| /dports/science/cdk/cdk-cdk-2.3/base/data/src/main/java/org/openscience/cdk/protein/data/ |
| H A D | PDBMonomer.java | 52 private String resSeq; field in PDBMonomer
104 return resSeq; in getResSeq()
116 public void setResSeq(String resSeq) { in setResSeq() argument
117 this.resSeq = resSeq; in setResSeq()
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| H A D | PDBAtom.java | 62 private String resSeq; field in PDBAtom
108 resSeq = null; in initValues()
307 resSeq = newResSeq; in setResSeq()
317 return resSeq; in getResSeq()
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| /dports/science/cdk/cdk-cdk-2.3/base/silent/src/main/java/org/openscience/cdk/silent/ |
| H A D | PDBMonomer.java | 51 private String resSeq; field in PDBMonomer
103 return resSeq; in getResSeq()
115 public void setResSeq(String resSeq) { in setResSeq() argument
116 this.resSeq = resSeq; in setResSeq()
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| H A D | PDBAtom.java | 61 private String resSeq; field in PDBAtom
107 resSeq = null; in initValues()
305 resSeq = newResSeq; in setResSeq()
315 return resSeq; in getResSeq()
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| /dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/topology/ |
| H A D | PQRParser.py | 160 chainID, resSeq, x, y, z, charge,
164 resSeq, x, y, z, charge,
171 resSeq, x, y, z, charge, radius) = fields
175 resid = int(resSeq)
178 resid = int(resSeq[:-1])
179 icode = resSeq[-1]
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/extensions/ |
| H A D | contact.py | 77 …resSeq,thisatom.residue.name,thisatom.residue.resSeq, thisatom.residue.chainID,thisatom.name,thata…
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| H A D | hbond.py | 60 (residue.resSeq, residue.name, residue.resSeq, residue.chainID, name)
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/graph_cut/ |
| H A D | utils.py | 41 … pKa1.pKaGroup.name, res1.chainID, str(res1.resSeq), state1,
42 … pKa2.pKaGroup.name, res2.chainID, str(res2.resSeq), state2)
52 location = str(pKa.residue.resSeq)
79 group.name, res.chainID, str(res.resSeq), state1,
80 group.name, res.chainID, str(res.resSeq), state2)
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| /dports/biology/protomol/protomol/framework/io/ |
| H A D | PDBWriter.cpp | 47 string resSeq = toString(a.residueNum); in write() local
50 resSeq = string(1,'A'+(a.residueNum-10000)/1000)+string(toString(a.residueNum%1000)); in write()
55 resSeq = "-1"; in write()
78 getLeftFill(resSeq,PDB::PDBAtom::L_RES_SEQ)); in write()
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| H A D | PDBReader.cpp | 90 int resSeq = toInt(str); in read() local
93 resSeq = (str[0] - 'A') * 1000 + 10000 + toInt(string(&str[1],&str[4])); in read()
97 resSeq = -1; in read()
108 resSeq, in read()
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/pdb2pka/ |
| H A D | pka_routines.py | 368 key = residue.name + '_' + residue.chainID + '_' + str(residue.resSeq)
383 key = 'NTR' + '_' + residue.chainID + '_' + str(residue.resSeq)
386 key = 'CTR' + '_' + residue.chainID + '_' + str(residue.resSeq)
438 pKa.residue.resSeq,
1373 CM.set_calc('background %s %s' %(pKa.residue.resSeq,state))
1542 CM.set_calc('Desolv solv %s %s' %(pKa.residue.resSeq,state))
1555 CM.set_calc('Desolv prot %s %s' %(pKa.residue.resSeq,state))
1933 text += " in residue %s %i" % (residue.name, residue.resSeq)
1960 text += " in residue %s %i" % (residue.name, residue.resSeq)
2159 PDB2PKAError( "no neutral state for " + str(residue.resSeq))
[all …]
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| H A D | charge_mon.py | 41 … self.cv.create_text(x_count,self.calc,text='%3d' %residue.resSeq,anchor='nw',fill=fill)
42 self.res_pos[residue.resSeq]=x_count
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/src/ |
| H A D | structures.py | 190 self.resSeq = sampleAtom.resSeq
221 text = "%s %s %i%s" % (self.name, self.chainID, self.resSeq, self.iCode)
334 self.resSeq = value
586 self.resSeq = atom.resSeq
650 tstr = "%d" % self.resSeq
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| H A D | protein.py | 99 resSeq = record.resSeq
110 if resSeq != previousAtom.resSeq or \
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| H A D | aa.py | 75 self.resSeq = sampleAtom.resSeq
736 self.resSeq = sampleAtom.resSeq
817 self.resSeq = sampleAtom.resSeq
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| /dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/generic/ |
| H A D | valist.c | 243 Valist *thee, Vio *sock, int *resSeq) { in Valist_readPDBResidueNumber() argument
292 *resSeq = ti; in Valist_readPDBResidueNumber()
350 int *resSeq, /* Set to residue number */ in Valist_readPDB_throughXYZ() argument
378 if (Valist_readPDBResidueNumber(thee, sock, resSeq) == VRC_FAILURE) { in Valist_readPDB_throughXYZ()
414 Vnm_print(1, "Valist_readPDB: resSeq = %d\n", *resSeq); in Valist_readPDB_throughXYZ()
