// Normal Spectrophore(TM): test all values
void test01(OpenBabel::OBMol* mol)
{
OpenBabel::OBSpectrophore s;
s.SetNormalization(OpenBabel::OBSpectrophore::NoNormalization);
s.SetResolution(3.0);
s.SetAccuracy(OpenBabel::OBSpectrophore::AngStepSize20);
s.SetStereo(OpenBabel::OBSpectrophore::NoStereoSpecificProbes);
std::vector<double> r = s.GetSpectrophore(mol);
OB_REQUIRE( (r[0] > 1.598) && (r[0] < 1.600) );
OB_REQUIRE( (r[1] > 1.576) && (r[1] < 1.578) );
OB_REQUIRE( (r[2] > 1.169) && (r[2] < 1.171) );
OB_REQUIRE( (r[3] > 3.760) && (r[3] < 3.762) );
OB_REQUIRE( (r[4] > 5.174) && (r[4] < 5.176) );
OB_REQUIRE( (r[5] > 5.780) && (r[5] < 5.782) );
OB_REQUIRE( (r[6] > 3.796) && (r[6] < 3.798) );
OB_REQUIRE( (r[7] > 3.712) && (r[7] < 3.714) );
OB_REQUIRE( (r[8] > 4.650) && (r[8] < 4.652) );
OB_REQUIRE( (r[9] > 7.736) && (r[9] < 7.738) );
OB_REQUIRE( (r[10] > 7.949) && (r[10] < 7.951) );
OB_REQUIRE( (r[11] > 4.868) && (r[11] < 4.870) );
OB_REQUIRE( (r[12] > 2.707) && (r[12] < 2.709) );
OB_REQUIRE( (r[13] > 3.470) && (r[13] < 3.472) );
OB_REQUIRE( (r[14] > 6.698) && (r[14] < 6.800) );
OB_REQUIRE( (r[15] > 9.485) && (r[15] < 9.487) );
OB_REQUIRE( (r[16] > 7.667) && (r[16] < 7.669) );
OB_REQUIRE( (r[17] > 8.881) && (r[17] < 8.883) );
OB_REQUIRE( (r[18] > 4.899) && (r[18] < 4.902) );
OB_REQUIRE( (r[19] > 7.478) && (r[19] < 7.480) );
OB_REQUIRE( (r[20] > 9.323) && (r[20] < 9.325) );
OB_REQUIRE( (r[21] > 10.292) && (r[21] < 10.294) );
OB_REQUIRE( (r[22] > 12.955) && (r[22] < 12.957) );
OB_REQUIRE( (r[23] > 10.334) && (r[23] < 10.336) );
OB_REQUIRE( (r[24] > 4.020) && (r[24] < 4.022) );
OB_REQUIRE( (r[25] > 3.813) && (r[25] < 3.815) );
OB_REQUIRE( (r[26] > 2.946) && (r[26] < 2.948) );
OB_REQUIRE( (r[27] > 6.380) && (r[27] < 6.382) );
OB_REQUIRE( (r[28] > 11.003) && (r[28] < 11.005) );
OB_REQUIRE( (r[29] > 8.278) && (r[29] < 8.280) );
OB_REQUIRE( (r[30] > 6.548) && (r[30] < 6.550) );
OB_REQUIRE( (r[31] > 7.135) && (r[31] < 7.137) );
OB_REQUIRE( (r[32] > 8.612) && (r[32] < 8.614) );
OB_REQUIRE( (r[33] > 13.181) && (r[33] < 13.183) );
OB_REQUIRE( (r[34] > 13.743) && (r[34] < 13.745) );
OB_REQUIRE( (r[35] > 9.083) && (r[35] < 9.085) );
OB_REQUIRE( (r[36] > 0.458) && (r[36] < 0.460) );
OB_REQUIRE( (r[37] > 0.641) && (r[37] < 0.643) );
OB_REQUIRE( (r[38] > 2.171) && (r[38] < 2.173) );
OB_REQUIRE( (r[39] > 2.752) && (r[39] < 2.754) );
OB_REQUIRE( (r[40] > 2.347) && (r[40] < 2.349) );
OB_REQUIRE( (r[41] > 2.604) && (r[41] < 2.606) );
OB_REQUIRE( (r[42] > 1.613) && (r[42] < 1.615) );
OB_REQUIRE( (r[43] > 3.165) && (r[43] < 3.167) );
OB_REQUIRE( (r[44] > 3.390) && (r[44] < 3.392) );
OB_REQUIRE( (r[45] > 3.131) && (r[45] < 3.133) );
OB_REQUIRE( (r[46] > 4.104) && (r[46] < 4.106) );
OB_REQUIRE( (r[47] > 2.874) && (r[47] < 2.876) );
}
// With modified resolution
void test03(OpenBabel::OBMol* mol)
{
OpenBabel::OBSpectrophore s;
s.SetNormalization(OpenBabel::OBSpectrophore::NoNormalization);
s.SetResolution(10.0);
s.SetAccuracy(OpenBabel::OBSpectrophore::AngStepSize20);
s.SetStereo(OpenBabel::OBSpectrophore::NoStereoSpecificProbes);
std::vector<double> r = s.GetSpectrophore(mol);
OB_REQUIRE( (r[1] > 0.146) && (r[1] < 0.147) );
OB_REQUIRE( (r[13] > 0.327) && (r[13] < 0.328) );
OB_REQUIRE( (r[25] > 0.359) && (r[25] < 0.360) );
OB_REQUIRE( (r[37] > 0.061) && (r[37] < 0.062) );
}
