johnmay

<plugin>
  <groupId>com.google.code.maven-replacer-plugin</groupId>
  <artifactId>replacer</artifactId>
  <version>1.5.3</version>
  <executions>
    <execution>
      <id>JavaEE to Jakarta</id>
      <phase>generate-sources</phase>
      <goals>
        <goal>replace</goal>

johnmay

import sys

import daylight
from daylight import Smiles, Smirks

def output(smiin, smirks, smiout, comment):
  print ("%s\t%s\t%s\t%s" % (smiin, smirks, smiout, comment))

def main(fname):
	file = open(fname, 'r')

johnmay

c12cccc1C=CC=C2.*[Zr](*)(Cl)Cl.c12cccc1C=CC=C2 |m:9:0.1.2.3.4,11:14.15.16.17.18| h5-
c12cccc1C=CC=C2.*[Zr](*)(Cl)Cl.c12cccc1C=CC=C2 |m:9:0.4.5.6.7.8,11:14.18.19.20.21.22| h6-
c12cccc1C=CC=C2.*[Zr](*)(Cl)Cl.c12cccc1C=CC=C2 |m:9:5.6.7.8,11:19.20.21.22| h4-

johnmay

[Fe]
  NextMove03242216572D

  1  0  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15
M  END
$$$$
[FeH]
  NextMove03242216572D

johnmay

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>

typedef struct array_list
{
    char *arrayType;
    size_t arraySize;
    void *address;

johnmay

bridged
  CDK     0322221734

  8  9  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

johnmay

Testing a 7 valent carbon
SMILES_IN = C(C)(C)(C)(C)(C)(C)C
INCHI_OUT = InChI=1S/C8H21/c1-8(2,3,4,5,6)7/h1-7H3

*** Open Babel Warning  in InChI code
  #1 :Accepted unusual valence(s): C(7)

CDK yes
ChemDraw yes
OpenBabel yes

johnmay

[john@***** scratch]$ more tmp.txt 
* Input_File: "tmp.inchi"
Structure: 1. (No struct name)
InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H
AuxInfo=1/0/N:1,2,3,4,5,6/E:(2,3)(4,5)/rA:6CCCCCN/rB:d1;s1;s2;d3;d4s5;/rC:;;;;;;
[john@talkie scratch]$ INCHI-1-BIN/linux/64bit/inchi-1 tmp.txt -OutputSDF output.sdf
InChI version 1, Software v. 1.06 (inchi-1 executable) 
Linux 64-bit Build (gcc 4.8.5 20150623 (Red Hat 4.8.5-39)) of Dec 19 2020 21:02:16

Opened log file 'tmp.txt.log'

johnmay

[john@***** scratch]$ INCHI-1-BIN/linux/64bit/inchi-1 -inchi2struct tmp.inchi -OutputSDF output.sdf
InChI version 1, Software v. 1.06 (inchi-1 executable) 
Linux 64-bit Build (gcc 4.8.5 20150623 (Red Hat 4.8.5-39)) of Dec 19 2020 21:02:16

Opened log file 'tmp.inchi.log'
Opened input file 'tmp.inchi'
Opened output file 'output.sdf'
Opened problem file 'tmp.inchi.prb'
The command line used:
"INCHI-1-BIN/linux/64bit/inchi-1 -inchi2struct tmp.inchi -OutputSDF output.sdf"

johnmay

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE CDXML SYSTEM "http://www.cambridgesoft.com/xml/cdxml.dtd" >
<CDXML
 CreationProgram="ChemDraw 14.0.0.118"
 Name="Human_Body.cdx"
 BoundingBox="5.57 2.92 538.65 658.35"
 WindowPosition="0 0"
 WindowSize="0 0"
 FractionalWidths="yes"
 InterpretChemically="yes"