MolWriters.h
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//
// Copyright (C) 2002-2017 Greg Landrum, Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_MOLWRITERS_H_
#define _RD_MOLWRITERS_H_
#include <RDGeneral/types.h>
#include <string>
#include <iostream>
#include <GraphMol/ROMol.h>
namespace RDKit {
static int defaultConfId = -1;
class RDKIT_FILEPARSERS_EXPORT MolWriter {
public:
virtual ~MolWriter() {}
virtual void write(const ROMol &mol, int confId = defaultConfId) = 0;
virtual void flush() = 0;
virtual void close() = 0;
virtual void setProps(const STR_VECT &propNames) = 0;
virtual unsigned int numMols() const = 0;
};
//! The SmilesWriter is for writing molecules and properties to
//! delimited text files.
class RDKIT_FILEPARSERS_EXPORT SmilesWriter : public MolWriter {
/******************************************************************************
* A Smiles Table writer - this is how it is used
* - create a SmilesWriter with a output file name (or a ostream), a
*delimiter,
* and a list of properties that need to be written out
* - then a call is made to the write function for each molecule that needs
*to
* be written out
******************************************************************************/
public:
/*!
\param fileName : filename to write to ("-" to write to stdout)
\param delimiter : delimiter to use in the text file
\param nameHeader : used to label the name column in the output. If this
is provided as the empty string, no names will be
written.
\param includeHeader : toggles inclusion of a header line in the output
\param isomericSmiles : toggles generation of isomeric SMILES
\param kekuleSmiles : toggles the generation of kekule SMILES
*/
SmilesWriter(const std::string &fileName, const std::string &delimiter = " ",
const std::string &nameHeader = "Name",
bool includeHeader = true, bool isomericSmiles = true,
bool kekuleSmiles = false);
//! \overload
SmilesWriter(std::ostream *outStream, std::string delimiter = " ",
std::string nameHeader = "Name", bool includeHeader = true,
bool takeOwnership = false, bool isomericSmiles = true,
bool kekuleSmiles = false);
~SmilesWriter();
//! \brief set a vector of property names that are need to be
//! written out for each molecule
void setProps(const STR_VECT &propNames);
//! \brief write a new molecule to the file
void write(const ROMol &mol, int confId = defaultConfId);
//! \brief flush the ostream
void flush() {
PRECONDITION(dp_ostream, "no output stream");
try {
dp_ostream->flush();
} catch (...) {
try {
if (dp_ostream->good()) dp_ostream->setstate(std::ios::badbit);
} catch (const std::runtime_error &) {
}
}
};
//! \brief close our stream (the writer cannot be used again)
void close() {
flush();
if (df_owner) {
delete dp_ostream;
df_owner = false;
}
dp_ostream = nullptr;
};
//! \brief get the number of molecules written so far
unsigned int numMols() const { return d_molid; };
private:
// local initialization
void init(const std::string &delimiter, const std::string &nameHeader,
bool includeHeader, bool isomericSmiles, bool kekuleSmiles);
// dumps a header line to the output stream
void dumpHeader() const;
std::ostream *dp_ostream;
bool df_owner;
bool df_includeHeader; // whether or not to include a title line
unsigned int d_molid; // the number of the molecules we wrote so far
std::string d_delim; // delimiter string between various records
std::string d_nameHeader; // header for the name column in the output file
STR_VECT d_props; // list of property name that need to be written out
bool df_isomericSmiles; // whether or not to do isomeric smiles
bool df_kekuleSmiles; // whether or not to do kekule smiles
};
//! The SDWriter is for writing molecules and properties to
//! SD files
class RDKIT_FILEPARSERS_EXPORT SDWriter : public MolWriter {
/**************************************************************************************
* A SD file ( or stream) writer - this is how it is used
* - create a SDMolWriter with a output file name (or a ostream),
* and a list of properties that need to be written out
* - then a call is made to the write function for each molecule that needs
*to be written out
**********************************************************************************************/
public:
/*!
\param fileName : filename to write to ("-" to write to stdout)
*/
SDWriter(const std::string &fileName);
SDWriter(std::ostream *outStream, bool takeOwnership = false);
~SDWriter();
//! \brief set a vector of property names that are need to be
//! written out for each molecule
void setProps(const STR_VECT &propNames);
//! \brief return the text that would be written to the file
static std::string getText(const ROMol &mol, int confId = defaultConfId,
bool kekulize = true, bool force_V3000 = false,
int molid = -1, STR_VECT *propNames = NULL);
//! \brief write a new molecule to the file
void write(const ROMol &mol, int confId = defaultConfId);
//! \brief flush the ostream
void flush() {
PRECONDITION(dp_ostream, "no output stream");
try {
dp_ostream->flush();
} catch (...) {
try {
if (dp_ostream->good()) dp_ostream->setstate(std::ios::badbit);
} catch (const std::runtime_error &) {
}
}
};
//! \brief close our stream (the writer cannot be used again)
void close() {
flush();
if (df_owner) {
delete dp_ostream;
df_owner = false;
}
dp_ostream = nullptr;
};
//! \brief get the number of molecules written so far
unsigned int numMols() const { return d_molid; };
void setForceV3000(bool val) { df_forceV3000 = val; };
bool getForceV3000() const { return df_forceV3000; };
void setKekulize(bool val) { df_kekulize = val; };
bool getKekulize() const { return df_kekulize; };
private:
void writeProperty(const ROMol &mol, const std::string &name);
std::ostream *dp_ostream;
bool df_owner;
unsigned int d_molid; // the number of the molecules we wrote so far
STR_VECT d_props; // list of property name that need to be written out
bool df_forceV3000; // force writing the mol blocks as V3000
bool df_kekulize; // toggle kekulization of molecules on writing
};
//! The TDTWriter is for writing molecules and properties to
//! TDT files
class RDKIT_FILEPARSERS_EXPORT TDTWriter : public MolWriter {
/**************************************************************************************
* A TDT file ( or stream) writer - this is how it is used
* - create a TDTWriter with a output file name (or a ostream),
* and a list of properties that need to be written out
* - then a call is made to the write function for each molecule that needs
*to be written out
**********************************************************************************************/
public:
/*!
