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
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/commandlineParser.h>
#include <BALL/MATHS/angle.h>
#include <BALL/STRUCTURE/peptideBuilder.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/STRUCTURE/peptides.h>
#include <vector>
#include <iostream>
#include "version.h"
using namespace std;
using namespace BALL;
void usage (const char *progname);
int main (int argc, char **argv)
{
CommandlineParser parpars("PeptideBuilder", "build a peptide ", VERSION, String(__DATE__), "Preparation");
parpars.registerMandatoryInputFile("i", "input torsion-file");
parpars.registerMandatoryOutputFile("o", "peptide output pdb-file");
String man = "This tool creates a peptide by a given torsion file. The amino acids shall be given in three letter code, the phi, psi, and omega angles shall be given in degree.\n\nExample:\n\n# aa phi psi omega\n\nA -180 140\n\nC -180 180\n\nG -90 -140\n\nP -65 -40 0 # cis\n\nT -120 -90\n\nP -78 146 180 # trans";
parpars.setToolManual(man);
parpars.setSupportedFormats("i", "txt");
parpars.setSupportedFormats("o", "pdb");
parpars.parse(argc, argv);
// initialize the peptide builder
BALL::Peptides::PeptideBuilder* pb = new BALL::Peptides::PeptideBuilder;
// "link" the fragment db for adding missing information
FragmentDB fdb("");
pb->setFragmentDB(&fdb);
// read the torsion file (format AA, PHI, PSI)
// e.g. ALA 109 65
LineBasedFile torsion_file(parpars.get("i"), std::ios::in);
vector<String> fields;
while (torsion_file.LineBasedFile::readLine())
{
// get the line
String aa_torsion = torsion_file.getLine();
if ((aa_torsion.countFields(" ")>0) && (aa_torsion(0,1) != "#"))
{
fields.clear();
aa_torsion.split(fields);
// split and check
// either expect a line
// G
// A -180 140
// or
// A -180 140 180 # some comment
if ( (fields.size() != 1)
&& ( (fields.size()<3)
|| ((fields.size()>3) && (fields[3] != "#") && (fields[4] != "#")) ))
{
Log.error() << "Error in while reading file " << parpars.get("i") << " in line " << aa_torsion << endl;
}
String aa = fields[0];
// assume a helix if no angles given
float phi = 300;
float psi = 310;
float omega = 0.;
if (fields.size()>1)
{
phi = fields[1].toFloat();
psi = fields[2].toFloat();
}
if ((fields.size()>4) && (fields[3] != "#"))
omega = fields[3].toFloat();
char test_aa = aa.toChar();
if (Peptides::IsOneLetterCode(test_aa))
{
aa = Peptides::ThreeLetterCode(test_aa);
}
// check
// we need three letter code, angles should be given in degree (phi than psi)
if (!Peptides::IsThreeLetterCode(aa))
{
Log.error() << "Error while reading line " << aa_torsion << " : amino acid shall be given in three letter code." << endl;
}
// append the peptide
pb->addAminoAcid(aa, Angle(phi, false), Angle(psi, false), Angle(omega, false));
}
}
// now build the peptide
Protein* prot = pb->construct();
cout << " a peptide " << Peptides::GetSequence(*prot) << endl;
cout << " was build";
/*
for (ResidueIterator res_it= prot->beginResidue(); +res_it; ++res_it)
{
cout << res_it->getName() << " " << res_it->getTorsionPhi().toDegree() << " " << res_it->getTorsionPsi().toDegree() << " " << res_it->getTorsionOmega().toDegree() << endl;
}
*/
// give sensible names
String pep_name = parpars.get("peptide_name");
pb->setChainName(pep_name);
pb->setProteinName(pep_name);
// normalize the names
prot->apply(fdb.normalize_names);
// build the missing bonds
prot->apply(fdb.build_bonds);
// add missing hydrogens
prot->apply(fdb.add_hydrogens);
// store
PDBFile out_file(parpars.get("o"), std::ios::out);
out_file << *prot;
out_file.close();
cout << " and stored as " << parpars.get("o") << endl;
return 0;
}
|
