This is the basic modelling facility to build and modify
united- (or all-) atom structures. Most activities are
changing the topology of the structures, although the forge
menu can also be addressed from here.
Atoms may be attached to existing ones, by picking those
(left button). If attachment can be done in more than a
single conformation, the user can toggle through the various
possibilities by keeping the left-hand button pressed and
repeatedly pressing the middle button. After releasing the
left button this feature is lost. An atom picked with the
middle button will be removed. The type of the added atom is
indicated as the menu header. The type of bonding (single,
double, triple) applied is also indicated (1, 2, 3).
Regarding atom types, there is no distinction into various
subtypes for the same chemical symbol! This must not be
considered a drawback, because the force field makes proper
recognition and treatment.
Topology Changes, Building [dTp]
n: open new entry (C2H6)
Here a new entry (ethane) will be generated. Except for
option m, this is the only way to do so. All other com
mands modify existing structures. The new entry will be
placed at the center of the visibility volume.
m: open SMILES entry
A SMILES code can be typed (pasted) into a string
requester. Then Moloc generates a new entry with the
topology of the given SMILES and a 'de novo\q conforma
tion.
t: change default atom type
The atom type to be added under option a is set here.
This is only relevant for non-zero bond type.
0,1,2,3: single, double, triple bond
If the bond type indicator is zero, single bonds are
inserted when using the bond option (b). However, in
this case the atom option (a) is altered such that upon
its selection a separate atom addition menu is entered.
Thus, the case zero restores the type of functionality,
as it was in older versions of Moloc (see
following Section).
a: add and delete atoms
Atoms may be attached to existing ones, by picking
those (left button). If attachment can be done in more
than a single conformation, the user can toggle through
the various possibilities by keeping the left-hand but
ton pressed and repeatedly pressing the middle button.
After releasing the left button this feature is lost.
An atom picked with the middle button will be removed.
The type of the added atom is indicated as the menu
header. The type of bonding (single, double, triple)
applied is also indicated (s, d, t). Regarding atom
types, there is no distinction into various subtypes
for the same chemical symbol! This must not be consid
ered a drawback, because the force field makes proper
recognition and treatment.
c: change atom types
Every atom picked will change its core number to the one
indicated by the menu header. H-counts will be adjusted
properly if possible. The last change made can be taken
back by picking the atom with the middle button.
b: add and delete bonds
Pick (left mouse button) the two atoms to be bonded to
generate a new bond. An erroneous first pick can be
undone by picking again with the middle button. The
multiplicity of the bond is as indicated in the menu,
and corresponding H-count adjustments are made at the
bonded atoms. To delete a bond, pick it with the middle
mouse button. a deleted bond is always assumed to have
been single!
s: add selected substituents
When this option is chosen a limited choice of avail
able substituents is presented before the actual build
ing can take place. The substituents are added by
picking atoms. The last addition can be removed again
by M picking the atom of attachment. As long as the L-
button is kept down after picking, one has the possi
bility to change the stereochemistry of the attachment.
M-clicks switch between stereoisomers (L is still
pressed). By pressing in addition the R-button, M-
clicks change the rotamer. In case you are afraid to
break your fingers, adjust the conformation with the
frg tool.
l: add local entries
A copy of any local entry (picked first) can be taken
over to another entry (picked second). If the trans
ferred entry is not repositioned, its origin becomes
invisible under the action.
i: identify (condense) bonds or atoms
The two atoms or bonds to be identified must me in dif
ferent fragments of the same entry. The two items to be
identified must be picked (left button). The fragment
picked first will be moved. This happens immediately
for atoms. For bonds, the direction of condensation
must be indicated by picking in addition a pair of cor
responding end atoms.
d: delete sets
Here, you are dropped into the set tool. All atoms which
belong to the current set are deleted upon leaving the
tool.
f: forge structures
u: united atoms (remove H's)
When picking an entry, all its explicit Hydrogen atoms
are removed and the H-count of the affected heavy atoms
are correspondingly augmented.
h: check modify silent H's (see Section on the
MAB-force field)
k: keep (add) H's explicitly
The silent Hydrogens of a picked structure will be
replaced by explicit ones.
o: optimize active structures
The optimizer menu is entered. Because freshly built
structures may have queer geometries no default mask is
used here. Some of the mask options may prevent sensi
ble relaxation!
p: print smi
If an entry is picked, its SMILES code is written to the
text port. This code is not unique which must be taken
into account when using it for the software package
Daylight!
r: generate scratch coordinates
The program generates a 'de novo\q conformation for the
picked entry.
Add and Delete Atoms, Change Core Numbers
If the bond type indicator is set to (c) atoms types are
changed by picking. The type they are changed to is given in
the menu header. Some changes may be awkward with respect to
Hydrogen counts. Consequently, these counts should be
checked afterwards!
1, 2, 3, c: bond type indicator
Choosing this point changes the applied bond type by
toggling through the three options: 1(ingle), 2(ouble),
3(riple) bond. The fourth option (c) changes the func
tionality to changing atom types. In this case the
picked atoms change their core number to the one indi
cated in the menu header. When choosing the change
option (c) in dTp, Tis is the initial modus.
C: carbon
N: nitrogen
O: oxygen
P: phosphorous
S: sulfur
o: others
Any atom type (below Fm) can be chosen by entering its
chemical symbol. However, not all of them will be
treated properly by the force field, or even by the
building routines.