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#include <stdlib.h> |
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#include <stdio.h> |
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#include <check.h> |
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#include <freesasa.h> |
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#include <freesasa_internal.h> |
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#include <classifier.h> |
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#include "tools.h" |
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struct atom { |
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const char *a; |
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const char *b; |
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const double radius; |
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const int class; |
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}; |
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#define ali_C 2.00 |
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#define aro_C 1.75 |
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#define car_O 1.40 |
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#define car_C 1.55 |
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#define ami_N 1.55 |
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#define hyd_O 1.40 |
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#define sulf 2.00 |
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#define sele 1.90 |
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#define phos 1.80 |
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#define unk_P 1.5 |
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#define r_unk -1.0 |
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#define APO FREESASA_ATOM_APOLAR |
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#define POL FREESASA_ATOM_POLAR |
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#define UNK FREESASA_ATOM_UNKNOWN |
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#define NUC 3 |
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#define naa 20 |
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const char *aa[naa] = {"ALA", "ARG", "ASN", "ASP", "CYS", "GLN", "GLU", |
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"GLY", "HIS", "ILE", "LEU", "LYS", "MET", "PHE", |
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"PRO", "SER", "THR", "TRP", "TYR", "VAL"}; |
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#define n_other 6 |
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const char *other_aa[n_other] = {"GLX", "SEC", "PYL", "PYH", "ASX", "CSE"}; |
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#define n_capping 2 |
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const char *capping[n_capping] = {"ACE","NH2"}; |
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#define n_nuc 13 |
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const char *nuc[n_nuc] = {"DA","DC","DG","DT","DU","DI","A","C","G","T","U","I","N"}; |
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const struct atom atoms[] = { |
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{"ALA"," C ",car_C,POL}, {"ALA"," O ",car_O,POL}, {"ALA"," CA ",ali_C,APO}, |
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{"ALA"," N ",ami_N,POL}, {"ALA"," CB ",ali_C,APO}, {"ALA"," X ",r_unk,UNK}, |
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{"ARG"," C ",car_C,POL}, {"ARG"," O ",car_O,POL}, {"ARG"," CA ",ali_C,APO}, |
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{"ARG"," N ",ami_N,POL}, {"ARG"," CB ",ali_C,APO}, {"ARG"," CG ",ali_C,APO}, |
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{"ARG"," CD ",ali_C,APO}, {"ARG"," CZ ",ali_C,APO}, {"ARG"," NE ",ami_N,POL}, |
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{"ARG"," NH1",ami_N,POL}, {"ARG"," NH2",ami_N,POL}, {"ARG"," X ",r_unk,UNK}, |
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{"ASN"," C ",car_C,POL}, {"ASN"," O ",car_O,POL}, {"ASN"," CA ",ali_C,APO}, |
