Dear all,
first thanks for reading this, I am new to OpenBabel and to this mailing
list,
be sure I will appreciate your advise.
I developed a software to visualize/analyse/edit atomistic models, very
recently
I decided to use the OpenBabel library to read/output coordinates files
in various
format, bellow you will find the code I wrote to read coordinates files
via babel.
While playing with my software and the newly inserted OpenBabel
read/write functions,
I noticed something rather odd when reading rather larger coordinates
files,
and I would like to get a better idea of what is going on.
When the connectivity of the system is rather large, well that it my
guess after few trial
and error sessions, it can takes a very long time to open the coordinate
file,
and I am just talking about some time spend around the '.ReadFile()'
instruction,
as an example you use this file (silica glass SiO2 with 3000 atoms in
PDB format, written using Babel):
https://ipcms-cloud.u-strasbg.fr/owncloud/index.php/s/70C7b9Z04adVauD
I also noticed that other PDB file where the bonds are described can be
opened very quickly.
My guess is, that Babel is analysing the connectivity, ie. looking for
bonds, am I correct ?
Is this the reason why it is so slow for this kind of coordinates is
because Babel looking for bonds ?
If yes is there a way to turn off this analyses before it begins ?
If yes I am wrong what can I do to speed up the opening process ?
Thanks in advance for your lights on the matter.
Best regards.
Sébastien Le Roux
--------------------------------------------------------------------------------------------------------------------------------------------------
int read_this_file_using_babel (char * this_format, char * this_file)
{
OBConversion conv;
if(conv.SetInFormat(this_format))
{
OBMol mol;
if(conv.ReadFile(& mol, this_file))
{
// It does read the file !
if (mol.HasData(OBGenericDataType::UnitCell))
{
OBUnitCell * uc = (OBUnitCell
*)mol.GetData(OBGenericDataType::UnitCell);
// My code is mostly in C, so I have to send back the data I
need to the C part.
save_babel_unit_cell_details (uc->GetA(), uc->GetB(),
uc->GetC(), uc->GetAlpha() , uc->GetBeta(), uc->GetGamma());
if (strcmp(this_format, "cif") == 0) uc -> FillUnitCell (& mol);
}
int atoms = mol.NumAtoms ();
int * lot;
lot = (int *)calloc(atoms, sizeof(int));
double ** coords;
coords = (double **)calloc(atoms, sizeof(double *));
int i = 0;
FOR_ATOMS_OF_MOL (atom, mol)
{
lot[i] = atom -> GetAtomicNum();
coords[i] = (double *)calloc(3, sizeof(double));
coords[i][0] = atom -> GetX();
coords[i][1] = atom -> GetY();
coords[i][2] = atom -> GetZ();
i ++;
}
// My code is mostly in C, so I have to send back the data I need
to the C part.
save_babel_molecule_details (atoms, lot, coords);
free (lot);
free (coords);
mol.Clear();
return 0;
}
else
{
// Error reading file
return 1;
}
}
else
{
// Error with this format
return 2;
}
}
--
===========================================================
Dr. Sébastien Le Roux
Ingénieur de Recherche CNRS
Institut de Physique et Chimie des Matériaux de Strasbourg
Département des Matériaux Organiques
23, rue du Loess
BP 43
F-67034 Strasbourg Cedex 2, France
E-mail: sebastien.ler...@ipcms.unistra.fr
Webpage: http://www.ipcms.unistra.fr/?page_id=14965&lang=en
RINGS project: http://rings-code.sourceforge.net/
ISAACS project: http://isaacs.sourceforge.net/
Fax: +33 3 88 10 72 46
Phone: +33 3 88 10 71 58
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