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Searched defs:protein (Results 1 – 25 of 158) sorted by relevance

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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/
H A Doutput.py55 def writePDB(protein, file=None, filename=None, hydrogens=False, options=None): argument
89 def writePQR(protein, label=None, hydrogens=False, options=None): argument
150 def writePKA(protein, filename=None, reference="neutral", direction="folding", options=None): argument
186 def printTmProfile(protein, reference="neutral", window=[0., 14., 1.], Tm=[0.,0.], Tms=None, ref=No… argument
202 def printResult(protein, verbose=False): argument
209 def printPKASection(protein, verbose=False): argument
223 def getDeterminantSection(protein, verbose=False): argument
248 def getSummarySection(protein, verbose=False): argument
265 def getFoldingProfileSection(protein, direction="folding", reference="neutral", window=[0., 14., 1.… argument
308 def getChargeProfileSection(protein, verbose=False, options=None): argument
H A Dmutate.py48 def optimizeMutationDeterminants(protein, mutation=None, atoms=None, alignment=None, version=None, … argument
89 def optimizeMultipleMutations(protein, mutations=None, atoms=None, alignment=None, version=None, op… argument
140 def generateChainList(mutation, protein, atoms=None): argument
162 def makeMutatedProtein(protein, mutation=None, atoms=None, alignment=None, options=None): argument
396 def mutateAtomsDictionaryUsingAlignment(protein, atoms=None, mutation=None, options=None): argument
465 def mutateAtomsDictionary_old(protein, atoms=None, mutation=None, options=None): argument
733 def recastIntoDictionary(input_mutation=None, alignment=None, protein=None, chains=None): argument
1009 def mutateAtomsDictionaryUsingOverlap(protein=None, atoms=None, mutation=None, options=None): argument
1156 def makeCompositeAtomsDictionary(protein=None, pdbfiles=None, options=None): argument
H A Dcalculator.py356 def BackBoneReorganization(protein): argument
378 def TmProfile(protein, reference="neutral", grid=[0., 14., 0.1], Tm=None, Tms=None, ref=None, optio… argument
421 def ChargeProfile(protein, options=None): argument
434 def pI(protein, pI=7.0, options=None): argument
476 def bracketingPI(protein, bracket=[0.0, 14.0]): argument
H A Dprotonator.py77 def protonate(self, protein=None): argument
336 def protonate(self, protein=None): argument
345 def protonate_protein(self, protein): argument
404 def remove_all_hydrogen_atoms_from_protein(self, protein): argument
432 def set_charges(self, protein, standard_protonation_states = 1): argument
H A Dprotonate.py102 def protonate_protein(self, protein): argument
168 def remove_all_hydrogen_atoms_from_protein(self, protein): argument
195 def set_charges(self, protein, standard_protonation_states = 1): argument
/dports/science/py-oddt/oddt-0.7/oddt/scoring/descriptors/
H A D__init__.py87 protein=None, argument
149 def build(self, ligands, protein=None): argument
217 protein=None, argument
246 def build(self, ligands, protein=None): argument
319 def __init__(self, protein=None, vina_scores=None): argument
330 def set_protein(self, protein): argument
334 def build(self, ligands, protein=None): argument
364 def __init__(self, protein=None, vina_scores=None): argument
384 def set_protein(self, protein): argument
388 def build(self, ligands, protein=None): argument
H A Dbinana.py15 def __init__(self, protein=None): argument
182 def set_protein(self, protein): argument
196 def build(self, ligands, protein=None): argument
/dports/biology/jalview/jalview/test/jalview/util/
H A DMapListTest.java265 int[] protein = new int[] { 1, 4 }; in testLocateInFrom_noIntrons() local
296 int[] protein = { 1, 4 }; in testLocateInFrom_withIntrons() local
317 int[] protein = { 11, 14 }; in testGetOverlapsInFrom_withIntrons() local
352 int[] protein = { 1, 1, 3, 4, 6, 6 }; in testGetOverlapsInTo_withIntrons() local
395 int[] protein = new int[] { 1, 4 }; in testLocateInTo_noIntrons() local
437 int[] protein = { 1, 1, 3, 4, 6, 6 }; in testLocateInTo_withIntrons() local
471 int[] protein = new int[] { 1, 4 }; in testEquals() local
533 int[] protein = { 1, 1, 3, 4, 6, 6 }; in testConstructor() local
578 int[] protein = { 1, 1, 2, 3, 6, 6 }; in testConstructor_mergeRanges() local
621 int[] protein = { 1, 1, 3, 4, 6, 6 }; in testGetInverse() local
[all …]
