| Keyword |
Aliases |
Arg |
Set |
Description |
| id |
|
int |
N |
molecular id |
| index |
|
int |
N |
index on the molecule list |
| numatoms |
|
int |
N |
number of atoms |
| name |
|
str |
N |
the name of the molecule (usually the name of the file) |
| filename |
|
str |
N |
list of filenames for all files loaded for this molecule |
| filetype |
|
str |
N |
list of file types for this molecule |
| database |
|
str |
N |
list of databases for this molecule |
| accession |
|
str |
N |
list of database accession codes for this molecule |
| remarks |
|
str |
N |
list of freeform remarks for this molecule |
| active |
|
bool |
Y |
is/make the molecule active |
| drawn |
displayed |
bool |
Y |
is/make the molecule drawn |
| fixed |
|
bool |
Y |
is/make the molecule fixed |
| top |
|
bool |
Y |
is/make the molecule top |
| center |
|
vector |
Y |
get/set the coordinate used as the center |
| center_matrix |
|
matrix |
Y |
get/set the centering matrix |
| rotate_matrix |
|
matrix |
Y |
get/set the rotation matrix |
| scale_matrix |
|
matrix |
Y |
get/set the scaling matrix |
| global_matrix |
|
matrix |
Y |
get/set the global (rotation/scaling) matrix |
| view_matrix |
|
matrix |
N |
get/set the overall viewing matrix |
| numreps |
|
int |
N |
the number of representations |
| selection i |
|
string |
N |
the string for the i'th selection |
| rep i |
|
string |
N |
the string for the i'th representation |
| color i |
colour |
string |
N |
the string for the i'th coloring method |
| numframes |
|
int |
N |
number of animation frames |
| frame |
|
int |
Y |
current frame number |
| timesteps |
|
int |
Y |
number of elapsed timesteps in an interactive simulation |
| angles |
|
list |
Y |
topology angle types and definitions {type a1 a2 a3} |
| dihedrals |
|
list |
Y |
topology dihedral types and definitions {type a1 a2 a3 a4} |
| impropers |
|
list |
Y |
topology improper types and definitions {type a1 a2 a3 a4} |
| bond |
|
float |
N |
the bond energy (for the current frame) |
| angle |
|
float |
N |
the angle energy |
| dihedral |
|
float |
N |
the dihedral energy |
| improper |
|
float |
N |
the improper energy |
| vdw |
|
float |
N |
the van der Waal energy |
| electrostatic |
elec |
float |
N |
the electrostatic energy |
| hbond |
|
float |
N |
the hydrogen bond energy |
| kinetic |
|
float |
N |
the total kinetic energy |
| potential |
|
float |
N |
the total potential energy |
| energy |
|
float |
N |
the total energy |
| temperature |
temp |
float |
N |
the overall temperature |
| pressure |
|
float |
Y |
the simulation pressure |
| volume |
|
float |
Y |
the simulation volume |
| efield |
|
float |
Y |
efield |
| alpha |
|
float |
Y |
unit cell angle alpha in degrees (for the current frame) |
| beta |
|
float |
Y |
unit cell angle beta in degrees (for the current frame) |
| gamma |
|
float |
Y |
unit cell angle gamma in degrees (for the current frame) |
| a |
|
float |
Y |
unit cell length a in Angstroms (for the current frame) |
| b |
|
float |
Y |
unit cell length b in Angstroms (for the current frame) |
| c |
|
float |
Y |
unit cell length c in Angstroms (for the current frame) |