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{"ASN"," N ",ami_N,POL}, {"ASN"," CB ",ali_C,APO}, {"ASN"," CG ",car_C,POL}, |
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{"ASN"," OD1",car_O,POL}, {"ASN"," ND2",ami_N,POL}, {"ASN"," Y ",r_unk,UNK}, |
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{"ASP"," C ",car_C,POL}, {"ASP"," O ",car_O,POL}, {"ASP"," CA ",ali_C,APO}, |
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{"ASP"," N ",ami_N,POL}, {"ASP"," CB ",ali_C,APO}, {"ASP"," CG ",car_C,POL}, |
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{"ASP"," OD1",car_O,POL}, {"ASP"," OD2",car_O,POL}, {"ASP"," Y ",r_unk,UNK}, |
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{"CYS"," C ",car_C,POL}, {"CYS"," O ",car_O,POL}, {"CYS"," CA ",ali_C,APO}, |
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{"CYS"," N ",ami_N,POL}, {"CYS"," CB ",ali_C,APO}, {"CYS"," SG ",sulf,POL}, |
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{"CYS"," X ",r_unk,UNK}, |
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{"GLN"," C ",car_C,POL}, {"GLN"," O ",car_O,POL}, {"GLN"," CA ",ali_C,APO}, |
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{"GLN"," N ",ami_N,POL}, {"GLN"," CB ",ali_C,APO}, {"GLN"," CG ",ali_C,APO}, |
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{"GLN"," CD ",car_C,POL}, {"GLN"," OE1",car_O,POL}, {"GLN"," NE2",ami_N,POL}, |
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{"GLN"," Y ",r_unk,UNK}, |
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{"GLU"," C ",car_C,POL}, {"GLU"," O ",car_O,POL}, {"GLU"," CA ",ali_C,APO}, |
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{"GLU"," N ",ami_N,POL}, {"GLU"," CB ",ali_C,APO}, {"GLU"," CG ",ali_C,APO}, |
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{"GLU"," CD ",car_C,POL}, {"GLU"," OE1",car_O,POL}, {"GLU"," OE2",car_O,POL}, |
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{"GLU"," Y ",r_unk,UNK}, |
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{"GLY"," C ",car_C,POL}, {"GLY"," O ",car_O,POL}, {"GLY"," CA ",ali_C,APO}, |
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{"GLY"," N ",ami_N,POL}, {"GLY"," X ",r_unk,UNK}, |
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{"HIS"," C ",car_C,POL}, {"HIS"," O ",car_O,POL}, {"HIS"," CA ",ali_C,APO}, |
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{"HIS"," N ",ami_N,POL}, {"HIS"," CB ",ali_C,APO}, {"HIS"," CG ",aro_C,APO}, |
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{"HIS"," ND1",ami_N,POL}, {"HIS"," CD2",aro_C,APO}, {"HIS"," NE2",ami_N,POL}, |
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{"HIS"," CE1",aro_C,APO}, {"HIS"," X ",r_unk,UNK}, |
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{"ILE"," C ",car_C,POL}, {"ILE"," O ",car_O,POL}, {"ILE"," CA ",ali_C,APO}, |
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{"ILE"," N ",ami_N,POL}, {"ILE"," CB ",ali_C,APO}, {"ILE"," CG1",ali_C,APO}, |
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{"ILE"," CG2",ali_C,APO}, {"ILE"," CD1",ali_C,APO}, {"ILE"," X ",r_unk,UNK}, |
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{"LEU"," C ",car_C,POL}, {"LEU"," O ",car_O,POL}, {"LEU"," CA ",ali_C,APO}, |
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{"LEU"," N ",ami_N,POL}, {"LEU"," CB ",ali_C,APO}, {"LEU"," CG ",ali_C,APO}, |
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{"LEU"," CD1",ali_C,APO}, {"LEU"," CD2",ali_C,APO}, {"LEU"," X ",r_unk,UNK}, |
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{"LYS"," C ",car_C,POL}, {"LYS"," O ",car_O,POL}, {"LYS"," CA ",ali_C,APO}, |
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{"LYS"," N ",ami_N,POL}, {"LYS"," CB ",ali_C,APO}, {"LYS"," CG ",ali_C,APO}, |
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{"LYS"," CG ",ali_C,APO}, {"LYS"," CD ",ali_C,APO}, {"LYS"," CE ",ali_C,APO}, |
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{"LYS"," NZ ",ami_N,POL}, {"LYS"," X ",r_unk,UNK}, |
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{"MET"," C ",car_C,POL}, {"MET"," O ",car_O,POL}, {"MET"," CA ",ali_C,APO}, |
