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Commit e0d2c132 by maarten
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met prolsq remark 3 

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@362 a1961a4f-ab94-4bcc-80e8-33b5a54de466
parent 9a54b6b9
Showing with 124 additions and 0 deletions
src/Cif2PDB.cpp
......@@ -1853,6 +1853,128 @@ void WriteRemark3XPlor(ostream& pdbFile, Datablock& db)
<< RM3("") << endl;
}
void WriteRemark3ProlSQ(ostream& pdbFile, Datablock& db)
{
auto refine = db["refine"].front();
auto pdbx_refine = db["pdbx_refine"].front();
auto hist = db["refine_hist"].front();
auto reflns = db["reflns"].front();
auto analyze = db["refine_analyze"].front();
auto& ls_restr = db["refine_ls_restr"];
pdbFile << RM3("") << endl
<< RM3(" DATA USED IN REFINEMENT.") << endl
<< RM3(" RESOLUTION RANGE HIGH (ANGSTROMS) : ", 5, 2) << Ff(refine, "ls_d_res_high") << endl
<< RM3(" RESOLUTION RANGE LOW (ANGSTROMS) : ", 5, 2) << Ff(refine, "ls_d_res_low") << endl
<< RM3(" DATA CUTOFF (SIGMA(F)) : ", 6, 3) << Ff(refine, "pdbx_ls_sigma_F") << endl
<< RM3(" COMPLETENESS FOR RANGE (%) : ", 5, 2) << Ff(refine, "ls_percent_reflns_obs") << endl
<< RM3(" NUMBER OF REFLECTIONS : ", 12, 6) << Fi(refine, "ls_number_reflns_obs") << endl
<< RM3("") << endl
<< RM3(" FIT TO DATA USED IN REFINEMENT.") << endl
<< RM3(" CROSS-VALIDATION METHOD : ") << Fs(refine, "pdbx_ls_cross_valid_method") << endl
<< RM3(" FREE R VALUE TEST SET SELECTION : ") << Fs(refine, "pdbx_R_Free_selection_details") << endl
<< RM3(" R VALUE (WORKING + TEST SET) : ", 7, 3) << Ff(refine, "ls_R_factor_obs") << endl
<< RM3(" R VALUE (WORKING SET) : ", 7, 3) << Ff(refine, "ls_R_factor_R_work") << endl
<< RM3(" FREE R VALUE : ", 7, 3) << Ff(refine, "ls_R_factor_R_free") << endl
<< RM3(" FREE R VALUE TEST SET SIZE (%) : ", 7, 3) << Ff(refine, "ls_percent_reflns_R_free") << endl
<< RM3(" FREE R VALUE TEST SET COUNT : ", 12, 6) << Fi(refine, "ls_number_reflns_R_free") << endl
<< RM3("") << endl
<< RM3(" FIT/AGREEMENT OF MODEL WITH ALL DATA.") << endl
<< RM3(" R VALUE (WORKING + TEST SET, NO CUTOFF) : ") << Fs(refine, "R_factor_all_no_cutoff") << endl
<< RM3(" R VALUE (WORKING SET, NO CUTOFF) : ") << Fs(refine, "R_factor_obs_no_cutoff") << endl
<< RM3(" FREE R VALUE (NO CUTOFF) : ") << Fs(pdbx_refine, "free_R_factor_no_cutoff") << endl
<< RM3(" FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : ") << Fs(pdbx_refine, "free_R_val_test_set_size_perc_no_cutoff") << endl
<< RM3(" FREE R VALUE TEST SET COUNT (NO CUTOFF) : ") << Fs(pdbx_refine, "free_R_val_test_set_ct_no_cutoff") << endl
<< RM3(" TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : ") << Fs(refine, "ls_number_reflns_all") << endl
<< RM3("") << endl
<< RM3(" NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.") << endl
<< RM3(" PROTEIN ATOMS : ", 12, 6) << Fi(hist, "pdbx_number_atoms_protein") << endl
<< RM3(" NUCLEIC ACID ATOMS : ", 12, 6) << Fi(hist, "pdbx_number_atoms_nucleic_acid") << endl
<< RM3(" HETEROGEN ATOMS : ", 12, 6) << Fi(hist, "pdbx_number_atoms_ligand") << endl
<< RM3(" SOLVENT ATOMS : ", 12, 6) << Fi(hist, "number_atoms_solvent") << endl
// << RM3(" ALL ATOMS : ", 12, 6) << Fi(hist, "pdbx_number_atoms_protein") << endl
<< RM3("") << endl
<< RM3(" B VALUES.") << endl
<< RM3(" B VALUE TYPE : ", 7, 2) << Fs(refine, "pdbx_TLS_residual_ADP_flag") << endl
<< RM3(" FROM WILSON PLOT (A**2) : ", 7, 2) << Ff(reflns, "B_iso_Wilson_estimate") << endl
<< RM3(" MEAN B VALUE (OVERALL, A**2) : ", 7, 2) << Ff(refine, "B_iso_mean") << endl
<< RM3(" OVERALL ANISOTROPIC B VALUE.") << endl
<< RM3(" B11 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[1][1]") << endl
<< RM3(" B22 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[2][2]") << endl
<< RM3(" B33 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[3][3]") << endl
<< RM3(" B12 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[1][2]") << endl
<< RM3(" B13 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[1][3]") << endl
<< RM3(" B23 (A**2) : ", -7, 2) << Ff(refine, "aniso_B[2][3]") << endl
<< RM3("") << endl
<< RM3(" ESTIMATED OVERALL COORDINATE ERROR.") << endl
<< RM3(" ESU BASED ON R VALUE (A) : ", 7, 2) << Ff(analyze, "pdbx_overall_ESU_R") << endl
<< RM3(" ESU BASED ON FREE R VALUE (A) : ", 7, 2) << Ff(analyze, "pdbx_overall_ESU_R_Free") << endl
<< RM3(" ESU BASED ON MAXIMUM LIKELIHOOD (A) : ", 7, 2) << Ff(analyze, "overall_SU_ML") << endl
