Copyright © 2020, Molsoft LLC Nov 14 2024
|
[ iarray | integer | label | logical | macro | map | matrix | MIMEL | mmff . | mmcif | Mol | mol2 | more | trajectory | mute ]
A basic ICM class for arrays of integers: {5, 7, -100, 10} See also: Iarray , Tointeger , read iarray.
numbers may exist in the ICM-shell as a named variable or a constant (e.g. 123,2,-45 ). There are several dozen predefined integer variables. Integers may be mentioned in arithmetic expressions, commands and functions. Examples: born = 1957 + 5 # she is 5 years younger now = 1996 # lets pretend we live in 1996 if (now - born > 28) print "no, you are not 28, you are 27!"
usually a string displayed in the ICM graphics window. Types of labels:
display "Below lies a black abyss" To delete it delete label i_labelNumber e.g. delete label 2 To show: show labels
may exist in ICM-shell as a named variable or a constant (only two possibilities: yes and no ) You can use exclamation mark for negation ( !) and two operations: and ( & ) and or ( | ) There is a number of predefined logical variables. Logicals can be used in arithmetic expressions, most frequently in if ( logical ) ... expressions. Examples: l_nowIamDoingAStupidThing = yes & yes l_Polite = no # another logical variable if (Error & !l_Polite) print "And what do you think you are doing?"
a group of ICM commands in a separate named function with arguments. Many advanced ICM tools are implemented as macros (e.g. icmPocketFinder. See description macro in the command section. See also user-defined (or icm-shell) functions which are the same as macros but may return a value and be nested.
a real function defined on a three-dimensional grid. Usually it is an electron density map or grid potential. This ICM-shell object contains a descriptor (or header) with the following information:
Maps can be read, calculated from structure factors, and created as a result of map arithmetics. Maps of 7 types (plus subtypes) of grid potentials can also be calculated with the make map potential command. To create an empty map you may do the following: build string "A" # just to some object in shell make map potential name="x" !a_ {0. 0. 0. 10. 10. 10.} 1. # a trick with empty cell and grid size 1. for i=1,Nof(m,1) for j=1,Nof(m,2) for k=1,Nof(m,3) x[i,j,k]= Random(1.,3.) endfor endfor endfor x = Bracket( x Box(x) ) # a trick to update map stats
The make map potential
The last map loaded or created becomes the current map.
The current map is a convenient default for commands
requiring map as an argument.
m = Smooth(m_ge)*2. - 1. + m_gc # does not make much sense See also: icm.map
a set of real numbers organized in rows and columns. The ICM-shell allows arbitrary size matrices [n,m], access to its elements ( M[i,j] ), rows ( M[i] ), columns ( M[1:i,j] ) or any sub-matrix ( M[i1:i2,j1:j2] ). Basic matrix operations such as
reading ( read matrix "a" ), assignment ( M_new=Transpose(M_old) ) or function Matrix ( e.g. M=Matrix(4,8)). Appending an array as matrix row.This can be done with the add matrix [ M ] R command. If the matrix is not specified a new matrix will be created. E.g. add matrix M {1. 2.} # creates new matrix M add matrix M {3. 4.} # appends the second row to M Making a matrix from table columns.The Matrix ( T S_columnNames ) returns a matrix with selected columns. E.g. group table t {1. 2.} "A" {3. 3.} "B" M = Matrix(t Name(t)) # returns a matrix Converting a matrix into table columns The inverse operation of the previous Matrix function is the following: Table ( M [ S_columnNamesToBeCreated ] E.g. T = Table(M {"AA","BB"}) Matrix-related functions are the following:
Examples: a=Matrix(4,5) # create a matrix, simple assignment a[1,1]=9. # a single matrix element a[2,?]={1. 2. 3. 4. 5.} # assign only the 2-nd row a[?,3]={1. 2. 3. 4.} # assign only the 3-nd column a[2:3,1:2]=Random(-1.,1.,2,2) # assign only the 2x2 submatrixBy simple arithmetic operations with matrices you can
an abbreviation of Modified IMage ELectrostatics algorithm ( Abagyan and Totrov, 1994) developed for fast evaluation of both internal Coulomb and electrostatic polarization free energy for large molecules. This term has no analytical derivatives and has no effect on local energy minimization. It can be a part of the energy function in global optimization such as montecarlo or ssearch . Three components of MIMEL can be shown using the show energy command. They are:
See also:
