C++ Example Search.C
ABOUT THIS EXAMPLE:
This example shows how to use the Search function to fulfill a query of arbitrary complexity. In this case, we find the (x, y, z) coordinates of every alpha carbon atom in chain A of the 5HVP molecule, using the atom_site category. Note that the Search function takes three optional arguments of note, none of which are used here, viz., an unsigned int fromRowIndex, which specifies a row from which to begin the search, a const eSearchDir searchDir, which specifies the direction of the search, and a const eSearchType searchType, which specifies the type of the search (e.g., find rows with values equal to target values, greater than target values, etc.).
BUILD INSTRUCTIONS:
Files: Search.C, 5HVP.cif
Save Search.C to/path/to/cifparse-obj-vX.X-prod-src/parser-test-app-vX.X/src/Save the CIF file anywhere, e.g.,/path/to/cifparse-obj-vX.X-prod-src/parser-test-app-vX.X/bin/Add Search.ext to the BASE_MAIN_FILES list in the Makefile in/path/to/cifparse-obj.vX.X-prod-src/parser-test-app-vX.XExecutemakein the same directory as the Makefilecdto bin, where the executable has been made, and run./Search /path/to/5HVP.cif
Functions of Note
#include "CifFile.h"
- string CifFile::GetFirstBlockName() ►
- Returns the first data block name. CifFile inherits this method from TableView.
Related:
CifFile::GetBlockNames(vector<string>& blockNames). - Block& CifFile::GetBlock(const string& blockName) ►
- Retrieves a data block specified by some blockName. CifFile inherits this method from TableView.
- ISTable& Block::GetTable(const string& name) ►
- Retrieves a table (i.e., category) within the block, specified by some name.
#include "ISTable.h"
- void Search(vector<unsigned int>& res, const vector<string>& targets, const vector<string>& colNames, const unsigned int fromRowIndex = 0, const eSearchDir searchDir = eFORWARD, const eSearchType searchType = eEQUAL, const string& indexName = string()) ►
- Propagates res with the indices of every row whose attributes colNames have the values targets.
- void ISTable::GetRow(vector<string>& row, const unsigned int rowIndex, const string& fromColName = string(), const string& toColName = string()) ►
- Returns the row in the zero-indexed category table specified by some rowIndex. Related:
vector<string>& ISTable::GetRow(const unsigned int rowIndex).
Basic Sample Output
./Search 5HVP.cif
99 atoms found:
(29.970, 38.922, 4.561)
(29.636, 36.572, 1.593)
(28.879, 33.060, 2.829)
(29.513, 30.113, 0.468)
(27.327, 27.003, 0.728)
(29.974, 24.273, 0.856)
(28.869, 23.997, 4.484)
(25.689, 24.716, 6.375)
(25.415, 28.480, 6.613)
(25.452, 28.653, 10.471)
(25.970, 31.965, 12.332)
-------truncated-------
(13.908, 32.611, 7.947)
(13.090, 35.152, 5.233)
(11.249, 37.435, 7.675)
(14.550, 38.372, 9.439)
(16.951, 37.736, 6.539)
(15.383, 40.593, 4.616)
(15.952, 42.771, 7.692)
(19.718, 42.404, 7.594)
(19.906, 42.920, 3.781)
(20.463, 39.289, 2.946)
(20.506, 38.362, -0.735)
(21.255, 35.231, -2.813)
(23.596, 35.908, -5.720)
(24.853, 33.899, -8.704)
/*************************
* Search.C
*
* For some CIF file, determine the (x, y, z) Cartesian coordinates
* of every alpha carbon atom in the A chain.
*
* Method: Perform a Search query on the atom_site category table.
*
* Highlighted lines contain footnoted references or explanations.
*************************/
#include <iostream>
#include <string>
#include <vector>
#include "CifFile.h"
#include "CifParserBase.h"
#include "ISTable.h"
int main(int argc, char **argv)
{
// The name of the CIF file
string cifFileName = argv[1];
// A string to hold any parsing diagnostics
string diagnostics;
// Create CIF file and parser objects
CifFile *cifFileP = new CifFile;
CifParser *cifParserP = new CifParser(cifFileP);
// Parse the CIF file
cifParserP->Parse(cifFileName, diagnostics);
// Delete the CIF parser, as it is no longer needed
delete cifParserP;
// Display any diagnostics
if (!diagnostics.empty())
{
std::cout << "Diagnostics: " << std::endl << diagnostics << std::endl;
}
// Get the first data block name in the CIF file
string firstBlockName = cifFileP->GetFirstBlockName();
// Retrieve the first data block
Block &block = cifFileP->GetBlock(firstBlockName);
// Retrieve the table corresponding to the atom_site category, which delineates atomic constituents1
ISTable& atom_site = block.GetTable("atom_site");
// Will hold the atom_site row indices of any atoms fulfilling our search query
vector<unsigned int> results;
// Holds attribute names and their target values
vector<string> colNames, targets;
// We want alpha carbons in chain A2
colNames.push_back("label_atom_id");
targets.push_back("CA");
colNames.push_back("auth_asym_id");
targets.push_back("A");
// Perform the search, propagating the results vector with atom indices
atom_site.Search(results, targets, colNames);
// Retrieve and display the coordinates of every atom satisfying our query
std::cout << results.size() << " atoms found: \n";
vector<string> coords;
for (unsigned int i = 0; i < results.size(); ++i)
{
atom_site.GetRow(coords, results[i], "Cartn_x", "Cartn_z");3
std::cout << "(" << coords[0] << ", " << coords[1] << ", " << coords[2] << ")" << std::endl;
}
return 0;
}