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Merge pull request #2637 from dkoes/segnames
Support for segment names in pdb files
This commit is contained in:
Geoff Hutchison
GitHub
commit
283cc846ac
@ -79,6 +79,8 @@ namespace OpenBabel {
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//! MODRES records for modified residues:
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//! http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_36.html
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void SetName(const std::string &resname);
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//! \brief Set the segment name of this residue (max four characters)
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void SetSegName(const std::string &segname);
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//! Set the residue number (in the sequence)
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void SetNum(const unsigned int resnum);
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void SetNum(const std::string resnum);
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@ -104,6 +106,8 @@ namespace OpenBabel {
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//! \return The residue name
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std::string GetName(void) const;
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//! \return The residue segment name
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std::string GetSegName(void) const;
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//! \return The residue number (in the sequence)
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int GetNum(void);
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std::string GetNumString(void);
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@ -177,6 +181,7 @@ namespace OpenBabel {
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unsigned int _reskey;//!< Residue key ID -- see SetResidueKeys()
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std::string _resnum;//!< Residue number (i.e., in file) 23, 1B, etc.
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std::string _resname;//!<Residue text name
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std::string _segname;//!<Segment text name
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char _insertioncode;//!<PBB insertion code
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std::vector<bool> _hetatm;//!< Is a given atom a HETAM
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@ -514,8 +514,9 @@ namespace OpenBabel
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unsigned int i;
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char buffer[BUFF_SIZE];
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char type_name[10], padded_name[10];
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char the_res[10];
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char type_name[10] = {0,}, padded_name[10] = {0,};
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char the_res[10] = {0,};
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char segname[10] = {0,};
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char the_chain = ' ';
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const char *element_name;
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int res_num;
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@ -688,6 +689,8 @@ namespace OpenBabel
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snprintf(type_name,5,"%s",(char*)res->GetAtomID(atom).c_str());
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the_chain = res->GetChain();
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snprintf(segname,5,"%s", (char*)res->GetSegName().c_str());
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//two char. elements are on position 13 and 14 one char. start at 14
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if (strlen(OBElements::GetSymbol(atom->GetAtomicNum())) == 1)
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{
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@ -724,6 +727,7 @@ namespace OpenBabel
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type_name[4] = '\0';
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res_num = 1;
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the_insertioncode=' ';
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strcpy(segname," ");
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}
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element_name = OBElements::GetSymbol(atom->GetAtomicNum());
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@ -745,7 +749,7 @@ namespace OpenBabel
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occup = occup_fp->GetGenericValue();
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}
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snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d%c %8.3f%8.3f%8.3f%6.2f 0.00 %2s%2s\n",
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snprintf(buffer, BUFF_SIZE, "%s%5d %-4s %-3s %c%4d%c %8.3f%8.3f%8.3f%6.2f 0.00 %4s%2s%2s\n",
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het?"HETATM":"ATOM ",
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i,
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type_name,
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@ -757,6 +761,7 @@ namespace OpenBabel
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atom->GetY(),
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atom->GetZ(),
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occup,
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segname,
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element_name,
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scharge);
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ofs << buffer;
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@ -911,6 +916,15 @@ namespace OpenBabel
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/* insertion code */
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char insertioncode = sbuf.substr(27-6-1,1)[0];
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if (' '==insertioncode) insertioncode=0;
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/* segname */
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string segname;
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if (sbuf.size() > 67) {
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segname = sbuf.substr(66,4);
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if(segname == " ") { //unset should be empty string
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segname = string();
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}
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}
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/* element */
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string element = " ";
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if (sbuf.size() > 71)
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@ -1129,14 +1143,16 @@ namespace OpenBabel
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|| res->GetName() != resname
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|| res->GetNumString() != resnum
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|| res->GetChain() != chain
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|| res->GetInsertionCode() != insertioncode)
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|| res->GetInsertionCode() != insertioncode
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|| res->GetSegName() != segname)
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{
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vector<OBResidue*>::iterator ri;
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for (res = mol.BeginResidue(ri) ; res ; res = mol.NextResidue(ri))
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if (res->GetName() == resname
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&& res->GetNumString() == resnum
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&& static_cast<int>(res->GetChain()) == chain
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&& static_cast<int>(res->GetInsertionCode()) == insertioncode) {
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&& static_cast<int>(res->GetInsertionCode()) == insertioncode
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&& res->GetSegName() == segname) {
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if (insertioncode) fprintf(stderr,"I: identified residue wrt insertion code: '%c'\n",insertioncode);
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break;
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}
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@ -1147,6 +1163,7 @@ namespace OpenBabel
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res->SetName(resname);
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res->SetNum(resnum);
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res->SetInsertionCode(insertioncode);
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res->SetSegName(segname);
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}
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}
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@ -961,6 +961,11 @@ namespace OpenBabel
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SetResidueKeys(_resname.c_str(), _reskey, _aakey);
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}
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void OBResidue::SetSegName(const string &name)
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{
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_segname = name;
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}
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void OBResidue::SetNum(const unsigned int resnum)
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{
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stringstream temp;
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@ -1037,6 +1042,11 @@ namespace OpenBabel
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return _resname;
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}
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string OBResidue::GetSegName(void) const
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{
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return _segname;
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}
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std::string OBResidue::GetNumString(void)
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{
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return _resnum;
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@ -18,10 +18,55 @@ and so you can quickly develop the tests and try them out.
