Python PDBAtom.yの例

コード例 #1

ファイル: make_mt_cncntr.py プロジェクト: klyshko/MT

pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")

pdbstr1   = 'ATOM     14   CB ALA A   7       8.120  -0.000  52.923  0.00  8.12         A'
pdbat1    = PDBAtom(pdbstr1)
pdbstr2   = 'ATOM     14   CB GLY A   7       8.120  -0.000  52.923  0.00  8.12         A'
pdbat2    = PDBAtom(pdbstr2)

chains   = [chr(i) for i in range(ord('A'), ord('M')+1)]
for chain in chains:
		for mon in range(MT_len):	
			R 		 = R_MT
			pdbat2.z  = 0.0
			pdbat1.z  = 2*r_mon*mon + z_step*(ord(chain) - ord('A'))
			alpha = alpha_step*(ord(chain) - ord('A'))
			pdbat2.y = -alpha
			pdbat2.x = 0.0
			x = R*cos(-alpha)
			y = R*sin(-alpha)
			pdbat1.chainid    = chain
			pdbat2.chainid    = chain
			pdbat1.x          = x
			pdbat1.y          = y
			pdbat1.residueseq = mon/2 + 1
			pdbat2.residueseq = mon/2 + 1
			pdbat1.number     = mon + MT_len*(ord(chain)-ord(chains[0])) + 1 
			pdbat2.number     = mon + MT_len*(ord(chain)-ord(chains[0])) + 1 
			if mon%2 == 0:
					pdbat1.name = 'CA'
					pdbat2.name = 'CA'
			else:

コード例 #2

ファイル: make_mt.py プロジェクト: ykjawale/MT

chains = [chr(i) for i in range(ord('A'), ord('M') + 1)]
for chain in chains:
    for mon in range(MT_len):
        if (MT_len - mon) < tail_len:
            if delete == True and chain == chains[len(chains) - 1]:
                break
            R = R_MT + (tail_len - (MT_len - mon)) * 2 * r_mon * sin(
                theta_tail)  #tail_step*(tail_len - (MT_len - mon))
            pdbat2.z = theta_tail  #atan(tail_step/z_step)
            pdbat1.z = 2 * r_mon * mon + z_step * (ord(chain) - ord('A'))
        else:
            R = R_MT
            pdbat2.z = 0.0
            pdbat1.z = 2 * r_mon * mon + z_step * (ord(chain) - ord('A'))
        alpha = alpha_step * (ord(chain) - ord('A'))
        pdbat2.y = -alpha
        pdbat2.x = 0.0
        x = R * cos(-alpha)
        y = R * sin(-alpha)
        pdbat1.chainid = chain
        pdbat2.chainid = chain
        pdbat1.x = x
        pdbat1.y = y
        pdbat1.residueseq = mon / 2 + 1
        pdbat2.residueseq = mon / 2 + 1
        pdbat1.number = mon + MT_len * (ord(chain) - ord(chains[0])) + 1
        pdbat2.number = mon + MT_len * (ord(chain) - ord(chains[0])) + 1
        if mon % 2 == 0:
            pdbat1.name = 'CA'
            pdbat2.name = 'CA'
        else:

コード例 #3

ファイル: random_concentration_w-o_ring.py プロジェクト: klyshko/MT

		break

pdbxyzfilename = 'volxyz_{}.pdb'.format(int(conc))
pdbangfilename = 'volang_{}.pdb'.format(int(conc))

pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")

pdbstr1   = 'ATOM     14   CB ALA A   7       8.120  -0.000  52.923  0.00  8.12         A'
pdbat1    = PDBAtom(pdbstr1)
pdbstr2   = 'ATOM     14   CB GLY A   7       8.120  -0.000  52.923  0.00  8.12         A'
pdbat2    = PDBAtom(pdbstr2)

for atom in atoms:
	pdbat1.x = atom[0]
	pdbat1.y = atom[1]
	pdbat1.z = atom[2]
	pdbat1.chainid    = 'A'
	pdbat1.residueseq = atoms.index(atom) + 1
	pdbat1.number     = 2 * atoms.index(atom) + 1 
	pdbat1.name = 'CA'
	pdbxyz.write("%s\n" % str(pdbat1))

	pdbat1.x = atom[0]
	pdbat1.y = atom[1]
	pdbat1.z = atom[2]+2*r_mon
	pdbat1.chainid    = 'A'
	pdbat1.residueseq = atoms.index(atom) + 1
	pdbat1.number     = 2 * atoms.index(atom) + 2 
	pdbat1.name = 'CB'
	pdbxyz.write("%s\n" % str(pdbat1))

