Dear Greg,
I will usse the new BSD license thanks for this advice.
Can you tell me the method to reproduce the red line of your
following python code in c++ from a recent publication, I would like
to compute the MMFF of a molecule but this failed in clang/emscripten:
#!/usr/bin/env python
# build 3D coordinates from SMILES and optimize
# geometry with the MMFF94s force field
fromrdkit importChem
fromrdkit.Chem importAllChem
smi = 'O=C(O)C(c1ccc(cc1)CCN4CCC(c2nc3ccccc3n2CCOCC)CC4)(C)C'
mol = Chem.MolFromSmiles(smi)
molH = Chem.AddHs(mol)
AllChem.EmbedMolecule(molH)
AllChem.MMFFOptimizeMolecule(molH, 'MMFF94s')
# save MMFF-optimized 3D coordinates
Chem.MolToMolFile(molH, 'bilastine.mol')
for the embedmolecule & addHs following methods work:
intEmbedmolecule3D()
{
returnRDKit::DGeomHelpers::EmbedMolecule(*rdmol);
}
voidaddHs()
{
returnRDKit::MolOps::addHs(*rdmol);
}
I have a issue to expose MMFFOptimizeMolecule:
std::pair<int, double> MMFFoptimizeMolecule()
{
return RDKit::MMFF::MMFFOptimizeMolecule(*rdmol);
}
In file included from ../rdmol.cpp:12:
In file included from code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h:13:
*code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:66:62: **error:
**unknown type name 'MMFFMolProperties'*
ForceFields::ForceField *constructForceField(ROMol &mol,
MMFFMolProperties *mmffMolProperties,
* ^*
*code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:83:9: **error:
**unknown type name 'MMFFMolProperties'*
MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field);
* ^*
*code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:85:9: **error:
**unknown type name 'MMFFMolProperties'*
MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field);
* ^*
*code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:87:9: **error:
**unknown type name 'MMFFMolProperties'*
MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field);
* ^*
*code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:89:9: **error:
**unknown type name 'MMFFMolProperties'*
MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field);
* ^*
*code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:91:9: **error:
**unknown type name 'MMFFMolProperties'*
MMFFMolProperties *mmffMolProperties, ForceFields::ForceField *field,
* ^*
*code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:93:49: **error:
**unknown type name 'MMFFMolProperties'*
void addVdW(const ROMol &mol, int confId, MMFFMolProperties
*mmffMolProperties,
* ^*
*code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:96:49: **error:
**unknown type name 'MMFFMolProperties'*
void addEle(const ROMol &mol, int confId, MMFFMolProperties
*mmffMolProperties,
* ^*
In file included from ../rdmol.cpp:12:
*code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h:46:30: **error:
**expected ';' after expression*
MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
* ^*
;
*code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h:46:13: **error: **no
member named 'MMFFMolProperties' in namespace 'RDKit::MMFF'*
MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
* ~~~~~~^*
*code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h:46:31: **error: **use of
undeclared identifier 'mmffMolProperties'*
MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
* ^*
*code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h:47:11: **error: **use of
undeclared identifier 'mmffMolProperties'*
if (mmffMolProperties.isValid()) {
best regards,
*Dr. Guillaume GODIN***
Project Manager
Innovation
CORPORATER&D DIVISION
DIRECTLINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
*Firmenich SA***
RUEDESJEUNES1 | CASEPOSTALE239 | CH-1211 GENEVE8
------------------------------------------------------------------------
*De :* Greg Landrum [[email protected]]
*Envoyé :* mercredi, 13. mai 2015 06:49
*À :* Guillaume GODIN
*Cc :* [email protected]
*Objet :* Re: [Rdkit-discuss] licence type
Dear Guillaume,
On Wed, May 13, 2015 at 6:35 AM, Guillaume GODIN
<[email protected]
<mailto:[email protected]>> wrote:
Dear All,
I would like to port RDKit to nodejs.
What is the licence type I should take ?
The RDKit's license, the "new BSD" license, is compatible with all
open-source licenses that I'm aware of, so the decision is really up
to you.
I, of course, favor the new BSD license or the Apache license. Both
allow people who use the code a great deal of flexibility.
-greg
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