\param fileName : filename to write to ("-" to write to stdout)
*/
TDTWriter(const std::string &fileName);
TDTWriter(std::ostream *outStream, bool takeOwnership = false);
~TDTWriter();
//! \brief set a vector of property names that are need to be
//! written out for each molecule
void setProps(const STR_VECT &propNames);
//! \brief write a new molecule to the file
void write(const ROMol &mol, int confId = defaultConfId);
//! \brief flush the ostream
void flush() {
PRECONDITION(dp_ostream, "no output stream");
try {
dp_ostream->flush();
} catch (...) {
try {
if (dp_ostream->good()) dp_ostream->setstate(std::ios::badbit);
} catch (const std::runtime_error &) {
}
}
};
//! \brief close our stream (the writer cannot be used again)
void close() {
// if we've written any mols, finish with a "|" line
if (dp_ostream && d_molid > 0) {
*dp_ostream << "|\n";
}
flush();
if (df_owner) {
delete dp_ostream;
df_owner = false;
}
dp_ostream = nullptr;
};
//! \brief get the number of molecules written so far
unsigned int numMols() const { return d_molid; };
void setWrite2D(bool state = true) { df_write2D = state; };
bool getWrite2D() const { return df_write2D; };
void setWriteNames(bool state = true) { df_writeNames = state; };
bool getWriteNames() const { return df_writeNames; };
void setNumDigits(unsigned int numDigits) { d_numDigits = numDigits; };
unsigned int getNumDigits() const { return d_numDigits; };
private:
void writeProperty(const ROMol &mol, const std::string &name);
std::ostream *dp_ostream;
bool df_owner;
unsigned int d_molid; // the number of molecules we wrote so far
STR_VECT d_props; // list of property name that need to be written out
bool df_write2D; // write 2D coordinates instead of 3D
bool df_writeNames; // write a name record for each molecule
unsigned int
d_numDigits; // number of digits to use in our output of coordinates;
};
//! The PDBWriter is for writing molecules to Brookhaven Protein
//! DataBank format files.
class RDKIT_FILEPARSERS_EXPORT PDBWriter : public MolWriter {
public:
PDBWriter(const std::string &fileName, unsigned int flavor = 0);
PDBWriter(std::ostream *outStream, bool takeOwnership = false,
unsigned int flavor = 0);
~PDBWriter();
//! \brief write a new molecule to the file
void write(const ROMol &mol, int confId = defaultConfId);
void setProps(const STR_VECT &){};
//! \brief flush the ostream
void flush() {
PRECONDITION(dp_ostream, "no output stream");
try {
dp_ostream->flush();
} catch (...) {
try {
if (dp_ostream->good()) dp_ostream->setstate(std::ios::badbit);
} catch (const std::runtime_error &) {
}
}
};
//! \brief close our stream (the writer cannot be used again)
void close() {
flush();
if (df_owner) {
delete dp_ostream;
df_owner = false;
}
dp_ostream = nullptr;
};
//! \brief get the number of molecules written so far
unsigned int numMols() const { return d_count; };
private:
std::ostream *dp_ostream;
unsigned int d_flavor;
unsigned int d_count;
bool df_owner;
};
} // namespace RDKit
#endif
ROMol.h
Defines the primary molecule class ROMol as well as associated typedefs.
types.h
RDKit::PDBWriter
Definition: MolWriters.h:276
RDKit::SDWriter
Definition: MolWriters.h:124
RDKIT_FILEPARSERS_EXPORT
#define RDKIT_FILEPARSERS_EXPORT
Definition: export.h:216
RDKit::MolWriter
Definition: MolWriters.h:24
RDKit::STR_VECT
std::vector< std::string > STR_VECT
Definition: Dict.h:29
RDKit::ROMol
Definition: ROMol.h:171
RDKit::SmilesWriter
Definition: MolWriters.h:36
RDKit::PDBWriter::numMols
unsigned int numMols() const
get the number of molecules written so far
Definition: MolWriters.h:312
RDKit::PDBWriter::setProps
void setProps(const STR_VECT &)
Definition: MolWriters.h:286
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::defaultConfId
static int defaultConfId
Definition: MolWriters.h:23
RDKit::PDBWriter::close
void close()
close our stream (the writer cannot be used again)
Definition: MolWriters.h:302
PRECONDITION
#define PRECONDITION(expr, mess)
Definition: Invariant.h:109
RDKit::TDTWriter
Definition: MolWriters.h:198
RDKit::PDBWriter::flush
void flush()
flush the ostream
Definition: MolWriters.h:289
RDKit::MolWriter::~MolWriter
virtual ~MolWriter()
Definition: MolWriters.h:26
export.h