Copyright © 2020, Molsoft LLC Jun 5 2024
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[ defCell | accFunction | gapFunction | I_out | M_out | R_out | R_2out | S_out | S_proteinTags | swissFields | readMolNames | Selection variable | as_out | as2_out | vs_out ]
the real array of the default cell parameters. This definition is used in the Resolution and MaxHKL functions if cell parameters are not provided as arguments. Default: {1. 1. 1. 90. 90. 90.}
This definition is effectively implemented in the Align( seq_1 seq_2 area ) }, Score functions and find database command. Default: {0.33 2.35 0.211, -15.0}. See also: alignMethod .
the real array of the gap penalty parameters, which represent a piecewise-linear concave function (as described in Batalov and Abagyan, 1999). ATTENTION: at the present time this gapFunction is only active when alignMethod =2. The first two values replace gapOpen and gapExtension traditional values. If present, the third element of the array represents the length of the gap, starting at which further gapExtensions become equal to the fourth element of the array. Likewise, if more elements are present, they represent pairs of the threshold lengths of the gap and the new gapExtensions values. For example, gapFunction = {2.4 0.15 10. 0.05 20. 0.}means that
Default: {2.4 0.15}. Recommended (put it in your _startup file): gapFunction = {2.4 0.15 10.} This set will produce fast and structure-like alignments. See also alignMethod, and accFunction (the accessibility attenuation parameters).
an integer array in which the output of some commands is stored.
matrix in which the output of some commands is stored.
real array in which the output of some commands is stored. Functions returning in R_out:
auxiliary rarray. Used in addition to R_out.
string array in which the output of some commands is stored.
sarray of sequence patterns that can be used for detection or deleting those tags from a sequence using Trim ( seq S_tags ) function.
string array of SWISS-PROT fields to be read by default in read sequence swiss If the field name starts from a minus ('-'), this field will be ignored in the feature table list. Also note that variable i_2out (after read sequence) contains the beginning of mature sequence. Example: swissFields={"-HELIX ","-COIL ","-STRAND","-TURN "} # to suppress the FT records with the secondary structure info
string array in which the SDF-file comment fields containing database compound identifier and description are preset. There is a standard place where database compound identifier should be stored in SDF (MOL)-files. This is the first line of the entry. However most of the database providers got used to leaving this line empty. Instead they put identifier and description in the end of the file in the following fashion: ... M END > <CAT_NO> R150002 > <NAME> (5-OXO-HEXAHYDRO-PYRANO[3,2-B]PYRROL-1-YL)-ACETIC ACID METHYL ESTER $$$$In this particular case before using such database set readMolNames = {"<CAT_NO>" "<NAME>"} # useful for Sigma-Aldrich files Another example: readMolNames = {"<CODE>" "<IUPAC_NAME>"} # useful for ACD database
Selections of atoms, residues, molecules, objects or internal variables (torsions, planar angles, bond lengths) can be stored in variables. Examples: cc = a_//ca # created named selection variable cc show cc & a_/3:15 # use it in the expressionIn this case the named selection cc is a true ICM-shell variable, not just an alias for the Ca selection. Please do not confuse it with another useful mechanism which allows you to use a string in a selection. This mechanism is used in scripts and macros. Example: cc = "a_//ca" # in this case cc is a string, not a selection show $cc & a_/3:15 # $cc is replaced by a_//ca before parsing How to store and exchange selections in strings:Examples of using the String ( os|ms|rs [name|number] ) function to return a residue selection: l_showResCodeInSelection = yes # the default res_str = String( Res(Sphere( a_H [1] a_A//!h*,ca,c,n,o 3.5 ))) # same as with option String(.. name) show res_str a_2c0cb.b/^T159,^S205,^K209,^Y224,^V248,^Y275,^L305,^M356,^N361 # or l_showResCodeInSelection = no res_str = String( Res(Sphere( a_H [1] a_A//!h*,ca,c,n,o 3.5 ))) # same as with option String(.. number) show res_str a_2c0cb.b/159,205,209,224,248,275,305,356,361However, be careful with using it in an arbitrary case at the atomic level since it may lead to a string that is too long.
an atom/residue/molecule/object selection variable where some commands or functions store their output: If atoms a_1./3/ca,c,n relate to atoms a_2./45/ca,c,n, then the first set will end up in as_out and the second in as2_out.
the second set of atoms ( selection ) returned by the following commands and functions: See also: as_out.
The variable selection where some commands or functions store their output:
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