// With normalization towards unit std and zero mean
void test06(OpenBabel::OBMol* mol)
{
OpenBabel::OBSpectrophore s;
s.SetNormalization(OpenBabel::OBSpectrophore::NormalizationTowardsZeroMeanAndUnitStd);
s.SetResolution(3.0);
s.SetAccuracy(OpenBabel::OBSpectrophore::AngStepSize20);
s.SetStereo(OpenBabel::OBSpectrophore::NoStereoSpecificProbes);
std::vector<double> r = s.GetSpectrophore(mol);
OB_REQUIRE( (r[4] > 0.388) && (r[4] < 0.389) );
OB_REQUIRE( (r[16] > -0.061) && (r[16] < -0.060) );
OB_REQUIRE( (r[28] > 0.887) && (r[28] < 0.888) );
OB_REQUIRE( (r[40] > -0.084) && (r[40] < -0.083) );
}
// With increased accuracy
void test02(OpenBabel::OBMol* mol)
{
OpenBabel::OBSpectrophore s;
s.SetNormalization(OpenBabel::OBSpectrophore::NoNormalization);
s.SetResolution(3.0);
s.SetAccuracy(OpenBabel::OBSpectrophore::AngStepSize5);
s.SetStereo(OpenBabel::OBSpectrophore::NoStereoSpecificProbes);
std::vector<double> r = s.GetSpectrophore(mol);
OB_REQUIRE( (r[0] > 1.644) && (r[0] < 1.645) );
OB_REQUIRE( (r[12] > 2.724) && (r[12] < 2.725) );
OB_REQUIRE( (r[24] > 4.043) && (r[24] < 4.044) );
OB_REQUIRE( (r[36] > 0.458) && (r[36] < 0.459) );
}
// With normalization towards unit std
void test05(OpenBabel::OBMol* mol)
{
OpenBabel::OBSpectrophore s;
s.SetNormalization(OpenBabel::OBSpectrophore::NormalizationTowardsUnitStd);
s.SetResolution(3.0);
s.SetAccuracy(OpenBabel::OBSpectrophore::AngStepSize20);
s.SetStereo(OpenBabel::OBSpectrophore::NoStereoSpecificProbes);
std::vector<double> r = s.GetSpectrophore(mol);
OB_REQUIRE( (r[3] > 1.698) && (r[3] < 1.699) );
OB_REQUIRE( (r[15] > 3.147) && (r[15] < 3.148) );
OB_REQUIRE( (r[27] > 1.823) && (r[27] < 1.824) );
OB_REQUIRE( (r[39] > 2.539) && (r[39] < 2.540) );
}
// With normalization towards zero mean
void test04(OpenBabel::OBMol* mol)
{
OpenBabel::OBSpectrophore s;
s.SetNormalization(OpenBabel::OBSpectrophore::NormalizationTowardsZeroMean);
s.SetResolution(3.0);
s.SetAccuracy(OpenBabel::OBSpectrophore::AngStepSize20);
s.SetStereo(OpenBabel::OBSpectrophore::NoStereoSpecificProbes);
std::vector<double> r = s.GetSpectrophore(mol);
OB_REQUIRE( (r[2] > -3.145) && (r[2] < -3.144) );
OB_REQUIRE( (r[14] > -1.152) && (r[14] < -1.151) );
OB_REQUIRE( (r[26] > -4.949) && (r[26] < -4.948) );
OB_REQUIRE( (r[38] > -0.267) && (r[38] < -0.266) );
}
// All stereo probes
void test09(OpenBabel::OBMol* mol)
{
OpenBabel::OBSpectrophore s;
s.SetNormalization(OpenBabel::OBSpectrophore::NoNormalization);
s.SetResolution(3.0);
s.SetAccuracy(OpenBabel::OBSpectrophore::AngStepSize20);
s.SetStereo(OpenBabel::OBSpectrophore::AllStereoSpecificProbes);
std::vector<double> r = s.GetSpectrophore(mol);
OB_REQUIRE( (r[0] > 1.150) && (r[0] < 1.151) );
OB_REQUIRE( (r[1] > 3.149) && (r[1] < 3.150) );
OB_REQUIRE( (r[2] > 3.209) && (r[2] < 3.210) );
OB_REQUIRE( (r[3] > 3.174) && (r[3] < 3.175) );
OB_REQUIRE( (r[4] > 3.569) && (r[4] < 3.570) );
OB_REQUIRE( (r[5] > 3.304) && (r[5] < 3.305) );
OB_REQUIRE( (r[6] > 3.051) && (r[6] < 3.052) );
OB_REQUIRE( (r[7] > 4.562) && (r[7] < 4.563) );
OB_REQUIRE( (r[8] > 6.095) && (r[8] < 6.096) );
OB_REQUIRE( (r[9] > 5.226) && (r[9] < 5.227) );
OB_REQUIRE( (r[10] > 4.518) && (r[10] < 4.519) );
OB_REQUIRE( (r[11] > 5.049) && (r[11] < 5.050) );
OB_REQUIRE( (r[12] > 6.967) && (r[12] < 6.968) );
OB_REQUIRE( (r[13] > 5.714) && (r[13] < 5.715) );
OB_REQUIRE( (r[14] > 4.741) && (r[14] < 4.742) );
