Mercurial > repos > guerler > springsuite

annotate spring_package/Molecule.py @ 17:c790d25086dc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
author guerler
date Wed, 28 Oct 2020 05:11:56 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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