<< RM3(" ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A) : ", 7, 2) << Ff(analyze, "overall_SU_B") << endl
<< RM3("") << endl
<< RM3(" RMS DEVIATIONS FROM IDEAL VALUES.") << endl
<< RM3(" DISTANCE RESTRAINTS. RMS SIGMA") << endl
<< RM3(" BOND LENGTH (A) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_bond_d", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_bond_d", "dev_ideal_target") << endl
<< RM3(" ANGLE DISTANCE (A) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_angle_d", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_angle_d", "dev_ideal_target") << endl
<< RM3(" INTRAPLANAR 1-4 DISTANCE (A) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_planar_d", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_planar_d", "dev_ideal_target") << endl
<< RM3(" H-BOND OR METAL COORDINATION (A) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_hb_or_metal_coord", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_hb_or_metal_coord", "dev_ideal_target") << endl
<< RM3("") << endl
<< RM3(" PLANE RESTRAINT (A) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_plane_restr", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_plane_restr", "dev_ideal_target") << endl
<< RM3(" CHIRAL-CENTER RESTRAINT (A**3) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_chiral_restr", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_chiral_restr", "dev_ideal_target") << endl
<< RM3("") << endl
<< RM3(" NON-BONDED CONTACT RESTRAINTS.") << endl
<< RM3(" SINGLE TORSION (A) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_singtor_nbd", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_singtor_nbd", "dev_ideal_target") << endl
<< RM3(" MULTIPLE TORSION (A) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_multtor_nbd", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_multtor_nbd", "dev_ideal_target") << endl
<< RM3(" H-BOND (X...Y) (A) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_xyhbond_nbd", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_xyhbond_nbd", "dev_ideal_target") << endl
<< RM3(" H-BOND (X-H...Y) (A) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_xhyhbond_nbd", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_xhyhbond_nbd", "dev_ideal_target") << endl
<< RM3("") << endl
<< RM3(" CONFORMATIONAL TORSION ANGLE RESTRAINTS.") << endl
<< RM3(" SPECIFIED (DEGREES) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_special_tor", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_special_tor", "dev_ideal_target") << endl
<< RM3(" PLANAR (DEGREES) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_planar_tor", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_planar_tor", "dev_ideal_target") << endl
<< RM3(" STAGGERED (DEGREES) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_staggered_tor", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_staggered_tor", "dev_ideal_target") << endl
<< RM3(" TRANSVERSE (DEGREES) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_transverse_tor", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_transverse_tor", "dev_ideal_target") << endl
<< RM3("") << endl
<< RM3(" ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA") << endl
<< RM3(" MAIN-CHAIN BOND (A**2) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_mcbond_it", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_mcbond_it", "dev_ideal_target") << endl
<< RM3(" MAIN-CHAIN ANGLE (A**2) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_mcangle_it", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_mcangle_it", "dev_ideal_target") << endl
<< RM3(" SIDE-CHAIN BOND (A**2) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_scbond_it", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_scbond_it", "dev_ideal_target") << endl
<< RM3(" SIDE-CHAIN ANGLE (A**2) : ", 7, 3) << Ff(ls_restr, cif::Key("type") == "p_scangle_it", "dev_ideal") << " ; "
<< Ff(ls_restr, cif::Key("type") == "p_scangle_it", "dev_ideal_target") << endl
<< RM3("") << endl;
}
void WriteRemark3(ostream& pdbFile, Datablock& db)
{
string program, authors;
......@@ -1916,6 +2038,8 @@ void WriteRemark3(ostream& pdbFile, Datablock& db)
WriteRemark3Shelxl(pdbFile, db);
else if (cif::iequals(program, "PHENIX"))
WriteRemark3Phenix(pdbFile, db);
else if (cif::iequals(program, "PROLSQ") or cif::iequals(program, "NUCLSQ"))
WriteRemark3ProlSQ(pdbFile, db);
}
for (auto r: db["refine"])
......
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