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import unittest
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from testbabel import run_exec, executable, BaseTest
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from testbindings import pybel
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class TestPDBFormat(BaseTest):
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"""A series of tests relating to PDB"""
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def testSegname(self):
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"""Test that different segments are put in different residues"""
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self.pdbin = '''ATOM 102 N CYS A 16 59.916 27.715 54.719 1.00 30.93 AAAA N
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ATOM 104 C CYS A 16 61.349 29.663 54.116 1.00 31.27 AAAA C
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ATOM 105 O CYS A 16 62.398 30.296 54.175 1.00 31.42 AAAA O
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ATOM 106 CB CYS A 16 62.233 27.349 54.045 1.00 30.95 AAAA C
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ATOM 107 SG CYS A 16 62.584 25.823 54.921 1.00 31.06 AAAA S
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ATOM 2492 N CYS A 16 46.752 17.445 54.719 1.00 30.93 B N
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ATOM 2493 CA CYS A 16 45.412 16.879 54.750 1.00 31.03 B C
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ATOM 2494 C CYS A 16 45.319 15.497 54.116 1.00 31.27 B C
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ATOM 2495 O CYS A 16 44.270 14.864 54.175 1.00 31.42 B O
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ATOM 2496 CB CYS A 16 44.435 17.811 54.045 1.00 30.95 B C
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ATOM 2497 SG CYS A 16 44.084 19.337 54.921 1.00 31.06 B S
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'''
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self.pdbout = '''ATOM 1 N CYS A 16 59.916 27.715 54.719 1.00 0.00 AAAA N
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ATOM 2 C CYS A 16 61.349 29.663 54.116 1.00 0.00 AAAA C
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ATOM 3 O CYS A 16 62.398 30.296 54.175 1.00 0.00 AAAA O
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ATOM 4 CB CYS A 16 62.233 27.349 54.045 1.00 0.00 AAAA C
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ATOM 5 SG CYS A 16 62.584 25.823 54.921 1.00 0.00 AAAA S
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ATOM 6 N CYS A 16 46.752 17.445 54.719 1.00 0.00 B N
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ATOM 7 CA CYS A 16 45.412 16.879 54.750 1.00 0.00 B C
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ATOM 8 C CYS A 16 45.319 15.497 54.116 1.00 0.00 B C
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ATOM 9 O CYS A 16 44.270 14.864 54.175 1.00 0.00 B O
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ATOM 10 CB CYS A 16 44.435 17.811 54.045 1.00 0.00 B C
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ATOM 11 SG CYS A 16 44.084 19.337 54.921 1.00 0.00 B S '''
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output, error = run_exec(self.pdbin,
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"obabel -ipdb -opdb")
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#pull out only atoms
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outatoms = '\n'.join([line for line in output.split('\n') if line.startswith('ATOM')])
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self.assertEqual(outatoms, self.pdbout)
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#skip if bindings not present
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if pybel:
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mol = pybel.readstring('pdb',self.pdbin)
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self.assertTrue(len(mol.residues) == 2)
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cnts = {'AAAA':0,'B':0}
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for a in mol.atoms:
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r = a.OBAtom.GetResidue()
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cnts[r.GetSegName().strip()] += 1
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self.assertEqual(cnts['AAAA'],5)
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self.assertEqual(cnts['B'],6)
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def testInsertionCodes(self):
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"""
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Testing a PDB entry with insertion codes to distinguish residues
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