OB_REQUIRE( (r[15] > 5.948) && (r[15] < 5.949) );
OB_REQUIRE( (r[16] > 5.890) && (r[16] < 5.891) );
OB_REQUIRE( (r[17] > 7.335) && (r[17] < 7.336) );
OB_REQUIRE( (r[18] > 1.147) && (r[18] < 1.148) );
OB_REQUIRE( (r[19] > 3.170) && (r[19] < 3.171) );
OB_REQUIRE( (r[20] > 3.174) && (r[20] < 3.175) );
OB_REQUIRE( (r[21] > 3.339) && (r[21] < 3.340) );
OB_REQUIRE( (r[22] > 3.669) && (r[22] < 3.670) );
OB_REQUIRE( (r[23] > 3.108) && (r[23] < 3.109) );
OB_REQUIRE( (r[24] > 3.160) && (r[24] < 3.161) );
OB_REQUIRE( (r[25] > 4.886) && (r[25] < 4.887) );
OB_REQUIRE( (r[26] > 6.239) && (r[26] < 6.240) );
OB_REQUIRE( (r[27] > 5.184) && (r[27] < 5.185) );
OB_REQUIRE( (r[28] > 4.438) && (r[28] < 4.439) );
OB_REQUIRE( (r[29] > 5.232) && (r[29] < 5.233) );
OB_REQUIRE( (r[30] > 6.973) && (r[30] < 6.974) );
OB_REQUIRE( (r[31] > 5.545) && (r[31] < 5.546) );
OB_REQUIRE( (r[32] > 4.827) && (r[32] < 4.828) );
OB_REQUIRE( (r[33] > 5.804) && (r[33] < 5.805) );
OB_REQUIRE( (r[34] > 5.809) && (r[34] < 5.810) );
OB_REQUIRE( (r[35] > 7.107) && (r[35] < 7.108) );
OB_REQUIRE( (r[36] > 2.015) && (r[36] < 2.016) );
OB_REQUIRE( (r[37] > 8.571) && (r[37] < 8.572) );
OB_REQUIRE( (r[38] > 5.878) && (r[38] < 5.879) );
OB_REQUIRE( (r[39] > 7.161) && (r[39] < 7.162) );
OB_REQUIRE( (r[40] > 5.824) && (r[40] < 5.825) );
OB_REQUIRE( (r[41] > 5.744) && (r[41] < 5.745) );
OB_REQUIRE( (r[42] > 5.676) && (r[42] < 5.677) );
OB_REQUIRE( (r[43] > 8.814) && (r[43] < 8.815) );
OB_REQUIRE( (r[44] > 9.347) && (r[44] < 9.348) );
OB_REQUIRE( (r[45] > 8.610) && (r[45] < 8.611) );
OB_REQUIRE( (r[46] > 6.540) && (r[46] < 6.541) );
OB_REQUIRE( (r[47] > 9.610) && (r[47] < 9.611) );
OB_REQUIRE( (r[48] > 13.544) && (r[48] < 13.545) );
OB_REQUIRE( (r[49] > 8.755) && (r[49] < 8.756) );
OB_REQUIRE( (r[50] > 9.704) && (r[50] < 9.705) );
OB_REQUIRE( (r[51] > 9.714) && (r[51] < 9.715) );
OB_REQUIRE( (r[52] > 9.948) && (r[52] < 9.949) );
OB_REQUIRE( (r[53] > 10.934) && (r[53] < 10.935) );
OB_REQUIRE( (r[54] > 1.986) && (r[54] < 1.987) );
OB_REQUIRE( (r[55] > 8.473) && (r[55] < 8.474) );
OB_REQUIRE( (r[56] > 5.681) && (r[56] < 5.682) );
OB_REQUIRE( (r[57] > 7.358) && (r[57] < 7.359) );
OB_REQUIRE( (r[58] > 5.874) && (r[58] < 5.875) );
OB_REQUIRE( (r[59] > 5.997) && (r[59] < 5.998) );
OB_REQUIRE( (r[60] > 5.596) && (r[60] < 5.597) );
OB_REQUIRE( (r[61] > 9.362) && (r[61] < 9.363) );
OB_REQUIRE( (r[62] > 9.389) && (r[62] < 9.390) );
OB_REQUIRE( (r[63] > 9.566) && (r[63] < 9.567) );
OB_REQUIRE( (r[64] > 6.162) && (r[64] < 6.163) );
OB_REQUIRE( (r[65] > 8.745) && (r[65] < 8.746) );
OB_REQUIRE( (r[66] > 12.694) && (r[66] < 12.695) );
OB_REQUIRE( (r[67] > 8.925) && (r[67] < 8.926) );
OB_REQUIRE( (r[68] > 8.854) && (r[68] < 8.855) );
OB_REQUIRE( (r[69] > 9.599) && (r[69] < 9.600) );
OB_REQUIRE( (r[70] > 10.087) && (r[70] < 10.088) );
OB_REQUIRE( (r[71] > 10.454) && (r[71] < 10.455) );
OB_REQUIRE( (r[72] > 2.432) && (r[72] < 2.433) );
OB_REQUIRE( (r[73] > 5.466) && (r[73] < 5.467) );
OB_REQUIRE( (r[74] > 7.455) && (r[74] < 7.456) );
OB_REQUIRE( (r[75] > 5.584) && (r[75] < 5.585) );
OB_REQUIRE( (r[76] > 5.687) && (r[76] < 5.688) );
OB_REQUIRE( (r[77] > 5.350) && (r[77] < 5.351) );
OB_REQUIRE( (r[78] > 5.879) && (r[78] < 5.880) );
OB_REQUIRE( (r[79] > 8.811) && (r[79] < 8.812) );
OB_REQUIRE( (r[80] > 10.500) && (r[80] < 10.501) );
