Feature Requests item #2871242, was opened at 2009-10-01 10:52
Message generated for change (Tracker Item Submitted) made by nobody
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: gaussian format: partial charges
Initial Comment:
Hi,
It seems that babel is well capable of reading in gaussian calculated Mulliken
charges. However, charges provided by more sophisticated algorithms (opt=mk for
example) are not read even if they are calculated. Including support for better
partial charges would make sense because Mulliken charges typically don't make
any sense.
Quick look in the gaussformat.cpp shows that only Mulliken charges are
interpreted. I tested a bit, and adding the following code after Mulliken code,
should do the trick (same code as for Mulliken with small changes):
else if(strstr(buffer,"Charges from ESP fit") != NULL )
{
hasPartialCharges = true;
ifs.getline(buffer,BUFF_SIZE); // column headings
ifs.getline(buffer,BUFF_SIZE); // column headings
ifs.getline(buffer,BUFF_SIZE);
tokenize(vs,buffer);
while (vs.size() >= 3 &&
strstr(buffer,"------------------------------------------")
== NULL)
{
atom = mol.GetAtom(atoi(vs[0].c_str()));
if (!atom)
break;
atom->SetPartialCharge(atof(vs[2].c_str()));
if (!ifs.getline(buffer,BUFF_SIZE)) break;
tokenize(vs,buffer);
}
}
In addition, one needs to add a correct value for the pair data that is set
later in the code.
I hope that this comment is useful.
Regards,
Tapani Kinnunen (takinnun at hotmail.com)
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