flex_align Command Help
Command: $SCHRODINGER/utilities/flex_align
flex_align - Uses the shape_screen technology to flexibly align a set of
structures to a flexible template, then reports the alignments associated
with the template conformer that yielded the highest average similarity to
all structures.
Usage: flex_align -screen <screenFile>
-shape <shapeFile>
-JOB <jobName>
[-rigid screen|shape|both [-title <propName>]]
[-norm 1|2|3|4]
[-best]
[-align <smartsFile> [-atoms]]
[-hydrogens]
[-atomTypes mmod|element|qsar]
[-atomWeights <propName>]
[-pharm [-fd <fdFile>] [-rad <radFile>]]
[-flexSearchMethod rapid|thorough|rdkit]
[-flexMaxConfs <maxConfs>]
[-flexConfsPerBond <numPerBond>]
[-flexMaxRelEnergy <energy>]
[-flexAmideOption vary|orig|trans]
[-refine [-refineSearchMethod rapid|thorough|rdkit]
[-refineMaxConfs <maxConfs>]
[-refineConfsPerBond <numPerBond>]
[-refineMaxRelEnergy <energy>]
[-refineAmideOption vary|orig|trans]]
[-refineReport <numAlign>]
[-save]
[-HOST <host>]
[-LOCAL]
[-TMPDIR <dir>]
[-WAIT]
[-INTERVAL <n>]
[-NICE]
[-HELP]
-screen <screenFile> - Maestro or SD file containing the
structures to align.
-shape <shapeFile> - Maestro or SD file containing the
template structure. If <shapeFile> and
<screenFile> are the same, all pairs of
of structures in the file will be rigidly
aligned to see which one is most suitable
as a template. <shapeFile> cannot be the
same as <screenFile> when -rigid is used.
-JOB <jobName> - Job name. Aligned structures will be
written to <jobName>_flex_align.maegz.
-rigid screen|shape|both - <screenFile> and/or <shapeFile> contains
pre-computed conformers, so don't flex.
Consecutive structures with identical
titles and connectivities will be treated
as conformers of the same molecule.
-title <propName> - Use property <propName> as the source of
titles. Valid only with -rigid.
-norm 1|2|3|4 - Similarity normalization scheme. The
similarity between the template A and a
screening molecule B is a function of
the overlap O(A,B) between the two, and
the self-overlaps O(A,A) and O(B,B):
Sim(A,B) = O(A,B)/f(O(A,A), O(B,B))
The normalization scheme determines the
form of the function f:
1 --> f = max{O(A,A), O(B,B)} (default)
2 --> f = min{O(A,A), O(B,B)}
3 --> f = O(A,A)
4 --> f = O(B,B)
-best - Report the best alignment found for each
structure in <screenFile>. This may not
yield a good consensus alignment because
the best alignment doesn't always come
from the same template conformer.
-align <smartsFile> - Align screening structures onto specific
atoms in the shape query using SMARTS
matching rules. Each rule consists of a
SMARTS pattern followed by a list of atoms
that define the desired mapping onto the
shape query. For example, if the shape
query contains a pyridine ring composed of
atoms C12, N13, C14, C15, C16 and C17, and
one wishes to match this to a benzene or
pyridine ring in a screening structure, the
following rule could be used:
c1[n,c]cccc1 12,13,14,15,16,17
When a screening structure is processed,
all possible mappings of the SMARTS are
identified, and the matched screening
structure atoms are aligned onto the list
of shape query atoms. The alignment that
yields the highest similarity is retained.
To align onto multiple, disconnected shape
query substructures, a separate rule can be
provided for each substructure, with one
rule per line. This option cannot be used
in combination with -pharm.
-atoms Report atom lists for all possible matches
to the shape query and exit. Use this flag
if you do not know the correct atom list
for any of the rules.
-hydrogens - Consider hydrogens attached to non-carbon
atoms when computing shape similarity.
By default, all hydrogens are ignored.
-atomTypes mmod|element|qsar - Consider atom types when computing
similarities. If this option is used,
overlapping volumes will be computed only
between atoms of the same type, so that
alignments will favor superposition of
chemically similar atoms. The supported
atom typing schemes are:
1. mmod - MacroModel atom types.
2. element - Elemental types.
3. qsar - Phase QSAR atom types:
D - H-bond donor hydrogen
H - hydrophobic/non-polar
N - negative ionic
P - positive ionic
W - electron-withdrawing
X - other
-atomWeights <propName> - Use real atom-level property <propName>
in <shapeFile> to weight overlap with
template atoms. This is achieved by
scaling the radius of each template atom
by the cube root of its weight. Values
in the range 0 to 1 are recommended.
Valid only when <shapeFile> is a Maestro
file.
-pharm Treat each shape and screening structure
as a collection of pharmacophoric sites,
whose locations are assigned by applying
Phase pharmacophore feature definitions.
Overlapping volumes will be computed only
between sites of the same type. May not
be used with the following: -hydrogens,
-atomTypes, -atomWeights.
-fd <fdFile> Pharmacophore feature definition file.
If omitted, the feature definitions in
the Schrodinger software installation
will be used. Valid only with -pharm.
-rad <radFile> Pharmacophore feature radii. Each line
in <radFile> should contain a feature
type (A,D,H,N,P,R,X,Y,Z), followed by a
radius in angstroms, with one or more
spaces separating the two fields. The
default radius for each feature type is
2.0. Valid only with -pharm.
-flexSearchMethod rapid|thorough|rdkit
- On-the-fly conformer search method. The
default is "rapid". This and other flex
options are not valid with -rigid both.
-flexMaxConfs <maxConfs> - Maximum number of on-the-fly conformers.
the default is 100.
-flexConfsPerBond <numPerBond> - Number of on-the-fly conformers to retain
per rotatable bond in the structure. The
total number of conformers is bounded by
the product of <numPerBond> and the
number of rotatable bonds. Note that if
<maxConfs> is increased, <numPerBond> may
have to be increased as well in order to
retain additional conformers for more
rigid structures. The default is 10.
-flexMaxRelEnergy <energy> - On-the-fly conformational energy window
in kJ/mol. The default is 16.0.
-flexAmideOption vary|orig|trans - On-the-fly amide torsion sampling. The
default is "vary".
-refine - Generate additional conformers for each
consensus alignment to see if a higher
similarity to the template conformer can be
achieved. Refine options are not valid with
-best. Note the following defaults, some of
which differ from the -flex* defaults:
-refineSearchMethod thorough
-refineMaxConfs 1000
-refineConfsPerBond 100
-refineMaxRelEnergy 16.0
-refineAmideOption vary
-refineReport <numAlign> - Report up to <numAlign> refined alignments
for each compound. The default is 1.
-save - Save all shape_screen job files.
-HOST <host> - Run job on remote host. Only single-CPU
jobs are supported.
-LOCAL - Store temporary job files in current
directory.
-TMPDIR <dir> - Store temporary job files in <dir>.
-WAIT - Do not return prompt until job completes.
-INTERVAL <n> - Update log file every <n> seconds.
-NICE - Run job at reduced priority.