Fragment Commands
This chapter describes a number of ChemShell commands that
operate on the ChemShell data structure describing
a molecule or crystal (also known as the fragment structure). In order to keep
the data structure in memory, the fragment has to be
declared.
The c_create command is used to setup the fragment structure. See
also the z_to_c command described in the Z-matrix section.
List of Functions in this section:
c_create
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
Identifier for the resulting fragment object |
| last argument |
Tcl List
|
yes |
- |
Fragment contents |
Description:
c_create creates a fragment object from a set of input records, the
following is the simplest form:
c_create coords=c {
coordinates angstrom
o 0. 0. 0.
h 0. 1. 0.
h 0. -0.5 1.0
}
The valid fields are as follows
coordinates: subsequent records define the position of the atoms. Each input
record has the form
symbol x y z
Optionally, an atomic charge may be presented as well. If the
charge is omitted, it is assumed to be undefined (this is not the same as
setting it to zero). The charge may be optionally
be preceeded by the keyword "charge".
shells Subsequent records define the position of shells. Each input
line consists of:
symbol x y z charge
bqs To define point charge positions. Each subsequent
record has the form
symbol x y z charge
space_group Allows the specification of a space group on the next record,
which can be presented as a number or a symbol, e.g.
space_group
p-1
cell_constants Allows the specification of crystallographic
cell parameters, presented (for 3D systems) as
cell_constants
a b c alpha beta gamma
and for slabs as
cell_constants
a b gamma
and for polymers as
cell_constants
a
Note that if a cell_constants record is presented, it is assumed
that coordinates ,shells , and bqs are
presented in fractional (or, for 1 and 2D, mixed) units.
cell Allows the specification of real-space periodicity
information. Depending on the dimensionality of the system, either
1, 2, or 3 records may be presented, each specifying a real-space vector
defining the corresponding cell vector
cell
x1 y1 z1
x2 y2 z2
x3 y3 z3
When cell is presented, it is assumed that the coordinates will be
in real-space (cartesian) form.
The coordinates bqs, shells and cell keywords
may be optionally followed by a unit specification
(e.g. angstrom above) to indicate the unit of length used. The default
is au.
connect: specifies how the fragment's connectivity table should be generated. Valid
values are covalent (default), ionic or no for an empty connection table.
See the connect command for details of the covalent and
ionic modes. Note that the connectivity method used is not stored in the fragment file, so
the mode should always be specified when reconnecting the fragment if you do not want to use
the default.
The following Tcl functions will change a molecule definition. Unless
otherwise specified, each command takes a coords= argument
to specify the molecule under examination.
and in some cases a result= argument to indicate the destination.
Other arguments are used as indicated in the examples below.
List of Functions in this section:
set_molecule_charge
set_atom_charge
set_bq_charge
set_shell_charge
unset_charges
add_atom_entry
add_shell_entry
replace_atom_entry
replace_bq_entry
replace_shell_entry
delete_atom_entry
delete_shell_entry
add_connection
delete_connection
set_cell
set_element_data
extend_fragment
connect
c_merge_fragments
set_atom_residue
unset_residues
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| charge |
real |
yes |
- |
charge to assign |
Description:
Assign a charge to a fragment
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment |
| atom_number |
integer |
yes |
- |
atom index |
| charge |
real |
yes |
- |
atom charge |
Description:
Sets the charge value for the atom
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment |
| bq_number |
integer |
yes |
- |
bq index |
| charge |
real |
yes |
- |
bq charge |
Description:
Sets the charge value for the BQ centre
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment |
| shell_number |
integer |
yes |
- |
shell index |
| charge |
real |
yes |
- |
shell charge |
Description:
Sets the charge value for the shell
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment |
Description:
Resets the flag denoting that atomic charges are stored for
the fragment object
add_atom_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| atom_entry |
Tcl List
|
yes |
- |
Atom data (Symbol,x,y,z) |
| atom_number |
integer |
no |
- |
atom number of required atom after insertion |
Description:
Add a new atom, adding to the end of the list,
unless atomnumber= was specified, in which case the
new atom is inserted
If the system is periodic,
the fractional cell information is also updated (the
latter assuming P1 symmetry, which may mean that warning messages
are generated later if equivalent atoms are added.
