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Include iCode field in residue numbers. making them one character lon…
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…ger.
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@mittinatten
mittinatten committed Oct 14, 2017
1 parent 87ce31d commit cc480b3
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Showing 9 changed files with 86 additions and 88 deletions.
4 changes: 1 addition & 3 deletions bindings/python/test.py
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Expand Up @@ -96,7 +96,7 @@ def testStructure(self):
self.assertTrue(s.chainLabel(1) == 'A')
self.assertTrue(s.atomName(1) == ' CA ')
self.assertTrue(s.residueName(1) == 'MET')
self.assertTrue(s.residueNumber(1) == ' 1')
self.assertTrue(s.residueNumber(1) == ' 1 ')

s2 = Structure("data/1ubq.pdb",Classifier("share/oons.config"))
self.assertTrue(s.nAtoms() == 602)
Expand Down Expand Up @@ -298,7 +298,6 @@ def testBioPDB(self):
# coordinates (due to rounding errors) we set the
# tolerance as high as 1e-3
result = calc(s1, Parameters({'algorithm' : LeeRichards, 'n-slices' : 20}))
print(result.totalArea())
self.assertTrue(math.fabs(result.totalArea() - 4804.055641) < 1e-3)
sasa_classes = classifyResults(result, s1)
self.assertTrue(math.fabs(sasa_classes['Polar'] - 2504.217302) < 1e-3)
Expand All @@ -308,7 +307,6 @@ def testBioPDB(self):
self.assertTrue(math.fabs(result.totalArea() - 4834.716265) < 1e-3)
self.assertTrue(math.fabs(sasa_classes['Polar'] - 2515.821238) < 1e-3)
self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2318.895027) < 1e-3)
print(result.totalArea())


if __name__ == '__main__':
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2 changes: 1 addition & 1 deletion src/pdb.c
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Expand Up @@ -315,7 +315,7 @@ write_pdb_impl(FILE *output,
// Write TER and ENDMDL lines
strncpy(buf2, &buf[6], 5);
buf2[5]='\0';
fprintf(output,"TER %5d %4s %c%4s\nENDMDL\n",
fprintf(output,"TER %5d %4s %c%5s\nENDMDL\n",
atoi(buf2)+1, last_res_name, last_chain[0], last_res_number);

fflush(output);
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2 changes: 1 addition & 1 deletion src/pdb.h
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Expand Up @@ -17,7 +17,7 @@

#define PDB_ATOM_NAME_STRL 4 //!< Length of strings with atom names, such as `" CA "`.
#define PDB_ATOM_RES_NAME_STRL 3 //!< Length of string with residue names, such as `"ALA"`.
#define PDB_ATOM_RES_NUMBER_STRL 4 //!< Length of string with residue number, such as `" 123"`.
#define PDB_ATOM_RES_NUMBER_STRL 5 //!< Length of string with residue number, such as `" 123"`.
#define PDB_ATOM_SYMBOL_STRL 2 //!< Length for string with element symbol, such "FE"
#define PDB_LINE_STRL 80 //!< Length of a line in PDB file.
#define PDB_MAX_LINE_STRL 120 //!< for reading, allows nonstandard input with extra fields
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2 changes: 1 addition & 1 deletion src/rsa.c
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Expand Up @@ -87,7 +87,7 @@ rsa_print_residue(FILE *output,
resi_str = freesasa_node_residue_number(residue);
chain = freesasa_node_name(freesasa_node_parent(residue))[0];