H A DMappingUtilsTest.java229 AlignmentI protein = loadAlignment(">Seq1\nK\n>Seq2\nL\n>Seq3\nQ\n", in testMapSequenceGroup_sequences() local
396 AlignmentI protein = loadAlignment( in setupMappedAlignments() local
520 AlignmentI protein = loadAlignment(">Seq1\nKA\n>Seq2\nLQ\n>Seq3\nQV\n", in testMapSequenceGroup_columns() local
604 AlignmentI protein = loadAlignment( in testMapSequenceGroup_region() local
838 SequenceI protein = new Sequence("Seq2", "-T-AS", 5, 7); in testMapEditCommand() local
1412 AlignmentI protein = new Alignment( in testMapSequenceGroup_sharedDataset() local
/dports/science/cdk/cdk-cdk-2.3/storage/pdb/src/main/java/org/openscience/cdk/tools/
H A DProteinBuilderTool.java60 …public static IBioPolymer addAminoAcidAtNTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand… in addAminoAcidAtNTerminus()
84 …public static IBioPolymer addAminoAcidAtCTerminus(IBioPolymer protein, IAminoAcid aaToAdd, IStrand… in addAminoAcidAtCTerminus()
130 IBioPolymer protein = builder.newInstance(IBioPolymer.class); in createProtein() local
167 … private static IBioPolymer addAminoAcid(IBioPolymer protein, IAminoAcid aaToAdd, IStrand strand) { in addAminoAcid()
/dports/science/cdk/cdk-cdk-2.3/descriptor/qsarprotein/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/
H A DAminoAcidCountDescriptorTest.java48 IBioPolymer protein = ProteinBuilderTool.createProtein("ARNDCFQEGHIPLKMSTYVW", in testAACount() local
61 …IBioPolymer protein = ProteinBuilderTool.createProtein("FF", SilentChemObjectBuilder.getInstance()… in testFCount() local
71 …IBioPolymer protein = ProteinBuilderTool.createProtein("TT", SilentChemObjectBuilder.getInstance()… in testTCount() local
/dports/biology/wise/wise2.4.1/src/dynlibsrc/
H A Dprotein.tex1 \section{protein} section in \\numhead0{#1}
9 \subsection{Object Protein}
/dports/science/py-oddt/oddt-0.7/oddt/docking/
H A DAutodockVina.py21 protein=None, argument
144 def set_protein(self, protein): argument
172 def score(self, ligands, protein=None): argument
218 def dock(self, ligands, protein=None): argument
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/
H A Dcompare.py45 def compareWithExperiment(protein, file=None, list=None, set=None, label="ALL", **argv): argument
144 def printDesolvationDistances(protein): argument
/dports/science/py-oddt/oddt-0.7/oddt/
H A Dfingerprints.py32 def InteractionFingerprint(ligand, protein, strict=True): argument
110 def SimpleInteractionFingerprint(ligand, protein, strict=True): argument
578 def SPLIF(ligand, protein, depth=1, size=4096, distance_cutoff=4.5): argument
708 def PLEC(ligand, protein, depth_ligand=2, depth_protein=4, distance_cutoff=4.5, argument
H A Dvirtualscreening.py170 def similarity(self, method, query, cutoff=0.9, protein=None): argument
230 def dock(self, engine, protein, *args, **kwargs): argument
254 def score(self, function, protein=None, *args, **kwargs): argument
H A Ddatasets.py124 def protein(self): member in _pdbbind_id
230 def protein(self): member in _dude_target
430 def protein(self): member in _CASFTarget
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/
H A Dapbs.py75 def runAPBS(self,protein, inputpath, routines, CM=None): argument
307 def get_potentials(self,protein): argument
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_writer/
H A Dwritedb_files.cpp268 bool protein, in CWriteDB_IndexFile()
412 bool protein, in CWriteDB_HeaderFile()
425 bool protein, in CWriteDB_SequenceFile()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_writer/
H A Dwritedb_files.cpp268 bool protein, in CWriteDB_IndexFile()
412 bool protein, in CWriteDB_HeaderFile()
425 bool protein, in CWriteDB_SequenceFile()
/dports/science/cdk/cdk-cdk-2.3/storage/pdb/src/test/java/org/openscience/cdk/tools/
H A DProteinBuilderToolTest.java35 …IBioPolymer protein = ProteinBuilderTool.createProtein("GAGA", SilentChemObjectBuilder.getInstance… in testCreateProtein() local
/dports/biology/exonerate/exonerate-2.4.0/test/data/
H A DMakefile.am2 SUBDIRS = cdna protein subdir
/dports/science/py-oddt/oddt-0.7/tests/
H A Dtest_surface.py14 protein = next(oddt.toolkit.readfile('pdb', os.path.join( variable
/dports/biology/jalview/jalview/src/jalview/appletgui/
H A DSplitFrame.java76 AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport in init() local
122 AlignmentViewport protein = cdna == topFrame.viewport in adjustLayout() local
/dports/misc/nut/nut-20.1/fltk/
H A DNutCharts.h34 float protein[1001]; variable

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