C++ signature :

bool isTopology(SireIO::SDF {lvalue})

num_atoms()

nAtoms( (SDF)arg1) -> int :

Return the total number of atoms.

C++ signature :

int nAtoms(SireIO::SDF {lvalue})

nAtoms( (SDF)arg1, (int)i) -> int :

Return the number of atoms in molecule i.

C++ signature :

int nAtoms(SireIO::SDF {lvalue},int)

num_frames()

nFrames( (SDF)arg1) -> int :

C++ signature :

int nFrames(SireIO::SDF {lvalue})

num_molecules()

nMolecules( (SDF)arg1) -> int :

Return the number of molecules loaded in this file

C++ signature :

int nMolecules(SireIO::SDF {lvalue})

parse_warnings()

parseWarnings( (SDF)arg1) -> object :

Return any warnings raised when parsing this file

C++ signature :

QStringList parseWarnings(SireIO::SDF {lvalue})

to_string()

toString( (SDF)arg1) -> object :

Return a string representation of this parser

C++ signature :

QString toString(SireIO::SDF {lvalue})

typename()

typeName() -> str :

Return the C++ name for this class

C++ signature :

char const* typeName()

what((SDF)arg1) → str :

Return the C++ name for this class

C++ signature :

char const* what(SireIO::SDF {lvalue})

sire.io.parser.TRAJ

alias of AmberTraj

class sire.io.parser.TRR

This class represents a Gromacs TRR (XDR file) trajectory.

assign((TRR)arg1, (TRR)other) → TRR :

C++ signature :

SireIO::TRR {lvalue} assign(SireIO::TRR {lvalue},SireIO::TRR)

clone((TRR)arg1) → TRR :

C++ signature :

SireIO::TRR clone(SireIO::TRR)

construct((TRR)arg1, (object)filename, (PropertyMap)map) → object :

Return this parser constructed from the passed filename

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::TRR {lvalue},QString,SireBase::PropertyMap)

construct( (TRR)arg1, (object)lines, (PropertyMap)map) -> object :

Return this parser constructed from the passed set of lines

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::TRR {lvalue},QStringList,SireBase::PropertyMap)

construct( (TRR)arg1, (System)system, (PropertyMap)map) -> object :

Return this parser constructed from the passed SireSystem::System

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::TRR {lvalue},SireSystem::System,SireBase::PropertyMap)

count((TRR)arg1) → int :

C++ signature :

int count(SireIO::TRR {lvalue})

format_description()

formatDescription( (TRR)arg1) -> object :

Return a description of the file format

C++ signature :

QString formatDescription(SireIO::TRR {lvalue})

format_name()

formatName( (TRR)arg1) -> object :

Return the format name that is used to identify this file format within Sire

C++ signature :

QString formatName(SireIO::TRR {lvalue})

format_suffix()

formatSuffix( (TRR)arg1) -> object :

Return the suffixes that TRR files will typically have

C++ signature :

QStringList formatSuffix(SireIO::TRR {lvalue})

get_frame()

getFrame( (TRR)arg1, (int)i) -> Frame :

C++ signature :

SireMol::Frame getFrame(SireIO::TRR {lvalue},int)

is_frame()

isFrame( (TRR)arg1) -> bool :

C++ signature :

bool isFrame(SireIO::TRR {lvalue})

is_text_file()

isTextFile( (TRR)arg1) -> bool :

This is not a text file

C++ signature :

bool isTextFile(SireIO::TRR {lvalue})

num_atoms()

nAtoms( (TRR)arg1) -> int :

Return the number of atoms whose coordinates are contained in this restart file

C++ signature :

int nAtoms(SireIO::TRR {lvalue})

num_frames()

nFrames( (TRR)arg1) -> int :

C++ signature :

int nFrames(SireIO::TRR {lvalue})

static parse((object)filename) → TRR :

Parse from the passed file

C++ signature :

