Shortcut: SKETCHMAP_PROJECTION

Module	dimred
Description	Usage
Read in a sketch-map projection
output value	type
the out-of-sample projections of the input arguments using the input sketch-map projection	scalar/vector

Details and examples

Read in a sketch-map projection

This shortcut can be used to read in a projection of a trajectory that was generated using SKETCHMAP. You can then use the coordinates that were read in to generate projections of other configurations. Examples of how this tool might be used are given in the last three papers cited below. In these papers, a sketch-map projection is computed from one particular set of data points. This sketch-map projection that was output was then used to analyse a second completely different data set.

An example input that illustrates how the sketch-map projection shortcut is used is shown below:

Click on the labels of the actions for more information on what each action computes

#SETTING INPUTFILES=regtest/dimred/rt-smap-read/smap.pdb
d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,4
d3The DISTANCE action with label d3 calculates the following quantities: Quantity    Type    Description  
d3 scalar the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6

smapThe PROJECT_POINTS action with label smap calculates the following quantities: Quantity    Type    Description  
smap.coord-1 scalar the coordinates of the points in the low dimensional space  This is the 1th of these quantities
smap.coord-2 scalar the coordinates of the points in the low dimensional space  This is the 2th of these quantities: SKETCHMAP_PROJECTIONRead in a sketch-map projection This action is a shortcut and it has hidden defaults. More details ...
    ARGthe list of arguments you would like to use in your definition of the path=d1,d2,d3 REFERENCEa pdb file containing the set of reference configurations=regtest/dimred/rt-smap-read/smap.pdb
    PROPERTYthe property to be used in the index=smap_coord-1,smap_coord-2 CGTOL The tolerance for the conjugate gradient minimization that finds the out of sample projections=1E-3
    WEIGHTthe weight of each individual landmark in the stress fucntion that is to be optimised=WEIGHT HIGH_DIM_FUNCTIONthe parameters of the switching function in the high dimensional space={SMAP R_0=4 A=3 B=2} LOW_DIM_FUNCTIONthe parameters of the switching function in the low dimensional space={SMAP R_0=4 A=1 B=2}
...
smap: SKETCHMAP_PROJECTIONRead in a sketch-map projection This action is a shortcut and uses the defaults shown here. More details ...
    ARGthe list of arguments you would like to use in your definition of the path=d1,d2,d3 REFERENCEa pdb file containing the set of reference configurations=regtest/dimred/rt-smap-read/smap.pdb
    PROPERTYthe property to be used in the index=smap_coord-1,smap_coord-2 CGTOL The tolerance for the conjugate gradient minimization that finds the out of sample projections=1E-3
    WEIGHTthe weight of each individual landmark in the stress fucntion that is to be optimised=WEIGHT HIGH_DIM_FUNCTIONthe parameters of the switching function in the high dimensional space={SMAP R_0=4 A=3 B=2} LOW_DIM_FUNCTIONthe parameters of the switching function in the low dimensional space={SMAP R_0=4 A=1 B=2}
 TYPE the manner in which distances are calculated=OPTIMAL-FAST
...
# PLUMED interprets the command:
# smap: SKETCHMAP_PROJECTION ...
#     ARG=d1,d2,d3 REFERENCE=regtest/dimred/rt-smap-read/smap.pdb
#     PROPERTY=smap_coord-1,smap_coord-2 CGTOL=1E-3
#     WEIGHT=WEIGHT HIGH_DIM_FUNCTION={SMAP R_0=4 A=3 B=2} LOW_DIM_FUNCTION={SMAP R_0=4 A=1 B=2}
# ...
# as follows (Click the red comment above to revert to the short version of the input):
smap_ref_d1The CONSTANT action with label smap_ref_d1 calculates the following quantities: Quantity    Type    Description  
smap_ref_d1 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=regtest/dimred/rt-smap-read/smap.pdb ARGread this single argument from the input rather than the atomic structure=d1
smap_ref_d2The CONSTANT action with label smap_ref_d2 calculates the following quantities: Quantity    Type    Description  
