/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h is in librdkit-dev 201503-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 | //
// Copyright (C) 2002-2013 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.
//
#ifndef _RD_FILEPARSERS_H
#define _RD_FILEPARSERS_H
#include <RDGeneral/types.h>
#include <GraphMol/RDKitBase.h>
#include <string>
#include <iostream>
#include <vector>
#include <exception>
#include <boost/shared_ptr.hpp>
namespace RDKit{
const int MOLFILE_MAXLINE=256;
std::string strip(const std::string &orig);
//-----
// mol files
//-----
typedef std::vector< RWMOL_SPTR > RWMOL_SPTR_VECT;
// \brief construct a molecule from MDL mol data in a stream
/*!
* \param inStream - stream containing the data
* \param line - current line number (used for error reporting)
* \param sanitize - toggles sanitization and stereochemistry
* perception of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param line - current line number (used for error reporting)
* \param strictParsing - if not set, the parser is more lax about correctness
* of the contents.
*
*/
RWMol *MolDataStreamToMol(std::istream *inStream, unsigned int &line,
bool sanitize=true,bool removeHs=true,
bool strictParsing=true);
// \overload
RWMol *MolDataStreamToMol(std::istream &inStream, unsigned int &line,
bool sanitize=true,bool removeHs=true,
bool strictParsing=true);
// \brief construct a molecule from an MDL mol block
/*!
* \param molBlock - string containing the mol block
* \param sanitize - toggles sanitization and stereochemistry
* perception of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param strictParsing - if set, the parser is more lax about correctness
* of the contents.
*/
RWMol *MolBlockToMol(const std::string &molBlock, bool sanitize=true,
bool removeHs=true,bool strictParsing=true);
// \brief construct a molecule from an MDL mol file
/*!
* \param fName - string containing the file name
* \param sanitize - toggles sanitization and stereochemistry
* perception of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param strictParsing - if set, the parser is more lax about correctness
* of the contents.
*/
RWMol *MolFileToMol(std::string fName, bool sanitize=true,
bool removeHs=true,bool strictParsing=true);
// \brief generates an MDL mol block for a molecule
/*!
* \param mol - the molecule in question
* \param includeStereo - toggles inclusion of stereochemistry information
* \param confId - selects the conformer to be used
* \param kekulize - triggers kekulization of the molecule before it is written
* \param forceV3000 - force generation a V3000 mol block (happens automatically with
* more than 999 atoms or bonds)
*/
std::string MolToMolBlock(const ROMol &mol,bool includeStereo=true,
int confId=-1,bool kekulize=true,bool forceV3000=false);
// \brief Writes a molecule to an MDL mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param includeStereo - toggles inclusion of stereochemistry information
* \param confId - selects the conformer to be used
* \param kekulize - triggers kekulization of the molecule before it is written
* \param forceV3000 - force generation a V3000 mol block (happens automatically with
* more than 999 atoms or bonds)
*/
void MolToMolFile(const ROMol &mol,std::string fName,bool includeStereo=true,
int confId=-1,bool kekulize=true,bool forceV3000=false);
//-----
// TPL handling:
//-----
//! \brief translate TPL data (BioCad format) into a multi-conf molecule
/*!
\param inStream: the stream from which to read
\param line: used to track the line number of errors
\param sanitize: toggles sanitization and stereochemistry
perception of the molecule
\param skipFirstConf: according to the TPL format description, the atomic
coords in the atom-information block describe the first
conformation and the first conf block describes second
conformation. The CombiCode, on the other hand, writes
the first conformation data both to the atom-information
block and to the first conf block. We want to be able to
read CombiCode-style tpls, so we'll allow this mis-feature
to be parsed when this flag is set.
*/
RWMol *TPLDataStreamToMol(std::istream *inStream, unsigned int &line,
bool sanitize=true,
bool skipFirstConf=false);
//! \brief construct a multi-conf molecule from a TPL (BioCad format) file
/*!
