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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: splitMMFFTestSuiteOptiFiles.C,v 1.1.8.1 2007/03/25 21:32:23 oliver Exp $
//
// A small program for spliting the Optimol log file from the MMFF94 test suite
// into smaller files, which are better to handle for parsing
#include <BALL/common.h>
#include <BALL/KERNEL/system.h>
#include <BALL/DATATYPE/string.h>
#include <BALL/SYSTEM/path.h>
#include <BALL/SYSTEM/fileSystem.h>
#include <BALL/FORMAT/lineBasedFile.h>
#include <BALL/SYSTEM/file.h>
#include <BALL/DATATYPE/hashSet.h>
// #define DEBUG
#ifdef DEBUG
#define LINE_PRINT Log.error() << infile.getLine() << " " << __LINE__ << std::endl;
#else
#define LINE_PRINT
#endif
using namespace std;
using namespace BALL;
void getAtomData(LineBasedFile& file, vector<String>& data)
{
while (file.readLine())
{
if (file.getLine().hasSubstring("OPTIMOL-LIST"))
{
file.skipLines(1);
return;
}
vector<String> fields;
Size size = file.getLine().split(fields);
Position pos = 0;
while (pos < size)
{
data.push_back(fields[pos + 2]);
pos += 3;
}
}
}
int main(int argc, char** argv)
{
if (argc != 3)
{
Log.error() << "Usage: splitMMFFTestSuiteOptiFiles <location of MMFF94_opti.log> <folder to write files>" << std::endl;
return 1;
}
vector<String> atoms_file_contents;
String file_name;
String dir = argv[2];
vector<String> file_names;
LineBasedFile infile(argv[1]);
Size nr_rings = 0;
Size nr_aromatic_rings = 0;
vector<String> fields;
while (infile.readLine())
{
LINE_PRINT
if (infile.getLine().hasSubstring("Structure Name:") ||
infile.getLine().hasSubstring("New Structure Name"))
{
file_name = infile.getLine().after(": ");
Log.error() << file_name << std::endl;
nr_aromatic_rings = 0;
nr_rings = 0;
}
else if (infile.getLine().hasSuffix("SUBRINGS"))
{
HashSet<String> lines;
while (!infile.getLine().hasSubstring("OPTIMOL-LIST"))
{
if (lines.has(infile.getLine()))
{
while (infile.getLine() != "" &&
!infile.getLine().hasSubstring("OPTIMOL"))
{
infile.readLine();
}
}
else if (infile.getLine().hasSuffix("SUBRINGS"))
{
infile.getLine().split(fields);
nr_rings += fields[3].toUnsignedShort();
lines.insert(infile.getLine());
}
else if (infile.getLine().hasSuffix("AROMATIC"))
{
nr_aromatic_rings++;
}
infile.readLine();
}
}
else if (infile.getLine().hasSuffix("****"))
{
File rings_file(dir + FileSystem::PATH_SEPARATOR + file_name + ".rings", std::ios::out);
rings_file << nr_rings << std::endl;
rings_file << nr_aromatic_rings << std::endl;
rings_file.close();
}
else if (infile.getLine().hasSubstring(" ATOM NAME TYPE"))
{
vector<String> atoms, names, types, symbols, charges, fcharges;
while (infile.readLine())
{
if (infile.getLine().hasSubstring("OPTIMOL")) break;
vector<String> fields;
Size size = infile.getLine().split(fields);
Position pos = 0;
while (pos < size)
{
atoms.push_back(fields[pos]);
names.push_back(fields[pos + 1]);
types.push_back(fields[pos + 2]);
pos += 3;
}
}
infile.skipLines(1);
getAtomData(infile, symbols);
getAtomData(infile, charges);
getAtomData(infile, fcharges);
File outfile(dir + FileSystem::PATH_SEPARATOR + file_name + ".atoms", std::ios::out);
Position pos = 0;
for (; pos < atoms.size(); pos++)
{
static char buf[800];
sprintf(buf, "%5s%5s%5s%7s%7s%7s",
atoms[pos].c_str(),
names[pos].c_str(),
types[pos].c_str(),
symbols[pos].c_str(),
charges[pos].c_str(),
fcharges[pos].c_str()
);
outfile << buf;
outfile << std::endl;
}
outfile.close();
}
else if (infile.getLine().hasSubstring("Total ENERGY (Kcal)"))
{
vector<String> fields;
File outfile(dir + FileSystem::PATH_SEPARATOR + file_name + ".results", std::ios::out);
for (Position pos = 0; pos < 16; pos ++)
