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Searched refs:pdblist (Results 1 – 25 of 28) sorted by relevance

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/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_PDBList.py29 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(
/dports/www/firefox-legacy/firefox-52.8.0esr/testing/web-platform/tests/tools/pytest/testing/
H A Dtest_pdb.py17 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 …]
/dports/lang/spidermonkey60/firefox-60.9.0/testing/web-platform/tests/tools/third_party/pytest/testing/
H A Dtest_pdb.py39 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 …]
/dports/lang/spidermonkey78/firefox-78.9.0/third_party/python/pytest/testing/
H A Dtest_pdb.py70 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 …]
/dports/lang/spidermonkey78/firefox-78.9.0/testing/web-platform/tests/tools/third_party/pytest/testing/
H A Dtest_pdb.py70 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/
H A Dmain.py79 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 …]
H A Dpka.py194 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)
H A Dmain_cgi.py495 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,
/dports/devel/py-pytest/pytest-4.6.11/testing/
H A Dtest_pdb.py81 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 …]
/dports/www/firefox/firefox-99.0/testing/web-platform/tests/tools/third_party/pytest/testing/
H A Dtest_debugging.py83 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 …]
/dports/mail/thunderbird/thunderbird-91.8.0/testing/web-platform/tests/tools/third_party/pytest/testing/
H A Dtest_debugging.py83 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 …]
/dports/www/firefox-esr/firefox-91.8.0/testing/web-platform/tests/tools/third_party/pytest/testing/
H A Dtest_debugging.py83 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 …]
/dports/biology/mafft/mafft-7.267-without-extensions/core/
H A Dmafft.tmpl230 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 …]
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/src/
H A Dprotein.py67 def __init__(self, pdblist, definition): argument
87 for record in pdblist: # Find number of chains
91 for record in pdblist:
H A Dpdb.py2287 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)
/dports/science/tinker/tinker/source/
H A Dpdb.f41 integer, allocatable :: pdblist(:)
H A Dxyzpdb.f140 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
H A Dfinal.f685 if (allocated(pdblist)) deallocate (pdblist)
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/
H A Dpka_old.py263 pdblist, errlist = readPDB(pdbfile)
291 myProtein = Protein(pdblist, dummydef)
310 … myProtein, myDefinition, Lig = ligff.initialize(myDefinition, ligfd, pdblist, verbose)
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/conf_avg/
H A DEnsemble_phimap.py141 pdblist, errlist = readPDB(pdbfile)
146 myProtein = Protein(pdblist, myDefinition)
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/ligandclean/
H A Dligff.py11 def initialize(definition, ligdesc, pdblist, verbose=0): argument
97 for line in pdblist:
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/
H A Dprotonate.py498 pdblist = pdb.readPDB(filename) variable
499 my_protein = protein.Protein(pdblist,'test.pdb')
H A Dbonds.py463 pdblist = pdb.readPDB(filename) variable
464 my_protein = protein.Protein(pdblist,'test.pdb')
H A Dprotonator.py744 pdblist = pdb.readPDB(filename) variable
745 my_protein = protein.Protein(pdblist,'test.pdb')
/dports/science/py-geometric/geometric-0.9.7.2/geometric/
H A DPDB.py2453 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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