vector2pdb

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vector2pdb is Eos's Command that creates PDB file by inputting parameter.


List of option

Main option

Option Essential/Optional Description Default
-o Optional Output: PDB stdout
-v Optional Input: Vector: (vx, vy, vz) (1, 0, 0)
-polar Optional Input: Vector[degree]: (phi, theta) (0, 0)
-polarz Optional Input: z-axis for polar: (zx, zy, zz) (0, 0, 1)
-polarx Optional Input: x-axis for polar: (xx, xy, xz) (1, 0, 0)
-ori Optional Input: origin: (sx, sy, sz) (0, 3, 0)
-step Optional Input: step: [A] 1.6
-n Optional Input: Number Of CA 20
-ID Optional Input: Chain ID A
-Res Optional Input: Chain ID GLY
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help  

-m details

Value Description
0

Execution example

Case: Options only essential

Outdata-vector2pdb.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.520000e+01 3.000000e+00 0.000000e+00

1.520000e+01

15.20 0.00 0.00


Option -v

Case: v=(1, 2, 3)

Outdata-v-vector2pdb.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

4.062400e+00 1.112470e+01 1.218715e+01

1.520002e+01

4.06 8.12 12.19


Option -polar

Case: polar=(30, 45), v=(1, 2, 3)

Outdata-polar-vector2pdb.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

9.308100e+00 8.374000e+00 1.074800e+01

1.520000e+01

9.31 5.37 10.75


Option -polarz

Case: polarz=(3, 2, 1), polar=(30, 45), v=(1, 2, 3)

Outdata-polarz-vector2pdb.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.377120e+01 9.259950e+00 -1.485850e+00

1.520002e+01

13.77 6.26 1.49


Option -polarx

Case: polarx=(1, 2, 3), polar=(30, 45), v=(1, 2, 3)

Outdata-polarx-vector2pdb.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

-1.781550e+00 8.668600e+00 1.399045e+01

1.519999e+01

1.78 5.67 13.99


Option -ori

Case: ori=(7, 3, 5), v=(1, 2, 3)

Outdata-ori-vector2pdb.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

1.106240e+01 1.112470e+01 1.718715e+01

1.520002e+01

4.06 8.12 12.19


Option -step

Case: step=3.2, v=(1, 2, 3)

Outdata-step-vector2pdb.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

8.124700e+00 1.924945e+01 2.437420e+01

3.039995e+01

8.12 16.25 24.37


Option -n

Case: n=30, v=(1, 2, 3)

Outdata-n-vector2pdb.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.200467e+00 1.540090e+01 1.860140e+01

2.320029e+01

6.20 12.40 18.60