fprintf(output, "RES %s %c%s ", abs->name, chain, resi_str);
fprintf(output, "RES %s %c%s ", abs->name, chain, resi_str);
if (rel->name != NULL) {
rsa_print_abs_rel(output, abs->total, rel->total);
rsa_print_abs_rel(output, abs->side_chain, rel->side_chain);
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2 changes: 1 addition & 1 deletion tests/data/1ubq.B.pdb
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Expand Up @@ -601,5 +601,5 @@ ATOM 599 CA GLY A 76 40.373 39.813 33.944 1.88 39.21
ATOM 600 C GLY A 76 40.031 39.992 35.432 1.61 5.69
ATOM 601 O GLY A 76 38.933 40.525 35.687 1.42 44.97
ATOM 602 OXT GLY A 76 40.862 39.575 36.251 1.46 44.20
TER 603 GLY A 76
TER 603 GLY A 76
ENDMDL
2 changes: 1 addition & 1 deletion tests/data/reference_bfactors.pdb
View file
Expand Up @@ -601,5 +601,5 @@ ATOM 599 CA GLY A 76 40.373 39.813 33.944 1.23 1.23
ATOM 600 C GLY A 76 40.031 39.992 35.432 1.23 1.23
ATOM 601 O GLY A 76 38.933 40.525 35.687 1.23 1.23
ATOM 602 OXT GLY A 76 40.862 39.575 36.251 1.23 1.23
TER 603 GLY A 76
TER 603 GLY A 76
ENDMDL
152 changes: 76 additions & 76 deletions tests/data/seq.reference
View file
@@ -1,78 +1,78 @@
# Residues in stdin
SEQ A 1 MET : 50.77
SEQ A 2 GLN : 77.34
SEQ A 3 ILE : 0.00
SEQ A 4 PHE : 56.45
SEQ A 5 VAL : 0.00
SEQ A 6 LYS : 98.42
SEQ A 7 THR : 23.60
SEQ A 8 LEU : 139.46
SEQ A 9 THR : 129.58
SEQ A 10 GLY : 67.39
SEQ A 11 LYS : 107.45
SEQ A 12 THR : 61.25
SEQ A 13 ILE : 2.70
SEQ A 14 THR : 61.41
SEQ A 15 LEU : 6.76
SEQ A 16 GLU : 140.39
SEQ A 17 VAL : 4.06
SEQ A 18 GLU : 102.53
SEQ A 19 PRO : 58.13
SEQ A 20 SER : 81.70
SEQ A 21 ASP : 32.83
SEQ A 22 THR : 47.89
SEQ A 23 ILE : 0.00
SEQ A 24 GLU : 119.57
SEQ A 25 ASN : 52.26
SEQ A 26 VAL : 0.00
SEQ A 27 LYS : 15.48
SEQ A 28 ALA : 44.91
SEQ A 29 LYS : 65.96
SEQ A 30 ILE : 0.00
SEQ A 31 GLN : 75.29
SEQ A 32 ASP : 129.20
SEQ A 33 LYS : 113.76
SEQ A 34 GLU : 66.80
SEQ A 35 GLY : 50.49
SEQ A 36 ILE : 28.39
SEQ A 37 PRO : 55.43
SEQ A 38 PRO : 49.32
SEQ A 39 ASP : 84.10
SEQ A 40 GLN : 39.95
SEQ A 41 GLN : 0.00
SEQ A 42 ARG : 90.69
SEQ A 43 LEU : 1.16
SEQ A 44 ILE : 31.09
SEQ A 45 PHE : 36.39
SEQ A 46 ALA : 73.44
SEQ A 47 GLY : 73.20
SEQ A 48 LYS : 101.09
SEQ A 49 GLN : 102.09
SEQ A 50 LEU : 5.00
SEQ A 51 GLU : 115.03
SEQ A 52 ASP : 61.18
SEQ A 53 GLY : 40.35
SEQ A 54 ARG : 122.25
SEQ A 55 THR : 30.77
SEQ A 56 LEU : 0.00
SEQ A 57 SER : 64.67
SEQ A 58 ASP : 87.83
SEQ A 59 TYR : 35.63
SEQ A 60 ASN : 113.50
SEQ A 61 ILE : 5.00
SEQ A 62 GLN : 123.98
SEQ A 63 LYS : 137.12
SEQ A 64 GLU : 99.99
SEQ A 65 SER : 21.74
SEQ A 66 THR : 55.29
SEQ A 67 LEU : 0.00
SEQ A 68 HIS : 77.90
SEQ A 69 LEU : 3.70
SEQ A 70 VAL : 37.85
SEQ A 71 LEU : 74.87
SEQ A 72 ARG : 119.71
SEQ A 73 LEU : 120.89
SEQ A 74 ARG : 213.93
SEQ A 75 GLY : 74.19
SEQ A 76 GLY : 142.20
SEQ A 1 MET : 50.77
SEQ A 2 GLN : 77.34
SEQ A 3 ILE : 0.00
SEQ A 4 PHE : 56.45
SEQ A 5 VAL : 0.00
SEQ A 6 LYS : 98.42
SEQ A 7 THR : 23.60
SEQ A 8 LEU : 139.46
SEQ A 9 THR : 129.58
SEQ A 10 GLY : 67.39
SEQ A 11 LYS : 107.45
SEQ A 12 THR : 61.25
SEQ A 13 ILE : 2.70
SEQ A 14 THR : 61.41
SEQ A 15 LEU : 6.76
SEQ A 16 GLU : 140.39
SEQ A 17 VAL : 4.06
SEQ A 18 GLU : 102.53
SEQ A 19 PRO : 58.13
SEQ A 20 SER : 81.70
SEQ A 21 ASP : 32.83
SEQ A 22 THR : 47.89
SEQ A 23 ILE : 0.00
SEQ A 24 GLU : 119.57
SEQ A 25 ASN : 52.26
SEQ A 26 VAL : 0.00
SEQ A 27 LYS : 15.48
SEQ A 28 ALA : 44.91
SEQ A 29 LYS : 65.96
SEQ A 30 ILE : 0.00
SEQ A 31 GLN : 75.29
SEQ A 32 ASP : 129.20
SEQ A 33 LYS : 113.76
SEQ A 34 GLU : 66.80
SEQ A 35 GLY : 50.49
SEQ A 36 ILE : 28.39
SEQ A 37 PRO : 55.43
SEQ A 38 PRO : 49.32
SEQ A 39 ASP : 84.10
SEQ A 40 GLN : 39.95
SEQ A 41 GLN : 0.00
SEQ A 42 ARG : 90.69
SEQ A 43 LEU : 1.16
SEQ A 44 ILE : 31.09
SEQ A 45 PHE : 36.39
SEQ A 46 ALA : 73.44
SEQ A 47 GLY : 73.20
SEQ A 48 LYS : 101.09
SEQ A 49 GLN : 102.09
SEQ A 50 LEU : 5.00
SEQ A 51 GLU : 115.03
SEQ A 52 ASP : 61.18
SEQ A 53 GLY : 40.35
SEQ A 54 ARG : 122.25
SEQ A 55 THR : 30.77
SEQ A 56 LEU : 0.00
SEQ A 57 SER : 64.67
SEQ A 58 ASP : 87.83
SEQ A 59 TYR : 35.63
SEQ A 60 ASN : 113.50
SEQ A 61 ILE : 5.00
SEQ A 62 GLN : 123.98
SEQ A 63 LYS : 137.12
SEQ A 64 GLU : 99.99
SEQ A 65 SER : 21.74
SEQ A 66 THR : 55.29
SEQ A 67 LEU : 0.00
SEQ A 68 HIS : 77.90
SEQ A 69 LEU : 3.70
SEQ A 70 VAL : 37.85
SEQ A 71 LEU : 74.87
SEQ A 72 ARG : 119.71
SEQ A 73 LEU : 120.89
SEQ A 74 ARG : 213.93
SEQ A 75 GLY : 74.19
SEQ A 76 GLY : 142.20

