/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | test_PDBList.py | 29 pdblist = PDBList(obsolete_pdb="unimportant") 30 url = pdblist.pdb_server + "/pub/pdb/data/status/latest/added.pdb" 31 entries = pdblist.get_status_list(url) 37 pdblist = PDBList(obsolete_pdb="unimportant") 38 entries = pdblist.get_all_entries() 46 pdblist = PDBList(obsolete_pdb="unimportant") 47 entries = pdblist.get_all_obsolete() 66 pdblist = PDBList(pdb=tmp, obsolete_pdb=os.path.join(tmp, "obsolete")) 70 pdblist.retrieve_pdb_file(
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/dports/www/firefox-legacy/firefox-52.8.0esr/testing/web-platform/tests/tools/pytest/testing/ |
H A D | test_pdb.py | 17 pdblist = [] 19 pdblist.append(args) 22 return pdblist 24 def test_pdb_on_fail(self, testdir, pdblist): argument 30 assert len(pdblist) == 1 31 tb = _pytest._code.Traceback(pdblist[0][0]) 34 def test_pdb_on_xfail(self, testdir, pdblist): argument 42 assert not pdblist 44 def test_pdb_on_skip(self, testdir, pdblist): argument 51 assert len(pdblist) == 0 [all …]
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/dports/lang/spidermonkey60/firefox-60.9.0/testing/web-platform/tests/tools/third_party/pytest/testing/ |
H A D | test_pdb.py | 39 def pdblist(self, request): member in TestPDB 41 pdblist = [] 44 pdblist.append(args) 48 return pdblist 50 def test_pdb_on_fail(self, testdir, pdblist): argument 56 assert len(pdblist) == 1 60 def test_pdb_on_xfail(self, testdir, pdblist): argument 68 assert not pdblist 70 def test_pdb_on_skip(self, testdir, pdblist): argument 77 assert len(pdblist) == 0 [all …]
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/dports/lang/spidermonkey78/firefox-78.9.0/third_party/python/pytest/testing/ |
H A D | test_pdb.py | 70 def pdblist(self, request): member in TestPDB 72 pdblist = [] 75 pdblist.append(args) 79 return pdblist 81 def test_pdb_on_fail(self, testdir, pdblist): argument 90 assert len(pdblist) == 1 105 assert not pdblist 107 def test_pdb_on_skip(self, testdir, pdblist): argument 117 assert len(pdblist) == 0 129 assert len(pdblist) == 0 [all …]
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/dports/lang/spidermonkey78/firefox-78.9.0/testing/web-platform/tests/tools/third_party/pytest/testing/ |
H A D | test_pdb.py | 70 def pdblist(self, request): member in TestPDB 72 pdblist = [] 75 pdblist.append(args) 79 return pdblist 81 def test_pdb_on_fail(self, testdir, pdblist): argument 90 assert len(pdblist) == 1 105 assert not pdblist 107 def test_pdb_on_skip(self, testdir, pdblist): argument 117 assert len(pdblist) == 0 129 assert len(pdblist) == 0 [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/ |
H A D | main.py | 79 def getOldHeader(pdblist): argument 84 for pdbObj in pdblist: 93 def printPQRHeader(pdblist, argument 171 header += getOldHeader(pdblist) 175 def runPDB2PQR(pdblist, ff, argument 264 for record in pdblist: 270 pdblist = pdblist_new 281 myProtein = Protein(pdblist, myDefinition) 692 pdblist, errlist = readPDB(pdbFile) 694 if len(pdblist) == 0 and len(errlist) == 0: [all …]
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H A D | pka.py | 194 pdblist, errlist = readPDB(pdbfile) 209 myProtein = Protein(pdblist, myDefinition) 212 myProtein, _, _ = ligff.initialize(myDefinition, ligand, pdblist, verbose) 278 pdblist, errlist = readPDB(pdbfile) 295 myProtein = Protein(pdblist, myDefinition) 298 myProtein, myDefinition, Lig = ligff.initialize(myDefinition, ligand, pdblist, verbose)
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H A D | main_cgi.py | 495 pdblist, errlist = readPDB(weboptions.pdbfile) 498 dummyprot = Protein(pdblist, dummydef) 499 if len(pdblist) == 0 and len(errlist) == 0: 584 header, lines, missedligands = runPDB2PQR(pdblist,
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/dports/devel/py-pytest/pytest-4.6.11/testing/ |
H A D | test_pdb.py | 81 def pdblist(self, request): member in TestPDB 83 pdblist = [] 86 pdblist.append(args) 90 return pdblist 92 def test_pdb_on_fail(self, testdir, pdblist): argument 101 assert len(pdblist) == 1 116 assert not pdblist 118 def test_pdb_on_skip(self, testdir, pdblist): argument 128 assert len(pdblist) == 0 140 assert len(pdblist) == 0 [all …]
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/dports/www/firefox/firefox-99.0/testing/web-platform/tests/tools/third_party/pytest/testing/ |