OB_REQUIRE( (r[81] > 9.302) && (r[81] < 9.304) );
OB_REQUIRE( (r[82] > 8.525) && (r[82] < 8.526) );
OB_REQUIRE( (r[83] > 9.723) && (r[83] < 9.724) );
OB_REQUIRE( (r[84] > 12.615) && (r[84] < 12.616) );
OB_REQUIRE( (r[85] > 9.912) && (r[85] < 9.913) );
OB_REQUIRE( (r[86] > 8.245) && (r[86] < 8.246) );
OB_REQUIRE( (r[87] > 10.045) && (r[87] < 10.046) );
OB_REQUIRE( (r[88] > 10.673) && (r[88] < 10.674) );
OB_REQUIRE( (r[89] > 12.036) && (r[89] < 12.037) );
OB_REQUIRE( (r[90] > 2.371) && (r[90] < 2.372) );
OB_REQUIRE( (r[91] > 5.658) && (r[91] < 5.659) );
OB_REQUIRE( (r[92] > 7.224) && (r[92] < 7.225) );
OB_REQUIRE( (r[93] > 5.556) && (r[93] < 5.557) );
OB_REQUIRE( (r[94] > 5.617) && (r[94] < 5.618) );
OB_REQUIRE( (r[95] > 5.240) && (r[95] < 5.241) );
OB_REQUIRE( (r[96] > 5.576) && (r[96] < 5.577) );
OB_REQUIRE( (r[97] > 9.171) && (r[97] < 9.172) );
OB_REQUIRE( (r[98] > 10.523) && (r[98] < 10.524) );
OB_REQUIRE( (r[99] > 9.109) && (r[99] < 9.110) );
OB_REQUIRE( (r[100] > 8.459) && (r[100] < 8.460) );
OB_REQUIRE( (r[101] > 9.413) && (r[101] < 9.414) );
OB_REQUIRE( (r[102] > 12.418) && (r[102] < 12.419) );
OB_REQUIRE( (r[103] > 10.191) && (r[103] < 10.192) );
OB_REQUIRE( (r[104] > 8.444) && (r[104] < 8.445) );
OB_REQUIRE( (r[105] > 10.295) && (r[105] < 10.296) );
OB_REQUIRE( (r[106] > 10.572) && (r[106] < 10.573) );
OB_REQUIRE( (r[107] > 12.187) && (r[107] < 12.188) );
OB_REQUIRE( (r[108] > 0.405) && (r[108] < 0.406) );
OB_REQUIRE( (r[109] > 2.217) && (r[109] < 2.218) );
OB_REQUIRE( (r[110] > 1.789) && (r[110] < 1.790) );
OB_REQUIRE( (r[111] > 2.424) && (r[111] < 2.425) );
OB_REQUIRE( (r[112] > 2.259) && (r[112] < 2.260) );
OB_REQUIRE( (r[113] > 1.872) && (r[113] < 1.873) );
OB_REQUIRE( (r[114] > 1.794) && (r[114] < 1.795) );
OB_REQUIRE( (r[115] > 2.502) && (r[115] < 2.503) );
OB_REQUIRE( (r[116] > 3.007) && (r[116] < 3.008) );
OB_REQUIRE( (r[117] > 2.563) && (r[117] < 2.564) );
OB_REQUIRE( (r[118] > 1.916) && (r[118] < 1.917) );
OB_REQUIRE( (r[119] > 2.708) && (r[119] < 2.709) );
OB_REQUIRE( (r[120] > 3.421) && (r[120] < 3.422) );
OB_REQUIRE( (r[121] > 2.706) && (r[121] < 2.707) );
OB_REQUIRE( (r[122] > 2.581) && (r[122] < 2.582) );
OB_REQUIRE( (r[123] > 2.838) && (r[123] < 2.839) );
OB_REQUIRE( (r[124] > 3.403) && (r[124] < 3.404) );
OB_REQUIRE( (r[125] > 3.637) && (r[125] < 3.638) );
OB_REQUIRE( (r[126] > 0.371) && (r[126] < 0.372) );
OB_REQUIRE( (r[127] > 2.238) && (r[127] < 2.239) );
OB_REQUIRE( (r[128] > 2.022) && (r[128] < 2.023) );
OB_REQUIRE( (r[129] > 2.330) && (r[129] < 2.331) );
OB_REQUIRE( (r[130] > 2.009) && (r[130] < 2.010) );
OB_REQUIRE( (r[131] > 1.968) && (r[131] < 1.969) );
OB_REQUIRE( (r[132] > 1.978) && (r[132] < 1.979) );
OB_REQUIRE( (r[133] > 2.682) && (r[133] < 2.683) );
OB_REQUIRE( (r[134] > 2.877) && (r[134] < 2.878) );
OB_REQUIRE( (r[135] > 2.494) && (r[135] < 2.495) );
OB_REQUIRE( (r[136] > 1.869) && (r[136] < 1.870) );
OB_REQUIRE( (r[137] > 2.450) && (r[137] < 2.451) );
OB_REQUIRE( (r[138] > 3.385) && (r[138] < 3.386) );
OB_REQUIRE( (r[139] > 2.565) && (r[139] < 2.566) );
OB_REQUIRE( (r[140] > 2.589) && (r[140] < 2.590) );
OB_REQUIRE( (r[141] > 3.011) && (r[141] < 3.012) );
OB_REQUIRE( (r[142] > 3.380) && (r[142] < 3.381) );
OB_REQUIRE( (r[143] > 3.848) && (r[143] < 3.849) );
}
// Mirror stereo probes
void test08(OpenBabel::OBMol* mol)
{
