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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/
H A Dcoupled_residues.py79 for residue in [residue1, residue2]:
87 interaction_energy = max(get_interaction(residue1,residue2), get_interaction(residue2,residue1))
97 interaction_energy = max(get_interaction(residue1,residue2), get_interaction(residue2,residue1))
114 default_pka1 = residue1.pKa_pro
124 residue1.calculateTotalPKA()
129 swapped_pka1 = residue1.pKa_pro
137 residue1.calculateTotalPKA()
290 determinants = residue1.determinants[0] + residue1.determinants[2]
309 … tagged_pka_print(' Original|',residue1.getDeterminantString(), [residue1.label, residue2.label])
318 residue1.calculateTotalPKA()
[all …]
H A Ddeterminants.py56 for residue1 in propka_residues:
59 if residue1 == residue2:
93 if 'ligand' not in [residue1.type, residue2.type]:
103 def addSidechainDeterminants(residue1, residue2, version=None): argument
142 if residue1.Q == residue2.Q:
144 if residue1.pKa_mod < residue2.pKa_mod:
154 residue1.determinants[0].append(newDeterminant1)
165 Q1 = residue1.Q
171 addCoulombAcidPair(residue1, residue2, value)
174 addCoulombBasePair(residue1, residue2, value)
[all …]
H A Dparameters.py420 def checkCooCooException(residue1, residue2): argument
432 def checkCooHisException(residue1, residue2): argument
443 def checkCysHisException(residue1, residue2): argument
454 def checkCysCysException(residue1, residue2): argument
784 key2 = residue1.resType
786 key1 = residue1.resType
798 resType1 = residue1.resType
827 Npair = residue1.Nmass + residue2.Nmass
1362 resType1 = residue1.resType
1415 name1 = lib.groupName(residue1.resName)
[all …]
H A Dversion.py569 Npair = residue1.Nmass + residue2.Nmass
625 def checkExceptions(self, residue1, residue2): argument
629 resType1 = residue1.resType
714 def checkExceptions(self, residue1, residue2): argument
718 resType1 = residue1.resType
803 def checkExceptions(self, residue1, residue2): argument
807 resType1 = residue1.resType
854 def checkExceptions(self, residue1, residue2): argument
893 resType1 = residue1.resType
949 resType1 = residue1.resType
[all …]
H A Diterative.py50 def addtoDeterminantList(residue1, residue2, distance, iterative_interactions, version): argument
62 atoms1 = residue1.makeDeterminantAtomList(residue2.resName, version=version)
63 atoms2 = residue2.makeDeterminantAtomList(residue1.resName, version=version)
69 dpka_max, cutoff = version.SideChainParameters[residue1.resType][residue2.resType]
70 weight = version.calculatePairWeight(residue1.Nmass, residue2.Nmass)
73 exception, hbond_value = version.checkExceptions(residue1, residue2)
74 if residue1.resType == "COO" and residue2.resType == "COO":
89 do_coulomb = version.checkCoulombPair(residue1, residue2, distance)
92 weight = version.calculatePairWeight(residue1.Nmass, residue2.Nmass)
98 pair = [residue1, residue2]
H A Ddebug.py120 residue1 = pair[0]
123 str += " %s %s" % (residue1.label, residue2.label)
152 residue1 = pair[0]
155 str += "'%s' '%s'" % (residue1.label, residue2.label)
H A Dcalculator.py55 def InterResidueDistance(residue1, residue2): argument
59 dX = residue1.x - residue2.x
60 dY = residue1.y - residue2.y
61 dZ = residue1.z - residue2.z
H A Dprotein.py233 for residue1 in CYSlist:
234 S1 = residue1.getAtom("SG")
236 if residue1 == residue2:
242 residue1.location = "BONDED"
244 residue1.pKa_mod = 99.99
H A Dbonds.py194 def connect_backbone(self, residue1, residue2): argument
197 self.find_bonds_for_residue_backbone(residue1)
203 for atom1 in residue1.atoms:
/dports/net/iaxmodem/iaxmodem-1.2.0/lib/spandsp/src/spandsp/
H A Dbiquad.h54 int32_t residue1; member
83 bq->residue1 = 0; in biquad2_init()
103 y += (2*bq->residue1 - bq->residue2); in biquad2()
104 bq->residue2 = bq->residue1; in biquad2()
105 bq->residue1 = y & 0x7FFF; in biquad2()
/dports/net/freeswitch/freeswitch-1.10.3.-release/libs/spandsp/src/spandsp/
H A Dbiquad.h52 int32_t residue1; member
81 bq->residue1 = 0; in biquad2_init()
101 y += (2*bq->residue1 - bq->residue2); in biquad2()
102 bq->residue2 = bq->residue1; in biquad2()
103 bq->residue1 = y & 0x7FFF; in biquad2()
/dports/comms/spandsp/spandsp-284fe91/src/spandsp/
H A Dbiquad.h52 int32_t residue1; member
81 bq->residue1 = 0; in biquad2_init()
101 y += (2*bq->residue1 - bq->residue2); in biquad2()
102 bq->residue2 = bq->residue1; in biquad2()
103 bq->residue1 = y & 0x7FFF; in biquad2()
/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_PDB_MMCIFIO.py61 residue1 = list(struct1.get_residues())[0]
63 self.io.set_structure(residue1)
77 residue1 = list(struct1.get_residues())[0]
80 parent = residue1.parent
84 self.io.set_structure(residue1)
102 residue1 = list(struct1.get_residues())[0]
104 residue1.parent = None # detach residue
107 self.io.set_structure(residue1)
