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/**********************************************************************
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Copyright (C) 2006 Chris Morley
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This file is part of the Open Babel project.
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For more information, see <http://openbabel.sourceforge.net/>
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This program is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation version 2 of the License.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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***********************************************************************/
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#include <openbabel/babelconfig.h>
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///Returns true if character is not one used in an InChI.
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bool inline isnic(char ch)
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//This set of characters could be extended
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static string nic("\"\'\\@<>!$%&{}[]");
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return nic.find(ch)!=string::npos;
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/// @brief Reads an InChI (possibly split) from an input stream and returns it as unsplit text.
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This function recovers a normal InChI from an input stream which
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contains other arbitary text. The InChI string can have
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extraneous characters inserted, for example because of word wrapping,
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provided it follows certain rules.
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Dmitrii Tchekhovskoi made a proposal for "InChI hyphenation".
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http://sourceforge.net/mailarchive/forum.php?thread_id=10200459&forum_id=45166
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The function here is consistent with this proposal but extends
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it, allowing a wider range of corrupted InChIs to be accepted.
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The original proposal was essentially:
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- When an InChI string is enclosed by " quote characters,
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any whitespace characters it contains (including new lines) are
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- Other extraneous strings can also be ignored, but this
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- The "InChI=" cannot be split.
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- The character that encloses a quoted InChI does not have to be "
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and can be any character that is not used in InChI - a NIC
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[never miss the opportunity for a TLA!]. This means that
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conflicts in systems which have other uses for the quote character
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- As well as whitespace characters (which are ignored), a quoted
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InChI can contain an extraneous string which starts and ends with
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a NIC. This allows inserted strings like <br /> to be ignored.
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However, only one such extraneous string is allowed.
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- There are no restrictions on splitting "InChI=" by whitespace
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characters, allowing a minimum column width of 1.
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If the splitting were by an extraneous string the minimum column
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The following are some examples of split InChIs.
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OpenBabel will find and convert 12 InChIs
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in this file, e.g. babel -iinchi getinchi.cpp -osmi
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First two unbroken examples, the first is unquoted
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InChI=1/CH4/h1H4 methane
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"InChI=1/C4H10O/c1-3-5-4-2/h3-4H2,1-2H3" diethyl ether
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Multiple white space splitting
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@InChI=1/C15H14O3/c1-11(15(16)17)18-
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14-10-6-5-9-13(14)12-7-3-2-4-8-12/h2
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Split with extraneous text, which starts and ends with a non-InChI character
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'InChI=1/C2H6O/c1-2-<br />3/h3H,2H2,1H3'
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Table with wrapped InChI column. (View with fixed font.)
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'InChI=1/CH4/h1H4' !flammable!
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'InChI=1/C2H2O4/c3-1 !toxic!
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'InChI=1/CH4O/c1-2/h !flammable! !toxic!
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'InChI=1/C10H5ClN2/c !no information!
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Quoted text in emails (but InChI is preserved after one break only).
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> "InChI=1/C4H7N3OS/c1-7(8)4-9-5-2-3-6-9/h
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> 2-4,8H,1H3/p+1/fC4H8N3OS/h5H/q+1/t9?"
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>> "InChI=1/C4H7N3OS/c1-7(8)4-9-5-2-3-6-9/
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>> h2-4,8H,1H3/p+1/fC4H8N3OS/h5H/q+1/t9?"
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Column width can be 1 if there is no extraneous text other than whitespace.
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(When there is an extraneous string with NICs the minimum column width is 2).
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string OBAPI GetInChI(istream& is);
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string GetInChI(istream& is)
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string prefix("InChI=");
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enum statetype {before_inchi, match_inchi, unquoted, quoted};
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statetype state = before_inchi;
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char ch, lastch=0, qch=0;
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size_t split_pos = 0;
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while((ch=is.get())!=EOF)
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if(state==before_inchi)
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if(ch==qch && state!=match_inchi)
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result.erase(split_pos);
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split_pos = result.size();
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if(state==match_inchi)
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if(prefix.compare(0,result.size(),result)==0) //true if correct
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if(result.size()==prefix.size())
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state = isnic(qch) ? quoted : unquoted;
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state = before_inchi;
added
removed
src/formats/getinchi.cpp