OpenBabel::OBSpectrophore s;
s.SetNormalization(OpenBabel::OBSpectrophore::NoNormalization);
s.SetResolution(3.0);
s.SetAccuracy(OpenBabel::OBSpectrophore::AngStepSize20);
s.SetStereo(OpenBabel::OBSpectrophore::MirrorStereoSpecificProbes);
std::vector<double> r = s.GetSpectrophore(mol);
OB_REQUIRE( (r[0] > 1.147) && (r[0] < 1.148) );
OB_REQUIRE( (r[1] > 3.170) && (r[1] < 3.171) );
OB_REQUIRE( (r[2] > 3.174) && (r[2] < 3.175) );
OB_REQUIRE( (r[3] > 3.339) && (r[3] < 3.340) );
OB_REQUIRE( (r[4] > 3.669) && (r[4] < 3.670) );
OB_REQUIRE( (r[5] > 3.108) && (r[5] < 3.109) );
OB_REQUIRE( (r[6] > 3.160) && (r[6] < 3.161) );
OB_REQUIRE( (r[7] > 4.886) && (r[7] < 4.887) );
OB_REQUIRE( (r[8] > 6.239) && (r[8] < 6.240) );
OB_REQUIRE( (r[9] > 5.184) && (r[9] < 5.185) );
OB_REQUIRE( (r[10] > 4.438) && (r[10] < 4.439) );
OB_REQUIRE( (r[11] > 5.232) && (r[11] < 5.233) );
OB_REQUIRE( (r[12] > 6.973) && (r[12] < 6.974) );
OB_REQUIRE( (r[13] > 5.545) && (r[13] < 5.546) );
OB_REQUIRE( (r[14] > 4.827) && (r[14] < 4.828) );
OB_REQUIRE( (r[15] > 5.804) && (r[15] < 5.805) );
OB_REQUIRE( (r[16] > 5.809) && (r[16] < 5.810) );
OB_REQUIRE( (r[17] > 7.107) && (r[17] < 7.108) );
OB_REQUIRE( (r[18] > 1.986) && (r[18] < 1.987) );
OB_REQUIRE( (r[19] > 8.473) && (r[19] < 8.474) );
OB_REQUIRE( (r[20] > 5.681) && (r[20] < 5.682) );
OB_REQUIRE( (r[21] > 7.358) && (r[21] < 7.359) );
OB_REQUIRE( (r[22] > 5.874) && (r[22] < 5.875) );
OB_REQUIRE( (r[23] > 5.997) && (r[23] < 5.998) );
OB_REQUIRE( (r[24] > 5.596) && (r[24] < 5.597) );
OB_REQUIRE( (r[25] > 9.362) && (r[25] < 9.363) );
OB_REQUIRE( (r[26] > 9.389) && (r[26] < 9.390) );
OB_REQUIRE( (r[27] > 9.566) && (r[27] < 9.567) );
OB_REQUIRE( (r[28] > 6.162) && (r[28] < 6.163) );
OB_REQUIRE( (r[29] > 8.745) && (r[29] < 8.746) );
OB_REQUIRE( (r[30] > 12.694) && (r[30] < 12.695) );
OB_REQUIRE( (r[31] > 8.925) && (r[31] < 8.926) );
OB_REQUIRE( (r[32] > 8.854) && (r[32] < 8.855) );
OB_REQUIRE( (r[33] > 9.599) && (r[33] < 9.600) );
OB_REQUIRE( (r[34] > 10.087) && (r[34] < 10.088) );
OB_REQUIRE( (r[35] > 10.454) && (r[35] < 10.455) );
OB_REQUIRE( (r[36] > 2.371) && (r[36] < 2.372) );
OB_REQUIRE( (r[37] > 5.658) && (r[37] < 5.659) );
OB_REQUIRE( (r[38] > 7.224) && (r[38] < 7.225) );
OB_REQUIRE( (r[39] > 5.556) && (r[39] < 5.557) );
OB_REQUIRE( (r[40] > 5.617) && (r[40] < 5.618) );
OB_REQUIRE( (r[41] > 5.240) && (r[41] < 5.241) );
OB_REQUIRE( (r[42] > 5.576) && (r[42] < 5.577) );
OB_REQUIRE( (r[43] > 9.171) && (r[43] < 9.172) );
OB_REQUIRE( (r[44] > 10.523) && (r[44] < 10.524) );
OB_REQUIRE( (r[45] > 9.109) && (r[45] < 9.110) );
OB_REQUIRE( (r[46] > 8.459) && (r[46] < 8.460) );
OB_REQUIRE( (r[47] > 9.413) && (r[47] < 9.414) );
OB_REQUIRE( (r[48] > 12.418) && (r[48] < 12.419) );
OB_REQUIRE( (r[49] > 10.191) && (r[49] < 10.192) );
OB_REQUIRE( (r[50] > 8.444) && (r[50] < 8.445) );
OB_REQUIRE( (r[51] > 10.295) && (r[51] < 10.296) );
OB_REQUIRE( (r[52] > 10.572) && (r[52] < 10.573) );
OB_REQUIRE( (r[53] > 12.187) && (r[53] < 12.188) );
OB_REQUIRE( (r[54] > 0.371) && (r[54] < 0.372) );
OB_REQUIRE( (r[55] > 2.238) && (r[55] < 2.239) );
OB_REQUIRE( (r[56] > 2.022) && (r[56] < 2.023) );
OB_REQUIRE( (r[57] > 2.330) && (r[57] < 2.331) );
OB_REQUIRE( (r[58] > 2.009) && (r[58] < 2.010) );
OB_REQUIRE( (r[59] > 1.968) && (r[59] < 1.969) );
OB_REQUIRE( (r[60] > 1.978) && (r[60] < 1.979) );
