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# This is statement is required by the build system to query build info
if __name__ == '__build__':
raise Exception
import sys
import os
import string
import Numeric
import Geometry
import copy
GUAAtoms = [ "N2", "O6", "C6", "C5", "N7", "C8", "N9", "C4", "N3", "C2", "N1" ]
def rotmat(phi, theta, psi, tx=0, ty=0, tz=0):
s1 = Numeric.sin(phi)
s2 = Numeric.sin(theta)
s3 = Numeric.sin(psi)
c1 = Numeric.cos(phi)
c2 = Numeric.cos(theta)
c3 = Numeric.cos(psi)
newmat = Numeric.array([
[ c2*c3, s2*s1*c3 - c1*s3, s2*c1*c3 + s1*s3, 0],
[ c2*s3, s2*s1*s3 + c1*c3, s2*c1*s3 - s1*c3, 0],
[-s2, c2*s1, c2*c1, 0],
[tx, ty, tz, 1]])
return newmat
def matrix_apply(crd, mat):
o = [crd[0], crd[1], crd[2], 1.0]
n = [0.0, 0.0, 0.0, 0.0]
for i in range(4):
for j in range(4):
n[i] = n[i] + o[j] * mat[j][i]
new = [None, None, None]
for i in range(3):
new[i] = (n[i]/n[3])
return new
class PDBRecord:
def __init__(self, type=None, anum=None, atom=None, residue=None, chain=None, rnum=None):
self.type = type
self.anum = anum
self.atom = atom
self.residue = residue
self.chain = chain
self.rnum = rnum
class PDB:
def __init__(self, filename = None, crds = None, records = None, connect = None):
if crds == None:
crds = []
if records == None:
records = []
self.records = records
self.crds = crds
self.connect = connect
if filename != None:
sys.stderr.write("Reading in new PDB %s\n" % filename)
self.Read(filename)
## note: we read the anum here, which doesn't necessarily correspond to the actual
## record number.
def Read(self, filename):
pdbfile = open(filename)
sys.stderr.write("Opened '%s' for reading as PDB\n" % filename)
while(1):
line = pdbfile.readline()
if line == '':
break
if line[0:4] == 'ATOM' or line[0:6] == 'HETATM':
type = string.strip(line[0:6])
anum = string.atoi(string.strip(line[7:11]))
atom = string.strip(line[12:17])
residue = string.strip(line[17:20])
chain = string.strip(line[21:22])
rnum = string.atoi(string.strip(line[23:26]))
x = string.atof(string.strip(line[31:38]))
y = string.atof(string.strip(line[39:46]))
z = string.atof(string.strip(line[47:54]))
self.records.append(PDBRecord(type, anum, atom, residue, chain, rnum))
self.crds.append((x,y,z))
self.crds = Numeric.array(self.crds)
def Write(self, filename):
self.pdbfd=open(filename,"w")
for i in range(len(self.records)):
record = self.records[i]
self.pdbfd.write("%-6s%5d %-4s%c%-4s%c%4d%c %8.3f%8.3f%8.3f\n" % \
( record.type, record.anum, record.atom,' ', record.residue,' ', record.rnum, ' ',
self.crds[i][0], self.crds[i][1], self.crds[i][2]))
self.pdbfd.write("TER\n")
if self.connect != None:
for i in self.connect:
self.pdbfd.write("CONECT")
for j in i:
self.pdbfd.write("%5d" % (j+1))
self.pdbfd.write("\n")
self.pdbfd.write("END\n")
self.pdbfd.close()
def Rotate(self,alpha, beta, gamma, tx, ty, tz):
r = rotmat(alpha, beta, gamma, tx, ty, tz)
self.RotateMatrix(r)
def RotateMatrix(self,r):
for i in range(len(self.crds)):
self.crds[i] = matrix_apply(self.crds[i], r)
def Center(self):
center = Numeric.add.reduce(self.crds) / len(self.crds)
self.crds = Numeric.subtract(self.crds, center)
def Print(self):
for i in self.records:
print i.type, i.anum, i.atom, i.residue, i.chain, i.rnum
def ReturnAnum(self, atom, rnum):
for i in range(len(self.records)):
record = self.records[i]
if record.atom == atom and record.rnum == rnum:
return i
sys.stderr.write("Unable to find atom '%s' in residue %d\n" % (atom, rnum))
return None
def CrdByName(self, atom, res):
x = self.ReturnAnum(atom, res)
if x == None:
return None
return self.crds[x]
def FixResNum(self):
rnum = 1
for i in range(len(self.records)):
newrnum = rnum
if i < len(self.records)-1 and \
self.records[i+1].rnum != self.records[i].rnum:
rnum = rnum + 1
self.records[i].rnum = newrnum
self.records[i].anum = i
def Copy(self):
crds = Numeric.array(self.crds)
records = copy.copy(self.records)
return PDB(None, crds, records)
def Append(self, struct2):
records = self.records + copy.copy(struct2.records)
crds = Numeric.concatenate((self.crds, struct2.crds))
return PDB(None, crds, records)
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