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| shell_entry |
Tcl List
|
yes |
- |
Shell data (Symbol,x,y,z,charge,parent core) |
| position |
string |
yes |
- |
how shell position is input (absolute or relative coordinates) |
Description:
Add a shell to the structural definition. If the system is periodic,
the fractional cell information is also updated (the
latter assuming P1 symmetry, which may mean that warning messages
are generated later if equivalent atoms are added.
The shell coordinates can be given either as absolute values
or relative to the corresponding core (the position argument must be given
to specify which has been used). Note that if absolute values are used,
the parent core will be assigned to the nearest core regardless of user input.
Internally the position is stored using
relative coordinates (so the shell will move when the core is moved).
replace_atom_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| atom_number |
integer |
yes |
- |
index of atom to replace |
| atom_entry |
Tcl List
|
yes |
- |
Atom data (symbol,x,y,z) |
Description:
Replace the specified atom.
replace_bq_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| bq_number |
integer |
yes |
- |
index of bq to replace |
| bq_entry |
Tcl List
|
yes |
- |
Bq data (Symbol,x,y,z,charge) |
Description:
Replace the specified point charge.
replace_shell_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| shell_number |
integer |
yes |
- |
index of shell to replace |
| shell_entry |
Tcl List
|
yes |
- |
Shell data (Symbol,x,y,z,charge,parent core) |
| position |
string |
yes |
- |
how shell position is input (absolute or relative coordinates) |
Description:
Replace the specified MD Shell.
The shell coordinates can be given either as absolute values
or relative to the corresponding core (the position argument must be given
to specify which has been used). Internally the position is stored using
relative coordinates (so the shell will move when the core is moved).
delete_atom_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| atom_number |
integer |
yes |
- |
index of atom to delete |
Description:
Delete the specified atom. If a shell is attached it will also be
deleted.
delete_shell_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| shell_number |
integer |
yes |
- |
index of shell to delete |
Description:
Delete the specified shell and transfer the charge on it to
the parent atom.
add_connection
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| i |
integer |
yes |
- |
first atom index |
| j |
integer |
yes |
- |
second atom index |
Description:
Add a connection table entry between the specified atoms.
delete_connection
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| i |
integer |
yes |
- |
first atom index |
| j |
integer |
yes |
- |
second atom index |
Description:
Deletes a connection table entry between the specified atoms.
set_cell
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| cell |
Tcl List |
yes |
- |
Unit cell |
Description:
Modify periodic boundary conditions
set_element_data
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| symbol |
text |
yes |
- |
Element symbol of required atom |
| field |
text |
yes |
- |
Element data entry to modify |
| value |
real |
yes |
- |
New value to assign. |
Description:
Modify an entry from the element data table. Valid values for the
field argument are covalent_radius, vdw_radius, atomic_number and atomic_symbol.
extend_fragment
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
origin fragment (must be periodic) |
| result |
Fragment tag
|
yes |
- |
target fragment (will be non-periodic) |
| cell_indices |
Tcl List
of 6 integers |
yes |
- |
Start/finish indices of cells required |
Description:
Replicate a fragment using the unit cell vectors. The range of the
extended lattice is given by six integers, specifying the start and
end cell indices in the x,y, and z directions. The example below will
generate a 3x3x3 block of cells.
extend_fragment coords=c result=c2 cell_indices= { -1 1 -1 1 -1 1}
connect
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| conn |
Fragment tag
|
yes |
- |
resulting fragment with connectivity table |
| mode |
string |
no |
covalent |
Use covalent or ionic radii (see below) |
| scale |
real |
no |
- |
Scale factor for radii used for test |
| toler |
real |
no |
- |
Tolerance for test |
Description:
Generates a connectivity table for a molecule, based
on internuclear separation and atomic radii. Atoms i and j
are considered to be connected when
R_ij < scale*(rad_i + rad_j) + toler
where R_ij is the internuclear distance, rad_i is the
radius of i, and scale and toler take values from the
input arguments, and if these are not presented,
from the global variables
chemsh_default_connectivity_scale
and
chemsh_default_connectivity_toler
By default covalent radii are used. An alternative ionic mode is available
for use with ionic solids and clusters, which uses approximate ionic radii instead.