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{"MET"," N ",ami_N,POL}, {"MET"," CB ",ali_C,APO}, {"MET"," CG ",ali_C,APO}, |
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{"MET"," SD ",sulf, POL}, {"MET"," CE ",ali_C,APO}, {"MET"," X ",r_unk,UNK}, |
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{"PHE"," C ",car_C,POL}, {"PHE"," O ",car_O,POL}, {"PHE"," CA ",ali_C,APO}, |
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{"PHE"," N ",ami_N,POL}, {"PHE"," CB ",ali_C,APO}, {"PHE"," CG ",aro_C,APO}, |
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{"PHE"," CD1",aro_C,APO}, {"PHE"," CD2",aro_C,APO}, {"PHE"," CE1",aro_C,APO}, |
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{"PHE"," CE2",aro_C,APO}, {"PHE"," CZ ",aro_C,APO}, {"PHE"," X ",r_unk,UNK}, |
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{"PRO"," C ",car_C,POL}, {"PRO"," O ",car_O,POL}, {"PRO"," CA ",ali_C,APO}, |
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{"PRO"," N ",ami_N,POL}, {"PRO"," CB ",aro_C,APO}, {"PRO"," CG ",aro_C,APO}, |
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{"PRO"," CD ",aro_C,APO}, {"PRO"," X ",r_unk,UNK}, |
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{"SER"," C ",car_C,POL}, {"SER"," O ",car_O,POL}, {"SER"," CA ",ali_C,APO}, |
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{"SER"," N ",ami_N,POL}, {"SER"," CB ",ali_C,APO}, {"SER"," OG ",hyd_O,POL}, |
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{"SER"," X ",r_unk,UNK}, |
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{"THR"," C ",car_C,POL}, {"THR"," O ",car_O,POL}, {"THR"," CA ",ali_C,APO}, |
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{"THR"," N ",ami_N,POL}, {"THR"," CB ",ali_C,APO}, {"THR"," OG1",hyd_O,POL}, |
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{"THR"," CG2",ali_C,APO}, {"THR"," X ",r_unk,UNK}, |
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{"TRP"," C ",car_C,POL}, {"TRP"," O ",car_O,POL}, {"TRP"," CA ",ali_C,APO}, |
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{"TRP"," N ",ami_N,POL}, {"TRP"," CB ",ali_C,APO}, {"TRP"," CG ",aro_C,APO}, |
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{"TRP"," CD1",aro_C,APO}, {"TRP"," CD2",aro_C,APO}, {"TRP"," NE1",ami_N,POL}, |
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{"TRP"," CE2",aro_C,APO}, {"TRP"," CE3",aro_C,APO}, {"TRP"," CZ2",aro_C,APO}, |
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{"TRP"," CZ3",aro_C,APO}, {"TRP"," CH2",aro_C,APO}, {"TRP"," X ",r_unk,UNK}, |
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{"TYR"," C ",car_C,POL}, {"TYR"," O ",car_O,POL}, {"TYR"," CA ",ali_C,APO}, |
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{"TYR"," N ",ami_N,POL}, {"TYR"," CB ",ali_C,APO}, {"TYR"," CG ",aro_C,APO}, |
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{"TYR"," CD1",aro_C,APO}, {"TYR"," CD2",aro_C,APO}, {"TYR"," CE1",aro_C,APO}, |
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{"TYR"," CE2",aro_C,APO}, {"TYR"," CZ ",aro_C,APO}, {"TYR"," OH ",hyd_O,POL}, |
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{"TYR"," X ",r_unk,UNK}, |
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{"VAL"," C ",car_C,POL}, {"VAL"," O ",car_O,POL}, {"VAL"," CA ",ali_C,APO}, |
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{"VAL"," N ",ami_N,POL}, {"VAL"," CB ",ali_C,APO}, {"VAL"," CG1",ali_C,APO}, |
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{"VAL"," CG2",ali_C,APO}, {"VAL"," X ",r_unk,UNK}, |
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{"ASX"," C ",car_C,POL}, {"ASX"," O ",car_O,POL}, {"ASX"," CA ",ali_C,APO}, |
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{"ASX"," N ",ami_N,POL}, {"ASX"," CB ",ali_C,APO}, {"ASX"," CG ",car_C,POL}, |
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{"ASX"," XD1",unk_P,POL}, {"ASX"," XD2",unk_P,POL}, {"ASX"," AD1",unk_P,POL}, |
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{"ASX"," AD2",unk_P,POL}, {"ASX"," Y ",r_unk,UNK}, |
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{"GLX"," C ",car_C,POL}, {"GLX"," O ",car_O,POL}, {"GLX"," CA ",ali_C,APO}, |