This word refers to the Merck molecular force field described in a series of 1994 and 1999 publications by Thomas Halgren. ICM can assign MMFF atom types using local chemical environment, formal charges and 3D topology. ICM also allows one to calculate the mmff94 energy and minimize it both in the cartesian space with free covalent geometry and in the internal coordinate space with fixed covalent geometry or user-defined geometrical constraints. See also:
A file with small molecule components of PDB can be found at the PDB ftp site. One entry from a components.cif file may looks like this: data_090 # _chem_comp.id 090 _chem_comp.name "N-(2,3-DIHYDRO-7,8-DIMETHOXYIMIDAZO[1,2-C] QUINAZOLIN-5-Y.." _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN ... loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_ordinal 090 OAU OAU O 0 1 N N N 43.937 13.173 32.712 -3.244 -5.748 0.338 1 090 CAO CAO C 0 1 N N N 43.419 12.319 32.005 -4.133 -5.838 1.182 2 090 CAP CAP C 0 1 Y N N 42.044 11.803 32.337 -4.940 -7.065 1.305 3 090 CAQ CAQ C 0 1 Y N N 41.453 10.822 31.543 -6.233 -7.001 1.769 4 090 NAR NAR N 0 1 Y N N 40.245 10.336 31.880 -7.027 -8.087 1.907 5 090 CAX CAX C 0 1 Y N N 39.597 10.758 32.985 -6.484 -9.275 1.559 6 090 CAW CAW C 0 1 Y N N 40.149 11.706 33.832 -5.192 -9.428 1.083 7 090 CAV CAV C 0 1 Y N N 41.389 12.225 33.504 -4.406 -8.288 0.955 8 ... # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 090 OAU CAO DOUB N N 1 090 CAO CAP SING N N 2 090 CAO NAN SING N N 3 090 CAP CAQ SING Y N 4 090 CAP CAV DOUB Y N 5 090 CAQ NAR DOUB Y N 6 .... data_091 # THE NEXT ENTRY ... The following commands will work on this kinds of files:
This word refers to the MDL Information Systems, Inc. SD-file format for small molecules (see trademarks). ICM can read and write molecules in this format. They may look like this: name jscorina 12209406473DS LongName 7 6 -0.0187 1.5258 0.0104 C 0 0 0 0 0 0.0021 -0.0041 0.0020 C 0 0 0 0 0 1.6831 2.1537 -0.0024 S 0 0 0 0 0 -1.4333 -0.5336 0.0129 C 0 0 0 0 0 2.0692 1.9811 -1.7665 C 0 0 0 0 0 -1.4126 -2.0635 0.0045 C 0 0 0 0 0 1.4620 3.1542 -2.5386 C 0 0 0 0 0 2 1 1 0 0 0 3 1 1 0 0 0 4 2 1 0 0 0 5 3 1 0 0 0 6 4 1 0 0 0 7 5 1 0 0 0 > <NSC> 19 > <CAS_RN> 638-46-0 $$$$ A multiple-mol file (or sdf file) can contain also numeric or text fields that will be converted into real , integer or sarray columns (arrays) in a chemical table. The conversion routine supports special values and the ND INF >number fields will be interpreted as numbers as well. See also:
This word refers to the Tripos file format for small molecules (see trademarks). ICM can read and write molecules in this format. The default extension for this type of file is .ml2. They may look like this: @<TRIPOS> MOLECULE a1 3 2 SMALL USER_CHARGES @<TRIPOS>ATOM 1 ho1 -2.0000 0.0000 -1.0000 H 1 hoh 0.3280 2 o -2.4944 0.0000 -1.8229 O 1 hoh -0.6550 3 ho2 -3.4149 0.0000 -1.5503 H 1 hoh 0.3280 @<TRIPOS>BOND 1 1 2 1 2 2 3 1The ATOM record contains the following fields: atom_id atom_name x y z atom_type [ subst_id [ subst_name [ charge [ status_bit ] ] ] ]
an internal ICM-viewer for the output of ICM commands, a little brother of the UNIX browser. Displays ICM output one screenful at a time. Control:
It is activated automatically under UNIX if the l_bufferedOutput parameter is set to yes .
a series of molecular conformations representing a Monte Carlo trajectory and saved in an ICM-formatted .trj binary file can be simply displayed or used for animated. The icm .mov files are not quicktime movies, or series of images. Instead, they contain a compressed series of geometrical parameters determining object geometry for each accepted montecarlo iteration. The frames of the trajectory file can be separately analyzed and further filtered with an ICM script. For example, one can generate a shorter trajectory file by retaining only the frames with lower energies. See also: display trajectory, load frame
an option in a number of commands (e.g. find pattern, find prosite, show tether, show energy, show area, show volume, etc). It is usually used in scripts when one wants to suppresses unnecessary output. In macro declaration, this option suppresses prompting for missing macro arguments.
|
Copyright© 1989-2024, Molsoft,LLC - All Rights Reserved. Copyright© 1989-2024, Molsoft,LLC - All Rights Reserved. This document contains proprietary and confidential information of Molsoft, LLC. The content of this document may not be disclosed to third parties, copied or duplicated in any form, in whole or in part, without the prior written permission from Molsoft, LLC. |