コード例 #4

ファイル: make_mt_cncntr.py プロジェクト: ykjawale/MT

pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")

pdbstr1 = 'ATOM     14   CB ALA A   7       8.120  -0.000  52.923  0.00  8.12         A'
pdbat1 = PDBAtom(pdbstr1)
pdbstr2 = 'ATOM     14   CB GLY A   7       8.120  -0.000  52.923  0.00  8.12         A'
pdbat2 = PDBAtom(pdbstr2)

chains = [chr(i) for i in range(ord('A'), ord('M') + 1)]
for chain in chains:
    for mon in range(MT_len):
        R = R_MT
        pdbat2.z = 0.0
        pdbat1.z = 2 * r_mon * mon + z_step * (ord(chain) - ord('A'))
        alpha = alpha_step * (ord(chain) - ord('A'))
        pdbat2.y = -alpha
        pdbat2.x = 0.0
        x = R * cos(-alpha)
        y = R * sin(-alpha)
        pdbat1.chainid = chain
        pdbat2.chainid = chain
        pdbat1.x = x
        pdbat1.y = y
        pdbat1.residueseq = mon / 2 + 1
        pdbat2.residueseq = mon / 2 + 1
        pdbat1.number = mon + MT_len * (ord(chain) - ord(chains[0])) + 1
        pdbat2.number = mon + MT_len * (ord(chain) - ord(chains[0])) + 1
        if mon % 2 == 0:
            pdbat1.name = 'CA'
            pdbat2.name = 'CA'
        else:

コード例 #5

ファイル: make_mt.py プロジェクト: klyshko/MT

pdbat2    = PDBAtom(pdbstr2)
chains   = [chr(i) for i in range(ord('A'), ord('M')+1)]
for chain in chains:
		for mon in range(MT_len):	
			if (MT_len - mon) < tail_len:
					if delete == True and chain == chains[len(chains) - 1]:
							break
					R 		= R_MT + (tail_len - (MT_len - mon))*2*r_mon*sin(theta_tail) #tail_step*(tail_len - (MT_len - mon))
					pdbat2.z = theta_tail #atan(tail_step/z_step)
					pdbat1.z = 2*r_mon*mon + z_step*(ord(chain) - ord('A'))
			else:
					R 		 = R_MT
					pdbat2.z  = 0.0
					pdbat1.z  = 2*r_mon*mon + z_step*(ord(chain) - ord('A'))
			alpha = alpha_step*(ord(chain) - ord('A'))
			pdbat2.y = -alpha
			pdbat2.x = 0.0
			x = R*cos(-alpha)
			y = R*sin(-alpha)
			pdbat1.chainid    = chain
			pdbat2.chainid    = chain
			pdbat1.x          = x
			pdbat1.y          = y
			pdbat1.residueseq = mon/2 + 1
			pdbat2.residueseq = mon/2 + 1
			pdbat1.number     = mon + MT_len*(ord(chain)-ord(chains[0])) + 1 
			pdbat2.number     = mon + MT_len*(ord(chain)-ord(chains[0])) + 1 
			if mon%2 == 0:
					pdbat1.name = 'CA'
					pdbat2.name = 'CA'
			else:

コード例 #6

        break

pdbxyzfilename = 'volxyz_{}.pdb'.format(int(conc))
pdbangfilename = 'volang_{}.pdb'.format(int(conc))

pdbxyz = open(pdbxyzfilename, "w")
pdbang = open(pdbangfilename, "w")

pdbstr1 = 'ATOM     14   CB ALA A   7       8.120  -0.000  52.923  0.00  8.12         A'
pdbat1 = PDBAtom(pdbstr1)
pdbstr2 = 'ATOM     14   CB GLY A   7       8.120  -0.000  52.923  0.00  8.12         A'
pdbat2 = PDBAtom(pdbstr2)

for atom in atoms:
    pdbat1.x = atom[0]
    pdbat1.y = atom[1]
    pdbat1.z = atom[2]
    pdbat1.chainid = 'A'
    pdbat1.residueseq = atoms.index(atom) + 1
    pdbat1.number = 2 * atoms.index(atom) + 1
    pdbat1.name = 'CA'
    pdbxyz.write("%s\n" % str(pdbat1))

    pdbat1.x = atom[0]
    pdbat1.y = atom[1]
    pdbat1.z = atom[2] + 2 * r_mon
    pdbat1.chainid = 'A'
    pdbat1.residueseq = atoms.index(atom) + 1
    pdbat1.number = 2 * atoms.index(atom) + 2
    pdbat1.name = 'CB'
    pdbxyz.write("%s\n" % str(pdbat1))