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{"GLX"," N ",ami_N,POL}, {"GLX"," CB ",ali_C,APO}, {"GLX"," CG ",ali_C,APO}, |
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{"GLX"," CD ",car_C,POL}, {"GLX"," XE1",unk_P,POL}, {"GLX"," XE2",unk_P,POL}, |
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{"GLX"," AE1",unk_P,POL}, {"GLX"," AE2",unk_P,POL}, {"GLX"," Y ",r_unk,UNK}, |
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{"CSE"," C ",car_C,POL}, {"CSE"," O ",car_O,POL}, {"CSE"," CA ",ali_C,APO}, |
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{"CSE"," N ",ami_N,POL}, {"CSE"," CB ",ali_C,APO}, {"CSE","SE ",sele,POL}, |
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{"CSE"," X ",r_unk,UNK}, |
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{"SEC"," C ",car_C,POL}, {"SEC"," O ",car_O,POL}, {"SEC"," CA ",ali_C,APO}, |
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{"SEC"," N ",ami_N,POL}, {"SEC"," CB ",ali_C,APO}, {"SEC","SE ",sele,POL}, |
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{"SEC"," X ",r_unk,UNK}, |
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{"PYL"," C ",car_C,POL}, {"PYL"," O ",car_O,POL}, {"PYL"," CA ",ali_C,APO}, |
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{"PYL"," N ",ami_N,POL}, {"PYL"," CB ",ali_C,APO}, {"PYL"," CG ",ali_C,APO}, |
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{"PYL"," CG ",ali_C,APO}, {"PYL"," CD ",ali_C,APO}, {"PYL"," CE ",ali_C,APO}, |
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{"PYL"," NZ ",ami_N,POL}, {"PYL"," O2 ",car_O,POL}, {"PYL"," C2 ",car_C,POL}, |
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{"PYL"," CA2",aro_C,APO}, {"PYL"," CB2",ali_C,APO}, {"PYL"," CG2",aro_C,APO}, |
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{"PYL"," CD2",aro_C,APO}, {"PYL"," CE2",aro_C,APO}, {"PYL"," N2 ",ami_N,POL}, |
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{"ACE"," C ",car_C,POL}, {"ACE"," O ",car_O,POL}, {"ACE"," CH3",ali_C,APO}, |
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{"NH2"," NH2",ami_N,POL}, |
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{" A"," P ",phos, POL}, {" A"," OP1",car_O,POL}, {" A"," OP2",car_O,POL}, |
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{" A"," OP3",car_O,POL}, {" A"," O5'",car_O,POL}, {" A"," C5'",ali_C,APO}, |
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{" A"," C4'",aro_C,APO}, {" A"," O4'",car_O,POL}, {" A"," C3'",aro_C,APO}, |
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{" A"," O3'",car_O,POL}, {" A"," C2'",aro_C,APO}, {" A"," O2'",car_O,POL}, |
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{" A"," C1'",aro_C,APO}, {" A"," N9 ",ami_N,POL}, {" A"," C8 ",aro_C,APO}, |
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{" A"," N7 ",ami_N,POL}, {" A"," C5 ",aro_C,APO}, {" A"," C6 ",aro_C,APO}, |
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{" A"," N6 ",ami_N,POL}, {" A"," N1 ",ami_N,POL}, {" A"," C2 ",aro_C,APO}, |
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{" A"," N3 ",ami_N,POL}, {" A"," C4 ",aro_C,APO}, |
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{" C"," P ",phos, POL}, {" C"," OP1",car_O,POL}, {" C"," OP2",car_O,POL}, |
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{" C"," OP3",car_O,POL}, {" C"," O5'",car_O,POL}, {" C"," C5'",ali_C,APO}, |
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{" C"," C4'",aro_C,APO}, {" C"," O4'",car_O,POL}, {" C"," C3'",aro_C,APO}, |
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{" C"," O3'",car_O,POL}, {" C"," C2'",aro_C,APO}, {" C"," O2'",car_O,POL}, |
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{" C"," C1'",aro_C,APO}, {" C"," N1 ",ami_N,POL}, {" C"," C2 ",aro_C,APO}, |
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{" C"," O2 ",car_O,POL}, {" C"," N3 ",ami_N,POL}, {" C"," C4 ",aro_C,APO}, |
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{" C"," N4 ",ami_N,POL}, {" C"," C5 ",aro_C,APO}, {" C"," C6 ",aro_C,APO}, |
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{" G"," P ",phos, POL}, {" G"," OP1",car_O,POL}, {" G"," OP2",car_O,POL}, |
