Dear Paolo,
I modify the Builder.h by adding this line under namespace:
class MMFFMolProperties;
I recompiled and now I have the following issues:
code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h:46:31: error: variable has
incomplete type 'MMFF::MMFFMolProperties'
MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
^
code/GraphMol/ForceFieldHelpers/MMFF/Builder.h:29:13: note: forward declaration
of 'RDKit::MMFF::MMFFMolProperties'
class MMFFMolProperties;
^
Dr. Guillaume GODIN
Project Manager
Innovation
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
________________________________
De : Paolo Tosco [[email protected]]
Envoyé : mercredi, 13. mai 2015 10:35
À : Guillaume GODIN; Greg Landrum
Cc : [email protected]
Objet : Re: [Rdkit-discuss] licence type
Dear Guillaume,
it looks like a forward declaration is missing there; try patching
Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h as follows:
*** ./Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h Wed May 13 09:32:12
2015
--- ./Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h Wed May 13 09:32:18 2015
***************
*** 26,31 ****
--- 26,32 ----
namespace RDKit {
class ROMol;
namespace MMFF {
+ class MMFFMolProperties;
//! Builds and returns a MMFF force field for a molecule
/*!
You'll only need to add the "class MMFFMolProperties;" line after "namespace
MMFF {". That should fix your problem. Would you please let me know if this
works for you?
Thank you, kind regards
Paolo
On 05/13/15 09:05, Guillaume GODIN wrote:
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
from rdkit import Chem
from rdkit.Chem import AllChem
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:
int Embedmolecule3D()
{
return RDKit::DGeomHelpers::EmbedMolecule(*rdmol);
}
void addHs()
{
return RDKit::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
CORPORATE R&D DIVISION
DIRECT LINE +41 (0)22 780 3645
MOBILE +41 (0)79 536 1039
Firmenich SA
RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
________________________________
De : Greg Landrum [[email protected]<mailto:[email protected]>]
Envoyé : mercredi, 13. mai 2015 06:49
À : Guillaume GODIN
Cc :
[email protected]<mailto:[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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