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Viewing changes to src/patty.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/patty.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"

#include "obutil.h"

#include "parsmart.h"

#include "patty.h"

// Simple programmable atom typer

// WPW - 070199

// Usage is in sample main below

namespace OpenBabel {

void patty::read_rules(const string &infile)

{

ifstream ifs, ifs1, *ifsP;

vector<string> vs;

char buffer[BUFF_SIZE];

char tmp_str[BUFF_SIZE];

char patty_dir[BUFF_SIZE];

_sp.resize(1000);

ifs.open(infile.c_str());

ifsP= &ifs;

if (!ifs)

{

if (getenv("BABEL_DATADIR") == NULL)

{

cerr << "The BABEL_DATADIR environment variable is not defined" << endl;

cerr << "Please define it so the program can find " << infile << endl;

exit(0);

}

else

strcpy(patty_dir,getenv("BABEL_DATADIR"));

strcat(patty_dir,FILE_SEP_CHAR);

strcat(patty_dir,infile.c_str());

ifs1.open(patty_dir);

ifsP= &ifs1;

// if (!ifs1)

// {

// cerr << "Could not open " << patty_dir << endl;

// exit(0);

// }

}

int i = 0;

if (!ifsP){

cerr << "Could not open " << patty_dir << endl;

exit(0);

}

while (ifsP->getline(buffer,BUFF_SIZE))

{

if (buffer[0] != '#')

{

tokenize(vs,buffer," \t\n");

if (vs.size() >= 2)

{

strcpy(tmp_str,vs[0].c_str());

_sp[i]->Init(tmp_str);

smarts.push_back(vs[0]);

typ.push_back(vs[1]);

i++;

}

_sp.resize(i);

}

void patty::assign_rules(vector<string> &rules)

{

vector<string> vs;

char buffer[BUFF_SIZE];

char tmp_str[BUFF_SIZE];

unsigned int i;

_sp.resize(1000);

for ( i = 0 ; i < rules.size() ; i++ )

{

strncpy(buffer, rules[i].c_str(), BUFF_SIZE);

if (buffer[0] != '#')

{

tokenize(vs,buffer," \t\n");

if (vs.size() >= 2)

{

strcpy(tmp_str,vs[0].c_str());

_sp[i]->Init(tmp_str);

smarts.push_back(vs[0]);

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typ.push_back(vs[1]);

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}

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else

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i--;

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}

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else

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i--;

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}

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_sp.resize(i);

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}

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void patty::assign_types(OBMol &mol,vector<string> &atm_typ)

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{

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atm_typ.resize(mol.NumAtoms()+1);

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for (unsigned int i = 0; i < _sp.size(); i++)

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{

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_sp[i]->Match(mol);

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vector<vector<int> > match = _sp[i]->GetMapList();

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//vector<vector<int> >& match = _sp[i]->GetMapList();

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if (match.size())

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{

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if (debug)

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cout << typ[i] << " " << smarts[i] << " matched " ;

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for (unsigned int j = 0; j < match.size(); j++)

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{

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if (debug)

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cout << match[j][0] << " ";

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atm_typ[match[j][0]] = typ[i];

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}

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if (debug)

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cout << endl;

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}

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}

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}

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void patty::assign_types(OBMol &mol,vector<int> &atm_typ)

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{

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atm_typ.resize(mol.NumAtoms()+1);

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for (unsigned int i = 0; i < _sp.size(); i++)

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{

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_sp[i]->Match(mol);

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vector<vector<int> > match = _sp[i]->GetMapList();

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//vector<vector<int> >& match = _sp[i]->GetMapList();

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if (match.size())

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{

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if (debug)

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cout << typ[i] << " " << smarts[i] << " matched " ;

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for (unsigned int j = 0; j < match.size(); j++)

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{

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if (debug)

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cout << match[j][0] << " ";

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atm_typ[match[j][0]] = type_to_int(typ[i]);

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}

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if (debug)

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cout << endl;

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}

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}

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}

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int patty::type_to_int(const string &type, bool failOnUndefined)

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{

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int result;

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switch(toupper(type.c_str()[0]))

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{

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case 'C' : // CAT - CATION

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result = PT_CATION;

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break;

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case 'A' :

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if (toupper(type.c_str()[1]) == 'N') // ANI - ANION

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result = PT_ANION;

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else

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result = PT_ACCEPTOR;

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break;

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case 'P' : // POL - POLAR

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result = PT_POLAR;

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break;

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case 'D' : // DON - DONOR

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result = PT_DONOR;

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break;

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case 'H' : // HYD - HYDROPHOBIC

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result = PT_HYDROPHOBIC;

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break;

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case 'M' : // Metal

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result = PT_METAL;

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break;

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case 'O' : // OTH - OTHER

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result = PT_OTHER;

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break;

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default :

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// This was added by Brian,

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// Behavior will fail if type is undefined

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if (failOnUndefined){

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cerr << "Unable to find type of feature passed in " << endl;

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cerr << "Feature passed in is " << type << endl;

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exit(-1);

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}else{

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result = 7;

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}

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}

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return(result);

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}

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}

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#ifdef I_EVER_BUY_A_MICHAEL_BOLTON_ALBUM

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int main(int argc, char *argv[])

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{

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OBMol mol(SDF,SDF);

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vector<string> types;

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ifstream ifs(argv[1]);

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if (!ifs)

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{

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cerr << "Could not open argv[1] " << endl;

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exit(0);

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}

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patty p("simple.txt");

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for (;;)

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{

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ifs >> mol;

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if (!mol.NumAtoms()) break;

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p.assign_types(mol,types);

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mol.Clear();

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}

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for (int i = 1; i < types.size(); i++)

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{

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cout << i << " " << types[i] << endl;

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}

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}

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#endif

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