avalontoolkit-discuss — Discussions and Feature Requests

[Avalontoolkit-discuss] SMILES valence model

[Noel O'B. <bao...@gm...>]

Hi there,

My previous emails have gone unanswered, but here is one last try...

The Avalon toolkit doesn't fully adhere to the SMILES valence model when
reading SMILES. Specifically, the spec describes that halides should only
be rounded up with implicit hydrogens to a valence of 1 when reading SMILES.

However, Avalon added a hydrogen to the chlorine in Cl(C)C and in
Cl(C)(C)(C)C. It also does this for the equivalent SMILES with bromine and
iodine. These six disagreements, if resolved, would allow the toolkit to
read SMILES exactly like Daylight.

I also note in passing that Avalon rejects, in error, the SMILES "[C@
@]1(Cl)(F)I.Br1".

Regards,
- Noel

[Avalontoolkit-discuss] Double-bond stereochemistry appearing and disappearing

[Noel O'B. <bao...@gm...>]

Hi there,

With C code similar to the following:
=======
  mol = SMIToMOL(argv[2], 0);
  ans = MOLToSMI(mol, DY_AROMATICITY);
  printf("%s\n", ans);
=======

...I find that double bond stereochemistry is not roundtripped. For example:
1. "FC=C(Cl)Br" is converted to "F/C=C(\Cl)\Br" (conflicting stereo symbols)
2. "F/C=C(Cl)/Br" is converted to "F/C=C(\Cl)\Br" (conflicting stereo
symbols and F is supposed to be trans to Br)

On the other hand, "FC=C(Cl)/Br" is correctly converted to "FC=C(Cl)Br"
(stereo not specified).

Am I doing something wrong, or is this a bug?

Regards,
   Noel (O'Boyle)

[Avalontoolkit-discuss] Incorrect number of Hs on P when reading aromatic SMILES

[Noel O'B. <bao...@gm...>]

Hi there,

I've been testing a large number of SMILES readers with a view to improving
quality and finding corner cases that should be resolved.

When reading the SMILES string c1cccc2c1p(c3c2cccc3)C, the Avalon toolkit
adds a hydrogen to the phosphorus, which I believe is an error (if it had a
hydrogen it should be written [pH]). If replaced with an 'n', no H is added.

Regards,
- Noel

Re: [Avalontoolkit-discuss] changes required to get code working on windows

[Rohde, B. <ber...@no...>]

The file local.h defines FALSE if it's not already defined. For some reason, this check didn't kick in.

Could you check if you can find out why FALSE is defined in your environment and what value other than 0 it has?

Cheers,

Bernd


Hi,

This morning I did a 32bit windows build of the code using Visual
Studio Express 2010. To get things working I had to make the following
mods:


glandrum@... ~/avalontoolkit
$ svn diff common
Index: common/patclean.c
===================================================================
--- common/patclean.c   (revision 2)
+++ common/patclean.c   (working copy)
@@ -845,14 +845,14 @@
    ssmatch_t *best_match;
    int problem_found, match_applied;

-   // check parameters
-   if (IsNULL(mp)  ||  IsNULL(ssp)) return (FALSE);
-
    int i, j, k, iatom, jatom;
    int symbol;
    struct reaccs_bond_t *bp, bm;
    neighbourhood_t neighbour_array[MAXATOMS], *nbp;

+   // check parameters
+   if(IsNULL(mp)  ||  IsNULL(ssp)) return 0;
+
    if (mp->n_atoms > MAXATOMS)
    {
       fprintf(stderr,"Too many atoms in molecule '%s'\n",mp->name);
Index: common/reaccsio.c
===================================================================
--- common/reaccsio.c   (revision 2)
+++ common/reaccsio.c   (working copy)
@@ -1357,7 +1357,7 @@
             {
                tempfile = tempnam(tempdir, (const char *)NULL);
                fp = fopen(tempfile, "wb+");
-               MyFree((char *)tempdir);
+               //MyFree((char *)tempdir);
                if (IsNULL(fp))
                {
                    MyFree((char *)tempfile);



-greg

[Avalontoolkit-discuss] changes required to get code working on windows

[Greg L. <gre...@gm...>]

Hi,

This morning I did a 32bit windows build of the code using Visual
Studio Express 2010. To get things working I had to make the following
mods:


glandrum@vielfrass ~/avalontoolkit
$ svn diff common
Index: common/patclean.c
===================================================================
--- common/patclean.c   (revision 2)
+++ common/patclean.c   (working copy)
@@ -845,14 +845,14 @@
    ssmatch_t *best_match;
    int problem_found, match_applied;

-   // check parameters
-   if (IsNULL(mp)  ||  IsNULL(ssp)) return (FALSE);
-
    int i, j, k, iatom, jatom;
    int symbol;
    struct reaccs_bond_t *bp, bm;
    neighbourhood_t neighbour_array[MAXATOMS], *nbp;

+   // check parameters
+   if(IsNULL(mp)  ||  IsNULL(ssp)) return 0;
+
    if (mp->n_atoms > MAXATOMS)
    {
       fprintf(stderr,"Too many atoms in molecule '%s'\n",mp->name);
Index: common/reaccsio.c
===================================================================
--- common/reaccsio.c   (revision 2)
+++ common/reaccsio.c   (working copy)
@@ -1357,7 +1357,7 @@
             {
                tempfile = tempnam(tempdir, (const char *)NULL);
                fp = fopen(tempfile, "wb+");
-               MyFree((char *)tempdir);
+               //MyFree((char *)tempdir);
                if (IsNULL(fp))
                {
                    MyFree((char *)tempfile);



-greg