527 int nlist, natoms, serial, resSeq; in Valist_readPDB() local
555 resName, &resSeq, &x, &y, &z) == VRC_FAILURE) { in Valist_readPDB()
621 int nlist, natoms, serial, resSeq; in Valist_readPQR() local
654 resName, &resSeq, &x, &y, &z) == VRC_FAILURE) { in Valist_readPQR()
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| /dports/math/parmetis/parmetis-4.0.3/metis/GKlib/ |
| H A D | pdb.c | 108 gk_free((void **)&p->resSeq, LTERM); in gk_freepdbf()
210 toFill->resSeq = (char *) gk_malloc (residues*sizeof(char),"residue seq"); in gk_readpdbfile()
234 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
247 toFill->cm[res-1].name = toFill->resSeq[res-1]; in gk_readpdbfile()
250 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
334 fprintf(FPOUT,"%c",pb->resSeq[i]); in gk_writefastafrompdb()
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| /dports/math/py-PyMetis/PyMetis-2020.1/src/metis/GKlib/ |
| H A D | pdb.c | 108 gk_free((void **)&p->resSeq, LTERM); in gk_freepdbf()
210 toFill->resSeq = (char *) gk_malloc (residues*sizeof(char),"residue seq"); in gk_readpdbfile()
234 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
247 toFill->cm[res-1].name = toFill->resSeq[res-1]; in gk_readpdbfile()
250 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
334 fprintf(FPOUT,"%c",pb->resSeq[i]); in gk_writefastafrompdb()
|
| /dports/cad/gmsh/gmsh-4.9.2-source/contrib/metis/GKlib/ |
| H A D | pdb.c | 108 gk_free((void **)&p->resSeq, LTERM); in gk_freepdbf()
210 toFill->resSeq = (char *) gk_malloc (residues*sizeof(char),"residue seq"); in gk_readpdbfile()
234 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
247 toFill->cm[res-1].name = toFill->resSeq[res-1]; in gk_readpdbfile()
250 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
334 fprintf(FPOUT,"%c",pb->resSeq[i]); in gk_writefastafrompdb()
|
| /dports/math/libmesh/libmesh-1.6.2/contrib/metis/GKlib/ |
| H A D | pdb.c | 108 gk_free((void **)&p->resSeq, LTERM); in gk_freepdbf()
210 toFill->resSeq = (char *) gk_malloc (residues*sizeof(char),"residue seq"); in gk_readpdbfile()
234 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
247 toFill->cm[res-1].name = toFill->resSeq[res-1]; in gk_readpdbfile()
250 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
334 fprintf(FPOUT,"%c",pb->resSeq[i]); in gk_writefastafrompdb()
|
| /dports/science/octopus/octopus-10.5/external_libs/metis-5.1/GKlib/ |
| H A D | pdb.c | 107 gk_free((void **)&p->resSeq, LTERM); in gk_freepdbf()
209 toFill->resSeq = (char *) gk_malloc (residues*sizeof(char),"residue seq"); in gk_readpdbfile()
233 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
246 toFill->cm[res-1].name = toFill->resSeq[res-1]; in gk_readpdbfile()
249 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
333 fprintf(FPOUT,"%c",pb->resSeq[i]); in gk_writefastafrompdb()
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| /dports/math/metis/metis-5.1.0/GKlib/ |
| H A D | pdb.c | 108 gk_free((void **)&p->resSeq, LTERM); in gk_freepdbf()
210 toFill->resSeq = (char *) gk_malloc (residues*sizeof(char),"residue seq"); in gk_readpdbfile()
234 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
247 toFill->cm[res-1].name = toFill->resSeq[res-1]; in gk_readpdbfile()
250 toFill->resSeq[res] = gk_threetoone(rname); in gk_readpdbfile()
334 fprintf(FPOUT,"%c",pb->resSeq[i]); in gk_writefastafrompdb()
|
| /dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/library/ |
| H A D | SequenceSplitWorker.cpp | 191 DNASequence &resSeq = *iter; in sl_onTaskFinished() local
192 …QString name = resSeq.getName() + " " + U1AnnotationUtils::buildLocationString(ssT->getInputAnnota… in sl_onTaskFinished()
196 resSeq.info[DNAInfo::ID] = name; in sl_onTaskFinished()
199 SharedDbiDataHandler seqId = context->getDataStorage()->putSequence(resSeq); in sl_onTaskFinished()
|
| /dports/science/py-geometric/geometric-0.9.7.2/geometric/ |
| H A D | PDB.py | 229 self.resSeq = None
269 self.resSeq = toInt(line[22:26].strip())
319 self.resSeq = toInt(line[22:26].strip())
371 self.resSeq = toInt(line[22:26].strip())
498 if self.resSeq < 100000:
499 tstr = "%d" % self.resSeq
501 tstr = hex(self.resSeq)[2:]
715 self.resSeq = toInt(line[22:26].strip())
784 if self.resSeq < 100000:
785 tstr = "%d" % self.resSeq
[all …]
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| /dports/editors/libreoffice/libreoffice-7.2.6.2/svl/source/passwordcontainer/ |
| H A D | passwordcontainer.cxx | 409 ::rtl::ByteSequence resSeq( aSeq.getLength() ); in DecodePasswords()
412 … reinterpret_cast<sal_uInt8*>(resSeq.getArray()), resSeq.getLength() ); in DecodePasswords()
414 …OUString aPasswd( reinterpret_cast<char*>(resSeq.getArray()), resSeq.getLength(), RTL_TEXTENCODING… in DecodePasswords()
459 ::rtl::ByteSequence resSeq(aSeq.getLength()+1); in EncodePasswords()
462 … reinterpret_cast<sal_uInt8*>(resSeq.getArray()), resSeq.getLength() ); in EncodePasswords()
495 return getAsciiLine( resSeq ); in EncodePasswords()
|