H A D | test_debugging.py | 83 def pdblist(self, request): member in TestPDB 85 pdblist = [] 88 pdblist.append(args) 92 return pdblist 94 def test_pdb_on_fail(self, testdir, pdblist): argument 103 assert len(pdblist) == 1 118 assert not pdblist 120 def test_pdb_on_skip(self, testdir, pdblist): argument 130 assert len(pdblist) == 0 142 assert len(pdblist) == 0 [all …]
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/dports/mail/thunderbird/thunderbird-91.8.0/testing/web-platform/tests/tools/third_party/pytest/testing/ |
H A D | test_debugging.py | 83 def pdblist(self, request): member in TestPDB 85 pdblist = [] 88 pdblist.append(args) 92 return pdblist 94 def test_pdb_on_fail(self, testdir, pdblist): argument 103 assert len(pdblist) == 1 118 assert not pdblist 120 def test_pdb_on_skip(self, testdir, pdblist): argument 130 assert len(pdblist) == 0 142 assert len(pdblist) == 0 [all …]
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/dports/www/firefox-esr/firefox-91.8.0/testing/web-platform/tests/tools/third_party/pytest/testing/ |
H A D | test_debugging.py | 83 def pdblist(self, request): member in TestPDB 85 pdblist = [] 88 pdblist.append(args) 92 return pdblist 94 def test_pdb_on_fail(self, testdir, pdblist): argument 103 assert len(pdblist) == 1 118 assert not pdblist 120 def test_pdb_on_skip(self, testdir, pdblist): argument 130 assert len(pdblist) == 0 142 assert len(pdblist) == 0 [all …]
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/dports/biology/mafft/mafft-7.267-without-extensions/core/ |
H A D | mafft.tmpl | 230 pdblist="/dev/null" 800 pdblist="$1" 801 if [ ! -e "$pdblist" ]; then 802 echo "Cannot open $pdblist" 1>&2 905 cat "$pdblist" | tr "\r" "\n" | grep -v "^$" > $TMPFILE/pdblist 1880 if [ $pdblist != "/dev/null" ]; then 1910 cat seekout.str >> pdblist 1911 pdblist="tsukaimasu" 2198 if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then 2204 if [ $pdblist != "/dev/null" ]; then [all …]
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/src/ |
H A D | protein.py | 67 def __init__(self, pdblist, definition): argument 87 for record in pdblist: # Find number of chains 91 for record in pdblist:
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H A D | pdb.py | 2287 pdblist = [] # Array of parsed lines (as objects) 2292 return pdblist, errlist 2306 pdblist.append(obj) 2316 pdblist.append(obj) 2329 return pdblist, errlist 2345 pdblist = string.split(pdbline) 2346 pdbZ = random.choice(pdblist)
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/dports/science/tinker/tinker/source/ |
H A D | pdb.f | 41 integer, allocatable :: pdblist(:)
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H A D | xyzpdb.f | 140 if (.not. allocated(pdblist)) allocate (pdblist(maxatm)) 153 pdblist(i) = 0 283 kp = pdblist(k) 286 ipdb12(m,kp) = pdblist(i12(m,k)) 648 if (pdblist(i) .ne. 0) hetmol(molcule(i)) = .false. 694 kp = pdblist(k) 697 ipdb12(m,kp) = pdblist(i12(m,k)) 744 pdblist(icoord) = npdb
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H A D | final.f | 685 if (allocated(pdblist)) deallocate (pdblist)
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/ |
H A D | pka_old.py | 263 pdblist, errlist = readPDB(pdbfile) 291 myProtein = Protein(pdblist, dummydef) 310 … myProtein, myDefinition, Lig = ligff.initialize(myDefinition, ligfd, pdblist, verbose)
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/conf_avg/ |
H A D | Ensemble_phimap.py | 141 pdblist, errlist = readPDB(pdbfile) 146 myProtein = Protein(pdblist, myDefinition)
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/ligandclean/ |
H A D | ligff.py | 11 def initialize(definition, ligdesc, pdblist, verbose=0): argument 97 for line in pdblist:
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/ |
H A D | protonate.py | 498 pdblist = pdb.readPDB(filename) variable 499 my_protein = protein.Protein(pdblist,'test.pdb')
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H A D | bonds.py | 463 pdblist = pdb.readPDB(filename) variable 464 my_protein = protein.Protein(pdblist,'test.pdb')
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H A D | protonator.py | 744 pdblist = pdb.readPDB(filename) variable 745 my_protein = protein.Protein(pdblist,'test.pdb')
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/dports/science/py-geometric/geometric-0.9.7.2/geometric/ |
H A D | PDB.py | 2453 pdblist = [] # Array of parsed lines (as objects) 2467 pdblist.append(obj) 2474 pdblist.append(obj) 2487 return pdblist, errlist 2503 pdblist = string.split(pdbline) 2504 pdbZ = random.choice(pdblist)
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