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{" G"," OP3",car_O,POL}, {" G"," O5'",car_O,POL}, {" G"," C5'",ali_C,APO}, |
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{" G"," C4'",aro_C,APO}, {" G"," O4'",car_O,POL}, {" G"," C3'",aro_C,APO}, |
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{" G"," O3'",car_O,POL}, {" G"," C2'",aro_C,APO}, {" G"," O2'",car_O,POL}, |
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{" G"," C1'",aro_C,APO}, {" G"," N9 ",ami_N,POL}, {" G"," C8 ",aro_C,APO}, |
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{" G"," N7 ",ami_N,POL}, {" G"," C5 ",aro_C,APO}, {" G"," C6 ",aro_C,APO}, |
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{" G"," O6 ",car_O,POL}, {" G"," N1 ",ami_N,POL}, {" G"," C2 ",aro_C,APO}, |
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{" G"," N3 ",ami_N,POL}, {" G"," C4 ",aro_C,APO}, |
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{" T"," P ",phos, POL}, {" T"," OP1",car_O,POL}, {" T"," OP2",car_O,POL}, |
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{" T"," OP3",car_O,POL}, {" T"," O5'",car_O,POL}, {" T"," C5'",ali_C,APO}, |
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{" T"," C4'",aro_C,APO}, {" T"," O4'",car_O,POL}, {" T"," C3'",aro_C,APO}, |
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{" T"," O3'",car_O,POL}, {" T"," C2'",aro_C,APO}, {" T"," O2'",car_O,POL}, |
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{" T"," C1'",aro_C,APO}, {" T"," N1 ",ami_N,POL}, {" T"," C2 ",aro_C,APO}, |
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{" T"," O2 ",car_O,POL}, {" T"," N3 ",ami_N,POL}, {" T"," C4 ",aro_C,APO}, |
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{" T"," O4 ",car_O,POL}, {" T"," C5 ",aro_C,APO}, {" T"," C6 ",aro_C,APO}, |
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{" T"," C7 ",aro_C,APO}, |
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{" U"," P ",phos, POL}, {" U"," OP1",car_O,POL}, {" U"," OP2",car_O,POL}, |
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{" U"," OP3",car_O,POL}, {" U"," O5'",car_O,POL}, {" U"," C5'",ali_C,APO}, |
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{" U"," C4'",aro_C,APO}, {" U"," O4'",car_O,POL}, {" U"," C3'",aro_C,APO}, |
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{" U"," O3'",car_O,POL}, {" U"," C2'",aro_C,APO}, {" U"," O2'",car_O,POL}, |
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{" U"," C1'",aro_C,APO}, {" U"," N1 ",ami_N,POL}, {" U"," C2 ",aro_C,APO}, |
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{" U"," O2 ",car_O,POL}, {" U"," N3 ",ami_N,POL}, {" U"," C4 ",aro_C,APO}, |
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{" U"," O4 ",car_O,POL}, {" U"," C5 ",aro_C,APO}, {" U"," C6 ",aro_C,APO}, |
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{" I"," P ",phos, POL}, {" I"," OP1",car_O,POL}, {" I"," OP2",car_O,POL}, |
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{" I"," OP3",car_O,POL}, {" I"," O5'",car_O,POL}, {" I"," C5'",ali_C,APO}, |
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{" I"," C4'",aro_C,APO}, {" I"," O4'",car_O,POL}, {" I"," C3'",aro_C,APO}, |
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{" I"," O3'",car_O,POL}, {" I"," C2'",aro_C,APO}, {" I"," O2'",car_O,POL}, |
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{" I"," C1'",aro_C,APO}, {" I"," N9 ",ami_N,POL}, {" I"," C8 ",aro_C,APO}, |
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{" I"," N7 ",ami_N,POL}, {" I"," C5 ",aro_C,APO}, {" I"," C6 ",aro_C,APO}, |
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{" I"," N6 ",ami_N,POL}, {" I"," N1 ",ami_N,POL}, {" I"," C2 ",aro_C,APO}, |
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{" I"," N3 ",ami_N,POL}, {" I"," C4 ",aro_C,APO}, |
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{" DA"," P ",phos, POL}, {" DA"," OP1",car_O,POL}, {" DA"," OP2",car_O,POL}, |
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{" DA"," OP3",car_O,POL}, {" DA"," O5'",car_O,POL}, {" DA"," C5'",ali_C,APO}, |
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{" DA"," C4'",aro_C,APO}, {" DA"," O4'",car_O,POL}, {" DA"," C3'",aro_C,APO}, |