In this mode the distance cut-off is scaled down for ions of the same sign
to exclude "unintentional" coordination (therefore when using the ionic mode
atomic charges should be set and all shells assigned to atoms).
c_merge_fragments
Command Line Arguments
Description:
This command merges the fragments c1 and c2 and generates a single
fragment cmerged consisting of the overlay of the original fragments.
The ordering of the atoms in the resulting fragment are as follows:
first the atoms in fragment c1 in the same order as in that fragment,
then the atoms in fragment c2, with the exception of atoms close to
the atoms already defined in fragment c1. The atoms in c2 close to
the atoms in c1 are assumed to be duplicate and are therefore discarded
in the merging operation. The default values for the seed=, start=, and
end= arguments are 1, 1, and the number of atoms in the fragment, respectively.
c_merge_fragments base=c1 add=c2 result=cmerged
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment |
| atom_number |
integer |
yes |
- |
atom index |
| residue |
integer |
yes |
- |
number of the residue (charge group) the atom
belongs to |
Description:
Sets the number of the residue (charge group) the atom
belongs to
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment |
Description:
Resets the flag denoting that residue (charge group) information for the atoms
is stored for the fragment object
The following Tcl functions will return information on
a molecule definition. Each command takes a coords= argument
to specify the molecule under examination. Other arguments are
used as indicated in the examples below.
List of Functions in this section:
get_number_of_atoms
get_number_of_bqs
get_number_of_exts
get_molecule_name
get_molecule_charge
check_for_bond
check_molecule connectivity
get_connected_atoms
get_molecule_members
interatomic_distance
angle
dihedral
get_atom_entry
get_atom_charge
get_atom_znum
atom_charge_defined
get_bq_entry
get_shell_entry
get_ext_entry
get_cell
get_molecule_centre
get_molecule_radius
get_element_data
compare_fragments
bang
get_atom_residue
get_electric_bq_field
get_number_of_atoms
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
Description:
Returns the number of atoms in a fragment
get_number_of_bqs
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
Description:
Returns the number of bqs (point charges) in a fragment
get_number_of_exts
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
Description:
Returns the number of external sites in a fragment
get_molecule_name
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
Description:
Returns the title of the fragment
get_molecule_charge
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
Description:
Returns or modifies the internally stored charge, for example:
set old [get_molecule_charge coords=c ]
set_molecule_charge coords=c charge=2
set new [get_molecule_charge coords=c ]
puts stdout "old charge $old, new charge $new"
check_for_bond
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| i |
integer |
yes |
- |
first atom index |
| j |
integer |
yes |
- |
second atom index |
Description:
Returns 1 if a connection is stored between two atoms, 0 otherwise.
check_molecule connectivity
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
Description:
Returns 1 if a connectivity table is stored for the fragment, 0 otherwise.
get_connected_atoms
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| atom_number |
integer |
yes |
- |
reference atom |
Description:
Returns a Tcl list of atom numbers. The atom numbers listed are those connected
to the atom specified through the atom_number= argument.
set mol_list [get_connected_atoms coords=c atom_number=4]
puts stdout $mol_list
get_molecule_members
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| atom_number |
integer |
yes |
- |
reference atom |
| range |
integer |
no |
- |
number of bonds to search (default 9999) |
Description:
Returns a Tcl list of atom numbers. The atom numbers listed are those
connected to the atom specified through the atom_number=
argument up to range= number of bonds from the specified
atom. The default of the range= argument is 9999, which in
principle suffices to get all the atoms belonging to a molecule.
set mol_list [get_molecule_members coords=c atom_number=4 range=3]
puts stdout $mol_list
interatomic_distance
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| i |
integer |
yes |
- |
first atom index |
| j |
integer |
yes |
- |
second atom index |
| unit |
text |
no |
- |
specification of output unit (default au) |
Description:
Returns an interatomic separation in au.
set r12 [interatomic_distance coords=c i=1 j=2]
The unit=angstrom argument may be used to request the distance in Å.
angle
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| i |
integer |
yes |
- |
first atom index |
| j |
integer |
yes |
- |
second atom index |
| k |
integer |
yes |
- |
third atom index |
Description:
Returns the angle defined by atoms i-j-k in degrees.