6 changes: 3 additions & 3 deletions tests/test_pdb.c
View file
Expand Up @@ -58,11 +58,11 @@ START_TEST (test_pdb_lines)

//Res-number
freesasa_pdb_get_res_number(buf,lines[0]);
ck_assert_str_eq(buf," 74");
ck_assert_str_eq(buf," 74 ");
freesasa_pdb_get_res_number(buf,lines[1]);
ck_assert_str_eq(buf," 72");
ck_assert_str_eq(buf," 72 ");
freesasa_pdb_get_res_number(buf,lines[2]);
ck_assert_str_eq(buf," 83");
ck_assert_str_eq(buf," 83 ");

//coordinates
freesasa_pdb_get_coord(x,lines[0]);
Expand Down
2 changes: 1 addition & 1 deletion tests/test_structure.c
View file
Expand Up @@ -139,7 +139,7 @@ START_TEST (test_structure_1ubq)
// check at random atom to see that parsing was correct
ck_assert_str_eq(freesasa_structure_atom_res_name(s,8),"GLN");
ck_assert_str_eq(freesasa_structure_atom_name(s,8)," N ");
ck_assert_str_eq(freesasa_structure_atom_res_number(s,8)," 2");
ck_assert_str_eq(freesasa_structure_atom_res_number(s,8)," 2 ");
ck_assert_int_eq(freesasa_structure_atom_chain(s,8),'A');
ck_assert_str_eq(freesasa_structure_atom_symbol(s,8)," N");

Expand Down

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