SireIO::TRR parse(QString)

size((TRR)arg1) → int :

C++ signature :

int size(SireIO::TRR {lvalue})

to_string()

toString( (TRR)arg1) -> object :

C++ signature :

QString toString(SireIO::TRR {lvalue})

typename()

typeName() -> str :

C++ signature :

char const* typeName()

what((TRR)arg1) → str :

C++ signature :

char const* what(SireIO::TRR {lvalue})

write_to_file()

writeToFile( (TRR)arg1, (object)filename) -> object :

Write this binary file filename

C++ signature :

QStringList writeToFile(SireIO::TRR {lvalue},QString)

class sire.io.parser.XTC

This class represents a Gromacs XTC (XDR file) trajectory. This is a compressed trajectory format

assign((XTC)arg1, (XTC)other) → XTC :

C++ signature :

SireIO::XTC {lvalue} assign(SireIO::XTC {lvalue},SireIO::XTC)

clone((XTC)arg1) → XTC :

C++ signature :

SireIO::XTC clone(SireIO::XTC)

construct((XTC)arg1, (object)filename, (PropertyMap)map) → object :

Return this parser constructed from the passed filename

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::XTC {lvalue},QString,SireBase::PropertyMap)

construct( (XTC)arg1, (object)lines, (PropertyMap)map) -> object :

Return this parser constructed from the passed set of lines

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::XTC {lvalue},QStringList,SireBase::PropertyMap)

construct( (XTC)arg1, (System)system, (PropertyMap)map) -> object :

Return this parser constructed from the passed SireSystem::System

C++ signature :

SireBase::PropPtr<SireIO::MoleculeParser> construct(SireIO::XTC {lvalue},SireSystem::System,SireBase::PropertyMap)

count((XTC)arg1) → int :

C++ signature :

int count(SireIO::XTC {lvalue})

format_description()

formatDescription( (XTC)arg1) -> object :

Return a description of the file format

C++ signature :

QString formatDescription(SireIO::XTC {lvalue})

format_name()

formatName( (XTC)arg1) -> object :

Return the format name that is used to identify this file format within Sire

C++ signature :

QString formatName(SireIO::XTC {lvalue})

format_suffix()

formatSuffix( (XTC)arg1) -> object :

Return the suffixes that XTC files will typically have

C++ signature :

QStringList formatSuffix(SireIO::XTC {lvalue})

get_frame()

getFrame( (XTC)arg1, (int)i) -> Frame :

C++ signature :

SireMol::Frame getFrame(SireIO::XTC {lvalue},int)

is_frame()

isFrame( (XTC)arg1) -> bool :

C++ signature :

bool isFrame(SireIO::XTC {lvalue})

is_text_file()

isTextFile( (XTC)arg1) -> bool :

This is not a text file

C++ signature :

bool isTextFile(SireIO::XTC {lvalue})

num_atoms()

nAtoms( (XTC)arg1) -> int :

Return the number of atoms whose coordinates are contained in this restart file

C++ signature :

int nAtoms(SireIO::XTC {lvalue})

num_frames()

nFrames( (XTC)arg1) -> int :

C++ signature :

int nFrames(SireIO::XTC {lvalue})

static parse((object)filename) → XTC :

Parse from the passed file

C++ signature :

SireIO::XTC parse(QString)

size((XTC)arg1) → int :

C++ signature :

int size(SireIO::XTC {lvalue})

to_string()

toString( (XTC)arg1) -> object :

C++ signature :

QString toString(SireIO::XTC {lvalue})

typename()

typeName() -> str :

C++ signature :

char const* typeName()

what((XTC)arg1) → str :

C++ signature :

char const* what(SireIO::XTC {lvalue})

write_to_file()

writeToFile( (XTC)arg1, (object)filename) -> object :

Write this binary file filename

C++ signature :

QStringList writeToFile(SireIO::XTC {lvalue},QString)