\param fName: the name of the file from which to read
\param sanitize: toggles sanitization and stereochemistry
perception of the molecule
\param skipFirstConf: according to the TPL format description, the atomic
coords in the atom-information block describe the first
conformation and the first conf block describes second
conformation. The CombiCode, on the other hand, writes
the first conformation data both to the atom-information
block and to the first conf block. We want to be able to
read CombiCode-style tpls, so we'll allow this mis-feature
to be parsed when this flag is set.
*/
RWMol *TPLFileToMol(std::string fName,bool sanitize=true,
bool skipFirstConf=false);
std::string MolToTPLText(const ROMol &mol,
std::string partialChargeProp="_GasteigerCharge",
bool writeFirstConfTwice=false);
void MolToTPLFile(const ROMol &mol,std::string fName,
std::string partialChargeProp="_GasteigerCharge",
bool writeFirstConfTwice=false);
//-----
// MOL2 handling
//-----
typedef enum {
CORINA=0 //! supports output from Corina and some dbtranslate output
} Mol2Type;
// \brief construct a molecule from a Tripos mol2 file
/*!
*
* \param fName - string containing the file name
* \param sanitize - toggles sanitization of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param variant - the atom type definitions to use
*/
RWMol *Mol2FileToMol(std::string fName,bool sanitize=true,bool removeHs=true,
Mol2Type variant=CORINA);
// \brief construct a molecule from Tripos mol2 data in a stream
/*!
* \param inStream - stream containing the data
* \param sanitize - toggles sanitization of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param variant - the atom type definitions to use
*/
RWMol *Mol2DataStreamToMol(std::istream *inStream,bool sanitize=true,bool removeHs=true,
Mol2Type variant=CORINA);
// \overload
RWMol *Mol2DataStreamToMol(std::istream &inStream,bool sanitize=true,bool removeHs=true,
Mol2Type variant=CORINA);
// \brief construct a molecule from a Tripos mol2 block
/*!
* \param molBlock - string containing the mol block
* \param sanitize - toggles sanitization of the molecule
* \param removeHs - toggles removal of Hs from the molecule. H removal
* is only done if the molecule is sanitized
* \param variant - the atom type definitions to use
*/
RWMol *Mol2BlockToMol(const std::string &molBlock,bool sanitize=true,bool removeHs=true,
Mol2Type variant=CORINA);
RWMol *PDBBlockToMol(const char *str, bool sanitize=true,
bool removeHs=true, unsigned int flavor=0);
RWMol *PDBBlockToMol(const std::string &str, bool sanitize=true,
bool removeHs=true, unsigned int flavor=0);
RWMol *PDBDataStreamToMol(std::istream *inStream, bool sanitize=true,
bool removeHs=true, unsigned int flavor=0);
RWMol *PDBDataStreamToMol(std::istream &inStream, bool sanitize=true,
bool removeHs=true, unsigned int flavor=0);
RWMol *PDBFileToMol(const std::string &fname, bool sanitize=true,
bool removeHs=true, unsigned int flavor=0);
// \brief generates an PDB block for a molecule
/*!
* \param mol - the molecule in question
* \param confId - selects the conformer to be used
* \param flavor - controls what gets written:
* flavor & 1 : Write MODEL/ENDMDL lines around each record
* flavor & 2 : Don't write any CONECT records
* flavor & 4 : Write CONECT records in both directions
* flavor & 8 : Don't use multiple CONECTs to encode bond order
* flavor & 16 : Write MASTER record
* flavor & 32 : Write TER record
*/
std::string MolToPDBBlock(const ROMol &mol, int confId=-1, unsigned int flavor=0);
// \brief Writes a molecule to an MDL mol file
/*!
* \param mol - the molecule in question
* \param fName - the name of the file to use
* \param confId - selects the conformer to be used
* \param flavor - controls what gets written:
* flavor & 1 : Write MODEL/ENDMDL lines around each record
* flavor & 2 : Don't write any CONECT records
* flavor & 4 : Write CONECT records in both directions
* flavor & 8 : Don't use multiple CONECTs to encode bond order
* flavor & 16 : Write MASTER record
* flavor & 32 : Write TER record
*/
void MolToPDBFile(const ROMol &mol,const std::string &fname, int confId=-1, unsigned int flavor=0);
}
#endif
|