Mercurial > repos > guerler > springsuite
annotate spring_package/Molecule.py @ 19:dfd972ba93a4 draft
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
author | guerler |
---|---|
date | Wed, 28 Oct 2020 05:15:42 +0000 |
parents | c790d25086dc |
children |
rev | line source |
---|---|
17
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
1 class Molecule: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
2 def __init__(self, fileName = None): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
3 self.calpha = dict() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
4 self.biomol = dict() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
5 self.rotmat = dict() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
6 self.atoms = list() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
7 if fileName is not None: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
8 self.fromFile(fileName) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
9 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
10 def fromFile(self, fileName): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
11 biomolNumber = 0 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
12 biomolChains = list() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
13 with open(fileName) as file: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
14 for index, line in enumerate(file): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
15 key = line[0:6].strip() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
16 if key == "ATOM": |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
17 atom = line[12:16] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
18 atomNumber = line[6:11] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
19 chainName = line[21:22] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
20 if chainName not in self.calpha: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
21 self.calpha[chainName] = dict() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
22 x = self.toFloat(line[30:38]) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
23 y = self.toFloat(line[38:46]) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
24 z = self.toFloat(line[46:54]) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
25 occupancy = self.toFloat(line[54:60], optional=True) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
26 temperature = self.toFloat(line[54:60], optional=True) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
27 residue = line[17:20] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
28 residueNumber = self.toInt(line[22:26]) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
29 atomNumber = self.toInt(line[6:11]) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
30 atomName = line[12:16] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
31 atomDict = dict(x=x, y=y, z=z, |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
32 residue=residue, |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
33 occupancy=occupancy, |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
34 temperature=temperature, |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
35 atomNumber=atomNumber, |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
36 atomName=atomName, |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
37 residueNumber=residueNumber, |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
38 chainName=chainName) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
39 if atom.strip() == "CA": |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
40 self.calpha[chainName][residueNumber] = atomDict |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
41 self.atoms.append(atomDict) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
42 biokey = "REMARK 350 BIOMOLECULE:" |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
43 if line[0:len(biokey)] == biokey: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
44 biomolNumber = self.toInt(line[len(biokey):]) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
45 biokey = "REMARK 350 APPLY THE FOLLOWING TO CHAINS:" |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
46 nextLine = next(file) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
47 while nextLine[:len(biokey)] != biokey: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
48 nextLine = next(file) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
49 biomolChains = nextLine[len(biokey):].split(",") |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
50 biomolChains = list(map(lambda x: x.strip(), biomolChains)) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
51 biokey = "REMARK 350 AND CHAINS:" |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
52 nextLine = next(file) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
53 while nextLine[:len(biokey)] == biokey: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
54 moreChains = nextLine[len(biokey):].split(",") |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
55 moreChains = list(map(lambda x: x.strip(), moreChains)) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
56 biomolChains = biomolChains + moreChains |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
57 nextLine = next(file) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
58 biokey = "REMARK 350 BIOMT" |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
59 if nextLine[:len(biokey)] == biokey: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
60 biomolMatId1, biomolMat1 = self.getFloats(nextLine) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
61 nextLine = next(file) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
62 biomolMatId2, biomolMat2 = self.getFloats(nextLine) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
63 nextLine = next(file) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
64 biomolMatId3, biomolMat3 = self.getFloats(nextLine) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
65 if biomolMatId1 != biomolMatId2 or biomolMatId1 != biomolMatId3: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
66 raise Exception("Invalid rotation matrix format [%s]." % biomolMatId1) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
67 matrix = [biomolMat1, biomolMat2, biomolMat3] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
68 biomolChains = [c for c in biomolChains if c] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
69 if biomolNumber not in self.rotmat: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
70 self.rotmat[biomolNumber] = list() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
71 self.rotmat[biomolNumber].append(dict(chains=biomolChains, matrix=matrix)) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
72 removeChains = [] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
73 for chainName in self.calpha: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
74 if len(self.calpha[chainName]) == 0: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
75 removeChains.append(chainName) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
76 for chainName in removeChains: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
77 del self.calpha[chainName] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
78 if not self.calpha: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
79 raise Exception("Molecule has no atoms.") |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
80 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
81 def getFloats(self, nextLine): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
82 matId = self.toInt(nextLine[20:23]) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
83 matLine = nextLine[23:].split() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
84 matLine = list(map(lambda x: self.toFloat(x), matLine)) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
85 return matId, matLine |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
86 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
87 def createUnit(self, biomolNumber = 1): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
88 molecule = Molecule() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
89 chainCount = 0 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
90 for matrixDict in self.rotmat[biomolNumber]: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
91 for chain in matrixDict["chains"]: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
92 if chain in self.calpha: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
93 chainCopy = dict() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
94 for residue in self.calpha[chain]: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
95 chainCopy[residue] = self.calpha[chain][residue].copy() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
96 for atomNumber in chainCopy: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
97 atom = chainCopy[atomNumber] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
98 rotmat = matrixDict["matrix"] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
99 self.applyMatrix(atom, rotmat) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
100 if chain in molecule.calpha: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
101 chainName = chainCount |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
102 else: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
103 chainName = chain |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
104 molecule.calpha[chainName] = chainCopy |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
105 chainCount = chainCount + 1 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
106 return molecule |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
107 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
108 def applyMatrix(self, atom, rotmat): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
109 newx = atom["x"] * rotmat[0][0] + atom["y"] * rotmat[0][1] + atom["z"] * rotmat[0][2] + rotmat[0][3] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
110 newy = atom["x"] * rotmat[1][0] + atom["y"] * rotmat[1][1] + atom["z"] * rotmat[1][2] + rotmat[1][3] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
111 newz = atom["x"] * rotmat[2][0] + atom["y"] * rotmat[2][1] + atom["z"] * rotmat[2][2] + rotmat[2][3] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
112 atom["x"] = newx |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
113 atom["y"] = newy |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
114 atom["z"] = newz |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
115 return atom |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
116 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
117 def toFloat(self, x, optional=False): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
118 try: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
119 return float(x) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
120 except: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
121 if not optional: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
122 raise Exception("Invalid float conversion [%s]." % x) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
123 return 0.0 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
124 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
125 def toInt(self, x): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
126 try: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
127 return int(x) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
128 except: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
129 raise Exception("Invalid integer conversion [%s]." % x) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
130 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
131 def saveChain(self, chainName, outputName): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
132 print ("Writing PDB file to %s." % outputName) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
133 f = open(outputName, "w") |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
134 for residueNumber in sorted(self.calpha[chainName].keys()): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
135 ca = self.calpha[chainName][residueNumber] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
136 if ca["residue"] is not None: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
137 f.write(self.atomString(ca)) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
138 f.close() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
139 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
140 def save(self, outputName, append=False, chainName=None): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
141 print ("Writing atoms to PDB file to %s." % outputName) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
142 fileFlag = "+a" if append else "w" |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
143 f = open(outputName, fileFlag) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
144 for atom in self.atoms: |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
145 atom["chainName"] = chainName if chainName else atom["chainName"] |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
146 f.write(self.atomString(atom)) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
147 f.write("TER\n") |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
148 f.close() |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
149 |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
150 def atomString(self, atom): |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
151 return "ATOM %5d %s %s %s%4d %8.3f%8.3f%8.3f%6.2f%6.2f\n" % (atom["atomNumber"], atom["atomName"], atom["residue"], atom["chainName"], atom["residueNumber"], atom["x"], atom["y"], atom["z"], atom["occupancy"], atom["temperature"]) |
c790d25086dc
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
guerler
parents:
diff
changeset
|
152 |