void TextWriter::do_set_frame() {
if (file_name_.empty() /* || file_name_.find("%1%")== std::string::npos*/) {
IMP_FAILURE("Cannot set frame on writer without %1% being in the name.");
}
if (out_ != TextOutput()) {
do_close();
out_ = TextOutput();
}
open();
}
void CHARMMParameters::read_parameter_file(base::TextInput input_file) {
IMP_OBJECT_LOG;
const String BONDS_LINE = "BOND";
const String ANGLES_LINE = "ANGL";
const String ANGLES_LINE2 = "THETA";
const String DIHEDRALS_LINE = "DIHE";
const String DIHEDRALS_LINE2 = "PHI";
const String IMPROPER_LINE = "IMPR";
const String IMPROPER_LINE2 = "IMPHI";
const String NONBONDED_LINE = "NONB";
const String NONBONDED_LINE2 = "NBON";
enum { NONE, BONDS, ANGLES, DIHEDRALS, IMPROPERS, NONBONDED } section = NONE;
while (!input_file.get_stream().eof()) {
String line;
getline(input_file.get_stream(), line);
boost::trim(line); // remove all spaces
// skip comments or empty lines
if (line[0] == '!' || line[0] == '*' || line.length() == 0) continue;
if (line.substr(0, NONBONDED_LINE.length()) == NONBONDED_LINE
|| line.substr(0, NONBONDED_LINE2.length()) == NONBONDED_LINE2) {
section = NONBONDED;
getline(input_file.get_stream(), line); //remove second line of NONBONDED
} else if (line.substr(0, BONDS_LINE.length()) == BONDS_LINE) {
section = BONDS;
} else if (line.substr(0, ANGLES_LINE.length()) == ANGLES_LINE
|| line.substr(0, ANGLES_LINE2.length()) == ANGLES_LINE2) {
section = ANGLES;
} else if (line.substr(0, DIHEDRALS_LINE.length()) == DIHEDRALS_LINE
|| line.substr(0, DIHEDRALS_LINE2.length()) == DIHEDRALS_LINE2) {
section = DIHEDRALS;
} else if (line.substr(0, IMPROPER_LINE.length()) == IMPROPER_LINE
|| line.substr(0, IMPROPER_LINE2.length()) == IMPROPER_LINE2) {
section = IMPROPERS;
} else if (line.substr(0, 5) == "HBOND" || line.substr(0, 5) == "NBFIX") {
section = NONE;
} else if (line.substr(0, 3) == "END") {
break;
} else {
switch(section) {
case BONDS:
parse_bonds_parameters_line(line);
break;
case ANGLES:
parse_angles_parameters_line(line);
break;
case DIHEDRALS:
parse_dihedrals_parameters_line(line, dihedral_parameters_);
break;
case IMPROPERS:
parse_dihedrals_parameters_line(line, improper_parameters_);
break;
case NONBONDED:
parse_nonbonded_parameters_line(line);
break;
default:
break;
}
}
}
if(force_field_2_vdW_.size() == 0) {
IMP_FAILURE("NONBONDED params not found in Charmm parameter file");
}
}