dihedral
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| i |
integer |
yes |
- |
first atom index |
| j |
integer |
yes |
- |
second atom index |
| k |
integer |
yes |
- |
third atom index |
| l |
integer |
yes |
- |
fourth atom index |
Description:
Returns the torsion angle defined by atoms i-j-k-l in degrees.
get_atom_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| atom_number |
integer |
yes |
- |
index of atom to recover |
Description:
Returns information about an atom, consisting of the atom symbol and
x,y, and z coordinates for the requested atom. The following example loops
over all atoms retrieving the the atomic symbol and coordinates.
set n [get_number_of_atoms coords=c ]
for {set i 0} {$i < $n} {incr i} {
set atom [ get_atom_entry atom_number=$i coords=c]
puts stdout $atom
}
get_atom_charge
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| atom_number |
integer |
yes |
- |
index of atom |
Description:
Returns atom charge, or the string "undefined" if the charge
is not defined.
get_atom_znum
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| atom_number |
integer |
yes |
- |
index of atom |
Description:
Returns atomic number (Z) of the atom.
atom_charge_defined
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| atom_number |
integer |
yes |
- |
index of atom |
Description:
Returns 1 if the atom charge is defined, 0 otherwise.
get_bq_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| bq_number |
integer |
yes |
- |
index of bq to recover |
Description:
Returns information about a bq (point charge), consisting of the charge and
x,y, and z coordinates for the requested centre.
get_shell_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| shell_number |
integer |
yes |
- |
index of shell to recover |
| position |
string |
yes |
- |
how shell position is returned (absolute or relative coordinates) |
Description:
Returns information about a shell, consisting of the symbol,
x,y, and z coordinates, charge and parent core of the requested centre.
The shell coordinates can be returned either as absolute values
or relative to the corresponding core (the position argument must be given
to specify which to return). Internally the position is stored using
relative coordinates (so the shell will move when the core is moved).
get_ext_entry
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| ext_number |
integer |
yes |
- |
index of external site to recover |
Description:
Returns information about an external site, consisting of the charge and
x,y, and z coordinates for the requested centre.
get_cell
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
Description:
Return simulation cell as a Tcl list
0 elements for a non-periodic system
6 for a slab
9 for a 3-d system
get_molecule_centre
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
Description:
Return the centroid of the fragment, as a Tcl list of three real values.
get_molecule_radius
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
Description:
Return the radius of the smallest sphere, which, when
centred at the centroid of the fragment encloses all the atoms.
get_element_data
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| symbol |
text |
no |
- |
Element symbol of required atom type |
| atomic_number |
integer |
no |
- |
Atomic number of required atom type |
| field |
text |
yes |
- |
Required element data entry |
Description:
Return an entry from the element data table. It is possible to
provide either the symbol or the atomic number.
Valid values for the
field argument are covalent_radius, vdw_radius, atomic_number and atomic_symbol.
compare_fragments
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords1 |
Fragment tag
|
yes |
- |
First fragment |
| coords2 |
Fragment tag
|
yes |
- |
Second fragment |
| toler |
real |
no |
- |
Tolerance for tests (default 0.01 au). |
Description:
Check two fragments for matching coordinates and symbols.
bang
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag |
yes |
- |
input structure |
| toler |
floating point |
yes |
- |
tolerance used for generating connectivity |
| unit |
string |
yes |
- |
unit to use |
Description:
bang is a program to generate bond-length and angle listings. The bond
lengths, inter-bond angles, and proper torsion angles are printed
out. The tolerance is used in the same way as connect to determine
which parameters are listed. The unit may be angstrom or au, (au is
the default).
get_atom_residue
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| atom_number |
integer |
yes |
- |
index of atom |
Description:
Returns the number of the residue (charge group) the atom belongs to, or
the string "undefined" if the charge
is not defined.
get_electric_bq_field
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
| position |
Tcl List
of 3 real numbers |
no |
- |
Position to calculate the potential and the electric filed. |
| file |
string |
no |
- |
File name to which an xyz file is written
contining the atom positions and the electric field at that atom. |
Description:
To be used with fragments containing point charges as bq
entries. get_electric_bq_field calculates the electrostatic
potential and the electric field that the bqs cause at the atomic
positions. If position is specified, the potential and the
field are calculated there.