OB_REQUIRE( (r[61] > 2.682) && (r[61] < 2.683) );
OB_REQUIRE( (r[62] > 2.877) && (r[62] < 2.878) );
OB_REQUIRE( (r[63] > 2.494) && (r[63] < 2.495) );
OB_REQUIRE( (r[64] > 1.869) && (r[64] < 1.870) );
OB_REQUIRE( (r[65] > 2.450) && (r[65] < 2.451) );
OB_REQUIRE( (r[66] > 3.385) && (r[66] < 3.386) );
OB_REQUIRE( (r[67] > 2.565) && (r[67] < 2.566) );
OB_REQUIRE( (r[68] > 2.589) && (r[68] < 2.590) );
OB_REQUIRE( (r[69] > 3.011) && (r[69] < 3.012) );
OB_REQUIRE( (r[70] > 3.380) && (r[70] < 3.381) );
OB_REQUIRE( (r[71] > 3.848) && (r[71] < 3.849) );
}
// Unique stereo probes
void test07(OpenBabel::OBMol* mol)
{
OpenBabel::OBSpectrophore s;
s.SetNormalization(OpenBabel::OBSpectrophore::NoNormalization);
s.SetResolution(3.0);
s.SetAccuracy(OpenBabel::OBSpectrophore::AngStepSize20);
s.SetStereo(OpenBabel::OBSpectrophore::UniqueStereoSpecificProbes);
std::vector<double> r = s.GetSpectrophore(mol);
OB_REQUIRE( (r[0] > 1.150) && (r[0] < 1.151) );
OB_REQUIRE( (r[1] > 3.149) && (r[1] < 3.150) );
OB_REQUIRE( (r[2] > 3.209) && (r[2] < 3.210) );
OB_REQUIRE( (r[3] > 3.174) && (r[3] < 3.175) );
OB_REQUIRE( (r[4] > 3.569) && (r[4] < 3.570) );
OB_REQUIRE( (r[5] > 3.304) && (r[5] < 3.305) );
OB_REQUIRE( (r[6] > 3.051) && (r[6] < 3.052) );
OB_REQUIRE( (r[7] > 4.562) && (r[7] < 4.563) );
OB_REQUIRE( (r[8] > 6.095) && (r[8] < 6.096) );
OB_REQUIRE( (r[9] > 5.226) && (r[9] < 5.227) );
OB_REQUIRE( (r[10] > 4.518) && (r[10] < 4.519) );
OB_REQUIRE( (r[11] > 5.049) && (r[11] < 5.050) );
OB_REQUIRE( (r[12] > 6.967) && (r[12] < 6.968) );
OB_REQUIRE( (r[13] > 5.714) && (r[13] < 5.715) );
OB_REQUIRE( (r[14] > 4.741) && (r[14] < 4.742) );
OB_REQUIRE( (r[15] > 5.948) && (r[15] < 5.949) );
OB_REQUIRE( (r[16] > 5.890) && (r[16] < 5.891) );
OB_REQUIRE( (r[17] > 7.335) && (r[17] < 7.336) );
OB_REQUIRE( (r[18] > 2.015) && (r[18] < 2.016) );
OB_REQUIRE( (r[19] > 8.571) && (r[19] < 8.572) );
OB_REQUIRE( (r[20] > 5.878) && (r[20] < 5.879) );
OB_REQUIRE( (r[21] > 7.161) && (r[21] < 7.162) );
OB_REQUIRE( (r[22] > 5.824) && (r[22] < 5.825) );
OB_REQUIRE( (r[23] > 5.744) && (r[23] < 5.745) );
OB_REQUIRE( (r[24] > 5.676) && (r[24] < 5.677) );
OB_REQUIRE( (r[25] > 8.814) && (r[25] < 8.815) );
OB_REQUIRE( (r[26] > 9.347) && (r[26] < 9.348) );
OB_REQUIRE( (r[27] > 8.610) && (r[27] < 8.611) );
OB_REQUIRE( (r[28] > 6.540) && (r[28] < 6.541) );
OB_REQUIRE( (r[29] > 9.610) && (r[29] < 9.611) );
OB_REQUIRE( (r[30] > 13.544) && (r[30] < 13.545) );
OB_REQUIRE( (r[31] > 8.755) && (r[31] < 8.756) );
OB_REQUIRE( (r[32] > 9.704) && (r[32] < 9.705) );
OB_REQUIRE( (r[33] > 9.714) && (r[33] < 9.715) );
OB_REQUIRE( (r[34] > 9.948) && (r[34] < 9.949) );
OB_REQUIRE( (r[35] > 10.934) && (r[35] < 10.935) );
OB_REQUIRE( (r[36] > 2.432) && (r[36] < 2.433) );
OB_REQUIRE( (r[37] > 5.466) && (r[37] < 5.467) );
OB_REQUIRE( (r[38] > 7.455) && (r[38] < 7.456) );
OB_REQUIRE( (r[39] > 5.584) && (r[39] < 5.585) );
OB_REQUIRE( (r[40] > 5.687) && (r[40] < 5.688) );
OB_REQUIRE( (r[41] > 5.350) && (r[41] < 5.351) );
OB_REQUIRE( (r[42] > 5.879) && (r[42] < 5.880) );
OB_REQUIRE( (r[43] > 8.811) && (r[43] < 8.812) );
OB_REQUIRE( (r[44] > 10.500) && (r[44] < 10.501) );
OB_REQUIRE( (r[45] > 9.302) && (r[45] < 9.303) );
OB_REQUIRE( (r[46] > 8.525) && (r[46] < 8.526) );
OB_REQUIRE( (r[47] > 9.723) && (r[47] < 9.724) );
OB_REQUIRE( (r[48] > 12.615) && (r[48] < 12.616) );