smap_ref_d2 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=regtest/dimred/rt-smap-read/smap.pdb ARGread this single argument from the input rather than the atomic structure=d2
smap_ref_d3The CONSTANT action with label smap_ref_d3 calculates the following quantities: Quantity    Type    Description  
smap_ref_d3 vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=regtest/dimred/rt-smap-read/smap.pdb ARGread this single argument from the input rather than the atomic structure=d3
smap_dataThe MATRIX_PRODUCT_DIAGONAL action with label smap_data calculates the following quantities: Quantity    Type    Description  
smap_data vector a vector containing the diagonal elements of the matrix that obtaned by multiplying the two input matrices together: EUCLIDEAN_DISTANCECalculate the euclidean distance between two vectors of arguments More details SQUARED The squared distance should be calculated ARG2The point that we are calculating the distance to=d1,d2,d3 ARG1The poin that we are calculating the distance from=smap_ref_d1,smap_ref_d2,smap_ref_d3
smap_coord-1The CONSTANT action with label smap_coord-1 calculates the following quantities: Quantity    Type    Description  
smap_coord-1 scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
smap_coord-1_refThe CONSTANT action with label smap_coord-1_ref calculates the following quantities: Quantity    Type    Description  
smap_coord-1_ref vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=regtest/dimred/rt-smap-read/smap.pdb ARGread this single argument from the input rather than the atomic structure=smap_coord-1
smap_coord-2The CONSTANT action with label smap_coord-2 calculates the following quantities: Quantity    Type    Description  
smap_coord-2 scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
smap_coord-2_refThe CONSTANT action with label smap_coord-2_ref calculates the following quantities: Quantity    Type    Description  
smap_coord-2_ref vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=regtest/dimred/rt-smap-read/smap.pdb ARGread this single argument from the input rather than the atomic structure=smap_coord-2
WEIGHTThe CONSTANT action with label WEIGHT calculates the following quantities: Quantity    Type    Description  
WEIGHT scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
WEIGHT_refThe CONSTANT action with label WEIGHT_ref calculates the following quantities: Quantity    Type    Description  
WEIGHT_ref vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=regtest/dimred/rt-smap-read/smap.pdb ARGread this single argument from the input rather than the atomic structure=WEIGHT
smap_wsumThe SUM action with label smap_wsum calculates the following quantities: Quantity    Type    Description  
smap_wsum scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe vector/matrix/grid whose elements shuld be added together=WEIGHT_ref
smap_weightsThe CUSTOM action with label smap_weights calculates the following quantities: Quantity    Type    Description  
smap_weights vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=WEIGHT_ref,smap_wsum FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
smap_targThe MORE_THAN action with label smap_targ calculates the following quantities: Quantity    Type    Description  
smap_targ vector the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=smap_data SQUARED is the input quantity the square of the value that you would like to apply the switching function to SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=4 A=3 B=2}
smap: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input More details ARGthe projections of the landmark points=smap_coord-1_ref,smap_coord-2_ref TARGET1the matrix of target quantities that you would like to match=smap_targ FUNC1a function that is applied on the distances between the points in the low dimensional space={SMAP R_0=4 A=1 B=2} WEIGHTS1the matrix with the weights of the target quantities=smap_weights CGTOL the tolerance for the conjugate gradient minimization=1E-3
# --- End of included input --- 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=smap.* FILEthe name of the file on which to output these quantities=colvar