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{" DA"," O3'",car_O,POL}, {" DA"," C2'",aro_C,APO}, |
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{" DA"," C1'",aro_C,APO}, {" DA"," N9 ",ami_N,POL}, {" DA"," C8 ",aro_C,APO}, |
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{" DA"," N7 ",ami_N,POL}, {" DA"," C5 ",aro_C,APO}, {" DA"," C6 ",aro_C,APO}, |
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{" DA"," N6 ",ami_N,POL}, {" DA"," N1 ",ami_N,POL}, {" DA"," C2 ",aro_C,APO}, |
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{" DA"," N3 ",ami_N,POL}, {" DA"," C4 ",aro_C,APO}, |
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{" DC"," P ",phos, POL}, {" DC"," OP1",car_O,POL}, {" DC"," OP2",car_O,POL}, |
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{" DC"," OP3",car_O,POL}, {" DC"," O5'",car_O,POL}, {" DC"," C5'",ali_C,APO}, |
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{" DC"," C4'",aro_C,APO}, {" DC"," O4'",car_O,POL}, {" DC"," C3'",aro_C,APO}, |
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{" DC"," O3'",car_O,POL}, {" DC"," C2'",aro_C,APO}, |
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{" DC"," C1'",aro_C,APO}, {" DC"," N1 ",ami_N,POL}, {" DC"," C2 ",aro_C,APO}, |
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{" DC"," O2 ",car_O,POL}, {" DC"," N3 ",ami_N,POL}, {" DC"," C4 ",aro_C,APO}, |
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{" DC"," N4 ",ami_N,POL}, {" DC"," C5 ",aro_C,APO}, {" DC"," C6 ",aro_C,APO}, |
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{" DG"," P ",phos, POL}, {" DG"," OP1",car_O,POL}, {" DG"," OP2",car_O,POL}, |
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{" DG"," OP3",car_O,POL}, {" DG"," O5'",car_O,POL}, {" DG"," C5'",ali_C,APO}, |
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{" DG"," C4'",aro_C,APO}, {" DG"," O4'",car_O,POL}, {" DG"," C3'",aro_C,APO}, |
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{" DG"," O3'",car_O,POL}, {" DG"," C2'",aro_C,APO}, |
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{" DG"," C1'",aro_C,APO}, {" DG"," N9 ",ami_N,POL}, {" DG"," C8 ",aro_C,APO}, |
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{" DG"," N7 ",ami_N,POL}, {" DG"," C5 ",aro_C,APO}, {" DG"," C6 ",aro_C,APO}, |
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{" DG"," O6 ",car_O,POL}, {" DG"," N1 ",ami_N,POL}, {" DG"," C2 ",aro_C,APO}, |
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{" DG"," N3 ",ami_N,POL}, {" DG"," C4 ",aro_C,APO}, |
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{" DT"," P ",phos, POL}, {" DT"," OP1",car_O,POL}, {" DT"," OP2",car_O,POL}, |
|
|
{" DT"," OP3",car_O,POL}, {" DT"," O5'",car_O,POL}, {" DT"," C5'",ali_C,APO}, |
|
|
{" DT"," C4'",aro_C,APO}, {" DT"," O4'",car_O,POL}, {" DT"," C3'",aro_C,APO}, |
|
|
{" DT"," O3'",car_O,POL}, {" DT"," C2'",aro_C,APO}, |
|
|
{" DT"," C1'",aro_C,APO}, {" DT"," N1 ",ami_N,POL}, {" DT"," C2 ",aro_C,APO}, |
|
|
{" DT"," O2 ",car_O,POL}, {" DT"," N3 ",ami_N,POL}, {" DT"," C4 ",aro_C,APO}, |
|
|
{" DT"," O4 ",car_O,POL}, {" DT"," C5 ",aro_C,APO}, {" DT"," C6 ",aro_C,APO}, |
|
|
{" DT"," C7 ",aro_C,APO}, |
|
|
|
|
|
{" DU"," P ",phos, POL}, {" DU"," OP1",car_O,POL}, {" DU"," OP2",car_O,POL}, |
|
|
{" DU"," OP3",car_O,POL}, {" DU"," O5'",car_O,POL}, {" DU"," C5'",ali_C,APO}, |
|
|
{" DU"," C4'",aro_C,APO}, {" DU"," O4'",car_O,POL}, {" DU"," C3'",aro_C,APO}, |
|
|
{" DU"," O3'",car_O,POL}, {" DU"," C2'",aro_C,APO}, |
|
|
{" DU"," C1'",aro_C,APO}, {" DU"," N1 ",ami_N,POL}, {" DU"," C2 ",aro_C,APO}, |
|
|
{" DU"," O2 ",car_O,POL}, {" DU"," N3 ",ami_N,POL}, {" DU"," C4 ",aro_C,APO}, |
|
|
{" DU"," O4 ",car_O,POL}, {" DU"," C5 ",aro_C,APO}, {" DU"," C6 ",aro_C,APO}, |
|
|
|
|
|
{" DI"," P ",phos, POL}, {" DI"," OP1",car_O,POL}, {" DI"," OP2",car_O,POL}, |
|
|
{" DI"," OP3",car_O,POL}, {" DI"," O5'",car_O,POL}, {" DI"," C5'",ali_C,APO}, |
|
|
{" DI"," C4'",aro_C,APO}, {" DI"," O4'",car_O,POL}, {" DI"," C3'",aro_C,APO}, |
|
|
{" DI"," O3'",car_O,POL}, {" DI"," C2'",aro_C,APO}, |
|
|
{" DI"," C1'",aro_C,APO}, {" DI"," N9 ",ami_N,POL}, {" DI"," C8 ",aro_C,APO}, |