OB_REQUIRE( (r[49] > 9.912) && (r[49] < 9.913) );
OB_REQUIRE( (r[50] > 8.245) && (r[50] < 8.246) );
OB_REQUIRE( (r[51] > 10.045) && (r[51] < 10.046) );
OB_REQUIRE( (r[52] > 10.673) && (r[52] < 10.674) );
OB_REQUIRE( (r[53] > 12.036) && (r[53] < 12.037) );
OB_REQUIRE( (r[54] > 0.405) && (r[54] < 0.406) );
OB_REQUIRE( (r[55] > 2.217) && (r[55] < 2.218) );
OB_REQUIRE( (r[56] > 1.789) && (r[56] < 1.790) );
OB_REQUIRE( (r[57] > 2.424) && (r[57] < 2.425) );
OB_REQUIRE( (r[58] > 2.259) && (r[58] < 2.260) );
OB_REQUIRE( (r[59] > 1.872) && (r[59] < 1.873) );
OB_REQUIRE( (r[60] > 1.794) && (r[60] < 1.795) );
OB_REQUIRE( (r[61] > 2.502) && (r[61] < 2.503) );
OB_REQUIRE( (r[62] > 3.007) && (r[62] < 3.008) );
OB_REQUIRE( (r[63] > 2.563) && (r[63] < 2.564) );
OB_REQUIRE( (r[64] > 1.916) && (r[64] < 1.917) );
OB_REQUIRE( (r[65] > 2.708) && (r[65] < 2.709) );
OB_REQUIRE( (r[66] > 3.421) && (r[66] < 3.422) );
OB_REQUIRE( (r[67] > 2.706) && (r[67] < 2.707) );
OB_REQUIRE( (r[68] > 2.581) && (r[68] < 2.582) );
OB_REQUIRE( (r[69] > 2.838) && (r[69] < 2.839) );
OB_REQUIRE( (r[70] > 3.403) && (r[70] < 3.404) );
OB_REQUIRE( (r[71] > 3.637) && (r[71] < 3.638) );
}
void
showParameters(const OpenBabel::OBSpectrophore& spec, const std::string& ifile)
{
std::string msg;
std::cout << std::endl;
std::cout << "*******************************************" << std::endl;
std::cout << "SPECTROPHORE(TM) CALCULATOR: OBSPECTROPHORE" << std::endl;
std::cout << "*******************************************" << std::endl;
std::cout << std::endl;
std::cout << "Input file: " << ifile << std::endl;
OpenBabel::OBSpectrophore::NormalizationOption n = spec.GetNormalization();
switch (n)
{
case OpenBabel::OBSpectrophore::NoNormalization:
msg = "No";
break;
case OpenBabel::OBSpectrophore::NormalizationTowardsZeroMean:
msg = "ZeroMean";
break;
case OpenBabel::OBSpectrophore::NormalizationTowardsUnitStd:
msg = "UnitStd";
break;
case OpenBabel::OBSpectrophore::NormalizationTowardsZeroMeanAndUnitStd:
msg = "ZeroMeanAndUnitStd";
break;
}
std::cout << "Normalization: " << msg << std::endl;
OpenBabel::OBSpectrophore::AccuracyOption a = spec.GetAccuracy();
switch (a)
{
case OpenBabel::OBSpectrophore::AngStepSize1:
msg = "1";
break;
case OpenBabel::OBSpectrophore::AngStepSize2:
msg = "2";
break;
case OpenBabel::OBSpectrophore::AngStepSize5:
msg = "5";
break;
case OpenBabel::OBSpectrophore::AngStepSize10:
msg = "10";
break;
case OpenBabel::OBSpectrophore::AngStepSize15:
msg = "15";
break;
case OpenBabel::OBSpectrophore::AngStepSize20:
msg = "20";
break;
case OpenBabel::OBSpectrophore::AngStepSize30:
msg = "30";
break;
case OpenBabel::OBSpectrophore::AngStepSize36:
msg = "36";
break;
case OpenBabel::OBSpectrophore::AngStepSize45:
msg = "45";
break;
case OpenBabel::OBSpectrophore::AngStepSize60:
msg = "60";
break;
}
std::cout << "Accuracy: " << msg << " degrees" << std::endl;
OpenBabel::OBSpectrophore::StereoOption s = spec.GetStereo();
switch (s)
{
case OpenBabel::OBSpectrophore::NoStereoSpecificProbes:
msg = "No";
break;
case OpenBabel::OBSpectrophore::UniqueStereoSpecificProbes:
msg = "Unique";
break;
case OpenBabel::OBSpectrophore::MirrorStereoSpecificProbes:
msg = "Mirror";
break;
case OpenBabel::OBSpectrophore::AllStereoSpecificProbes:
msg = "All";
break;
}
std::cout << "Stereo treatment: " << msg << std::endl;
