Dear Eagon,
I will use MM2AtomTypeMatcherTest and MMFF94AtomTypeMatcherTest classes and get
back to you.
kind regards,
Aziz
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> From: cdk-user-requ...@lists.sourceforge.net
> Subject: Cdk-user Digest, Vol 42, Issue 4
> To: cdk-user@lists.sourceforge.net
> Date: Fri, 6 Nov 2009 12:03:38 +0000
>
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> Today's Topics:
>
> 1. Wrong atom types assignements (Aziz Yasri)
> 2. Re: Wrong atom types assignements (Egon Willighagen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 6 Nov 2009 11:17:59 +0100
> From: Aziz Yasri <aya...@hotmail.fr>
> Subject: [Cdk-user] Wrong atom types assignements
> To: <cdk-user@lists.sourceforge.net>
> Message-ID: <col104-w12d57fc85fae075676843eab...@phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear All,
>
> I am using cdk-1.2.3 version and trying to get forcefield parameters for some
> molecules. When I use the forcefieldConfigurator calss with mmff94 or mm2
> forcefield, I get wrong atom type names assignements. I have done this
> several times for many molecules and I get to the same conclusion. I have
> atached here the code (for one molcule) I am using that configures the
> forcefield, assigns the atom type names and print the atom type names for
> each atom in the molecule. I also attached the atom types obtained from the
> MMFF94 forcefield (REAL MMFF94) from other source and I know that there are
> correct.
>
> I don't know if I am doing someting wrong or the routine that assigns the
> atome types is not correct.
>
>
> here is the code:
>
> sp = SmilesParser(DefaultChemObjectBuilder.getInstance())
> mol =
> sp.parseSmiles("CN1CC2=C(N=CN2C2=C(C1=O)C(Cl)=CC=C2)C1=NOC(=N1)[...@](C)(O)CO")
> ffc = ForceFieldConfigurator();
> ffc.setForceFieldConfigurator("mmff94");
> ffc.assignAtomTyps(mol);
> atoms = mol.atoms().iterator()
> atom_ID = 1
> while atoms.hasNext():
> atom_i = atoms.next()
> print atom_ID,"Symbol :",atom_i.getSymbol()," Atom Type
> :",atom_i.getAtomTypeName()
> atom_ID += 1
>
>
>
> Mol code : CID10091748
> Mol smile : CN1CC2=C(N=CN2C2=C(C1=O)C(Cl)=CC=C2)C1=NOC(=N1)[...@](C)(O)CO
>
>
> MMFF94 REAL MMFF94
> 1 Symbol : C Atom Type : C C
> 2 Symbol : N Atom Type : N NC=O
> 3 Symbol : C Atom Type : C C
> 4 Symbol : C Atom Type : Car C5A
> 5 Symbol : C Atom Type : C5 C5B
> 6 Symbol : N Atom Type : N2OX N5B
> 7 Symbol : C Atom Type : C5 C5A
> 8 Symbol : N Atom Type : N2OX NPYL
> 9 Symbol : C Atom Type : Car Car
> 10 Symbol : C Atom Type : Car Car
> 11 Symbol : C Atom Type : C= C=
> 12 Symbol : O Atom Type : O= O=
> 13 Symbol : C Atom Type : Car Car
> 14 Symbol : Cl Atom Type : CL CL
> 15 Symbol : C Atom Type : Car Car
> 16 Symbol : C Atom Type : Car Car
> 17 Symbol : C Atom Type : Car Car
> 18 Symbol : C Atom Type : C5 C5B
> 19 Symbol : N Atom Type : N2OX N5A
> 20 Symbol : O Atom Type : Oar Oar
> 21 Symbol : C Atom Type : C5 C5A
> 22 Symbol : N Atom Type : N2OX N5B
> 23 Symbol : C Atom Type : C C
> 24 Symbol : C Atom Type : C C
> 25 Symbol : O Atom Type : O O
> 26 Symbol : C Atom Type : C C
> 27 Symbol : O Atom Type : O O
>
> MM2
> 1 Symbol : C Atom Type : C
> 2 Symbol : N Atom Type : N
> 3 Symbol : C Atom Type : C
> 4 Symbol : C Atom Type : Csp2
> 5 Symbol : C Atom Type : Csp2
> 6 Symbol : N Atom Type : NPYL
> 7 Symbol : C Atom Type : Csp2
> 8 Symbol : N Atom Type : N
> 9 Symbol : C Atom Type : Csp2
> 10 Symbol : C Atom Type : Csp2
> 11 Symbol : C Atom Type : Csp2
> 12 Symbol : O Atom Type : O=
> 13 Symbol : C Atom Type : Csp2
> 14 Symbol : Cl Atom Type : CL
> 15 Symbol : C Atom Type : Csp2
> 16 Symbol : C Atom Type : Csp2
> 17 Symbol : C Atom Type : Csp2
> 18 Symbol : C Atom Type : Csp2
> 19 Symbol : N Atom Type : NPYL
> 20 Symbol : O Atom Type : Oar
> 21 Symbol : C Atom Type : Csp2
> 22 Symbol : N Atom Type : NPYL
> 23 Symbol : C Atom Type : C
> 24 Symbol : C Atom Type : C
> 25 Symbol : O Atom Type : O
> 26 Symbol : C Atom Type : C
> 27 Symbol : O Atom Type : O
>
>
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> ------------------------------
>
> Message: 2
> Date: Fri, 6 Nov 2009 12:10:28 +0100
> From: Egon Willighagen <egon.willigha...@gmail.com>
> Subject: Re: [Cdk-user] Wrong atom types assignements
> To: Aziz Yasri <aya...@hotmail.fr>
> Cc: cdk-user@lists.sourceforge.net
> Message-ID:
> <6aeb064b0911060310j621d1a9dye0ca56606b80...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Aziz,
>
> On Fri, Nov 6, 2009 at 11:17 AM, Aziz Yasri <aya...@hotmail.fr> wrote:
> > I am using cdk-1.2.3 version and trying to get forcefield parameters for
> > some molecules. When I use the forcefieldConfigurator calss? with mmff94 or
> > mm2 forcefield, I get wrong atom type names assignements. I have done this
> > several times for many molecules and I get to the same conclusion. I have
> > atached here? the code (for one molcule) I am using that configures the
> > forcefield, assigns the atom type names and print the atom type names for
> > each atom in the molecule. I also attached the atom types obtained from the
> > MMFF94 forcefield (REAL MMFF94) from other source and I know that there are
> > correct.
> > I don't know if I am doing someting wrong or the routine that assigns the
> > atome types is not correct.
>
> I do not have experience with this part of the library, but can point
> you to the unit test classes, which might server as some comparision
> material. Please look at MM2AtomTypeMatcherTest [0] and
> MMFF94AtomTypeMatcherTest [1]. The main difference seems to be that
> these unit tests do no use the ForceFieldConfigurator, but
> AtomTypeMatchers for the two force fields.
>
> Could you try what those classes give for atom types? I think a unit
> tests using those atom type matcher classes at your below mentioned
> test case would be very interesting...
>
> Egon
>
> 0.http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=blob;f=src/test/org/openscience/cdk/atomtype/MM2AtomTypeMatcherTest.java;h=647c8e6ccff5167566e3a65b572ebac7bed2de0a;hb=681b3a129f34bbbb85264bfe92451918c395960e
> 1.http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cdk/cdk;a=blob;f=src/test/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcherTest.java;h=a3f6a2a7fdca8bb01c91328889f39c35b8042b75;hb=681b3a129f34bbbb85264bfe92451918c395960e
>
> --
> Post-doc @ Uppsala University
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
>
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