|
|
{" DI"," N7 ",ami_N,POL}, {" DI"," C5 ",aro_C,APO}, {" DI"," C6 ",aro_C,APO}, |
|
|
{" DI"," N6 ",ami_N,POL}, {" DI"," N1 ",ami_N,POL}, {" DI"," C2 ",aro_C,APO}, |
|
|
{" DI"," N3 ",ami_N,POL}, {" DI"," C4 ",aro_C,APO}, |
|
|
}; |
|
|
|
|
|
const int n_atom_types = sizeof(atoms)/sizeof(struct atom); |
|
|
|
|
|
static const freesasa_classifier *oons_c = &freesasa_oons_classifier; |
|
|
|
|
|
|
|
|
START_TEST (test_radius) |
|
|
{ |
|
|
char buf[50]; |
|
|
freesasa_set_verbosity(FREESASA_V_SILENT); |
|
|
for (int i = 0; i < n_atom_types; ++i) { |
|
|
const struct atom a = atoms[i]; |
|
|
double r1 = freesasa_classifier_radius(oons_c, a.a, a.b); |
|
|
ck_assert(float_eq(r1, a.radius, 1e-10)); |
|
|
} |
|
|
ck_assert(float_eq(freesasa_guess_radius(" H"), 1.10, 1e-10)); |
|
|
freesasa_set_verbosity(FREESASA_V_NORMAL); |
|
|
} |
|
|
END_TEST |
|
|
|
|
|
START_TEST (test_class) |
|
|
{ |
|
|
char buf[50]; |
|
|
for (int i = 0; i < n_atom_types; ++i) { |
|
|
const struct atom a = atoms[i]; |
|
|
int c = freesasa_classifier_class(oons_c, a.a, a.b); |
|
|
if (c == FREESASA_WARN) { ck_assert(a.class == UNK); continue; } |
|
|
sprintf(buf,"Classification error for %s %s %s %s", |
|
|
a.a, a.b, freesasa_classifier_class2str(c), |
|
|
freesasa_classifier_class2str(a.class)); |
|
|
ck_assert_msg(c == a.class, buf); |
|
|
} |
|
|
freesasa_set_verbosity(FREESASA_V_SILENT); |
|
|
ck_assert(freesasa_classifier_class(oons_c, "ABC", " X ") == FREESASA_ATOM_UNKNOWN); |
|
|
|
|
|
ck_assert(freesasa_classifier_class2str(100) == NULL); |
|
|
ck_assert(freesasa_classifier_class2str(-1) == NULL); |
|
|
ck_assert_str_eq(freesasa_classifier_class2str(FREESASA_ATOM_APOLAR), "Apolar"); |
|
|
ck_assert_str_eq(freesasa_classifier_class2str(FREESASA_ATOM_POLAR), "Polar"); |
|
|
ck_assert_str_eq(freesasa_classifier_class2str(FREESASA_ATOM_UNKNOWN), "Unknown"); |
|
|
freesasa_set_verbosity(FREESASA_V_NORMAL); |
|
|
} |
|
|
END_TEST |
|
|
|
|
|
|
|
|
START_TEST (test_residue) |
|
|
{ |
|
|
|
|
|
int nrt = freesasa_classify_n_residue_types(); |
|
|
for (int i = 0; i < nrt; ++i) { |
|
|
const char *res = freesasa_classify_residue_name(i); |
|
|
ck_assert_int_eq(freesasa_classify_residue(res),i); |
|
|
} |
|
|
|
|
|
|
|
|
for (int i = 0; i < naa; ++i) { |
|
|
ck_assert_int_lt(freesasa_classify_residue(aa[i]), naa); |
|
|
} |
|
|
|
|
|
ck_assert_int_ge(freesasa_classify_residue("UNK"), naa); |
|
|
ck_assert_int_ge(freesasa_classify_residue("XXX"), naa); |
|
|
|
|
|
for (int i = 0; i < n_other; ++i) { |
|
|
ck_assert_int_ge(freesasa_classify_residue(other_aa[i]), naa); |
|
|
} |
|
|
for (int i = 0; i < n_capping; ++i) { |
|
|
ck_assert_int_ge(freesasa_classify_residue(capping[i]), naa); |
|
|
} |
|
|
for (int i = 0; i < n_nuc; ++i) { |
|
|
ck_assert_int_ge(freesasa_classify_residue(nuc[i]), naa); |
|
|
} |
|
|
} |
|
|
END_TEST |
|
|
|
|
|
START_TEST (test_user) |
|
|
{ |
|
|
FILE *clf = fopen(SHAREDIR "oons.config", "r"); |
|
|
ck_assert(clf != NULL); |
|
|
|
|
|
freesasa_classifier* c = freesasa_classifier_from_file(clf); |
|
|
ck_assert(c != NULL); |
|
|
ck_assert(freesasa_classifier_class(c, "ALA", "CA") == FREESASA_ATOM_APOLAR); |
|
|
ck_assert(freesasa_classifier_class(c, "ALA", "O") == FREESASA_ATOM_POLAR); |
|
|
ck_assert(float_eq(freesasa_classifier_radius(c, "ALA","CA"), 2.0, 1e-5)); |
|
|
ck_assert(float_eq(freesasa_classifier_radius(c, "ALA","N"), 1.55, 1e-5)); |
|
|
|
|
|
for (int i = 0; i < 188; ++i) { |
|
|
const char *res_name = atoms[i].a, *atom_name = atoms[i].b; |
|
|
if (strcmp(atom_name," X ") == 0) continue; |
|
|
if (strcmp(atom_name," Y ") == 0) continue; |
|
|
ck_assert(float_eq(freesasa_classifier_radius(c, res_name, atom_name), |
|
|
freesasa_classifier_radius(oons_c, res_name, atom_name), 1e-5)); |
|
|
ck_assert(freesasa_classifier_class(c, res_name, atom_name) == |
|
|
freesasa_classifier_class(oons_c, res_name, atom_name)); |
|
|
} |
|
|
freesasa_set_verbosity(FREESASA_V_SILENT); |
|
|
ck_assert(freesasa_classifier_radius(c, "ALA", "X") < 0); |
|
|
ck_assert(freesasa_classifier_radius(c, "X", "CB") > 0); |
|
|
ck_assert(freesasa_classifier_radius(c, "X", "X") < 0); |
