inchi-gem

Ruby wrapper for InChI v1.06

Install

$ gem install inchi-gem

Usage

require 'inchi-gem'

rv = Inchi::ExtraInchiReturnValues.new
inchi = Inchi::molfileToInchi(molfile, rv, "-Polymers")
// "InChI=1B/C8H8Zz2/c9-6-8(10)7-4-2-1-3-5-7/h1-5,8H,6H2/z101-1-8(10-8,9-6)"

inchi05 = Inchi::molfileToInchi(molfile, rv, "-Polymers105")
// "InChI=1B/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2/z101-1-8(1.2)"

inchi = Inchi::molfileToInchi(sample_01, rv, "-Polymers -FoldCRU -NPZz -SAtZZ -LargeMolecules")
// "InChI=1B/C8H8Zz2/c9-6-8(10)7-4-2-1-3-5-7/h1-5,8H,6H2/z101-1-8(10-8,9-6)"

List options:

• LooseTSACheck (new in v. 1.06). Relax strictness of tetrahedral stereo ambiguity check for stereo atoms in (large) rings. Default: Use strict criteria (as in v. 1.05 and previous).
• Polymers Experimental support of simple polymers, current mode. Default: Disabled.
• Polymers105 (new in v. 1.06). Experimental support of simple polymers in legacy v. 1.05 mode. Default: Disabled.
• NoFrameShift (new in v. 1.06). Disable polymer CRU frame shift. Default: Attempt CRU frame shift.
• FoldCRU (new in v. 1.06). In polymer treatment, try to fold constitutional repeating units which themselves contain repeats. Default: Disabled.
• NPZz (new in v. 1.06). Allow non-polymer Zz pseudo element atoms. Default: Disabled.
• SAtZZ (new in v. 1.06). Allow stereo at atoms connected to Zz. Default: Disabled.
• LargeMolecules. Experimental support of molecules up to 32767 atoms. Default: Disabled.

Return value

Return information is saved in the ExtraInchiReturnValues struct param

struct ExtraInchiReturnValues {
  int returnCode; // return code, see the table below
  std::string messagePtr;
  std::string logPtr;
  std::string auxInfoPtr;
};

Example of warning inchi

require 'inchi-gem'

rv = Inchi::ExtraInchiReturnValues.new
inchi = Inchi::molfileToInchi(molfile, rv, "-Polymers")
puts rv.returnCode // 1
puts rv.messagePtr // "Accepted unusual valence(s): N(4); Metal was disconnected; Proton(s) added/removed"

Code	Value	Meaning
inchi_Ret_OKAY	0	Success; no errors or warnings
inchi_Ret_WARNING	1	Success; warning(s) issued
inchi_Ret_ERROR	2	Error: no InChI has been created
inchi_Ret_FATAL	3	Severe error: no InChI has been created (typically, memory allocation failure)
inchi_Ret_UNKNOWN	4	Unknown program error
inchi_Ret_BUSY	5	Previous call to InChI has not returned yet
inchi_Ret_EOF	-1	No structural data have been provided
inchi_Ret_SKIP	-2	Not used in InChI library

Test

$ rake test