本文整理汇总了C++中Topology::SetParmBox方法的典型用法代码示例。如果您正苦于以下问题:C++ Topology::SetParmBox方法的具体用法?C++ Topology::SetParmBox怎么用?C++ Topology::SetParmBox使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Topology
的用法示例。
在下文中一共展示了Topology::SetParmBox方法的4个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的C++代码示例。
示例1: Execute
Exec::RetType Exec_ParmBox::Execute(CpptrajState& State, ArgList& argIn) {
Box pbox;
bool nobox = false;
if ( argIn.hasKey("nobox") )
nobox = true;
else {
pbox.SetX( argIn.getKeyDouble("x",0) );
pbox.SetY( argIn.getKeyDouble("y",0) );
pbox.SetZ( argIn.getKeyDouble("z",0) );
pbox.SetAlpha( argIn.getKeyDouble("alpha",0) );
pbox.SetBeta( argIn.getKeyDouble("beta",0) );
pbox.SetGamma( argIn.getKeyDouble("gamma",0) );
}
Topology* parm = State.DSL().GetTopByIndex( argIn );
if (parm == 0) return CpptrajState::ERR;
if (nobox)
mprintf("\tRemoving box information from parm %i:%s\n", parm->Pindex(), parm->c_str());
else
// Fill in missing parm box information from specified parm
pbox.SetMissingInfo( parm->ParmBox() );
if (argIn.hasKey("truncoct")) pbox.SetTruncOct();
parm->SetParmBox( pbox );
parm->ParmBox().PrintInfo();
return CpptrajState::OK;
}
示例2: mprintf
/** Read file as a Tripos Mol2 file. */
int Parm_Mol2::ReadParm(FileName const& fname, Topology &parmOut) {
Mol2File infile;
if (infile.OpenRead(fname)) return 1;
mprintf(" Reading Mol2 file %s as topology file.\n",infile.Filename().base());
// Get @<TRIPOS>MOLECULE information
if (infile.ReadMolecule()) return 1;
parmOut.SetParmName( infile.Mol2Title(), infile.Filename() );
// Get @<TRIPOS>ATOM information
if (infile.ScanTo( Mol2File::ATOM)) return 1;
double XYZ[3];
for (int atom=0; atom < infile.Mol2Natoms(); atom++) {
if ( infile.Mol2XYZ(XYZ) ) return 1;
parmOut.AddTopAtom( infile.Mol2Atom(), infile.Mol2Residue(), XYZ );
}
// Get @<TRIPOS>BOND information [optional]
int at1 = 0;
int at2 = 0;
if (infile.ScanTo(Mol2File::BOND)==0) {
for (int bond=0; bond < infile.Mol2Nbonds(); bond++) {
if (infile.Mol2Bond(at1, at2)) return 1;
// mol2 atom #s start from 1
parmOut.AddBond(at1-1, at2-1);
}
needsBondSearch_ = false;
} else {
mprintf(" Mol2 file does not contain bond information.\n");
needsBondSearch_ = true;
}
// No box
parmOut.SetParmBox( Box() );
mprintf(" Mol2 contains %i atoms, %i residues,\n", parmOut.Natom(),parmOut.Nres());
//mprintf(" %i bonds to H, %i other bonds.\n", parmOut.NbondsWithH,parmOut.NbondsWithoutH);
infile.CloseFile();
return 0;
}
示例3: ReadParm
/** Read file as a Tinker file. */
int Parm_Tinker::ReadParm(FileName const& fname, Topology &parmOut) {
TinkerFile infile;
infile.SetTinkerName( fname );
if (infile.OpenTinker()) return 1;
mprintf("\tReading Tinker file %s as topology file.\n",infile.Filename().base());
// Allocate memory for coordinates.
double* Coords = new double[ infile.TinkerNatom() * 3 ];
std::vector<int> Bonds;
std::vector<Atom> Atoms = infile.ReadTinkerAtoms(Coords, Bonds);
if (Atoms.empty()) return 1;
// Use up to first 3 chars of title as residue name.
std::string resname;
for (std::string::const_iterator c = infile.TinkerTitle().begin();
c != infile.TinkerTitle().end(); ++c)
resname += *c;
if (resname.size() > 3) resname.resize(3);
Residue tinker_res( resname, 0, ' ', ' ' );
// Put atoms into topology
const double* XYZ = Coords;
for (std::vector<Atom>::const_iterator atom = Atoms.begin();
atom != Atoms.end();
++atom, XYZ += 3)
parmOut.AddTopAtom( *atom, tinker_res, XYZ );
delete[] Coords;
// Add bond information
for (std::vector<int>::const_iterator bond = Bonds.begin();
bond != Bonds.end(); bond += 2)
parmOut.AddBond( *bond, *(bond+1) );
// Try to set up residue info based on bonds.
if (parmOut.Setup_NoResInfo()) return 1;
// Set topology box info.
parmOut.SetParmBox( infile.TinkerBox() );
parmOut.SetParmName( infile.TinkerTitle(), infile.Filename() );
mprintf("\tTinker file contains %i atoms, %i residues,\n", parmOut.Natom(),parmOut.Nres());
//mprintf(" %i bonds to H, %i other bonds.\n", parmOut.NbondsWithH,parmOut.NbondsWithoutH);
infile.CloseFile();
return 0;
}
示例4: ReadParm
//.........这里部分代码省略.........
