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A basic ICM class for arrays of integers: {5, 7, -100, 10}

See also: Iarray , Tointeger , read iarray.

integer

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!" 

label

usually a string displayed in the ICM graphics window. Types of labels:

• atom label # toggled by LeftMB clicking
• residue label # toggled by LeftMB double clicking
• variable label
• free string label # drag it with the Middle mouse button.

 
 show labels 

 
 l_nowIamDoingAStupidThing = yes & yes      
 
 l_Polite = no                     # another logical variable 
 if (Error & !l_Polite) print "And what do you think you are doing?" 

This ICM-shell object contains a descriptor (or header) with the following information:

• cell type (space group number) and parameters {a, b, c, alpha, beta, gamma};
• lattice and sublattice specifications (sizes and offsets for columns, rows and sections);
• characteristics of the density values: the mean value, standard deviation, the minimum and the maximum values.
• correspondence between X,Y,Z and sections, rows and columns

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.
The following arithmetic operations between maps of compatible sizes are allowed: map+map, map+i, map+r, i+map, r+map map-map, map-i, map-r, i-map, r-map map*r, map*i, i*map, r*map, map*map map/r, map/i.
Map functions:

function	description
Box( map )	returns R_6box defining the map boundary
Bracket( )	same as Trim it also updates the map statistics, mean, stdev etc.
Cell( map )	returns R_6 crystallographic cell parameters of the map
Index( m_EDS )	returns various index cell dimensions
make grob map r_sigma [name= s_name ]	contour map
make grob g_contour add r_step	re-contour map at new sigma level
converting x-ray map: make map potential map_Xray [as] [R_6box] [r_gridCellSize] [smooth] [name=s] to convert an oblique map into a fast rectangular map.
Map( map I_3_or_6 [ simple ] )	a submap
Map( m_EDS cell )	returns a map in crystallographic cell
Index( m_EDS cell )	returns 3 xr-cell index dimensions
Min( map )	minimal value
Max( map )	maximal value
Nof( map )	total number of grid points
Rarray( map )	returns all values from 3D-grid points as a linear real array
Smooth( map [ expand] )	space-average the map values
Symgroup( map )	string with the symmetry group name
Trim( map, vMin vMax )	trim by values outside the range
Trim( map, R_6box )	set values outside the box to zero

Simple arithmetic operations are allowed with the maps (map1 and map2 must have the same dimensions):

• plus (map1 + map2, map + r ),
• minus (map1 - map2, map - r ),
• multiply (map1 * map2, map*r, r*map ),
• divide (map1 / map2, map/r ),

 
 m = Smooth(m_ge)*2. - 1. + m_gc  # does not make much sense 

See also: icm.map

• plus (M1 + M2),
• minus (M1 - M2),
• multiply (M1 * M2),
• concatenate rows ( M1 // M2 ),
• equal ( M1 == M2 ),
• not equal ( M1 != M2),
• Transpose(M), and
• inverse ( Power(M,-1) )

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:

• determinant of square matrix ( Det(M))
• principal components or "distance geometry" ( Disgeo (M)) function, i.e. if a given square matrix M[1:n,1:n] contains distances between n points find coordinates in (n-1) dimensional space and sort the space dimensions according to their contribution to the variation. If distances are 3-dimensional Euclidean distances, the first three coordinates will give you x,y,z.
• Eigen (M) function returns a matrix of eigenvectors; eigenvalues are stored in R_out
• Distance( alignment) - returns matrix of pairwise distances between sequences in an alignment.
• Max , Min , Mean and Sum functions return a row (actually a real array ) with maximal, minimal, mean, or total values in each column, respectively
• Nof(M) and Length(M) - return n and m, respectively for matrix M[1:n,1:m] .
• Power(M, i_exponent) calculates different integer powers of a matrix, including matrix inverse ( inmat=Power(M,-1)),
• Random(d1,d2,n,m) creates a matrix and fills it with random numbers,
• Rarray( M [1-7] ) returns matrix elements merged into an array. It can return merged rows (Rarray(M,1)), columns, upper and lower triangles with (3,4) or without (6,7) a diagonal; or only the diagonal (5).
• Rmsd(M) returns root-mean-square deviation,
• Trace(M) returns the trace of a square matrix,
• Xyz( as_select) returns a matrix of xyz coordinates of selected atoms.
• Distance( matrix) returns a matrix of pairwise distances between the row-vectors of the matrix.

 
 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 submatrix 

• solve a system of linear equations ( x=Power(A,-1)*B ),
• find best set of parameters x[1:m] which fits your model A[1:n,1:m] (n > m) to data vector B[1:n]. Minimum of (A*x-B) is found by 3 steps:

   
   M1=Transpose(A)*A 
   M2=Power(M1,-1) 
   x =(M2*Transpose(A))*B 
  

• Coulomb interactions of explicit atomic charges (note that it is divided by the dielConst ICM-shell parameter)
• "Self energy" (or interaction of explicit charges with their own images)
• "Cross energy" (or interaction of explicit charges with other charges' images)

See also:

• mimelDepth

• ffMethod - defines which force field to use
• read library mmff - sets the parameters set type mmff - identifies the atom types from the covalent geometry, formal charges, and bond types
• minimize

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:

• read table mmcif read table mmcif file.mmcif
• creating an index file for large mmcif file write index mmcif file.mmcif
• read index mmcif

mol or sdf format

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:

• read mol creates 3D object(s). (also write mol )
• read table mol - read an .sdf file into a table (can also be read by chunks)
• write table mol - writes to an .sdf file
• write index - creates an index to a large .sdf file for individual or chunk access
• Smiles( X [cartesian] ) # smiles with X,Y,[Z] coordinates,- an alternative to .sdf
• TOOLS.smilesXyzSeparator

 
@<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    1  

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It is activated automatically under UNIX if the l_bufferedOutput parameter is set to yes .