{
Size nr_fields = infile.getLine().split(fields);
if (nr_fields < 2 ||
infile.getLine().hasPrefix(" Bond Torsion"))
{
infile.readLine();
continue;
}
outfile << fields[nr_fields - 1] << " # ";
for (Position i = 0; i < nr_fields - 1; i++)
{
outfile << fields[i] << " ";
}
outfile << std::endl;
infile.readLine();
}
String rms = infile.getLine().after("=");
rms = rms.before("Kcal");
rms.trim();
outfile << rms << " # rms" << std::endl;
outfile.close();
}
/// stretch
else if (infile.getLine() == " I J I J CLASS LENGTH LENGTH DIFF. ENERGY CONSTANT")
{
File outfile(dir + FileSystem::PATH_SEPARATOR + file_name + ".stretch", std::ios::out);
infile.readLine();
while (infile.readLine() && infile.getLine() != "")
{
vector<String> fields;
infile.getLine().split(fields);
outfile << fields[0] << " " << fields[2] << " "
<< fields[6] << " " << fields[8] << " "
<< fields[11] << std::endl;
}
}
/// bend
else if (infile.getLine() == " I J K I J K CLASS ANGLE ANGLE DIFF. ENERGY CONSTANT")
{
File outfile(dir + FileSystem::PATH_SEPARATOR + file_name + ".bend", std::ios::out);
infile.readLine();
while (infile.readLine() && infile.getLine() != "")
{
vector<String> fields;
infile.getLine().split(fields);
// I J K type angle delta energy ka
outfile << fields[0] << " " << fields[1] << " "
<< fields[3] << " " << fields[7] << " "
<< fields[9] << " " << fields[10] << " "
<< fields[11] << " " << fields[12] << std::endl;
}
}
/// stretch bend
else if (infile.getLine() == " I J K I J K CLASS ANGLE ANGLE R(I,J) ENERGY I-J")
{
File outfile(dir + FileSystem::PATH_SEPARATOR + file_name + ".stretchbend", std::ios::out);
infile.readLine();
while (infile.readLine() && infile.getLine() != "")
{
vector<String> fields;
infile.getLine().split(fields);
// I J K type energy f_ij
outfile << fields[0] << " " << fields[1] << " "
<< fields[3] << " " << fields[7] << " "
<< fields[11] << " " << fields[12] << " " << std::endl;
}
}
/// torsions
else if (infile.getLine() == " I J K L I J K L CLASS ANGLE ENERGY V1 V2 V3")
{
File outfile(dir + FileSystem::PATH_SEPARATOR + file_name + ".torsions", std::ios::out);
infile.readLine();
while (infile.readLine() && infile.getLine() != "")
{
vector<String> fields;
infile.getLine().split(fields);
// I J K L type angle energy v1 v2 v3
outfile << fields[0] << " " << fields[1] << " "
<< fields[3] << " " << fields[5] << " "
<< fields[10] << " " << fields[11] << " "
<< fields[12] << " " << fields[13] << " "
<< fields[14] << " " << fields[15]
<< std::endl;
}
}
/// planes
else if (infile.getLine() == " I -- J -- K ... L I J K L ANGLE ENERGY CONSTANT")
{
File outfile(dir + FileSystem::PATH_SEPARATOR + file_name + ".planes", std::ios::out);
infile.readLine();
while (infile.readLine() && infile.getLine() != "")
{
vector<String> fields;
infile.getLine().split(fields);
// I J K L angle energy constant
outfile << fields[0] << " " << fields[1] << " "
<< fields[2] << " " << fields[3] << " "
<< fields[9] << " " << fields[10] << " "
<< fields[11]
<< std::endl;
}
}
/// non bonded
else if (infile.getLine() == " ATOM PAIR R VDW EREP EATTR EQ R* EPS")
{
File outfile(dir + FileSystem::PATH_SEPARATOR + file_name + ".nonbonded", std::ios::out);
infile.readLine();
while (infile.readLine() && infile.getLine() != "")
{
vector<String> fields;
infile.getLine().split(fields);
if (fields.size() < 11) break;
// ATOMPAIR R VDW EREP EATTR EQ R* EPS
outfile << fields[0] << " " << fields[2] << " "
<< fields[4] << " " << fields[5] << " "
<< fields[6] << " " << fields[7] << " "
<< fields[8] << " " << fields[9] << " "
<< fields[10] << std::endl;
}
}
}
return 0;
}
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