}
// Does this CIF contain multiple models?
int Nmodels = 0;
int model_col = block.ColumnIndex("pdbx_PDB_model_num");
if (model_col != -1) {
line = block.end();
--line;
Nmodels = convertToInteger( (*line)[model_col] );
if (Nmodels > 1)
mprintf("Warning: CIF '%s' contains %i models. Using first model for topology.\n",
fname.full(), Nmodels);
}
// Get essential columns
int COL[NENTRY];
for (int i = 0; i < (int)NENTRY; i++) {
COL[i] = block.ColumnIndex(Entries[i]);
if (COL[i] == -1) {
mprinterr("Error: In CIF file '%s' could not find entry '%s' in block '%s'\n",
fname.full(), Entries[i], block.Header().c_str());
return 1;
}
if (debug_>0) mprintf("DEBUG: '%s' column = %i\n", Entries[i], COL[i]);
}
// Get optional columns
int occ_col = block.ColumnIndex("occupancy");
int bfac_col = block.ColumnIndex("B_iso_or_equiv");
int icode_col = block.ColumnIndex("pdbx_PDB_ins_code");
int altloc_col = block.ColumnIndex("label_alt_id");
std::vector<AtomExtra> extra;
// Loop over all atom sites
int current_res = 0;
double XYZ[3];
double occupancy = 1.0;
double bfactor = 0.0;
char altloc = ' ';
char icode;
icode = ' ';
Frame Coords;
for (line = block.begin(); line != block.end(); ++line) {
// If more than 1 model check if we are done.
if (Nmodels > 1) {
if ( convertToInteger( (*line)[model_col] ) > 1 )
break;
}
if (occ_col != -1) occupancy = convertToDouble( (*line)[ occ_col ] );
if (bfac_col != -1) bfactor = convertToDouble( (*line)[ bfac_col ] );
if (altloc_col != -1) altloc = (*line)[ altloc_col ][0];
// '.' altloc means blank?
if (altloc == '.') altloc = ' ';
extra.push_back( AtomExtra(occupancy, bfactor, altloc) );
if (icode_col != -1) {
icode = (*line)[ icode_col ][0];
// '?' icode means blank
if (icode == '?') icode = ' ';
}
XYZ[0] = convertToDouble( (*line)[ COL[X] ] );
XYZ[1] = convertToDouble( (*line)[ COL[Y] ] );
XYZ[2] = convertToDouble( (*line)[ COL[Z] ] );
NameType currentResName( (*line)[ COL[RNAME] ] );
// It seems that in some CIF files, there doesnt have to be a residue
// number. Check if residue name has changed.
if ( (*line)[ COL[RNUM] ][0] == '.' ) {
Topology::res_iterator lastResidue = TopIn.ResEnd();
--lastResidue;
if ( currentResName != (*lastResidue).Name() )
current_res = TopIn.Nres() + 1;
} else
current_res = convertToInteger( (*line)[ COL[RNUM] ] );
TopIn.AddTopAtom( Atom((*line)[ COL[ANAME] ], " "),
Residue(currentResName, current_res, icode,
(*line)[ COL[CHAINID] ][0]) );
Coords.AddXYZ( XYZ );
}
if (TopIn.SetExtraAtomInfo( 0, extra )) return 1;
// Search for bonds // FIXME nobondsearch?
BondSearch( TopIn, Coords, Offset_, debug_ );
// Get title.
CIFfile::DataBlock const& entryblock = infile.GetDataBlock("_entry");
std::string ciftitle;
if (!entryblock.empty())
ciftitle = entryblock.Data("id");
TopIn.SetParmName( ciftitle, infile.CIFname() );
// Get unit cell parameters if present.
CIFfile::DataBlock const& cellblock = infile.GetDataBlock("_cell");
if (!cellblock.empty()) {
double cif_box[6];
cif_box[0] = convertToDouble( cellblock.Data("length_a") );
cif_box[1] = convertToDouble( cellblock.Data("length_b") );
cif_box[2] = convertToDouble( cellblock.Data("length_c") );
cif_box[3] = convertToDouble( cellblock.Data("angle_alpha") );
cif_box[4] = convertToDouble( cellblock.Data("angle_beta" ) );
cif_box[5] = convertToDouble( cellblock.Data("angle_gamma") );
mprintf("\tRead cell info from CIF: a=%g b=%g c=%g alpha=%g beta=%g gamma=%g\n",
cif_box[0], cif_box[1], cif_box[2], cif_box[3], cif_box[4], cif_box[5]);
TopIn.SetParmBox( Box(cif_box) );
}
return 0;
}