double r = spec.GetResolution();
std::cout << "Resolution: " << r << " Angstrom" << std::endl;
std::cout << std::endl;
}
int main(int argc,char **argv)
{
std::string ifile = "";
OpenBabel::OBSpectrophore::AccuracyOption accuracy = OpenBabel::OBSpectrophore::AngStepSize20;
OpenBabel::OBSpectrophore::StereoOption stereo = OpenBabel::OBSpectrophore::NoStereoSpecificProbes;
OpenBabel::OBSpectrophore::NormalizationOption normalization = OpenBabel::OBSpectrophore::NoNormalization;
double resolution = 3.0;
int c;
opterr = 0;
std::string msg;
while ((c = getopt(argc, argv, "ui:n:a:s:r:h")) != -1)
{
switch (c)
{
case 'u':
showImplementationDetails(argv[0]);
exit(1);
break;
case 'i':
if (!isValidValue('i', optarg))
{
msg = "Option -i is followed by an invalid argument: ";
msg += optarg;
showError(msg);
exit(1);
}
else
{
ifile = optarg;
}
break;
case 'n':
if (!isValidValue('n', optarg))
{
msg = "Option -n is followed by an invalid argument: ";
msg += optarg;
showError(msg);
exit(1);
}
else normalization = stringToNormalizationOption(optarg);
break;
case 'a':
if (!isValidValue('a', optarg))
{
msg = "Option -a is followed by an invalid argument: ";
msg += optarg;
showError(msg);
exit(1);
}
else accuracy = stringToAccuracyOption(optarg);
break;
case 's':
if (!isValidValue('s', optarg))
{
msg = "Option -s is followed by an invalid argument: ";
msg += optarg;
showError(msg);
exit(1);
}
else stereo = stringToStereoOption(optarg);
break;
case 'r':
if (!isValidValue('r', optarg))
{
msg = "Option -r is followed by an invalid argument: ";
msg += optarg;
showError(msg);
exit(1);
}
else
{
resolution = atof(optarg);
if (resolution <= 0)
{
msg = "Resolution -r should be larger than 0.0: ";
msg += optarg;
showError(msg);
exit(1);
}
}
break;
case 'h':
showHelp(argv[0]);
exit(0);
break;
case '?':
if ((optopt == 'i') ||
(optopt == 'n') ||
(optopt == 'a') ||
(optopt == 's') ||
(optopt == 'r'))
{
msg = "Option -";
msg += optopt;
msg += " requires an argument.";
showError(msg);
exit(1);
}
else
{
msg = "Unknown option -";
msg += optopt;
msg += ".";
showError(msg);
exit(1);
}
break;
default:
showError("Unknown option");
exit(1);
break;
}
}
// The input file (-i) is the only required option
if (ifile.empty())
{
msg = "Input file specification is required (option -i).";
showError(msg);
exit(1);
}
OpenBabel::OBConversion obconversion;
OpenBabel::OBFormat *format = obconversion.FormatFromExt(ifile.c_str());
if (!format)
{
msg = "Could not find file format for ";
msg += ifile;
showError(msg);
exit(1);
}
obconversion.SetInFormat(format);
std::ifstream ifs;
ifs.open(ifile.c_str());
obconversion.SetInStream(&ifs);
// Start calculations
OpenBabel::OBMol mol;
OpenBabel::OBSpectrophore spec;
spec.SetAccuracy(accuracy);
spec.SetNormalization(normalization);
spec.SetStereo(stereo);
spec.SetResolution(resolution);
showParameters(spec, ifile);
unsigned int count(0);
while (obconversion.Read(&mol))
{
std::vector<double> result = spec.GetSpectrophore(&mol);
if (result.empty()) {
std::cerr << "Error calculating Spectrophore from molecule number ";
std::cerr << count;
std::cerr << " (counting starts at 0)!";
std::cerr << std::endl;
}
else
{
std::cout << mol.GetTitle() << "\t";
for (unsigned int i(0); i < result.size(); ++i)
{
std::cout << result[i] << "\t";
}
std::cout << std::endl;
}
mol.Clear();
++count;
}
return 0;
}