H A Dtest_PDB_PDBIO.py99 residue1 = list(struct1.get_residues())[0]
102 parent = residue1.parent
105 self.io.set_structure(residue1)
106 self.assertIs(parent, residue1.parent)
120 residue1 = list(struct1.get_residues())[0]
123 parent = residue1.parent
127 self.io.set_structure(residue1)
145 residue1 = list(struct1.get_residues())[0]
147 residue1.parent = None # detach residue
150 self.io.set_structure(residue1)
/dports/biology/emboss/EMBOSS-6.6.0/ajax/core/
H A Dajdomain.c3887 AjPResidue residue1 = NULL; in ajPdbWriteDomain() local
4212 if(residue1->Mod != 1) in ajPdbWriteDomain()
4288 residue1->Pdb, in ajPdbWriteDomain()
4289 residue1->Id1, in ajPdbWriteDomain()
4290 residue1->Id3); in ajPdbWriteDomain()
4293 if(residue1->eNum != 0) in ajPdbWriteDomain()
4297 ajFmtPrintF(outf, "%-5S%-5c", residue1->eId, residue1->eType); in ajPdbWriteDomain()
4299 if(residue1->eType == 'H') in ajPdbWriteDomain()
4314 residue1->Phi, in ajPdbWriteDomain()
4315 residue1->Psi, in ajPdbWriteDomain()
[all …]
/dports/biology/ncbi-toolkit/ncbi/tools/
H A Dxmlblast.c375 Uint1 codon[4], residue1, residue2; in BXMLGetSeqLineForStdSeg() local
424 hsp->hseq[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
426 if (residue1 == residue2) in BXMLGetSeqLineForStdSeg()
427 hsp->midline[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
453 hsp->hseq[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
455 hsp->qseq[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
459 if (residue1 == residue2) in BXMLGetSeqLineForStdSeg()
494 hsp->hseq[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
504 hsp->hseq[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
525 hsp->qseq[abs_index] = residue1; in BXMLGetSeqLineForStdSeg()
[all …]
/dports/science/jmol/jmol-14.32.7/src/org/jmol/modelsetbio/
H A DAminoPolymer.java99 private void calcPhiPsiAngles2(AminoMonomer residue1, AminoMonomer residue2) { in calcPhiPsiAngles2() argument
111 P3 nitrogen1 = residue1.getNitrogenAtom(); in calcPhiPsiAngles2()
112 P3 alphacarbon1 = residue1.getLeadAtom(); in calcPhiPsiAngles2()
113 P3 carbon1 = residue1.getCarbonylCarbonAtom(); in calcPhiPsiAngles2()
120 residue1.setGroupParameter(T.psi, Measure.computeTorsion(nitrogen1, in calcPhiPsiAngles2()
124 residue1.setGroupParameter(T.omega, Measure.computeTorsion( in calcPhiPsiAngles2()
/dports/cad/openroad/OpenROAD-2.0/src/sta/dcalc/
H A DDmpDelayCalc.cc313 ComplexFloat pole1, residue1; in loadDelay() local
315 parasitics_->poleResidue(pole_residue, 0, pole1, residue1); in loadDelay()
317 && residue1.imag() == 0.0) { in loadDelay()
319 float k1 = residue1.real(); in loadDelay()
/dports/biology/py-biopython/biopython-1.79/Bio/Align/
H A DAlignInfo.py230 for residue1, residue2 in zip(seq1, seq2):
231 if residue1 in letters and residue2 in letters:
232 dictionary[(residue1, residue2)] += weight1 * weight2
H A D__init__.py910 for residue1, residue2 in zip(seq1, seq2):
911 if residue1 == "-":
915 m[(residue1, residue2)] += weight1 * weight2
/dports/math/psurface/psurface-2.0.0-13-gb5b6825/test/
H A Dsparsematrixtest.cpp78 Vector<ctype> residue1(3); in test() local
98 test1.BiCGSTAB(b1, result1, residue1, maxIter, tolerance); in test()
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/extensions/
H A Dresinter.py165 def get_residue_interaction_energy(residue1, residue2): argument
179 for pair in product(residue1.getAtoms(), residue2.getAtoms()):
H A Dnewresinter.py335 def get_residue_interaction_energy(residue1, residue2): argument
349 for pair in product(residue1.getAtoms(), residue2.getAtoms()):
/dports/biology/ncbi-toolkit/ncbi/api/
H A Dvalid.c24642 Int2 residue1, residue2; in PartialAtSpliceSiteOrGap() local
30788 residue1 = protseq [i]; in CdTransCheck()
30789 if (i == 0 && residue1 == '-') { in CdTransCheck()
30792 if (i == 0 && residue1 == 'X') { in CdTransCheck()
30795 if (residue1 == '*') { in CdTransCheck()
30801 if (residue1 == 'X') { in CdTransCheck()
31029 residue1 = protseq [i]; in CdTransCheck()
31035 if (residue1 != residue2) { in CdTransCheck()
31041 if (residue1 == 'B' || residue1 == 'Z' || residue1 == 'J') { in CdTransCheck()
31052 } else if (residue1 == '-') { in CdTransCheck()
[all …]
H A Dtxalign.c2172 Uint1 codon[4], residue1, residue2; in load_align_sum_for_StdSeg() local
2265 residue1 = AAForCodon(codon, genetic_code1); in load_align_sum_for_StdSeg()
2270 if (residue1 == residue2) in load_align_sum_for_StdSeg()
2273 asp->matrix[residue1][residue2] >0) in load_align_sum_for_StdSeg()
2285 while ((residue1=SeqPortGetResidue(spp2)) != SEQPORT_EOF) { in load_align_sum_for_StdSeg()
2291 if (residue1 == residue2) in load_align_sum_for_StdSeg()
2294 asp->matrix[residue1][residue2] >0) in load_align_sum_for_StdSeg()

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