If charges of the atoms are specified (e.g. by using fit_esp_charges), the command will also print the
electrostatic force on that atom caused by the bq charges in the fragment.
The following Tcl functions will return information on
a molecule definition. Each command takes a coords= argument
to specify the molecule under examination. Other arguments are
used as indicated in the examples below.
List of Functions in this section:
write_xyz
read_xyz
write_pdb
read_pdb
write_xtl
read_xtl
write_msi
list_molecule
c_prepare_input
write_xyz
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
Fragment to output |
| file |
text |
yes |
- |
Output file name |
Description:
Write out a fragment to a file in xyz format.
read_xyz
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
Fragment to create |
| file |
text |
yes |
- |
Input file name |
Description:
Read in a fragment from a file in xyz format.
write_pdb
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
Fragment to output |
| file |
text |
yes |
- |
Output file name |
| info_var |
keyword |
no |
none |
pdb meta info stored by read_pdb
(specified there also by info_var) |
| residues |
Tcl List
|
no |
none |
List of residues in the same format as required
for hdlcopt (see there). Atoms with no
residue in this list are assigned the residue "none". |
Description:
Write out a fragment to a file in pdb format. If a previous call of
read_pdb on a pdb file with the same number of atoms was made,
meta-informations such as residue names are reused. Otherwise they are guessed.
read_pdb
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
Fragment to create |
| file |
text |
yes |
- |
Input file name |
| info_var |
keyword |
no |
none |
save pdb meta info to be reused by write_pdb |
Description:
Read in a fragment from a file in pdb format.
write_xtl
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
Fragment to output |
| file |
text |
yes |
- |
Output file name |
Description:
Write out a fragment to a file in xtl format. This format can be used
to output periodic systems
read_xtl
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
Fragment to create |
| file |
text |
yes |
- |
Input file name |
Description:
Read a fragment object from a file in xtl format.
write_msi
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
Fragment to output |
| file |
text |
yes |
- |
Output file name |
Description:
Write out a fragment to a file in msi format.
list_molecule
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
Description:
Provide listing of fragment definition to stdout.
c_prepare_input
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to interrogate |
Description:
Provide listing of fragment definition to stdout in form suitable for
use by the c_create command. The resulting text is the return value,
use as follows
set data [ c_prepare_input coords=c ]
set fp [ open data.txt w ]
puts $fp $data
close $fp
List of Functions in this section:
c_shuffle
c_reorder
c_shuffle
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| result |
Fragment tag
|
yes |
- |
resultant fragment |
| indexlist |
Tcl List
|
yes |
- |
re-ordering matrix |
Description:
This command will change the order in which the cartesian atoms are listed. In
the example, atoms 5, 12, 3, and 8 in the original fragment c will appear as
atoms 1, 2, 3, and 4 in the resulting fragment cshuffled. The other atoms then
follow: number 1 will be 5, number 2 will be 6, number 4 will be 7, etc.
c_shuffle coords=c result=cshuffled indexlist= {5 12 3 8}
c_reorder
Command Line Arguments
| Argument |
Argument type |
Mandatory |
Default |
To specify |
| coords |
Fragment tag
|
yes |
- |
denotes fragment to modify |
| result |
Fragment tag
|
yes |
- |
resultant fragment |
| seed |
integer |
no |
- |
reference atom number |
| start |
integer |
no |
- |
start reordering from this atom |
| end |
integer |
no |
- |
finish reordering at this atom |
Description:
This command will change the order in which the cartesian atoms are listed on
the basis of their distance to a specific atom. The atom with respect to which the
distance is measured is specified by the seed= argument. The reordering may be
limited to a range of atoms in the original fragment by the start= and end=
arguments. In the example, atoms 6 through 12 in the original fragment c will be
reordered in increasing distance from atom 1 in the creordered fragment.
The default values for the seed=, start=, and end= arguments are 1, 1, and
the number of atoms in the fragment, respectively.
c_reorder coords=c result=creordered seed=1 start=6 end=12
|