|
|
ck_assert(freesasa_classifier_class(c, "ALA", "X") == FREESASA_ATOM_UNKNOWN); |
|
|
ck_assert(freesasa_classifier_class(c, "X", "CB") == FREESASA_ATOM_APOLAR); |
|
|
ck_assert(freesasa_classifier_class(c, "X", "X") == FREESASA_ATOM_UNKNOWN); |
|
|
freesasa_classifier_free(c); |
|
|
|
|
|
FILE *f = fopen(DATADIR "empty.pdb", "r"); |
|
|
c = freesasa_classifier_from_file(f); |
|
|
ck_assert(c==NULL); |
|
|
fclose(f); |
|
|
freesasa_classifier_free(c); |
|
|
|
|
|
f = fopen(DATADIR "err.config", "r"); |
|
|
c = freesasa_classifier_from_file(f); |
|
|
ck_assert(c==NULL); |
|
|
fclose(f); |
|
|
freesasa_classifier_free(c); |
|
|
freesasa_set_verbosity(FREESASA_V_NORMAL); |
|
|
} |
|
|
END_TEST |
|
|
|
|
|
START_TEST (test_backbone) |
|
|
{ |
|
|
ck_assert(freesasa_atom_is_backbone("C")); |
|
|
ck_assert(freesasa_atom_is_backbone(" C ")); |
|
|
ck_assert(freesasa_atom_is_backbone(" CA ")); |
|
|
ck_assert(freesasa_atom_is_backbone(" CA ")); |
|
|
ck_assert(freesasa_atom_is_backbone("CA")); |
|
|
ck_assert(freesasa_atom_is_backbone("N")); |
|
|
ck_assert(freesasa_atom_is_backbone("O")); |
|
|
ck_assert(freesasa_atom_is_backbone("OXT")); |
|
|
ck_assert(freesasa_atom_is_backbone("P")); |
|
|
ck_assert(freesasa_atom_is_backbone("OP1")); |
|
|
ck_assert(freesasa_atom_is_backbone("OP2")); |
|
|
ck_assert(freesasa_atom_is_backbone("O5'")); |
|
|
ck_assert(freesasa_atom_is_backbone("C5'")); |
|
|
ck_assert(freesasa_atom_is_backbone("C4'")); |
|
|
ck_assert(freesasa_atom_is_backbone("O4'")); |
|
|
ck_assert(freesasa_atom_is_backbone("C3'")); |
|
|
ck_assert(freesasa_atom_is_backbone("O3'")); |
|
|
ck_assert(freesasa_atom_is_backbone("C2'")); |
|
|
ck_assert(freesasa_atom_is_backbone("C1'")); |
|
|
ck_assert(freesasa_atom_is_backbone("") == 0); |
|
|
ck_assert(freesasa_atom_is_backbone("X") == 0); |
|
|
} |
|
|
END_TEST |
|
|
|
|
|
START_TEST (test_memerr) |
|
|
{ |
|
|
freesasa_set_verbosity(FREESASA_V_SILENT); |
|
|
set_fail_after(1); |
|
|
void *ptr[] = {freesasa_classifier_types_new(), |
|
|
freesasa_classifier_residue_new("ALA"), |
|
|
freesasa_classifier_new()}; |
|
|
set_fail_after(0); |
|
|
|
|
|
for (int i = 0; i < sizeof(ptr)/sizeof(void*); ++i) { |
|
|
ck_assert_ptr_eq(ptr[i], NULL); |
|
|
} |
|
|
|
|
|
for (int i = 1; i < 4; ++i) { |
|
|
struct classifier_types *types = freesasa_classifier_types_new(); |
|
|
struct classifier_residue *res = freesasa_classifier_residue_new("ALA"); |
|
|
struct freesasa_classifier *clf = freesasa_classifier_new(); |
|
|
int ret; |
|
|
|
|
|
if (i < 2) { |
|
|
set_fail_after(i); |
|
|
ret = freesasa_classifier_add_type(types,"a","A",1.0); |
|
|
set_fail_after(0); |
|
|
ck_assert_int_eq(ret, FREESASA_FAIL); |
|
|
} |
|
|
set_fail_after(i); |
|
|
ret = freesasa_classifier_add_atom(res,"A",1.0,0); |
|
|
set_fail_after(0); |
|
|
ck_assert_int_eq(ret, FREESASA_FAIL); |
|
|
|
|
|
set_fail_after(i); |
|
|
ret = freesasa_classifier_add_residue(clf,"A"); |
|
|
set_fail_after(0); |
|
|
ck_assert_int_eq(ret, FREESASA_FAIL); |
|
|
|
|
|
freesasa_classifier_types_free(types); |
|
|
freesasa_classifier_residue_free(res); |
|
|
freesasa_classifier_free(clf); |
|
|
} |
|
|
|
|
|
|
|
|
FILE *config = fopen(SHAREDIR "naccess.config","r"); |
|
|
for (int i = 1; i < 200; ++i) { |
|
|
set_fail_after(i); |
|
|
void *ptr = freesasa_classifier_from_file(config); |
|
|
set_fail_after(0); |
|
|
ck_assert_ptr_eq(ptr,NULL); |
|
|
rewind(config); |
|
|
} |
|
|
fclose(config); |
|
|
freesasa_set_verbosity(FREESASA_V_NORMAL); |
|
|
} |
|
|
END_TEST |
|
|
|
|
|
extern TCase * test_classifier_static(); |
|
|
|
|
|
Suite* classifier_suite() |
|
|
{ |
|
|
Suite *s = suite_create("Classify"); |
|
|
TCase *tc_core = tcase_create("Core"); |
|
|
tcase_add_test(tc_core,test_radius); |
|
|
tcase_add_test(tc_core,test_class); |
|
|
tcase_add_test(tc_core,test_residue); |
|
|
tcase_add_test(tc_core,test_user); |
|
|
tcase_add_test(tc_core,test_backbone); |
|
|
tcase_add_test(tc_core,test_memerr); |
|
|
|
|
|
TCase *tc_static = test_classifier_static(); |
|
|
|
|
|
suite_add_tcase(s,tc_core); |
|
|
suite_add_tcase(s,tc_static); |
|
|
|
|
|
return s; |
|
|
} |
|
|
|
