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Viewing changes to src/amber.cpp

Committer: Bazaar Package Importer
Author(s): Michael Banck
Date: 2002-02-01 01:19:44 UTC
Revision ID: james.westby@ubuntu.com-20020201011944-4a9guzcsnpezzawx

Tags: upstream-1.99

Import upstream version 1.99

files added:

AUTHORS

COPYING

ChangeLog

INSTALL

Makefile.in

README

THANKS

config.guess

config.sub

configure

configure.in

doc/FAQ

doc/Migration

doc/Primer.html

doc/babel.1

install-sh

ltconfig

ltmain.sh

missing

mkinstalldirs

src/Makefile

src/Makefile.in

src/StdAfx.cpp

src/StdAfx.h

src/Vector.cpp

src/Vector.h

src/alchemy.cpp

src/amber.cpp

src/aromatic.h

src/aromatic.txt

src/atom.cpp

src/atomtyp.h

src/atomtyp.txt

src/balst.cpp

src/base.cpp

src/base.h

src/bgf.cpp

src/bin2hex.pl

src/binary.cpp

src/binary.h

src/binary_io.cpp

src/binary_io.h

src/bitgrid.cpp

src/bitgrid.h

src/bitvec.cpp

src/bitvec.h

src/bond.cpp

src/box.cpp

src/c3d.cpp

src/cacao.cpp

src/cache.cpp

src/car.cpp

src/ccc.cpp

src/chains.cpp

src/chains.h

src/chdrw.cpp

src/chiral.cpp

src/chiral.h

src/commandline.cpp

src/commandline.h

src/csr.cpp

src/cssr.cpp

src/ctransform.cpp

src/ctransform.h

src/cwrap.cpp

src/cwrap.h

src/data.cpp

src/data.h

src/dmol.cpp

src/element.h

src/element.txt

src/extable.h

src/extable.txt

src/feat.cpp

src/fh.cpp

src/fileformat.cpp

src/fileformat.h

src/gamess.cpp

src/gaussian.cpp

src/generic.cpp

src/generic.h

src/ghemical.cpp

src/grid.cpp

src/grid.h

src/gromos96.cpp

src/hin.cpp

src/jaguar.cpp

src/main.cpp

src/matrix.cpp

src/matrix.h

src/mdl.cpp

src/mmod.cpp

src/mol.cpp

src/mol.h

src/mol2.cpp

src/molchrg.cpp

src/molchrg.h

src/molvector.cpp

src/molvector.h

src/mopac.cpp

src/mpqc.cpp

src/nwchem.cpp

src/obifstream.h

src/oblib.dsp

src/oblib.dsw

src/obutil.cpp

src/obutil.h

src/parsmart.cpp

src/parsmart.h

src/parsmi.cpp

src/patty.cpp

src/patty.h

src/pdb.cpp

src/phmodel.cpp

src/phmodel.h

src/phmodel.txt

src/phmodeldata.h

src/qchem.cpp

src/quat.c

src/rand.cpp

src/report.cpp

src/resdata.h

src/resdata.txt

src/ring.cpp

src/ring.h

src/rotor.cpp

src/rotor.h

src/smarts.cpp

src/smarts.h

src/smi.cpp

src/smi.h

src/tinker.cpp

src/tokenst.cpp

src/typer.cpp

src/typer.h

src/types.h

src/types.txt

src/unichem.cpp

src/version.h.in

src/xed.cpp

src/xyz.cpp

stamp-h.in

stamp.h

test

test/Makefile

test/Makefile.in

test/attype.00.smi

test/main.cpp

test/ringresults.txt

test/ringtest.cpp

test/smartsresults.txt

test/smartstest.cpp

test/smartstest.txt

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src/amber.cpp

/**********************************************************************

This program is free software; you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

GNU General Public License for more details.

***********************************************************************/

#include "mol.h"

namespace OpenBabel {

bool ReadAmberPrep(istream &ifs,OBMol &mol,char *title)

{

char buffer[BUFF_SIZE];

string str,str1;

OBAtom *atom;

OBInternalCoord *coord;

vector<string> vs;

vector<OBInternalCoord*> internals;

ttab.SetFromType("XYZ");

mol.BeginModify();

while (ifs.getline(buffer,BUFF_SIZE))

{

tokenize(vs,buffer);

if (vs.size() > 8)

{

atom = mol.NewAtom();

coord = new OBInternalCoord();

if (mol.NumAtoms() > 1)

coord->_a = mol.GetAtom(atoi(vs[4].c_str()));

if (mol.NumAtoms() > 2)

coord->_b = mol.GetAtom(atoi(vs[5].c_str()));

if (mol.NumAtoms() > 3)

coord->_c = mol.GetAtom(atoi(vs[6].c_str()));

coord->_dst = atof(vs[7].c_str());

coord->_ang = atof(vs[8].c_str());

coord->_tor = atof(vs[9].c_str());

internals.push_back(coord);

atom->SetAtomicNum(etab.GetAtomicNum(vs[1].c_str()));

ttab.SetToType("INT"); ttab.Translate(str,vs[1]);

atom->SetType(str);

if (!ifs.getline(buffer,BUFF_SIZE)) break;

tokenize(vs,buffer);

}

InternalToCartesian(internals,mol);

mol.EndModify();

mol.ConnectTheDots();

mol.SetTitle(title);

return(true);

}

} // namespace

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