Each frame in your input trajectory generates the three distances so one set of sketch-map coordinates are generated from each frame. Notice that if you want to generate projections of multiple input points at once you need to use PROJECT_POINTS directly rather than this wrapper.

The configurations of the landmark points in your sketch-map input file can also be defined in terms of a set of atomic positions. In this case the distance between the reference configurations and the instantaneous coordinates are calculated using RMSD. An input for this type of calculation is as follows:

Click on the labels of the actions for more information on what each action computes

#SETTING INPUTFILES=regtest/dimred/rt-mds-rmsd/embed.pdb.reference

smapThe PROJECT_POINTS action with label smap calculates the following quantities: Quantity    Type    Description  
smap.coord-1 scalar the coordinates of the points in the low dimensional space  This is the 1th of these quantities
smap.coord-2 scalar the coordinates of the points in the low dimensional space  This is the 2th of these quantities: SKETCHMAP_PROJECTIONRead in a sketch-map projection This action is a shortcut and it has hidden defaults. More details ...
   REFERENCEa pdb file containing the set of reference configurations=regtest/dimred/rt-mds-rmsd/embed.pdb.reference
   PROPERTYthe property to be used in the index=mds-1,mds-2 CGTOL The tolerance for the conjugate gradient minimization that finds the out of sample projections=1E-3
   WEIGHTthe weight of each individual landmark in the stress fucntion that is to be optimised=weights HIGH_DIM_FUNCTIONthe parameters of the switching function in the high dimensional space={SMAP R_0=4 A=3 B=2} LOW_DIM_FUNCTIONthe parameters of the switching function in the low dimensional space={SMAP R_0=4 A=1 B=2}
...
smap: SKETCHMAP_PROJECTIONRead in a sketch-map projection This action is a shortcut and uses the defaults shown here. More details ...
   REFERENCEa pdb file containing the set of reference configurations=regtest/dimred/rt-mds-rmsd/embed.pdb.reference
   PROPERTYthe property to be used in the index=mds-1,mds-2 CGTOL The tolerance for the conjugate gradient minimization that finds the out of sample projections=1E-3
   WEIGHTthe weight of each individual landmark in the stress fucntion that is to be optimised=weights HIGH_DIM_FUNCTIONthe parameters of the switching function in the high dimensional space={SMAP R_0=4 A=3 B=2} LOW_DIM_FUNCTIONthe parameters of the switching function in the low dimensional space={SMAP R_0=4 A=1 B=2}
 TYPE the manner in which distances are calculated=OPTIMAL-FAST
...
# PLUMED interprets the command:
# smap: SKETCHMAP_PROJECTION ...
#    REFERENCE=regtest/dimred/rt-mds-rmsd/embed.pdb.reference
#    PROPERTY=mds-1,mds-2 CGTOL=1E-3
#    WEIGHT=weights HIGH_DIM_FUNCTION={SMAP R_0=4 A=3 B=2} LOW_DIM_FUNCTION={SMAP R_0=4 A=1 B=2}
# ...
# as follows (Click the red comment above to revert to the short version of the input):
smap_dataThe RMSD action with label smap_data calculates the following quantities: Quantity    Type    Description  
smap_data vector a vector containing the RMSD between the instantaneous structure and each of the reference structures that were input: RMSDCalculate the RMSD with respect to a reference structure. More details SQUARED  This should be setted if you want MSD instead of RMSD  REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=regtest/dimred/rt-mds-rmsd/embed.pdb.reference TYPE the manner in which RMSD alignment is performed=OPTIMAL-FAST
mds-1The CONSTANT action with label mds-1 calculates the following quantities: Quantity    Type    Description  
mds-1 scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
mds-1_refThe CONSTANT action with label mds-1_ref calculates the following quantities: Quantity    Type    Description  
mds-1_ref vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=regtest/dimred/rt-mds-rmsd/embed.pdb.reference ARGread this single argument from the input rather than the atomic structure=mds-1
mds-2The CONSTANT action with label mds-2 calculates the following quantities: Quantity    Type    Description  
mds-2 scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
mds-2_refThe CONSTANT action with label mds-2_ref calculates the following quantities: Quantity    Type    Description  
mds-2_ref vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=regtest/dimred/rt-mds-rmsd/embed.pdb.reference ARGread this single argument from the input rather than the atomic structure=mds-2
weightsThe CONSTANT action with label weights calculates the following quantities: Quantity    Type    Description  
weights scalar the constant value that was read from the plumed input: CONSTANTCreate a constant value that can be passed to actions More details VALUEthe single number that you would like to store=1
weights_refThe CONSTANT action with label weights_ref calculates the following quantities: Quantity    Type    Description  
weights_ref vector the constant value that was read from the plumed input: PDB2CONSTANTCreate a constant value from a PDB input file More details REFERENCEa file in pdb format containing the reference structure=regtest/dimred/rt-mds-rmsd/embed.pdb.reference ARGread this single argument from the input rather than the atomic structure=weights
smap_wsumThe SUM action with label smap_wsum calculates the following quantities: Quantity    Type    Description  
smap_wsum scalar the SUM of the elements in the input value: SUMCalculate the sum of the arguments More details PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ARGthe vector/matrix/grid whose elements shuld be added together=weights_ref
smap_weightsThe CUSTOM action with label smap_weights calculates the following quantities: Quantity    Type    Description  
smap_weights vector the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=weights_ref,smap_wsum FUNCthe function you wish to evaluate=x/y PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
smap_targThe MORE_THAN action with label smap_targ calculates the following quantities: Quantity    Type    Description  
smap_targ vector the vector obtained by doing an element-wise application of a function that is one if the if the input is more than a threshold to the input vectors: MORE_THANUse a switching function to determine how many of the input variables are more than a certain cutoff. More details ARGthe values input to this function=smap_data SQUARED is the input quantity the square of the value that you would like to apply the switching function to SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={SMAP R_0=4 A=3 B=2}
smap: PROJECT_POINTSFind the projection of a point in a low dimensional space by matching the (transformed) distance between it and a series of reference configurations that were input More details ARGthe projections of the landmark points=mds-1_ref,mds-2_ref TARGET1the matrix of target quantities that you would like to match=smap_targ FUNC1a function that is applied on the distances between the points in the low dimensional space={SMAP R_0=4 A=1 B=2} WEIGHTS1the matrix with the weights of the target quantities=smap_weights CGTOL the tolerance for the conjugate gradient minimization=1E-3
# --- End of included input ---

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	scalar	the list of arguments you would like to use in your definition of the path

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	input	none	the list of arguments you would like to use in your definition of the path
REFERENCE	compulsory	none	a pdb file containing the set of reference configurations
TYPE	compulsory	OPTIMAL-FAST	the manner in which distances are calculated
PROPERTY	compulsory	none	the property to be used in the index
WEIGHT	compulsory	none	the weight of each individual landmark in the stress fucntion that is to be optimised
HIGH_DIM_FUNCTION	compulsory	none	the parameters of the switching function in the high dimensional space
LOW_DIM_FUNCTION	compulsory	none	the parameters of the switching function in the low dimensional space
CGTOL	compulsory	1E-6	The tolerance for the conjugate gradient minimization that finds the out of sample projections

References

More information about how this action can be used is available in the following articles:

Quantity	Type	Description
d1	scalar	the DISTANCE between this pair of atoms