1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/molFileFactory.h>
#include <BALL/FORMAT/genericMolFile.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/DOCKING/COMMON/constraints.h>
#include <BALL/DOCKING/COMMON/dockingAlgorithm.h>
#include <BALL/DATATYPE/options.h>
#include "version.h"
using namespace BALL;
using namespace std;
int main(int argc, char* argv[])
{
CommandlineParser parpars("InteractionConstraintDefiner", "define interaction constraint", VERSION, String(__DATE__), "Docking");
parpars.registerMandatoryStringParameter("res", "residue ID");
parpars.registerMandatoryDoubleParameter("s", "desired minimal interation (score) between ligand and specified residue(s)");
parpars.registerMandatoryDoubleParameter("p", "penalty value");
parpars.registerMandatoryOutputFile("o", "output configuration file");
parpars.registerOptionalInputFile(DockingAlgorithm::OPTION_FILE_PARAMETER_NAME, "input configuration file");
String man = "This tool allows to define interaction constraints for docking or scoring.\n\nThe constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: <chain-ID>:<residue-ID>, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17.\n\nOutput of this tool is a ini-file that contains the desired interaction constraint.";
parpars.setToolManual(man);
parpars.setSupportedFormats(DockingAlgorithm::OPTION_FILE_PARAMETER_NAME,"ini");
parpars.setSupportedFormats("o","ini");
parpars.parse(argc, argv);
Log.setMinLevel(cout, 10);
Options options;
list<Constraint*> constraints;
if (parpars.has(DockingAlgorithm::OPTION_FILE_PARAMETER_NAME))
{
DockingAlgorithm::readOptionFile(parpars.get(DockingAlgorithm::OPTION_FILE_PARAMETER_NAME), options, constraints);
}
vector<String> residue_IDs;
String res = parpars.get("res");
res.split(residue_IDs,",");
list<String> interaction_types;
interaction_types.push_back("vdW");
interaction_types.push_back("HB");
interaction_types.push_back("ES");
PharmacophoreConstraint* phC = new PharmacophoreConstraint(residue_IDs, interaction_types, parpars.get("s").toDouble(), parpars.get("p").toDouble());
String name = "InteractionConstraintDefiner on ";
name += parpars.get("res");
phC->setName(name);
constraints.push_back(phC);
/// Write output and clean everthing up
DockingAlgorithm::writeOptionFile(parpars.get("o"), options, constraints);
for (list<Constraint*>::iterator it = constraints.begin(); it != constraints.end(); it++)
{
delete *it;
}
return 0;
}
|
